From 4b0f078f72787a0c23dde0e2582d9a1b0b370f90 Mon Sep 17 00:00:00 2001 From: Carlo Antonio Pignedoli Date: Thu, 23 Jan 2025 17:13:13 +0000 Subject: [PATCH 01/12] fixing parser for v2024.3 --- aiida_cp2k/utils/parser.py | 16 +++++++++++++--- 1 file changed, 13 insertions(+), 3 deletions(-) diff --git a/aiida_cp2k/utils/parser.py b/aiida_cp2k/utils/parser.py index b9d7518c..f7043fd6 100644 --- a/aiida_cp2k/utils/parser.py +++ b/aiida_cp2k/utils/parser.py @@ -213,18 +213,28 @@ def parse_cp2k_output_advanced( # Note: with CELL_OPT/LBFGS there is no "STEP 0", while there is with CELL_OPT/BFGS if re.search(r"Informations at step", line): step = int(data[5]) + # Note fixes v2024.3 + if re.search(r"OPT\| Step number ", line): + step = int(data[3]) + if re.search(r"Maximum step size ", line): + max_step = float(data[-1]) if re.search(r"Max. step size =", line): max_step = float(data[-1]) + if re.search(r"RMS step size ", line): + rms_step = float(data[-1]) if re.search(r"RMS step size =", line): rms_step = float(data[-1]) + if re.search(r"Maximum gradient ", line): + max_grad = float(data[-1]) if re.search(r"Max. gradient =", line): max_grad = float(data[-1]) + if re.search(r"RMS gradient ", line): + rms_grad = float(data[-1]) if re.search(r"RMS gradient =", line): rms_grad = float(data[-1]) if ( - len(data) == 1 - and data[0] == "---------------------------------------------------" - ): + (len(data) == 1 and data[0] == "---------------------------------------------------") or (len(data) == 10 and data[0] == "OPT|" and data[2] =="peak")or (len(data) == 7 and data[0] == "OPT|" and data[2] =="peak") + ): print_now = True # 51('-') if re.search( r"Reevaluating energy at the minimum", line From baf86b30566f3d6898a75fc67768ca8ec6813ff6 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Thu, 23 Jan 2025 17:17:38 +0000 Subject: [PATCH 02/12] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- aiida_cp2k/utils/parser.py | 36 +++++++++++++++++++++++++++--------- 1 file changed, 27 insertions(+), 9 deletions(-) diff --git a/aiida_cp2k/utils/parser.py b/aiida_cp2k/utils/parser.py index f7043fd6..cb2886fa 100644 --- a/aiida_cp2k/utils/parser.py +++ b/aiida_cp2k/utils/parser.py @@ -213,28 +213,46 @@ def parse_cp2k_output_advanced( # Note: with CELL_OPT/LBFGS there is no "STEP 0", while there is with CELL_OPT/BFGS if re.search(r"Informations at step", line): step = int(data[5]) - # Note fixes v2024.3 + # Note fixes v2024.3 if re.search(r"OPT\| Step number ", line): step = int(data[3]) - if re.search(r"Maximum step size ", line): - max_step = float(data[-1]) + if re.search( + r"Maximum step size ", + line, + ): + max_step = float(data[-1]) if re.search(r"Max. step size =", line): max_step = float(data[-1]) - if re.search(r"RMS step size ", line): - rms_step = float(data[-1]) + if re.search( + r"RMS step size ", + line, + ): + rms_step = float(data[-1]) if re.search(r"RMS step size =", line): rms_step = float(data[-1]) - if re.search(r"Maximum gradient ", line): + if re.search( + r"Maximum gradient ", + line, + ): max_grad = float(data[-1]) if re.search(r"Max. gradient =", line): max_grad = float(data[-1]) - if re.search(r"RMS gradient ", line): + if re.search( + r"RMS gradient ", + line, + ): rms_grad = float(data[-1]) if re.search(r"RMS gradient =", line): rms_grad = float(data[-1]) if ( - (len(data) == 1 and data[0] == "---------------------------------------------------") or (len(data) == 10 and data[0] == "OPT|" and data[2] =="peak")or (len(data) == 7 and data[0] == "OPT|" and data[2] =="peak") - ): + ( + len(data) == 1 + and data[0] + == "---------------------------------------------------" + ) + or (len(data) == 10 and data[0] == "OPT|" and data[2] == "peak") + or (len(data) == 7 and data[0] == "OPT|" and data[2] == "peak") + ): print_now = True # 51('-') if re.search( r"Reevaluating energy at the minimum", line From 72e384227b4a8aba84360f373f88862c3a290898 Mon Sep 17 00:00:00 2001 From: Carlo Antonio Pignedoli Date: Fri, 24 Jan 2025 14:41:36 +0000 Subject: [PATCH 03/12] fix also for the restart handler --- aiida_cp2k/workchains/base.py | 2 +- examples/workchains/example_base_md_reftraj_restart.py | 7 +++++-- 2 files changed, 6 insertions(+), 3 deletions(-) diff --git a/aiida_cp2k/workchains/base.py b/aiida_cp2k/workchains/base.py index 3ed3caee..c092ff17 100644 --- a/aiida_cp2k/workchains/base.py +++ b/aiida_cp2k/workchains/base.py @@ -84,7 +84,7 @@ def restart_incomplete_calculation(self, calc): content_string = calc.outputs.retrieved.base.repository.get_object_content(calc.base.attributes.get('output_filename')) # CP2K was updating geometry - continue with that. - restart_geometry_transformation = "Max. gradient =" in content_string or "MD| Step number" in content_string + restart_geometry_transformation = "Max. gradient =" or "OPT| Maximum gradient " in content_string or "MD| Step number" in content_string end_inner_scf_loop = "Total energy: " in content_string # The message is written in the log file when the CP2K input parameter `LOG_PRINT_KEY` is set to True. if not (restart_geometry_transformation or end_inner_scf_loop or "Writing RESTART" in content_string): diff --git a/examples/workchains/example_base_md_reftraj_restart.py b/examples/workchains/example_base_md_reftraj_restart.py index 91b38c4d..71de62cd 100644 --- a/examples/workchains/example_base_md_reftraj_restart.py +++ b/examples/workchains/example_base_md_reftraj_restart.py @@ -57,7 +57,7 @@ def example_base(cp2k_code): "GLOBAL": { "RUN_TYPE": "MD", "PRINT_LEVEL": "LOW", - "WALLTIME": 4, + "WALLTIME": 2, "PROJECT": "aiida", }, "MOTION": { @@ -151,10 +151,13 @@ def example_base(cp2k_code): "basis": basis_file, "pseudo": pseudo_file, } - builder.cp2k.metadata.options.resources = { + builder.cp2k.metadata.options={ + "max_wallclock_seconds":100, + "resources" : { "num_machines": 1, "num_mpiprocs_per_machine": 1, } + } print("Submitted calculation...") outputs, calc_node = engine.run_get_node(builder) From 390b034762674c82c61009ea9f773d81f5dfc688 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Fri, 24 Jan 2025 14:41:53 +0000 Subject: [PATCH 04/12] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- .../workchains/example_base_md_reftraj_restart.py | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/examples/workchains/example_base_md_reftraj_restart.py b/examples/workchains/example_base_md_reftraj_restart.py index 71de62cd..ab1d99d7 100644 --- a/examples/workchains/example_base_md_reftraj_restart.py +++ b/examples/workchains/example_base_md_reftraj_restart.py @@ -151,12 +151,12 @@ def example_base(cp2k_code): "basis": basis_file, "pseudo": pseudo_file, } - builder.cp2k.metadata.options={ - "max_wallclock_seconds":100, - "resources" : { - "num_machines": 1, - "num_mpiprocs_per_machine": 1, - } + builder.cp2k.metadata.options = { + "max_wallclock_seconds": 100, + "resources": { + "num_machines": 1, + "num_mpiprocs_per_machine": 1, + }, } print("Submitted calculation...") From 85c6d4cec9870ff91d6abbd87d2ba05250b18f9e Mon Sep 17 00:00:00 2001 From: Carlo Antonio Pignedoli Date: Fri, 24 Jan 2025 15:47:17 +0000 Subject: [PATCH 05/12] bug fix --- aiida_cp2k/workchains/base.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/aiida_cp2k/workchains/base.py b/aiida_cp2k/workchains/base.py index c092ff17..742f3aaa 100644 --- a/aiida_cp2k/workchains/base.py +++ b/aiida_cp2k/workchains/base.py @@ -84,7 +84,7 @@ def restart_incomplete_calculation(self, calc): content_string = calc.outputs.retrieved.base.repository.get_object_content(calc.base.attributes.get('output_filename')) # CP2K was updating geometry - continue with that. - restart_geometry_transformation = "Max. gradient =" or "OPT| Maximum gradient " in content_string or "MD| Step number" in content_string + restart_geometry_transformation = "Max. gradient =" in content_string or "OPT| Maximum gradient " in content_string or "MD| Step number" in content_string end_inner_scf_loop = "Total energy: " in content_string # The message is written in the log file when the CP2K input parameter `LOG_PRINT_KEY` is set to True. if not (restart_geometry_transformation or end_inner_scf_loop or "Writing RESTART" in content_string): From b451e4a06a76603ea429a1b53d25ec94b0f80871 Mon Sep 17 00:00:00 2001 From: Aliaksandr Yakutovich Date: Tue, 28 Jan 2025 09:21:51 +0000 Subject: [PATCH 06/12] Add tests for CP2K v2024.3 --- test/outputs/GEO_OPT_v2024.3.out | 1841 ++++++++++++++++++++++++++++++ test/outputs/GEO_OPT_v9.1.out | 1778 +++++++++++++++++++++++++++++ test/test_parser.py | 56 +- 3 files changed, 3674 insertions(+), 1 deletion(-) create mode 100644 test/outputs/GEO_OPT_v2024.3.out create mode 100644 test/outputs/GEO_OPT_v9.1.out diff --git a/test/outputs/GEO_OPT_v2024.3.out b/test/outputs/GEO_OPT_v2024.3.out new file mode 100644 index 00000000..83ac37fa --- /dev/null +++ b/test/outputs/GEO_OPT_v2024.3.out @@ -0,0 +1,1841 @@ + DBCSR| CPU Multiplication driver BLAS (U) + DBCSR| Multrec recursion limit 512 (U) + DBCSR| Multiplication stack size 30000 (D) + DBCSR| Maximum elements for images UNLIMITED (U) + DBCSR| Multiplicative factor virtual images 1 (U) + DBCSR| Use multiplication densification F (D) + DBCSR| Multiplication size stacks 3 (U) + DBCSR| Use memory pool for CPU allocation F (U) + DBCSR| Number of 3D layers SINGLE (U) + DBCSR| Use MPI memory allocation F (U) + DBCSR| Use RMA algorithm F (U) + DBCSR| Use Communication thread T (U) + DBCSR| Communication thread load 87 (D) + DBCSR| MPI: My process id 0 + DBCSR| MPI: Number of processes 4 + DBCSR| OMP: Current number of threads 1 + DBCSR| OMP: Max number of threads 1 + DBCSR| ACC: Number of devices/node 1 + DBCSR| ACC: Number of stack-buffers per thread 8 (U) + DBCSR| ACC: Avoid driver after busy F (U) + DBCSR| ACC: Process inhomogeneous stacks T (U) + DBCSR| ACC: Min. flop for processing 0 (U) + DBCSR| ACC: Min. flop for sorting 4000 (U) + DBCSR| ACC: Number of binning bins 4096 (U) + DBCSR| ACC: Size of binning bins 16 (U) + DBCSR| ACC: GPU backend is enabled T (D) + DBCSR| Split modifier for TAS multiplication algorithm 1.0E+00 (U) + + + **** **** ****** ** PROGRAM STARTED AT 2025-01-22 10:22:17.809 + ***** ** *** *** ** PROGRAM STARTED ON nid006590 + ** **** ****** PROGRAM STARTED BY cpi + ***** ** ** ** ** PROGRAM PROCESS ID 278132 + **** ** ******* ** PROGRAM STARTED IN /capstor/scratch/cscs/cpi/aiida/2d/33 + /a915-92b7-437a-b835-9b7e41b4a8f5 + + CP2K| version string: CP2K version 2024.3 + CP2K| source code revision number: + CP2K| cp2kflags: omp libint fftw3 libxc elpa parallel scalapack cosma dbcsr_acc + CP2K| plumed2 spglib sirius offload_cuda spla_gemm_offloading + CP2K| is freely available from https://www.cp2k.org/ + CP2K| Program compiled at 1980-01-01 12:01:00 + CP2K| Program compiled on + CP2K| Program compiled for aarch64 + CP2K| Data directory path /users/cpi/src/cp2k/data + CP2K| Input file name aiida.inp + + GLOBAL| Force Environment number 1 + GLOBAL| Basis set file name BASIS_MOLOPT + GLOBAL| Potential file name POTENTIAL + GLOBAL| MM Potential file name MM_POTENTIAL + GLOBAL| Coordinate file name aiida.coords.xyz + GLOBAL| Method name CP2K + GLOBAL| Project name aiida + GLOBAL| Run type GEO_OPT + GLOBAL| FFT library FFTW3 + GLOBAL| Diagonalization library ELPA + GLOBAL| DGEMM library SPLA + GLOBAL| Minimum number of eigenvectors for ELPA usage 16 + GLOBAL| Orthonormality check for eigenvectors DISABLED + GLOBAL| Matrix multiplication library COSMA + GLOBAL| All-to-all communication in single precision F + GLOBAL| FFTs using library dependent lengths T + GLOBAL| Grid backend AUTO + GLOBAL| Global print level MEDIUM + GLOBAL| MPI I/O enabled T + GLOBAL| Total number of message passing processes 4 + GLOBAL| Number of threads for this process 1 + GLOBAL| This output is from process 0 + GLOBAL| Stack size for threads created by OpenMP (OMP_STACKSIZE) default + GLOBAL| CPU model name UNKNOWN + + MEMORY| system memory details [Kb] + MEMORY| rank 0 min max average + MEMORY| MemTotal 895967360 895967360 895967360 895967360 + MEMORY| MemFree 861433664 861433664 861433664 861433664 + MEMORY| Buffers 1536 1536 1536 1536 + MEMORY| Cached 10248832 10248832 10248832 10248832 + MEMORY| Slab 8339904 8339904 8339904 8339904 + MEMORY| SReclaimable 337152 337152 337152 337152 + MEMORY| MemLikelyFree 872021184 872021184 872021184 872021184 + + + *** Fundamental physical constants (SI units) *** + + *** Literature: B. J. Mohr and B. N. Taylor, + *** CODATA recommended values of the fundamental physical + *** constants: 2006, Web Version 5.1 + *** http://physics.nist.gov/constants + + Speed of light in vacuum [m/s] 2.99792458000000E+08 + Magnetic constant or permeability of vacuum [N/A**2] 1.25663706143592E-06 + Electric constant or permittivity of vacuum [F/m] 8.85418781762039E-12 + Planck constant (h) [J*s] 6.62606896000000E-34 + Planck constant (h-bar) [J*s] 1.05457162825177E-34 + Elementary charge [C] 1.60217648700000E-19 + Electron mass [kg] 9.10938215000000E-31 + Electron g factor [ ] -2.00231930436220E+00 + Proton mass [kg] 1.67262163700000E-27 + Fine-structure constant 7.29735253760000E-03 + Rydberg constant [1/m] 1.09737315685270E+07 + Avogadro constant [1/mol] 6.02214179000000E+23 + Boltzmann constant [J/K] 1.38065040000000E-23 + Atomic mass unit [kg] 1.66053878200000E-27 + Bohr radius [m] 5.29177208590000E-11 + + *** Conversion factors *** + + [u] -> [a.u.] 1.82288848426455E+03 + [Angstrom] -> [Bohr] = [a.u.] 1.88972613288564E+00 + [a.u.] = [Bohr] -> [Angstrom] 5.29177208590000E-01 + [a.u.] -> [s] 2.41888432650478E-17 + [a.u.] -> [fs] 2.41888432650478E-02 + [a.u.] -> [J] 4.35974393937059E-18 + [a.u.] -> [N] 8.23872205491840E-08 + [a.u.] -> [K] 3.15774647902944E+05 + [a.u.] -> [kJ/mol] 2.62549961709828E+03 + [a.u.] -> [kcal/mol] 6.27509468713739E+02 + [a.u.] -> [Pa] 2.94210107994716E+13 + [a.u.] -> [bar] 2.94210107994716E+08 + [a.u.] -> [atm] 2.90362800883016E+08 + [a.u.] -> [eV] 2.72113838565563E+01 + [a.u.] -> [Hz] 6.57968392072181E+15 + [a.u.] -> [1/cm] (wave numbers) 2.19474631370540E+05 + [a.u./Bohr**2] -> [1/cm] 5.14048714338585E+03 + + + CELL_TOP| Volume [angstrom^3]: 1475.364128 + CELL_TOP| Vector a [angstrom 12.424 0.000 0.000 |a| = 12.424154 + CELL_TOP| Vector b [angstrom 0.000 11.875 0.000 |b| = 11.874962 + CELL_TOP| Vector c [angstrom 0.000 0.000 10.000 |c| = 10.000004 + CELL_TOP| Angle (b,c), alpha [degree]: 90.000000 + CELL_TOP| Angle (a,c), beta [degree]: 90.000000 + CELL_TOP| Angle (a,b), gamma [degree]: 90.000000 + CELL_TOP| Numerically orthorhombic: YES + CELL_TOP| Periodicity XYZ + + GENERATE| Preliminary Number of Bonds generated: 0 + GENERATE| Achieved consistency in connectivity generation. + + CELL| Volume [angstrom^3]: 1475.364128 + CELL| Vector a [angstrom]: 12.424 0.000 0.000 |a| = 12.424154 + CELL| Vector b [angstrom]: 0.000 11.875 0.000 |b| = 11.874962 + CELL| Vector c [angstrom]: 0.000 0.000 10.000 |c| = 10.000004 + CELL| Angle (b,c), alpha [degree]: 90.000000 + CELL| Angle (a,c), beta [degree]: 90.000000 + CELL| Angle (a,b), gamma [degree]: 90.000000 + CELL| Numerically orthorhombic: YES + CELL| Periodicity XYZ + + CELL_REF| Volume [angstrom^3]: 1475.364128 + CELL_REF| Vector a [angstrom 12.424 0.000 0.000 |a| = 12.424154 + CELL_REF| Vector b [angstrom 0.000 11.875 0.000 |b| = 11.874962 + CELL_REF| Vector c [angstrom 0.000 0.000 10.000 |c| = 10.000004 + CELL_REF| Angle (b,c), alpha [degree]: 90.000000 + CELL_REF| Angle (a,c), beta [degree]: 90.000000 + CELL_REF| Angle (a,b), gamma [degree]: 90.000000 + CELL_REF| Numerically orthorhombic: YES + CELL_REF| Periodicity XYZ + + ******************************************************************************* + ******************************************************************************* + ** ** + ** ##### ## ## ** + ** ## ## ## ## ## ** + ** ## ## ## ###### ** + ** ## ## ## ## ## ##### ## ## #### ## ##### ##### ** + ** ## ## ## ## ## ## ## ## ## ## ## ## ## ## ** + ** ## ## ## ## ## ## ## #### ### ## ###### ###### ** + ** ## ### ## ## ## ## ## ## ## ## ## ## ** + ** ####### ##### ## ##### ## ## #### ## ##### ## ** + ** ## ## ** + ** ** + ** ... make the atoms dance ** + ** ** + ** Copyright (C) by CP2K developers group (2000-2024) ** + ** J. Chem. Phys. 152, 194103 (2020) ** + ** ** + ******************************************************************************* + + DFT| Spin restricted Kohn-Sham (RKS) calculation RKS + DFT| Multiplicity 1 + DFT| Number of spin states 1 + DFT| Charge 0 + DFT| Self-interaction correction (SIC) NO + DFT| Cutoffs: density 1.000000E-10 + DFT| gradient 1.000000E-10 + DFT| tau 1.000000E-10 + DFT| cutoff_smoothing_range 0.000000E+00 + DFT| XC density smoothing NONE + DFT| XC derivatives PW + + FUNCTIONAL| PBE: + FUNCTIONAL| J.P.Perdew, K.Burke, M.Ernzerhof, Phys. Rev. Letter, vol. 77, n 18, + FUNCTIONAL| pp. 3865-3868, (1996) {spin unpolarized} + + vdW POTENTIAL| Pair Potential + vdW POTENTIAL| DFT-D3 (Version 3.1) + vdW POTENTIAL| Potential Form: S. Grimme et al, JCP 132: 154104 (2010) + vdW POTENTIAL| Zero Damping + vdW POTENTIAL| Cutoff Radius [Bohr]: 28.35 + vdW POTENTIAL| s6 Scaling Factor: 1.0000 + vdW POTENTIAL| sr6 Scaling Factor: 1.2170 + vdW POTENTIAL| s8 Scaling Factor: 0.7220 + vdW POTENTIAL| Cutoff for CN calculation: 0.1000E-05 + + QS| Method: GPW + QS| Density plane wave grid type NON-SPHERICAL FULLSPACE + QS| Number of grid levels: 5 + QS| Density cutoff [a.u.]: 300.0 + QS| Multi grid cutoff [a.u.]: 1) grid level 300.0 + QS| 2) grid level 100.0 + QS| 3) grid level 33.3 + QS| 4) grid level 11.1 + QS| 5) grid level 3.7 + QS| Grid level progression factor: 3.0 + QS| Relative density cutoff [a.u.]: 20.0 + QS| Interaction thresholds: eps_pgf_orb: 1.0E-07 + QS| eps_filter_matrix: 0.0E+00 + QS| eps_core_charge: 1.0E-16 + QS| eps_rho_gspace: 1.0E-14 + QS| eps_rho_rspace: 1.0E-14 + QS| eps_gvg_rspace: 1.0E-07 + QS| eps_ppl: 1.0E-02 + QS| eps_ppnl: 1.0E-09 + + + ATOMIC KIND INFORMATION + + 1. Atomic kind: C Number of atoms: 2 + + Orbital Basis Set TZV2P-MOLOPT-GTH + + Number of orbital shell sets: 1 + Number of orbital shells: 8 + Number of primitive Cartesian functions: 7 + Number of Cartesian basis functions: 24 + Number of spherical basis functions: 22 + Norm type: 2 + + Normalised Cartesian orbitals: + + Set Shell Orbital Exponent Coefficient + + 1 1 2s 6.132625 -0.263661 + 2.625196 -0.231112 + 1.045457 0.042712 + 0.478316 0.306085 + 0.178617 0.065483 + 0.075145 0.000568 + 0.030287 0.000417 + + 1 2 3s 6.132625 0.131937 + 2.625196 0.414269 + 1.045457 -0.593590 + 0.478316 0.644922 + 0.178617 0.069203 + 0.075145 -0.145101 + 0.030287 0.008247 + + 1 3 4s 6.132625 -1.009391 + 2.625196 -0.608763 + 1.045457 -0.320627 + 0.478316 1.417678 + 0.178617 -0.917862 + 0.075145 0.286664 + 0.030287 -0.031483 + + 1 4 3px 6.132625 0.562677 + 2.625196 0.633910 + 1.045457 0.379157 + 0.478316 0.235193 + 0.178617 0.052379 + 0.075145 0.003677 + 0.030287 0.000105 + 1 4 3py 6.132625 0.562677 + 2.625196 0.633910 + 1.045457 0.379157 + 0.478316 0.235193 + 0.178617 0.052379 + 0.075145 0.003677 + 0.030287 0.000105 + 1 4 3pz 6.132625 0.562677 + 2.625196 0.633910 + 1.045457 0.379157 + 0.478316 0.235193 + 0.178617 0.052379 + 0.075145 0.003677 + 0.030287 0.000105 + + 1 5 4px 6.132625 -0.472364 + 2.625196 -0.221326 + 1.045457 -0.481781 + 0.478316 0.135466 + 0.178617 0.072281 + 0.075145 0.024920 + 0.030287 0.002706 + 1 5 4py 6.132625 -0.472364 + 2.625196 -0.221326 + 1.045457 -0.481781 + 0.478316 0.135466 + 0.178617 0.072281 + 0.075145 0.024920 + 0.030287 0.002706 + 1 5 4pz 6.132625 -0.472364 + 2.625196 -0.221326 + 1.045457 -0.481781 + 0.478316 0.135466 + 0.178617 0.072281 + 0.075145 0.024920 + 0.030287 0.002706 + + 1 6 5px 6.132625 -0.321125 + 2.625196 -0.513960 + 1.045457 -0.659092 + 0.478316 1.236398 + 0.178617 -0.279443 + 0.075145 0.042466 + 0.030287 -0.008547 + 1 6 5py 6.132625 -0.321125 + 2.625196 -0.513960 + 1.045457 -0.659092 + 0.478316 1.236398 + 0.178617 -0.279443 + 0.075145 0.042466 + 0.030287 -0.008547 + 1 6 5pz 6.132625 -0.321125 + 2.625196 -0.513960 + 1.045457 -0.659092 + 0.478316 1.236398 + 0.178617 -0.279443 + 0.075145 0.042466 + 0.030287 -0.008547 + + 1 7 4dx2 6.132625 0.874783 + 2.625196 0.375772 + 1.045457 0.653959 + 0.478316 0.191007 + 0.178617 0.018656 + 0.075145 0.003649 + 0.030287 -0.000011 + 1 7 4dxy 6.132625 1.515169 + 2.625196 0.650856 + 1.045457 1.132690 + 0.478316 0.330834 + 0.178617 0.032314 + 0.075145 0.006321 + 0.030287 -0.000019 + 1 7 4dxz 6.132625 1.515169 + 2.625196 0.650856 + 1.045457 1.132690 + 0.478316 0.330834 + 0.178617 0.032314 + 0.075145 0.006321 + 0.030287 -0.000019 + 1 7 4dy2 6.132625 0.874783 + 2.625196 0.375772 + 1.045457 0.653959 + 0.478316 0.191007 + 0.178617 0.018656 + 0.075145 0.003649 + 0.030287 -0.000011 + 1 7 4dyz 6.132625 1.515169 + 2.625196 0.650856 + 1.045457 1.132690 + 0.478316 0.330834 + 0.178617 0.032314 + 0.075145 0.006321 + 0.030287 -0.000019 + 1 7 4dz2 6.132625 0.874783 + 2.625196 0.375772 + 1.045457 0.653959 + 0.478316 0.191007 + 0.178617 0.018656 + 0.075145 0.003649 + 0.030287 -0.000011 + + 1 8 5dx2 6.132625 3.037532 + 2.625196 0.636556 + 1.045457 2.577237 + 0.478316 -0.930692 + 0.178617 0.140536 + 0.075145 -0.022558 + 0.030287 0.000345 + 1 8 5dxy 6.132625 5.261160 + 2.625196 1.102547 + 1.045457 4.463906 + 0.478316 -1.612005 + 0.178617 0.243416 + 0.075145 -0.039072 + 0.030287 0.000598 + 1 8 5dxz 6.132625 5.261160 + 2.625196 1.102547 + 1.045457 4.463906 + 0.478316 -1.612005 + 0.178617 0.243416 + 0.075145 -0.039072 + 0.030287 0.000598 + 1 8 5dy2 6.132625 3.037532 + 2.625196 0.636556 + 1.045457 2.577237 + 0.478316 -0.930692 + 0.178617 0.140536 + 0.075145 -0.022558 + 0.030287 0.000345 + 1 8 5dyz 6.132625 5.261160 + 2.625196 1.102547 + 1.045457 4.463906 + 0.478316 -1.612005 + 0.178617 0.243416 + 0.075145 -0.039072 + 0.030287 0.000598 + 1 8 5dz2 6.132625 3.037532 + 2.625196 0.636556 + 1.045457 2.577237 + 0.478316 -0.930692 + 0.178617 0.140536 + 0.075145 -0.022558 + 0.030287 0.000345 + + Atomic covalent radius [Angstrom]: 0.770 + + Atomic van der Waals radius [Angstrom]: 1.700 + + GTH Potential information for GTH-PBE-q4 + + Description: Goedecker-Teter-Hutter pseudopotential + Goedecker et al., PRB 54, 1703 (1996) + Hartwigsen et al., PRB 58, 3641 (1998) + Krack, TCA 114, 145 (2005) + + Gaussian exponent of the core charge distribution: 4.364419 + Electronic configuration (s p d ...): 2 2 + + Parameters of the local part of the GTH pseudopotential: + + rloc C1 C2 C3 C4 + 0.338471 -8.803674 1.339211 + + Parameters of the non-local part of the GTH pseudopotential: + + l r(l) h(i,j,l) + + 0 0.302576 9.622487 + 1 0.291507 + + 2. Atomic kind: H Number of atoms: 4 + + Orbital Basis Set TZV2P-MOLOPT-GTH + + Number of orbital shell sets: 1 + Number of orbital shells: 5 + Number of primitive Cartesian functions: 7 + Number of Cartesian basis functions: 9 + Number of spherical basis functions: 9 + Norm type: 2 + + Normalised Cartesian orbitals: + + Set Shell Orbital Exponent Coefficient + + 1 1 2s 11.478000 0.129129 + 3.700759 0.177012 + 1.446884 0.141285 + 0.716815 0.245670 + 0.247919 0.094768 + 0.066918 0.004062 + 0.021708 -0.000053 + + 1 2 3s 11.478000 -0.079256 + 3.700759 -0.152992 + 1.446884 0.015066 + 0.716815 -0.331234 + 0.247919 0.210690 + 0.066918 0.058630 + 0.021708 -0.003429 + + 1 3 4s 11.478000 -0.246880 + 3.700759 0.023016 + 1.446884 -1.109374 + 0.716815 1.524652 + 0.247919 -0.227968 + 0.066918 -0.037343 + 0.021708 0.005696 + + 1 4 3px 11.478000 0.325290 + 3.700759 0.187466 + 1.446884 0.443300 + 0.716815 0.267738 + 0.247919 0.088285 + 0.066918 0.019092 + 0.021708 0.000629 + 1 4 3py 11.478000 0.325290 + 3.700759 0.187466 + 1.446884 0.443300 + 0.716815 0.267738 + 0.247919 0.088285 + 0.066918 0.019092 + 0.021708 0.000629 + 1 4 3pz 11.478000 0.325290 + 3.700759 0.187466 + 1.446884 0.443300 + 0.716815 0.267738 + 0.247919 0.088285 + 0.066918 0.019092 + 0.021708 0.000629 + + 1 5 4px 11.478000 -1.727188 + 3.700759 -0.598393 + 1.446884 -3.813128 + 0.716815 1.901151 + 0.247919 -0.262425 + 0.066918 0.006339 + 0.021708 0.007345 + 1 5 4py 11.478000 -1.727188 + 3.700759 -0.598393 + 1.446884 -3.813128 + 0.716815 1.901151 + 0.247919 -0.262425 + 0.066918 0.006339 + 0.021708 0.007345 + 1 5 4pz 11.478000 -1.727188 + 3.700759 -0.598393 + 1.446884 -3.813128 + 0.716815 1.901151 + 0.247919 -0.262425 + 0.066918 0.006339 + 0.021708 0.007345 + + Atomic covalent radius [Angstrom]: 0.320 + + Atomic van der Waals radius [Angstrom]: 1.090 + + GTH Potential information for GTH-PBE-q1 + + Description: Goedecker-Teter-Hutter pseudopotential + Goedecker et al., PRB 54, 1703 (1996) + Hartwigsen et al., PRB 58, 3641 (1998) + Krack, TCA 114, 145 (2005) + + Gaussian exponent of the core charge distribution: 12.500000 + Electronic configuration (s p d ...): 1 + + Parameters of the local part of the GTH pseudopotential: + + rloc C1 C2 C3 C4 + 0.200000 -4.178900 0.724463 + + + MOLECULE KIND INFORMATION + + + All atoms are their own molecule, skipping detailed information + + + TOTAL NUMBERS AND MAXIMUM NUMBERS + + Total number of - Atomic kinds: 2 + - Atoms: 6 + - Shell sets: 6 + - Shells: 36 + - Primitive Cartesian functions: 42 + - Cartesian basis functions: 84 + - Spherical basis functions: 80 + + Maximum angular momentum of- Orbital basis functions: 2 + - Local part of the GTH pseudopotential: 2 + - Non-local part of the GTH pseudopotential: 0 + + + MODULE QUICKSTEP: ATOMIC COORDINATES IN ANGSTROM + + Atom Kind Element X Y Z Z(eff) Mass + 1 1 C 6 6.877573 5.937481 5.000001 4.0000 12.0107 + 2 1 C 6 5.546581 5.937481 5.000002 4.0000 12.0107 + 3 2 H 1 7.424154 6.874961 5.000004 1.0000 1.0079 + 4 2 H 1 7.424153 5.000000 5.000000 1.0000 1.0079 + 5 2 H 1 5.000000 6.874962 5.000000 1.0000 1.0079 + 6 2 H 1 5.000000 5.000000 5.000004 1.0000 1.0079 + + + + SCF PARAMETERS Density guess: RESTART + -------------------------------------------------------- + max_scf: 40 + max_scf_history: 0 + max_diis: 4 + -------------------------------------------------------- + eps_scf: 1.00E-06 + eps_scf_history: 0.00E+00 + eps_diis: 1.00E-01 + eps_eigval: 1.00E-05 + -------------------------------------------------------- + level_shift [a.u.]: 0.000000 + -------------------------------------------------------- + Outer loop SCF in use + No variables optimised in outer loop + eps_scf 1.00E-06 + max_scf 50 + No outer loop optimization + step_size 5.00E-01 + + PW_GRID| Information for grid number 1 + PW_GRID| Grid distributed over 4 processors + PW_GRID| Real space group dimensions 4 1 + PW_GRID| the grid is blocked: NO + PW_GRID| Cutoff [a.u.] 300.0 + PW_GRID| spherical cutoff: NO + PW_GRID| Bounds 1 -94 94 Points: 189 + PW_GRID| Bounds 2 -87 87 Points: 175 + PW_GRID| Bounds 3 -75 74 Points: 150 + PW_GRID| Volume element (a.u.^3) 0.2007E-02 Volume (a.u.^3) 9956.2508 + PW_GRID| Grid span FULLSPACE + PW_GRID| Distribution Average Max Min + PW_GRID| G-Vectors 1240312.5 1240407 1240218 + PW_GRID| G-Rays 6562.5 6563 6562 + PW_GRID| Real Space Points 1240312.5 1260000 1233750 + + PW_GRID| Information for grid number 2 + PW_GRID| Number of the reference grid 1 + PW_GRID| Grid distributed over 4 processors + PW_GRID| Real space group dimensions 4 1 + PW_GRID| the grid is blocked: NO + PW_GRID| Cutoff [a.u.] 100.0 + PW_GRID| spherical cutoff: NO + PW_GRID| Bounds 1 -52 52 Points: 105 + PW_GRID| Bounds 2 -52 52 Points: 105 + PW_GRID| Bounds 3 -44 43 Points: 88 + PW_GRID| Volume element (a.u.^3) 0.1026E-01 Volume (a.u.^3) 9956.2508 + PW_GRID| Grid span FULLSPACE + PW_GRID| Distribution Average Max Min + PW_GRID| G-Vectors 242550.0 242655 242445 + PW_GRID| G-Rays 2310.0 2311 2309 + PW_GRID| Real Space Points 242550.0 249480 240240 + + PW_GRID| Information for grid number 3 + PW_GRID| Number of the reference grid 1 + PW_GRID| Grid distributed over 4 processors + PW_GRID| Real space group dimensions 4 1 + PW_GRID| the grid is blocked: NO + PW_GRID| Cutoff [a.u.] 33.3 + PW_GRID| spherical cutoff: NO + PW_GRID| Bounds 1 -31 31 Points: 63 + PW_GRID| Bounds 2 -30 29 Points: 60 + PW_GRID| Bounds 3 -25 24 Points: 50 + PW_GRID| Volume element (a.u.^3) 0.5268E-01 Volume (a.u.^3) 9956.2508 + PW_GRID| Grid span FULLSPACE + PW_GRID| Distribution Average Max Min + PW_GRID| G-Vectors 47250.0 47313 47187 + PW_GRID| G-Rays 750.0 751 749 + PW_GRID| Real Space Points 47250.0 48000 45000 + + PW_GRID| Information for grid number 4 + PW_GRID| Number of the reference grid 1 + PW_GRID| Grid distributed over 4 processors + PW_GRID| Real space group dimensions 4 1 + PW_GRID| the grid is blocked: NO + PW_GRID| Cutoff [a.u.] 11.1 + PW_GRID| spherical cutoff: NO + PW_GRID| Bounds 1 -17 17 Points: 35 + PW_GRID| Bounds 2 -16 16 Points: 33 + PW_GRID| Bounds 3 -15 14 Points: 30 + PW_GRID| Volume element (a.u.^3) 0.2873 Volume (a.u.^3) 9956.2508 + PW_GRID| Grid span FULLSPACE + PW_GRID| Distribution Average Max Min + PW_GRID| G-Vectors 8662.5 8680 8645 + PW_GRID| G-Rays 247.5 248 247 + PW_GRID| Real Space Points 8662.5 8910 7920 + + PW_GRID| Information for grid number 5 + PW_GRID| Number of the reference grid 1 + PW_GRID| Grid distributed over 4 processors + PW_GRID| Real space group dimensions 4 1 + PW_GRID| the grid is blocked: NO + PW_GRID| Cutoff [a.u.] 3.7 + PW_GRID| spherical cutoff: NO + PW_GRID| Bounds 1 -10 10 Points: 21 + PW_GRID| Bounds 2 -10 9 Points: 20 + PW_GRID| Bounds 3 -9 8 Points: 18 + PW_GRID| Volume element (a.u.^3) 1.317 Volume (a.u.^3) 9956.2508 + PW_GRID| Grid span FULLSPACE + PW_GRID| Distribution Average Max Min + PW_GRID| G-Vectors 1890.0 1911 1869 + PW_GRID| G-Rays 90.0 91 89 + PW_GRID| Real Space Points 1890.0 2160 1800 + + POISSON| Solver PERIODIC + POISSON| Periodicity XYZ + + RS_GRID| Information for grid number 1 + RS_GRID| Bounds 1 -94 94 Points: 189 + RS_GRID| Bounds 2 -87 87 Points: 175 + RS_GRID| Bounds 3 -75 74 Points: 150 + RS_GRID| Real space fully replicated + RS_GRID| Group size 1 + + RS_GRID| Information for grid number 2 + RS_GRID| Bounds 1 -52 52 Points: 105 + RS_GRID| Bounds 2 -52 52 Points: 105 + RS_GRID| Bounds 3 -44 43 Points: 88 + RS_GRID| Real space fully replicated + RS_GRID| Group size 1 + + RS_GRID| Information for grid number 3 + RS_GRID| Bounds 1 -31 31 Points: 63 + RS_GRID| Bounds 2 -30 29 Points: 60 + RS_GRID| Bounds 3 -25 24 Points: 50 + RS_GRID| Real space fully replicated + RS_GRID| Group size 1 + + RS_GRID| Information for grid number 4 + RS_GRID| Bounds 1 -17 17 Points: 35 + RS_GRID| Bounds 2 -16 16 Points: 33 + RS_GRID| Bounds 3 -15 14 Points: 30 + RS_GRID| Real space fully replicated + RS_GRID| Group size 1 + + RS_GRID| Information for grid number 5 + RS_GRID| Bounds 1 -10 10 Points: 21 + RS_GRID| Bounds 2 -10 9 Points: 20 + RS_GRID| Bounds 3 -9 8 Points: 18 + RS_GRID| Real space fully replicated + RS_GRID| Group size 1 + + BFGS| Use rational function optimization for step estimation: NO + BFGS| Use model Hessian for initial guess: YES + BFGS| Restart Hessian: NO + BFGS| Trust radius: 0.100 + + ******************************************************************************* + *** STARTING GEOMETRY OPTIMIZATION *** + *** BFGS *** + ******************************************************************************* + + Number of electrons: 12 + Number of occupied orbitals: 6 + Number of molecular orbitals: 6 + + Number of orbital functions: 80 + Number of independent orbital functions: 80 + + Extrapolation method: initial_guess + + *** WARNING in qs_initial_guess.F:306 :: User requested to restart the *** + *** wavefunction from the file named: ./parent_calc/aiida-RESTART.wfn. *** + *** This file does not exist. Please check the existence of the file or *** + *** change properly the value of the keyword WFN_RESTART_FILE_NAME. *** + *** Calculation continues using ATOMIC GUESS. *** + + + Atomic guess: The first density matrix is obtained in terms of atomic orbitals + and electronic configurations assigned to each atomic kind + + Guess for atomic kind: C + + Electronic structure + Total number of core electrons 2.00 + Total number of valence electrons 4.00 + Total number of electrons 6.00 + Multiplicity not specified + S [ 2.00] 2.00 + P 2.00 + + + ******************************************************************************* + Iteration Convergence Energy [au] + ******************************************************************************* + 1 0.106529 -5.270272483724 + 2 0.700070E-01 -5.275253796046 + 3 0.257977E-03 -5.278907327451 + 4 0.489006E-04 -5.278907347137 + 5 0.128506E-06 -5.278907348859 + + Energy components [Hartree] Total Energy :: -5.278907348859 + Band Energy :: -1.297504853113 + Kinetic Energy :: 3.437573111170 + Potential Energy :: -8.716480460029 + Virial (-V/T) :: 2.535649476576 + Core Energy :: -8.301868323195 + XC Energy :: -1.382083082551 + Coulomb Energy :: 4.405044056886 + Total Pseudopotential Energy :: -11.773288188249 + Local Pseudopotential Energy :: -12.379139771299 + Nonlocal Pseudopotential Energy :: 0.605851583050 + Confinement :: 0.338467538844 + + Orbital energies State L Occupation Energy[a.u.] Energy[eV] + + 1 0 2.000 -0.478379 -13.017346 + + 1 1 2.000 -0.170374 -4.636105 + + + Total Electron Density at R=0: 0.000341 + + Guess for atomic kind: H + + Electronic structure + Total number of core electrons 0.00 + Total number of valence electrons 1.00 + Total number of electrons 1.00 + Multiplicity not specified + S 1.00 + + + ******************************************************************************* + Iteration Convergence Energy [au] + ******************************************************************************* + 1 0.363633E-02 -0.424359639014 + 2 0.457201E-03 -0.424374328003 + 3 0.158035E-04 -0.424374562686 + 4 0.544881E-08 -0.424374562963 + + Energy components [Hartree] Total Energy :: -0.424374562963 + Band Energy :: -0.197817388557 + Kinetic Energy :: 0.463739149097 + Potential Energy :: -0.888113712060 + Virial (-V/T) :: 1.915114809241 + Core Energy :: -0.479953896523 + XC Energy :: -0.245504363650 + Coulomb Energy :: 0.301083697210 + Total Pseudopotential Energy :: -0.962570132454 + Local Pseudopotential Energy :: -0.962570132454 + Nonlocal Pseudopotential Energy :: 0.000000000000 + Confinement :: 0.188770868335 + + Orbital energies State L Occupation Energy[a.u.] Energy[eV] + + 1 0 1.000 -0.197817 -5.382885 + + + Total Electron Density at R=0: 0.235042 + Re-scaling the density matrix to get the right number of electrons + # Electrons Trace(P) Scaling factor + 12 12.000 1.000 + + + SCF WAVEFUNCTION OPTIMIZATION + + ----------------------------------- OT --------------------------------------- + Minimizer : CG : conjugate gradient + Preconditioner : FULL_SINGLE_INVERSE : inversion of + H + eS - 2*(Sc)(c^T*H*c+const)(Sc)^T + Precond_solver : DEFAULT + Line search : 2PNT : 2 energies, one gradient + stepsize : 0.08000000 energy_gap : 0.08000000 + eps_taylor : 0.10000E-15 max_taylor : 4 + ----------------------------------- OT --------------------------------------- + + Step Update method Time Convergence Total energy Change + ------------------------------------------------------------------------------ + 1 OT CG 0.80E-01 1.1 0.17512196 -12.5028932274 -1.25E+01 + 2 OT LS 0.11E+00 0.4 -13.2453329267 + 3 OT CG 0.11E+00 0.5 0.18341009 -13.2135556628 -7.11E-01 + 4 OT LS 0.40E-01 0.4 -12.7550925871 + 5 OT CG 0.40E-01 0.5 0.12115962 -13.4170797323 -2.04E-01 + 6 OT LS 0.69E-01 0.4 -13.6163466937 + 7 OT CG 0.69E-01 0.5 0.05205595 -13.6435520317 -2.26E-01 + 8 OT LS 0.86E-01 0.4 -13.6849570018 + 9 OT CG 0.86E-01 0.5 0.04097937 -13.6864314319 -4.29E-02 + 10 OT LS 0.56E-01 0.4 -13.7030296708 + 11 OT CG 0.56E-01 0.5 0.01793871 -13.7093395632 -2.29E-02 + 12 OT LS 0.12E+00 0.4 -13.7160026579 + 13 OT CG 0.12E+00 0.5 0.01365114 -13.7186417031 -9.30E-03 + 14 OT LS 0.11E+00 0.4 -13.7237671340 + 15 OT CG 0.11E+00 0.5 0.00799310 -13.7237818723 -5.14E-03 + 16 OT LS 0.77E-01 0.4 -13.7246631327 + 17 OT CG 0.77E-01 0.5 0.00402713 -13.7249554286 -1.17E-03 + 18 OT LS 0.12E+00 0.4 -13.7253552974 + 19 OT CG 0.12E+00 0.5 0.00296731 -13.7254079429 -4.53E-04 + 20 OT LS 0.81E-01 0.4 -13.7255469840 + 21 OT CG 0.81E-01 0.5 0.00158232 -13.7255792418 -1.71E-04 + 22 OT LS 0.12E+00 0.4 -13.7256424831 + 23 OT CG 0.12E+00 0.5 0.00109803 -13.7256486715 -6.94E-05 + 24 OT LS 0.95E-01 0.4 -13.7256747307 + 25 OT CG 0.95E-01 0.5 0.00053776 -13.7256760581 -2.74E-05 + 26 OT LS 0.10E+00 0.4 -13.7256830883 + 27 OT CG 0.10E+00 0.5 0.00040747 -13.7256831227 -7.06E-06 + 28 OT LS 0.95E-01 0.4 -13.7256869091 + 29 OT CG 0.95E-01 0.5 0.00025423 -13.7256869259 -3.80E-06 + 30 OT LS 0.93E-01 0.4 -13.7256883664 + 31 OT CG 0.93E-01 0.5 0.00010646 -13.7256883675 -1.44E-06 + 32 OT LS 0.16E+00 0.4 -13.7256887296 + 33 OT CG 0.16E+00 0.5 0.00010431 -13.7256888132 -4.46E-07 + 34 OT LS 0.71E-01 0.4 -13.7256886850 + 35 OT CG 0.71E-01 0.5 0.00005050 -13.7256889992 -1.86E-07 + 36 OT LS 0.12E+00 0.4 -13.7256890608 + 37 OT CG 0.12E+00 0.5 0.00002865 -13.7256890734 -7.42E-08 + 38 OT LS 0.13E+00 0.4 -13.7256890994 + 39 OT CG 0.13E+00 0.5 0.00002180 -13.7256890996 -2.62E-08 + 40 OT LS 0.68E-01 0.4 -13.7256891004 + + Leaving inner SCF loop after reaching 40 steps. + + + Electronic density on regular grids: -12.0000000000 -0.0000000000 + Core density on regular grids: 12.0000000000 -0.0000000000 + Total charge density on r-space grids: -0.0000000000 + Total charge density g-space grids: -0.0000000000 + + Overlap energy of the core charge distribution: 0.00000236921509 + Self energy of the core charge distribution: -32.31191168900799 + Core Hamiltonian energy: 10.29782692711844 + Hartree energy: 13.16260376609334 + Exchange-correlation energy: -4.87374882252720 + Dispersion energy: -0.00046165125791 + + Total energy: -13.72568910036622 + + outer SCF iter = 1 RMS gradient = 0.22E-04 energy = -13.7256891004 + + ----------------------------------- OT --------------------------------------- + Minimizer : CG : conjugate gradient + Preconditioner : FULL_SINGLE_INVERSE : inversion of + H + eS - 2*(Sc)(c^T*H*c+const)(Sc)^T + Precond_solver : DEFAULT + Line search : 2PNT : 2 energies, one gradient + stepsize : 0.08000000 energy_gap : 0.08000000 + eps_taylor : 0.10000E-15 max_taylor : 4 + ----------------------------------- OT --------------------------------------- + + Step Update method Time Convergence Total energy Change + ------------------------------------------------------------------------------ + 1 OT CG 0.80E-01 0.9 0.00000955 -13.7256891074 -7.77E-09 + 2 OT LS 0.16E+00 0.4 -13.7256891100 + 3 OT CG 0.16E+00 0.5 0.00000524 -13.7256891108 -3.42E-09 + 4 OT LS 0.13E+00 0.4 -13.7256891116 + 5 OT CG 0.13E+00 0.5 0.00000134 -13.7256891116 -8.40E-10 + 6 OT LS 0.14E+00 0.4 -13.7256891117 + 7 OT CG 0.14E+00 0.5 0.00000042 -13.7256891117 -6.22E-11 + + *** SCF run converged in 7 steps *** + + + Electronic density on regular grids: -12.0000000000 -0.0000000000 + Core density on regular grids: 12.0000000000 -0.0000000000 + Total charge density on r-space grids: -0.0000000000 + Total charge density g-space grids: -0.0000000000 + + Overlap energy of the core charge distribution: 0.00000236921509 + Self energy of the core charge distribution: -32.31191168900799 + Core Hamiltonian energy: 10.29787686915676 + Hartree energy: 13.16256223674835 + Exchange-correlation energy: -4.87375724654942 + Dispersion energy: -0.00046165125791 + + Total energy: -13.72568911169511 + + outer SCF iter = 2 RMS gradient = 0.42E-06 energy = -13.7256891117 + outer SCF loop converged in 2 iterations or 47 steps + + + !-----------------------------------------------------------------------------! + Mulliken Population Analysis + + # Atom Element Kind Atomic population Net charge + 1 C 1 4.164086 -0.164086 + 2 C 1 4.164086 -0.164086 + 3 H 2 0.917957 0.082043 + 4 H 2 0.917957 0.082043 + 5 H 2 0.917957 0.082043 + 6 H 2 0.917957 0.082043 + # Total charge 12.000000 0.000000 + + !-----------------------------------------------------------------------------! + + !-----------------------------------------------------------------------------! + Hirshfeld Charges + + #Atom Element Kind Ref Charge Population Net charge + 1 C 1 4.000 4.896 -0.896 + 2 C 1 4.000 4.896 -0.896 + 3 H 2 1.000 0.549 0.451 + 4 H 2 1.000 0.549 0.451 + 5 H 2 1.000 0.549 0.451 + 6 H 2 1.000 0.549 0.451 + + Total Charge 0.014 + !-----------------------------------------------------------------------------! + + ENERGY| Total FORCE_EVAL ( QS ) energy [a.u.]: -13.725689111701852 + + OPT| ************************************************************************** + OPT| Step number 0 + OPT| Optimization method BFGS + OPT| Total energy [hartree] -13.7256891117 + OPT| Used time [s] 23.842 + OPT| ************************************************************************** + OPT| Estimated peak process memory [MiB] 1079 + + -------------------------- + OPTIMIZATION STEP: 1 + -------------------------- + + Number of electrons: 12 + Number of occupied orbitals: 6 + Number of molecular orbitals: 6 + + Number of orbital functions: 80 + Number of independent orbital functions: 80 + + Parameters for the always stable predictor-corrector (ASPC) method: + + ASPC order: 0 + + B(1) = 1.000000 + + Extrapolation method: ASPC + + + SCF WAVEFUNCTION OPTIMIZATION + + ----------------------------------- OT --------------------------------------- + Minimizer : CG : conjugate gradient + Preconditioner : FULL_SINGLE_INVERSE : inversion of + H + eS - 2*(Sc)(c^T*H*c+const)(Sc)^T + Precond_solver : DEFAULT + Line search : 2PNT : 2 energies, one gradient + stepsize : 0.08000000 energy_gap : 0.08000000 + eps_taylor : 0.10000E-15 max_taylor : 4 + ----------------------------------- OT --------------------------------------- + + Step Update method Time Convergence Total energy Change + ------------------------------------------------------------------------------ + 1 OT CG 0.80E-01 0.4 0.00101148 -13.7260965450 -1.37E+01 + 2 OT LS 0.20E+00 0.4 -13.7261281142 + 3 OT CG 0.20E+00 0.5 0.00030205 -13.7261465312 -5.00E-05 + 4 OT LS 0.14E+00 0.4 -13.7261487233 + 5 OT CG 0.14E+00 0.5 0.00008172 -13.7261494859 -2.95E-06 + 6 OT LS 0.14E+00 0.4 -13.7261497044 + 7 OT CG 0.14E+00 0.5 0.00001960 -13.7261497044 -2.19E-07 + 8 OT LS 0.19E+00 0.4 -13.7261497205 + 9 OT CG 0.19E+00 0.5 0.00000383 -13.7261497219 -1.75E-08 + 10 OT LS 0.20E+00 0.4 -13.7261497226 + 11 OT CG 0.20E+00 0.5 0.00000087 -13.7261497226 -7.20E-10 + + *** SCF run converged in 11 steps *** + + + Electronic density on regular grids: -12.0000000000 -0.0000000000 + Core density on regular grids: 12.0000000000 -0.0000000000 + Total charge density on r-space grids: -0.0000000000 + Total charge density g-space grids: -0.0000000000 + + Overlap energy of the core charge distribution: 0.00000221816287 + Self energy of the core charge distribution: -32.31191168900799 + Core Hamiltonian energy: 10.27764059020297 + Hartree energy: 13.17625315507601 + Exchange-correlation energy: -4.86766614436412 + Dispersion energy: -0.00046785269954 + + Total energy: -13.72614972262980 + + outer SCF iter = 1 RMS gradient = 0.87E-06 energy = -13.7261497226 + outer SCF loop converged in 1 iterations or 11 steps + + + !-----------------------------------------------------------------------------! + Mulliken Population Analysis + + # Atom Element Kind Atomic population Net charge + 1 C 1 4.163747 -0.163747 + 2 C 1 4.163747 -0.163747 + 3 H 2 0.918127 0.081873 + 4 H 2 0.918127 0.081873 + 5 H 2 0.918127 0.081873 + 6 H 2 0.918127 0.081873 + # Total charge 12.000000 -0.000000 + + !-----------------------------------------------------------------------------! + + !-----------------------------------------------------------------------------! + Hirshfeld Charges + + #Atom Element Kind Ref Charge Population Net charge + 1 C 1 4.000 4.896 -0.896 + 2 C 1 4.000 4.896 -0.896 + 3 H 2 1.000 0.549 0.451 + 4 H 2 1.000 0.549 0.451 + 5 H 2 1.000 0.549 0.451 + 6 H 2 1.000 0.549 0.451 + + Total Charge 0.014 + !-----------------------------------------------------------------------------! + + ENERGY| Total FORCE_EVAL ( QS ) energy [a.u.]: -13.726149722666458 + + OPT| ************************************************************************** + OPT| Step number 1 + OPT| Optimization method BFGS + OPT| Total energy [hartree] -13.7261497227 + OPT| Effective energy change [hartree] -0.0004606110 + OPT| Predicted energy change [hartree] -0.0003565862 + OPT| Scaling factor 0.0000000000 + OPT| Step size 0.0376199090 + OPT| Trust radius 0.1000000000 + OPT| Decrease in energy YES + OPT| Used time [s] 5.343 + OPT| + OPT| Maximum step size 0.0376199090 + OPT| Convergence limit for maximum step size 0.0030000000 + OPT| Maximum step size is converged NO + OPT| + OPT| RMS step size 0.0189431999 + OPT| Convergence limit for RMS step size 0.0015000000 + OPT| RMS step size is converged NO + OPT| + OPT| Maximum gradient 0.0015528293 + OPT| Convergence limit for maximum gradient 0.0004500000 + OPT| Maximum gradient is converged NO + OPT| + OPT| RMS gradient 0.0007719361 + OPT| Convergence limit for RMS gradient 0.0003000000 + OPT| RMS gradient is converged NO + OPT| ************************************************************************** + OPT| Estimated peak process memory after this step [MiB] 1079 + + -------------------------- + OPTIMIZATION STEP: 2 + -------------------------- + + Number of electrons: 12 + Number of occupied orbitals: 6 + Number of molecular orbitals: 6 + + Number of orbital functions: 80 + Number of independent orbital functions: 80 + + Parameters for the always stable predictor-corrector (ASPC) method: + + ASPC order: 0 + + B(1) = 2.000000 + B(2) = -1.000000 + + Extrapolation method: ASPC + + + SCF WAVEFUNCTION OPTIMIZATION + + ----------------------------------- OT --------------------------------------- + Minimizer : CG : conjugate gradient + Preconditioner : FULL_SINGLE_INVERSE : inversion of + H + eS - 2*(Sc)(c^T*H*c+const)(Sc)^T + Precond_solver : DEFAULT + Line search : 2PNT : 2 energies, one gradient + stepsize : 0.08000000 energy_gap : 0.08000000 + eps_taylor : 0.10000E-15 max_taylor : 4 + ----------------------------------- OT --------------------------------------- + + Step Update method Time Convergence Total energy Change + ------------------------------------------------------------------------------ + 1 OT CG 0.80E-01 0.4 0.00061049 -13.7261733873 -1.37E+01 + 2 OT LS 0.21E+00 0.4 -13.7261850037 + 3 OT CG 0.21E+00 0.5 0.00015176 -13.7261923873 -1.90E-05 + 4 OT LS 0.15E+00 0.4 -13.7261930827 + 5 OT CG 0.15E+00 0.5 0.00003549 -13.7261932214 -8.34E-07 + 6 OT LS 0.13E+00 0.4 -13.7261932609 + 7 OT CG 0.13E+00 0.5 0.00001187 -13.7261932617 -4.02E-08 + 8 OT LS 0.17E+00 0.4 -13.7261932672 + 9 OT CG 0.17E+00 0.5 0.00000235 -13.7261932675 -5.82E-09 + 10 OT LS 0.20E+00 0.4 -13.7261932677 + 11 OT CG 0.20E+00 0.5 0.00000052 -13.7261932677 -2.68E-10 + + *** SCF run converged in 11 steps *** + + + Electronic density on regular grids: -12.0000000000 -0.0000000000 + Core density on regular grids: 12.0000000000 -0.0000000000 + Total charge density on r-space grids: -0.0000000000 + Total charge density g-space grids: -0.0000000000 + + Overlap energy of the core charge distribution: 0.00000212715790 + Self energy of the core charge distribution: -32.31191168900799 + Core Hamiltonian energy: 10.26566042888386 + Hartree energy: 13.18454564204831 + Exchange-correlation energy: -4.86401939920950 + Dispersion energy: -0.00047037761701 + + Total energy: -13.72619326774442 + + outer SCF iter = 1 RMS gradient = 0.52E-06 energy = -13.7261932677 + outer SCF loop converged in 1 iterations or 11 steps + + + !-----------------------------------------------------------------------------! + Mulliken Population Analysis + + # Atom Element Kind Atomic population Net charge + 1 C 1 4.163480 -0.163480 + 2 C 1 4.163480 -0.163480 + 3 H 2 0.918260 0.081740 + 4 H 2 0.918260 0.081740 + 5 H 2 0.918260 0.081740 + 6 H 2 0.918260 0.081740 + # Total charge 12.000000 -0.000000 + + !-----------------------------------------------------------------------------! + + !-----------------------------------------------------------------------------! + Hirshfeld Charges + + #Atom Element Kind Ref Charge Population Net charge + 1 C 1 4.000 4.896 -0.896 + 2 C 1 4.000 4.896 -0.896 + 3 H 2 1.000 0.549 0.451 + 4 H 2 1.000 0.549 0.451 + 5 H 2 1.000 0.549 0.451 + 6 H 2 1.000 0.549 0.451 + + Total Charge 0.014 + !-----------------------------------------------------------------------------! + + ENERGY| Total FORCE_EVAL ( QS ) energy [a.u.]: -13.726193267757864 + + OPT| ************************************************************************** + OPT| Step number 2 + OPT| Optimization method BFGS + OPT| Total energy [hartree] -13.7261932678 + OPT| Effective energy change [hartree] -0.0000435451 + OPT| Predicted energy change [hartree] -0.0000436237 + OPT| Scaling factor 0.0000000000 + OPT| Step size 0.0155526727 + OPT| Trust radius 0.1000000000 + OPT| Decrease in energy YES + OPT| Used time [s] 5.376 + OPT| + OPT| Maximum step size 0.0155526727 + OPT| Convergence limit for maximum step size 0.0030000000 + OPT| Maximum step size is converged NO + OPT| + OPT| RMS step size 0.0076510488 + OPT| Convergence limit for RMS step size 0.0015000000 + OPT| RMS step size is converged NO + OPT| + OPT| Maximum gradient 0.0003036619 + OPT| Convergence limit for maximum gradient 0.0004500000 + OPT| Maximum gradient is converged YES + OPT| + OPT| RMS gradient 0.0001078140 + OPT| Convergence limit for RMS gradient 0.0003000000 + OPT| RMS gradient is converged YES + OPT| ************************************************************************** + OPT| Estimated peak process memory after this step [MiB] 1079 + + -------------------------- + OPTIMIZATION STEP: 3 + -------------------------- + + Number of electrons: 12 + Number of occupied orbitals: 6 + Number of molecular orbitals: 6 + + Number of orbital functions: 80 + Number of independent orbital functions: 80 + + Parameters for the always stable predictor-corrector (ASPC) method: + + ASPC order: 1 + + B(1) = 2.500000 + B(2) = -2.000000 + B(3) = 0.500000 + + Extrapolation method: ASPC + + + SCF WAVEFUNCTION OPTIMIZATION + + ----------------------------------- OT --------------------------------------- + Minimizer : CG : conjugate gradient + Preconditioner : FULL_SINGLE_INVERSE : inversion of + H + eS - 2*(Sc)(c^T*H*c+const)(Sc)^T + Precond_solver : DEFAULT + Line search : 2PNT : 2 energies, one gradient + stepsize : 0.08000000 energy_gap : 0.08000000 + eps_taylor : 0.10000E-15 max_taylor : 4 + ----------------------------------- OT --------------------------------------- + + Step Update method Time Convergence Total energy Change + ------------------------------------------------------------------------------ + 1 OT CG 0.80E-01 0.4 0.00017484 -13.7261921885 -1.37E+01 + 2 OT LS 0.15E+00 0.4 -13.7261930449 + 3 OT CG 0.15E+00 0.5 0.00006751 -13.7261932739 -1.09E-06 + 4 OT LS 0.14E+00 0.4 -13.7261934271 + 5 OT CG 0.14E+00 0.5 0.00001289 -13.7261934275 -1.54E-07 + 6 OT LS 0.18E+00 0.4 -13.7261934343 + 7 OT CG 0.18E+00 0.5 0.00000255 -13.7261934346 -7.06E-09 + 8 OT LS 0.17E+00 0.4 -13.7261934349 + 9 OT CG 0.17E+00 0.5 0.00000043 -13.7261934349 -2.72E-10 + + *** SCF run converged in 9 steps *** + + + Electronic density on regular grids: -12.0000000000 -0.0000000000 + Core density on regular grids: 12.0000000000 -0.0000000000 + Total charge density on r-space grids: -0.0000000000 + Total charge density g-space grids: -0.0000000000 + + Overlap energy of the core charge distribution: 0.00000212008668 + Self energy of the core charge distribution: -32.31191168900799 + Core Hamiltonian energy: 10.26484863897842 + Hartree energy: 13.18511914232630 + Exchange-correlation energy: -4.86378114729310 + Dispersion energy: -0.00047049995297 + + Total energy: -13.72619343486265 + + outer SCF iter = 1 RMS gradient = 0.43E-06 energy = -13.7261934349 + outer SCF loop converged in 1 iterations or 9 steps + + + !-----------------------------------------------------------------------------! + Mulliken Population Analysis + + # Atom Element Kind Atomic population Net charge + 1 C 1 4.163453 -0.163453 + 2 C 1 4.163453 -0.163453 + 3 H 2 0.918274 0.081726 + 4 H 2 0.918274 0.081726 + 5 H 2 0.918273 0.081727 + 6 H 2 0.918273 0.081727 + # Total charge 12.000000 -0.000000 + + !-----------------------------------------------------------------------------! + + !-----------------------------------------------------------------------------! + Hirshfeld Charges + + #Atom Element Kind Ref Charge Population Net charge + 1 C 1 4.000 4.896 -0.896 + 2 C 1 4.000 4.896 -0.896 + 3 H 2 1.000 0.549 0.451 + 4 H 2 1.000 0.549 0.451 + 5 H 2 1.000 0.549 0.451 + 6 H 2 1.000 0.549 0.451 + + Total Charge 0.014 + !-----------------------------------------------------------------------------! + + ENERGY| Total FORCE_EVAL ( QS ) energy [a.u.]: -13.726193434870929 + + OPT| ************************************************************************** + OPT| Step number 3 + OPT| Optimization method BFGS + OPT| Total energy [hartree] -13.7261934349 + OPT| Effective energy change [hartree] -0.0000001671 + OPT| Predicted energy change [hartree] -0.0000001203 + OPT| Scaling factor 0.0000000000 + OPT| Step size 0.0003463702 + OPT| Trust radius 0.1000000000 + OPT| Decrease in energy YES + OPT| Used time [s] 4.514 + OPT| + OPT| Maximum step size 0.0003463702 + OPT| Convergence limit for maximum step size 0.0030000000 + OPT| Maximum step size is converged YES + OPT| + OPT| RMS step size 0.0001827720 + OPT| Convergence limit for RMS step size 0.0015000000 + OPT| RMS step size is converged YES + OPT| + OPT| Maximum gradient 0.0000728784 + OPT| Convergence limit for maximum gradient 0.0004500000 + OPT| Maximum gradient is converged YES + OPT| + OPT| RMS gradient 0.0000258819 + OPT| Convergence limit for RMS gradient 0.0003000000 + OPT| RMS gradient is converged YES + OPT| ************************************************************************** + OPT| Estimated peak process memory after this step [MiB] 1081 + + ******************************************************************************* + *** GEOMETRY OPTIMIZATION COMPLETED *** + ******************************************************************************* + + Reevaluating energy at the minimum + + Number of electrons: 12 + Number of occupied orbitals: 6 + Number of molecular orbitals: 6 + + Number of orbital functions: 80 + Number of independent orbital functions: 80 + + Parameters for the always stable predictor-corrector (ASPC) method: + + ASPC order: 2 + + B(1) = 2.800000 + B(2) = -2.800000 + B(3) = 1.200000 + B(4) = -0.200000 + + Extrapolation method: ASPC + + + SCF WAVEFUNCTION OPTIMIZATION + + ----------------------------------- OT --------------------------------------- + Minimizer : CG : conjugate gradient + Preconditioner : FULL_SINGLE_INVERSE : inversion of + H + eS - 2*(Sc)(c^T*H*c+const)(Sc)^T + Precond_solver : DEFAULT + Line search : 2PNT : 2 energies, one gradient + stepsize : 0.08000000 energy_gap : 0.08000000 + eps_taylor : 0.10000E-15 max_taylor : 4 + ----------------------------------- OT --------------------------------------- + + Step Update method Time Convergence Total energy Change + ------------------------------------------------------------------------------ + 1 OT CG 0.80E-01 0.4 0.00022600 -13.7261909453 -1.37E+01 + 2 OT LS 0.18E+00 0.4 -13.7261924800 + 3 OT CG 0.18E+00 0.5 0.00008436 -13.7261931992 -2.25E-06 + 4 OT LS 0.13E+00 0.4 -13.7261933785 + 5 OT CG 0.13E+00 0.5 0.00002003 -13.7261934190 -2.20E-07 + 6 OT LS 0.16E+00 0.4 -13.7261934335 + 7 OT CG 0.16E+00 0.5 0.00000429 -13.7261934340 -1.50E-08 + 8 OT LS 0.19E+00 0.4 -13.7261934348 + 9 OT CG 0.19E+00 0.5 0.00000086 -13.7261934348 -8.28E-10 + + *** SCF run converged in 9 steps *** + + + Electronic density on regular grids: -12.0000000000 -0.0000000000 + Core density on regular grids: 12.0000000000 -0.0000000000 + Total charge density on r-space grids: -0.0000000000 + Total charge density g-space grids: -0.0000000000 + + Overlap energy of the core charge distribution: 0.00000212008668 + Self energy of the core charge distribution: -32.31191168900799 + Core Hamiltonian energy: 10.26485101565855 + Hartree energy: 13.18511786800448 + Exchange-correlation energy: -4.86378224962235 + Dispersion energy: -0.00047049995297 + + Total energy: -13.72619343483359 + + outer SCF iter = 1 RMS gradient = 0.86E-06 energy = -13.7261934348 + outer SCF loop converged in 1 iterations or 9 steps + + + The electron density is written in cube file format to the file: + + aiida-ELECTRON_DENSITY-1_3.cube + + !-----------------------------------------------------------------------------! + Mulliken Population Analysis + + # Atom Element Kind Atomic population Net charge + 1 C 1 4.163454 -0.163454 + 2 C 1 4.163452 -0.163452 + 3 H 2 0.918274 0.081726 + 4 H 2 0.918274 0.081726 + 5 H 2 0.918274 0.081726 + 6 H 2 0.918274 0.081726 + # Total charge 12.000000 0.000000 + + !-----------------------------------------------------------------------------! + + !-----------------------------------------------------------------------------! + Hirshfeld Charges + + #Atom Element Kind Ref Charge Population Net charge + 1 C 1 4.000 4.896 -0.896 + 2 C 1 4.000 4.896 -0.896 + 3 H 2 1.000 0.549 0.451 + 4 H 2 1.000 0.549 0.451 + 5 H 2 1.000 0.549 0.451 + 6 H 2 1.000 0.549 0.451 + + Total Charge 0.014 + !-----------------------------------------------------------------------------! + + Eigenvalues of the occupied subspace spin 1 + --------------------------------------------- + -0.68412780 -0.51657878 -0.41454219 -0.36888136 + -0.30660434 -0.24103549 + Fermi Energy [eV] : -6.558909 + + Lowest Eigenvalues of the unoccupied subspace spin 1 + ----------------------------------------------------- + OT| Eigensolver reached convergence in 53 iterations + -0.02897857 + + HOMO - LUMO gap [eV] : 5.770362 + + ENERGY| Total FORCE_EVAL ( QS ) energy [a.u.]: -13.726193434833586 + + ------------------------------------------------------------------------------- + - - + - DBCSR STATISTICS - + - - + ------------------------------------------------------------------------------- + COUNTER TOTAL BLAS SMM ACC + flops 6 x 1 x 6 144 0.0% 0.0% 100.0% (*) + flops 1 x 1 x 1 594 0.0% 0.0% 100.0% (*) + flops 6 x 1 x 9 864 0.0% 0.0% 100.0% (*) + flops 9 x 1 x 6 864 0.0% 0.0% 100.0% (*) + flops 6 x 1 x 22 1056 0.0% 0.0% 100.0% (*) + flops 22 x 1 x 6 1056 0.0% 0.0% 100.0% (*) + flops 7 x 1 x 7 2646 0.0% 0.0% 100.0% (*) + flops 7 x 7 x 9 7056 0.0% 0.0% 100.0% + flops 1 x 1 x 9 7416 0.0% 0.0% 100.0% (*) + flops 7 x 7 x 22 8624 0.0% 0.0% 100.0% + flops 1 x 1 x 22 9064 0.0% 0.0% 100.0% (*) + flops 9 x 1 x 1 11520 0.0% 0.0% 100.0% (*) + flops 7 x 1 x 9 13608 0.0% 0.0% 100.0% (*) + flops 9 x 1 x 7 13608 0.0% 0.0% 100.0% (*) + flops 22 x 1 x 1 14080 0.0% 0.0% 100.0% (*) + flops 7 x 1 x 22 16632 0.0% 0.0% 100.0% (*) + flops 22 x 1 x 7 16632 0.0% 0.0% 100.0% (*) + flops 9 x 7 x 9 36288 0.0% 0.0% 100.0% + flops 22 x 7 x 9 44352 0.0% 0.0% 100.0% + flops 9 x 7 x 22 44352 0.0% 0.0% 100.0% + flops 22 x 7 x 22 54208 0.0% 0.0% 100.0% + flops 6 x 6 x 6 151200 0.0% 0.0% 100.0% + flops 9 x 1 x 9 352512 0.0% 0.0% 100.0% (*) + flops 22 x 1 x 9 430848 0.0% 0.0% 100.0% (*) + flops 9 x 1 x 22 430848 0.0% 0.0% 100.0% (*) + flops 22 x 1 x 22 526592 0.0% 0.0% 100.0% (*) + flops 6 x 6 x 9 588384 0.0% 0.0% 100.0% + flops 6 x 6 x 22 719136 0.0% 0.0% 100.0% + flops 9 x 6 x 6 808704 0.0% 0.0% 100.0% + flops 22 x 9 x 6 969408 0.0% 0.0% 100.0% + flops 9 x 22 x 6 969408 0.0% 0.0% 100.0% + flops 22 x 6 x 6 988416 0.0% 0.0% 100.0% + flops 9 x 9 x 6 991440 0.0% 0.0% 100.0% + flops 22 x 22 x 6 1777248 0.0% 0.0% 100.0% + flops 9 x 6 x 9 3483648 0.0% 0.0% 100.0% + flops 22 x 6 x 9 4257792 0.0% 0.0% 100.0% + flops 9 x 6 x 22 4257792 0.0% 0.0% 100.0% + flops 22 x 6 x 22 5203968 0.0% 0.0% 100.0% + + *** WARNING in dbcsr_mm_sched.F:613 :: (*) ACC Untuned kernels, consider *** + *** to run the ACC tuning procedure for them *** + + flops inhomo. stacks 0 0.0% 0.0% 0.0% + flops total 27.212008E+06 0.0% 0.0% 100.0% + flops max/rank 13.390016E+06 0.0% 0.0% 100.0% + matmuls inhomo. stacks 0 0.0% 0.0% 0.0% + matmuls total 21022 0.0% 0.0% 100.0% + number of processed stacks 11446 0.0% 0.0% 100.0% + average stack size 0.0 0.0 1.8 + marketing flops 30.373304E+06 + ------------------------------------------------------------------------------- + # multiplications 2012 + max memory usage/rank 19.240976E+09 + # max total images/rank 1 + # max 3D layers 1 + # MPI messages exchanged 16096 + MPI messages size (bytes): + total size 24.055240E+06 + min size 0.000000E+00 + max size 12.800000E+03 + average size 1.494486E+03 + MPI breakdown and total messages size (bytes): + size <= 128 10029 9264 + 128 < size <= 8192 4619 5511576 + 8192 < size <= 32768 1448 18534400 + 32768 < size <= 131072 0 0 + 131072 < size <= 4194304 0 0 + 4194304 < size <= 16777216 0 0 + 16777216 < size 0 0 + ------------------------------------------------------------------------------- + - - + - DBCSR MESSAGE PASSING PERFORMANCE - + - - + ------------------------------------------------------------------------------- + ROUTINE CALLS AVE VOLUME [Bytes] + MP_Bcast 39 12. + MP_Allreduce 6659 8. + MP_Alltoall 7695 268. + MP_ISend 16060 535. + MP_IRecv 16060 444. + ------------------------------------------------------------------------------- + + ------------------------------------------------------------------------------- + - - + - DBM STATISTICS - + - - + ------------------------------------------------------------------------------- + M x N x K COUNT PERCENT + ------------------------------------------------------------------------------- + + ------------------------------------------------------------------------------- + - - + - GRID STATISTICS - + - - + ------------------------------------------------------------------------------- + LP KERNEL BACKEND COUNT PERCENT + 2 collocate ortho GPU 244104 32.65% + 3 collocate ortho GPU 178848 23.92% + 2 integrate ortho GPU 122052 16.32% + 3 integrate ortho GPU 100044 13.38% + 4 collocate ortho GPU 61364 8.21% + 4 integrate ortho GPU 38458 5.14% + 5 integrate ortho GPU 2668 0.36% + 0 collocate general CPU 60 0.01% + 1 collocate ortho CPU 56 0.01% + 0 integrate general CPU 30 0.00% + 2 collocate ortho CPU 28 0.00% + 1 integrate general CPU 24 0.00% + ------------------------------------------------------------------------------- + + MEMORY| Estimated peak process memory [MiB] 1092 + + ------------------------------------------------------------------------------- + ---- MULTIGRID INFO ---- + ------------------------------------------------------------------------------- + count for grid 1: 51002 cutoff [a.u.] 300.00 + count for grid 2: 44201 cutoff [a.u.] 100.00 + count for grid 3: 42021 cutoff [a.u.] 33.33 + count for grid 4: 31383 cutoff [a.u.] 11.11 + count for grid 5: 25502 cutoff [a.u.] 3.70 + total gridlevel count : 194109 + + ------------------------------------------------------------------------------- + - - + - MESSAGE PASSING PERFORMANCE - + - - + ------------------------------------------------------------------------------- + + ROUTINE CALLS AVE VOLUME [Bytes] + MP_Group 5 + MP_Bcast 1761 198884. + MP_Allreduce 5437 187. + MP_Sync 91 + MP_Alltoall 1342 47249250. + MP_SendRecv 1488 2581353. + MP_ISendRecv 777 2772741. + MP_Wait 777 + MP_comm_split 86 + MP_Write_All 4 1175592. + ------------------------------------------------------------------------------- + + + ------------------------------------------------------------------------------- + - - + - R E F E R E N C E S - + - - + ------------------------------------------------------------------------------- + + CP2K version 2024.3, the CP2K developers group (2024). + CP2K is freely available from https://www.cp2k.org/ . + + T. D. Kuehne, M. Iannuzzi, M. Del Ben, V. V. Rybkin, P. Seewald, F. Stein, T. + Laino, R. Z. Khaliullin, O. Schuett, F. Schiffmann, D. Golze, J. Wilhelm, S. + Chulkov, M. H. Bani-Hashemian, V. Weber, U. Borstnik, M. Taillefumier, A. S. + Jakobovits, A. Lazzaro, H. Pabst, T. Mueller, R. Schade, M. Guidon, S. + Andermatt, N. Holmberg, G. K. Schenter, A. Hehn, A. Bussy, F. Belleflamme, G. + Tabacchi, A. Gloess, M. Lass, I. Bethune, C. J. Mundy, C. Plessl, M. Watkins, + J. VandeVondele, M. Krack, J. Hutter. + J. Chem. Phys. 152, 194103 (2020). + CP2K: An electronic structure and molecular dynamics software package - + Quickstep: Efficient and accurate electronic structure calculations. + https://doi.org/10.1063/5.0007045 + + L. Goerigk, A. Hansen, C. Bauer, S. Ehrlich, A. Najibi, S. Grimme. + Phys. Chem. Chem. Phys. 19, 32184-32215 (2017). + A look at the density functional theory zoo with the advanced GMTKN55 database + for general main group thermochemistry, kinetics and noncovalent interactions. + https://doi.org/10.1039/C7CP04913G + + O. Schuett, P. Messmer, J. Hutter, J. VandeVondele. + Electronic Structure Calculations on Graphics Processing Units, 173-190 (2016). + GPU-Accelerated Sparse Matrix-Matrix Multiplication for Linear Scaling Density + Functional Theory. + https://doi.org/10.1002/9781118670712.ch8 + + J. Hutter, M. Iannuzzi, F. Schiffmann, J. VandeVondele. + WIREs Comput Mol Sci. 4, 15-25 (2014). + CP2K: atomistic simulations of condensed matter systems. + https://doi.org/10.1002/wcms.1159 + + U. Borstnik, J. VandeVondele, V. Weber, J. Hutter. + Parallel Comput. 40, 47-58 (2014). + Sparse matrix multiplication: The distributed block-compressed sparse row + library. + https://doi.org/10.1016/j.parco.2014.03.012 + + A. Marek, V. Blum, R. Johanni, V. Havu, B. Lang, T. Auckenthaler, A. Heinecke, + H. Bungartz, H. Lederer. + J. Phys. Condens. Matter 26, 213201 (2014). + The ELPA library: scalable parallel eigenvalue solutions for electronic + structure theory and computational science. + https://doi.org/10.1088/0953-8984/26/21/213201 + + S. Grimme, S. Ehrlich, L. Goerigk. + J. Comput. Chem. 32, 1456 (2011). + Effect of the damping function in dispersion corrected density functional + theory. + https://doi.org/10.1002/jcc.21759 + + S. Grimme, J. Antony, S. Ehrlich, H. Krieg. + J. Chem. Phys. 132, 154104 (2010). + A consistent and accurate ab initio parametrization of density functional + dispersion correction (DFT-D) for the 94 elements H-Pu. + https://doi.org/10.1063/1.3382344 + + J. VandeVondele, J. Hutter. + J. Chem. Phys. 127, 114105 (2007). + Gaussian basis sets for accurate calculations on molecular systems in gas and + condensed phases. + https://doi.org/10.1063/1.2770708 + + T. D. Kühne, M. Krack, F. R. Mohamed, M. Parrinello. + Phys. Rev. Lett. 98, 066401 (2007). + Efficient and accurate Car-Parrinello-like approach to Born-Oppenheimer + molecular dynamics. + https://doi.org/10.1103/PhysRevLett.98.066401 + + J. VandeVondele, M. Krack, F. Mohamed, M. Parrinello, T. Chassaing, J. Hutter. + Comput. Phys. Commun. 167, 103-128 (2005). + QUICKSTEP: Fast and accurate density functional calculations using a mixed + Gaussian and plane waves approach. + https://doi.org/10.1016/j.cpc.2004.12.014 + + M. Krack. + Theor. Chem. Acc. 114, 145-152 (2005). + Pseudopotentials for H to Kr optimized for gradient-corrected + exchange-correlation functionals. + https://doi.org/10.1007/s00214-005-0655-y + + M. Frigo, S. G. Johnson. + Proc. IEEE 93, 216-231 (2005). + The design and implementation of FFTW3. + https://doi.org/10.1109/JPROC.2004.840301 + + J. Kolafa. + J. Comput. Chem. 25, 335-342 (2004). + Time-reversible always stable predictor-corrector method for molecular dynamics + of polarizable molecules. + https://doi.org/10.1002/jcc.10385 + + J. VandeVondele, J. Hutter. + J. Chem. Phys. 118, 4365-4369 (2003). + An efficient orbital transformation method for electronic structure + calculations. + https://doi.org/10.1063/1.1543154 + + C. Hartwigsen, S. Goedecker, J. Hutter. + Phys. Rev. B 58, 3641-3662 (1998). + Relativistic separable dual-space Gaussian pseudopotentials from H to Rn. + https://doi.org/10.1103/PhysRevB.58.3641 + + G. Lippert, J. Hutter, M. Parrinello. + Mol. Phys. 92, 477-487 (1997). + A hybrid Gaussian and plane wave density functional scheme. + https://doi.org/10.1080/002689797170220 + + S. Goedecker, M. Teter, J. Hutter. + Phys. Rev. B 54, 1703-1710 (1996). + Separable dual-space Gaussian pseudopotentials. + https://doi.org/10.1103/PhysRevB.54.1703 + + J. P. Perdew, K. Burke, M. Ernzerhof. + Phys. Rev. Lett. 77, 3865-3868 (1996). + Generalized gradient approximation made simple. + https://doi.org/10.1103/PhysRevLett.77.3865 + + + ------------------------------------------------------------------------------- + - - + - T I M I N G - + - - + ------------------------------------------------------------------------------- + SUBROUTINE CALLS ASD SELF TIME TOTAL TIME + MAXIMUM AVERAGE MAXIMUM AVERAGE MAXIMUM + CP2K 1 1.0 0.049 0.067 48.424 48.425 + cp_geo_opt 1 2.0 0.000 0.000 48.029 48.030 + geoopt_bfgs 1 3.0 0.003 0.005 48.029 48.030 + cp_eval_at 5 4.0 0.001 0.001 47.488 47.489 + qs_energies 5 5.8 0.001 0.001 45.638 45.640 + qs_forces 4 5.0 0.000 0.000 38.541 38.541 + scf_env_do_scf 5 6.8 0.000 0.001 37.981 37.981 + scf_env_do_scf_inner_loop 87 7.9 0.003 0.005 34.797 34.815 + rebuild_ks_matrix 91 9.8 0.000 0.000 33.864 33.867 + qs_ks_build_kohn_sham_matrix 91 10.8 0.013 0.014 33.863 33.867 + qs_ks_update_qs_env 93 8.9 0.001 0.001 32.088 32.091 + qs_vxc_create 91 11.8 0.002 0.002 28.989 28.995 + xc_rho_set_and_dset_create 91 13.8 0.215 0.218 25.476 25.835 + xc_functional_eval 91 14.8 0.001 0.002 21.144 21.490 + pbe_lda_eval 91 15.8 21.143 21.489 21.143 21.489 + xc_vxc_pw_create 50 12.7 0.240 0.241 17.375 17.378 + xc_exc_calc 41 12.9 0.129 0.131 11.612 11.620 + fft_wrap_pw1pw2 1342 13.7 0.013 0.013 9.646 9.804 + fft_wrap_pw1pw2_300 766 15.3 0.002 0.002 8.855 9.012 + xc_pw_derive 423 14.7 0.002 0.002 6.187 6.400 + dbcsr_multiply_generic 2012 12.5 0.039 0.040 5.784 6.084 + multiply_cannon 2012 13.5 0.098 0.101 4.267 5.464 + pw_gpu_c1dr3d_3d_ps 667 16.5 1.660 1.695 5.271 5.324 + multiply_cannon_loop 2012 14.5 0.146 0.158 3.966 5.186 + scf_post_calculation_gpw 5 6.8 0.000 0.000 5.085 5.085 + qs_rho_update_rho_low 92 8.9 0.000 0.001 4.794 4.862 + calculate_rho_elec 92 9.9 0.285 0.287 4.793 4.861 + pw_gpu_r3dc1d_3d_ps 675 14.9 1.208 1.227 4.359 4.573 + density_rs2pw 92 10.9 0.003 0.003 4.400 4.489 + multiply_cannon_multrec 4024 15.5 0.024 0.035 2.065 4.336 + dbcsr_mm_accdrv_process 6426 16.0 0.068 0.159 2.007 4.274 + jit_kernel_multiply 38 16.2 1.933 4.100 1.933 4.100 + mp_alltoall_z22v 1342 17.7 3.700 3.904 3.700 3.904 + make_lumo_gpw 1 7.0 0.000 0.000 3.406 3.408 + ot_eigensolver 1 8.0 0.001 0.001 3.401 3.401 + x_to_yz 667 17.5 1.198 1.223 3.312 3.343 + xc_pw_divergence 50 13.7 0.001 0.001 2.945 3.164 + init_scf_loop 6 7.8 0.000 0.000 3.164 3.164 + mp_waitall_1 65161 16.9 1.557 3.094 1.557 3.094 + multiply_cannon_metrocomm3 4024 15.5 0.003 0.004 1.147 2.756 + yz_to_x 675 15.9 0.754 0.767 2.341 2.508 + ot_mini 140 10.8 0.001 0.001 2.131 2.132 + qs_ot_get_derivative 73 11.8 0.001 0.001 1.959 2.049 + sum_up_and_integrate 50 11.7 0.001 0.001 1.930 1.982 + init_scf_run 5 6.8 0.000 0.000 1.952 1.952 + scf_env_initial_rho_setup 5 7.8 0.000 0.000 1.952 1.952 + integrate_v_rspace 50 12.7 0.003 0.004 1.845 1.897 + transfer_rs2pw 480 11.8 0.003 0.003 1.723 1.810 + qs_ks_update_qs_env_forces 4 6.0 0.000 0.000 1.780 1.781 + pw_derive 696 15.0 1.684 1.706 1.684 1.706 + pw_poisson_solve 91 11.8 0.001 0.001 1.670 1.681 + mp_sum_l 6467 12.8 0.978 1.634 0.978 1.634 + potential_pw2rs 50 13.7 0.008 0.008 1.557 1.558 + transfer_rs2pw_300 104 12.7 0.894 0.921 1.384 1.469 + calculate_first_density_matrix 1 9.0 0.002 0.002 1.332 1.362 + pw_copy 1211 14.2 1.191 1.238 1.191 1.238 + qs_scf_new_mos 87 8.9 0.000 0.000 1.051 1.057 + qs_scf_loop_do_ot 87 9.9 0.001 0.001 1.050 1.056 + write_available_results 5 7.8 0.000 0.000 1.050 1.050 + write_mo_free_results 5 8.8 0.634 0.635 1.049 1.050 + ot_scf_mini 87 10.9 0.002 0.002 0.970 0.971 + ------------------------------------------------------------------------------- + + The number of warnings for this run is : 2 + + ------------------------------------------------------------------------------- + **** **** ****** ** PROGRAM ENDED AT 2025-01-22 10:23:13.882 + ***** ** *** *** ** PROGRAM RAN ON nid006590 + ** **** ****** PROGRAM RAN BY cpi + ***** ** ** ** ** PROGRAM PROCESS ID 278132 + **** ** ******* ** PROGRAM STOPPED IN /capstor/scratch/cscs/cpi/aiida/2d/33 + /a915-92b7-437a-b835-9b7e41b4a8f5 diff --git a/test/outputs/GEO_OPT_v9.1.out b/test/outputs/GEO_OPT_v9.1.out new file mode 100644 index 00000000..f2e3845d --- /dev/null +++ b/test/outputs/GEO_OPT_v9.1.out @@ -0,0 +1,1778 @@ + DBCSR| CPU Multiplication driver BLAS + DBCSR| Multrec recursion limit 512 + DBCSR| Multiplication stack size 1000 + DBCSR| Maximum elements for images UNLIMITED + DBCSR| Multiplicative factor virtual images 1 + DBCSR| Use multiplication densification T + DBCSR| Multiplication size stacks 3 + DBCSR| Use memory pool for CPU allocation F + DBCSR| Number of 3D layers SINGLE + DBCSR| Use MPI memory allocation F + DBCSR| Use RMA algorithm F + DBCSR| Use Communication thread T + DBCSR| Communication thread load 87 + DBCSR| MPI: My node id 0 + DBCSR| MPI: Number of nodes 2 + DBCSR| OMP: Current number of threads 1 + DBCSR| OMP: Max number of threads 1 + DBCSR| Split modifier for TAS multiplication algorithm 1.0E+00 + + + **** **** ****** ** PROGRAM STARTED AT 2025-01-22 08:37:25.541 + ***** ** *** *** ** PROGRAM STARTED ON 4d88af77387d + ** **** ****** PROGRAM STARTED BY + ***** ** ** ** ** PROGRAM PROCESS ID 4189 + **** ** ******* ** PROGRAM STARTED IN /home/jovyan/aiida_run/27/dc/845f-632 + 3-402a-8e1d-7a53a3cd164d + + CP2K| version string: CP2K version 9.1 + CP2K| source code revision number: git:d8d7100 + CP2K| cp2kflags: omp libint fftw3 libxc elpa parallel mpi3 scalapack spglib + CP2K| is freely available from https://www.cp2k.org/ + CP2K| Program compiled at Sun Jan 9 17:21:00 UTC 2022 + CP2K| Program compiled on bos02-arm64-063 + CP2K| Program compiled for Linux-aarch64-gfortran + CP2K| Data directory path /usr/share/cp2k + CP2K| Input file name aiida.inp + + GLOBAL| Force Environment number 1 + GLOBAL| Basis set file name BASIS_MOLOPT + GLOBAL| Potential file name POTENTIAL + GLOBAL| MM Potential file name MM_POTENTIAL + GLOBAL| Coordinate file name aiida.coords.xyz + GLOBAL| Method name CP2K + GLOBAL| Project name aiida + GLOBAL| Run type GEO_OPT + GLOBAL| FFT library FFTW3 + GLOBAL| Diagonalization library ELPA + GLOBAL| Minimum number of eigenvectors for ELPA usage 16 + GLOBAL| Orthonormality check for eigenvectors DISABLED + GLOBAL| Matrix multiplication library ScaLAPACK + GLOBAL| All-to-all communication in single precision F + GLOBAL| FFTs using library dependent lengths T + GLOBAL| Grid backend AUTO + GLOBAL| Global print level MEDIUM + GLOBAL| MPI I/O enabled T + GLOBAL| Total number of message passing processes 2 + GLOBAL| Number of threads for this process 1 + GLOBAL| This output is from process 0 + GLOBAL| Stack size for threads created by OpenMP (OMP_STACKSIZE) default + GLOBAL| CPU model name UNKNOWN + + MEMORY| system memory details [Kb] + MEMORY| rank 0 min max average + MEMORY| MemTotal 24573204 24573204 24573204 24573204 + MEMORY| MemFree 19534960 19534960 19534960 19534960 + MEMORY| Buffers 596160 596160 596160 596160 + MEMORY| Cached 887728 887728 887728 887728 + MEMORY| Slab 1191824 1191824 1191824 1191824 + MEMORY| SReclaimable 1111204 1111204 1111204 1111204 + MEMORY| MemLikelyFree 22130052 22130052 22130052 22130052 + + + *** Fundamental physical constants (SI units) *** + + *** Literature: B. J. Mohr and B. N. Taylor, + *** CODATA recommended values of the fundamental physical + *** constants: 2006, Web Version 5.1 + *** http://physics.nist.gov/constants + + Speed of light in vacuum [m/s] 2.99792458000000E+08 + Magnetic constant or permeability of vacuum [N/A**2] 1.25663706143592E-06 + Electric constant or permittivity of vacuum [F/m] 8.85418781762039E-12 + Planck constant (h) [J*s] 6.62606896000000E-34 + Planck constant (h-bar) [J*s] 1.05457162825177E-34 + Elementary charge [C] 1.60217648700000E-19 + Electron mass [kg] 9.10938215000000E-31 + Electron g factor [ ] -2.00231930436220E+00 + Proton mass [kg] 1.67262163700000E-27 + Fine-structure constant 7.29735253760000E-03 + Rydberg constant [1/m] 1.09737315685270E+07 + Avogadro constant [1/mol] 6.02214179000000E+23 + Boltzmann constant [J/K] 1.38065040000000E-23 + Atomic mass unit [kg] 1.66053878200000E-27 + Bohr radius [m] 5.29177208590000E-11 + + *** Conversion factors *** + + [u] -> [a.u.] 1.82288848426455E+03 + [Angstrom] -> [Bohr] = [a.u.] 1.88972613288564E+00 + [a.u.] = [Bohr] -> [Angstrom] 5.29177208590000E-01 + [a.u.] -> [s] 2.41888432650478E-17 + [a.u.] -> [fs] 2.41888432650478E-02 + [a.u.] -> [J] 4.35974393937059E-18 + [a.u.] -> [N] 8.23872205491840E-08 + [a.u.] -> [K] 3.15774647902944E+05 + [a.u.] -> [kJ/mol] 2.62549961709828E+03 + [a.u.] -> [kcal/mol] 6.27509468713739E+02 + [a.u.] -> [Pa] 2.94210107994716E+13 + [a.u.] -> [bar] 2.94210107994716E+08 + [a.u.] -> [atm] 2.90362800883016E+08 + [a.u.] -> [eV] 2.72113838565563E+01 + [a.u.] -> [Hz] 6.57968392072181E+15 + [a.u.] -> [1/cm] (wave numbers) 2.19474631370540E+05 + [a.u./Bohr**2] -> [1/cm] 5.14048714338585E+03 + + + CELL_TOP| Volume [angstrom^3]: 1475.364128 + CELL_TOP| Vector a [angstrom 12.424 0.000 0.000 |a| = 12.424154 + CELL_TOP| Vector b [angstrom 0.000 11.875 0.000 |b| = 11.874962 + CELL_TOP| Vector c [angstrom 0.000 0.000 10.000 |c| = 10.000004 + CELL_TOP| Angle (b,c), alpha [degree]: 90.000000 + CELL_TOP| Angle (a,c), beta [degree]: 90.000000 + CELL_TOP| Angle (a,b), gamma [degree]: 90.000000 + CELL_TOP| Numerically orthorhombic: YES + + GENERATE| Preliminary Number of Bonds generated: 0 + GENERATE| Achieved consistency in connectivity generation. + + CELL| Volume [angstrom^3]: 1475.364128 + CELL| Vector a [angstrom]: 12.424 0.000 0.000 |a| = 12.424154 + CELL| Vector b [angstrom]: 0.000 11.875 0.000 |b| = 11.874962 + CELL| Vector c [angstrom]: 0.000 0.000 10.000 |c| = 10.000004 + CELL| Angle (b,c), alpha [degree]: 90.000000 + CELL| Angle (a,c), beta [degree]: 90.000000 + CELL| Angle (a,b), gamma [degree]: 90.000000 + CELL| Numerically orthorhombic: YES + + CELL_REF| Volume [angstrom^3]: 1475.364128 + CELL_REF| Vector a [angstrom 12.424 0.000 0.000 |a| = 12.424154 + CELL_REF| Vector b [angstrom 0.000 11.875 0.000 |b| = 11.874962 + CELL_REF| Vector c [angstrom 0.000 0.000 10.000 |c| = 10.000004 + CELL_REF| Angle (b,c), alpha [degree]: 90.000000 + CELL_REF| Angle (a,c), beta [degree]: 90.000000 + CELL_REF| Angle (a,b), gamma [degree]: 90.000000 + CELL_REF| Numerically orthorhombic: YES + + ******************************************************************************* + ******************************************************************************* + ** ** + ** ##### ## ## ** + ** ## ## ## ## ## ** + ** ## ## ## ###### ** + ** ## ## ## ## ## ##### ## ## #### ## ##### ##### ** + ** ## ## ## ## ## ## ## ## ## ## ## ## ## ## ** + ** ## ## ## ## ## ## ## #### ### ## ###### ###### ** + ** ## ### ## ## ## ## ## ## ## ## ## ## ** + ** ####### ##### ## ##### ## ## #### ## ##### ## ** + ** ## ## ** + ** ** + ** ... make the atoms dance ** + ** ** + ** Copyright (C) by CP2K developers group (2000-2021) ** + ** J. Chem. Phys. 152, 194103 (2020) ** + ** ** + ******************************************************************************* + + DFT| Spin restricted Kohn-Sham (RKS) calculation RKS + DFT| Multiplicity 1 + DFT| Number of spin states 1 + DFT| Charge 0 + DFT| Self-interaction correction (SIC) NO + DFT| Cutoffs: density 1.000000E-10 + DFT| gradient 1.000000E-10 + DFT| tau 1.000000E-10 + DFT| cutoff_smoothing_range 0.000000E+00 + DFT| XC density smoothing NONE + DFT| XC derivatives PW + FUNCTIONAL| ROUTINE=NEW + FUNCTIONAL| PBE: + FUNCTIONAL| J.P.Perdew, K.Burke, M.Ernzerhof, Phys. Rev. Letter, vol. 77, n 18, + FUNCTIONAL| pp. 3865-3868, (1996){spin unpolarized} + vdW POTENTIAL| Pair Potential + vdW POTENTIAL| DFT-D3 (Version 3.1) + vdW POTENTIAL| Potential Form: S. Grimme et al, JCP 132: 154104 (2010) + vdW POTENTIAL| Zero Damping + vdW POTENTIAL| Cutoff Radius [Bohr]: 28.35 + vdW POTENTIAL| s6 Scaling Factor: 1.0000 + vdW POTENTIAL| sr6 Scaling Factor: 1.2170 + vdW POTENTIAL| s8 Scaling Factor: 0.7220 + vdW POTENTIAL| Cutoff for CN calculation: 0.1000E-05 + + QS| Method: GPW + QS| Density plane wave grid type NON-SPHERICAL FULLSPACE + QS| Number of grid levels: 5 + QS| Density cutoff [a.u.]: 300.0 + QS| Multi grid cutoff [a.u.]: 1) grid level 300.0 + QS| 2) grid level 100.0 + QS| 3) grid level 33.3 + QS| 4) grid level 11.1 + QS| 5) grid level 3.7 + QS| Grid level progression factor: 3.0 + QS| Relative density cutoff [a.u.]: 20.0 + QS| Interaction thresholds: eps_pgf_orb: 1.0E-07 + QS| eps_filter_matrix: 0.0E+00 + QS| eps_core_charge: 1.0E-16 + QS| eps_rho_gspace: 1.0E-14 + QS| eps_rho_rspace: 1.0E-14 + QS| eps_gvg_rspace: 1.0E-07 + QS| eps_ppl: 1.0E-02 + QS| eps_ppnl: 1.0E-09 + + + ATOMIC KIND INFORMATION + + 1. Atomic kind: C Number of atoms: 2 + + Orbital Basis Set TZV2P-MOLOPT-GTH + + Number of orbital shell sets: 1 + Number of orbital shells: 8 + Number of primitive Cartesian functions: 7 + Number of Cartesian basis functions: 24 + Number of spherical basis functions: 22 + Norm type: 2 + + Normalised Cartesian orbitals: + + Set Shell Orbital Exponent Coefficient + + 1 1 2s 6.132625 -0.263661 + 2.625196 -0.231112 + 1.045457 0.042712 + 0.478316 0.306085 + 0.178617 0.065483 + 0.075145 0.000568 + 0.030287 0.000417 + + 1 2 3s 6.132625 0.131937 + 2.625196 0.414269 + 1.045457 -0.593590 + 0.478316 0.644922 + 0.178617 0.069203 + 0.075145 -0.145101 + 0.030287 0.008247 + + 1 3 4s 6.132625 -1.009391 + 2.625196 -0.608763 + 1.045457 -0.320627 + 0.478316 1.417678 + 0.178617 -0.917862 + 0.075145 0.286664 + 0.030287 -0.031483 + + 1 4 3px 6.132625 0.562677 + 2.625196 0.633910 + 1.045457 0.379157 + 0.478316 0.235193 + 0.178617 0.052379 + 0.075145 0.003677 + 0.030287 0.000105 + 1 4 3py 6.132625 0.562677 + 2.625196 0.633910 + 1.045457 0.379157 + 0.478316 0.235193 + 0.178617 0.052379 + 0.075145 0.003677 + 0.030287 0.000105 + 1 4 3pz 6.132625 0.562677 + 2.625196 0.633910 + 1.045457 0.379157 + 0.478316 0.235193 + 0.178617 0.052379 + 0.075145 0.003677 + 0.030287 0.000105 + + 1 5 4px 6.132625 -0.472364 + 2.625196 -0.221326 + 1.045457 -0.481781 + 0.478316 0.135466 + 0.178617 0.072281 + 0.075145 0.024920 + 0.030287 0.002706 + 1 5 4py 6.132625 -0.472364 + 2.625196 -0.221326 + 1.045457 -0.481781 + 0.478316 0.135466 + 0.178617 0.072281 + 0.075145 0.024920 + 0.030287 0.002706 + 1 5 4pz 6.132625 -0.472364 + 2.625196 -0.221326 + 1.045457 -0.481781 + 0.478316 0.135466 + 0.178617 0.072281 + 0.075145 0.024920 + 0.030287 0.002706 + + 1 6 5px 6.132625 -0.321125 + 2.625196 -0.513960 + 1.045457 -0.659092 + 0.478316 1.236398 + 0.178617 -0.279443 + 0.075145 0.042466 + 0.030287 -0.008547 + 1 6 5py 6.132625 -0.321125 + 2.625196 -0.513960 + 1.045457 -0.659092 + 0.478316 1.236398 + 0.178617 -0.279443 + 0.075145 0.042466 + 0.030287 -0.008547 + 1 6 5pz 6.132625 -0.321125 + 2.625196 -0.513960 + 1.045457 -0.659092 + 0.478316 1.236398 + 0.178617 -0.279443 + 0.075145 0.042466 + 0.030287 -0.008547 + + 1 7 4dx2 6.132625 0.874783 + 2.625196 0.375772 + 1.045457 0.653959 + 0.478316 0.191007 + 0.178617 0.018656 + 0.075145 0.003649 + 0.030287 -0.000011 + 1 7 4dxy 6.132625 1.515169 + 2.625196 0.650856 + 1.045457 1.132690 + 0.478316 0.330834 + 0.178617 0.032314 + 0.075145 0.006321 + 0.030287 -0.000019 + 1 7 4dxz 6.132625 1.515169 + 2.625196 0.650856 + 1.045457 1.132690 + 0.478316 0.330834 + 0.178617 0.032314 + 0.075145 0.006321 + 0.030287 -0.000019 + 1 7 4dy2 6.132625 0.874783 + 2.625196 0.375772 + 1.045457 0.653959 + 0.478316 0.191007 + 0.178617 0.018656 + 0.075145 0.003649 + 0.030287 -0.000011 + 1 7 4dyz 6.132625 1.515169 + 2.625196 0.650856 + 1.045457 1.132690 + 0.478316 0.330834 + 0.178617 0.032314 + 0.075145 0.006321 + 0.030287 -0.000019 + 1 7 4dz2 6.132625 0.874783 + 2.625196 0.375772 + 1.045457 0.653959 + 0.478316 0.191007 + 0.178617 0.018656 + 0.075145 0.003649 + 0.030287 -0.000011 + + 1 8 5dx2 6.132625 3.037532 + 2.625196 0.636556 + 1.045457 2.577237 + 0.478316 -0.930692 + 0.178617 0.140536 + 0.075145 -0.022558 + 0.030287 0.000345 + 1 8 5dxy 6.132625 5.261160 + 2.625196 1.102547 + 1.045457 4.463906 + 0.478316 -1.612005 + 0.178617 0.243416 + 0.075145 -0.039072 + 0.030287 0.000598 + 1 8 5dxz 6.132625 5.261160 + 2.625196 1.102547 + 1.045457 4.463906 + 0.478316 -1.612005 + 0.178617 0.243416 + 0.075145 -0.039072 + 0.030287 0.000598 + 1 8 5dy2 6.132625 3.037532 + 2.625196 0.636556 + 1.045457 2.577237 + 0.478316 -0.930692 + 0.178617 0.140536 + 0.075145 -0.022558 + 0.030287 0.000345 + 1 8 5dyz 6.132625 5.261160 + 2.625196 1.102547 + 1.045457 4.463906 + 0.478316 -1.612005 + 0.178617 0.243416 + 0.075145 -0.039072 + 0.030287 0.000598 + 1 8 5dz2 6.132625 3.037532 + 2.625196 0.636556 + 1.045457 2.577237 + 0.478316 -0.930692 + 0.178617 0.140536 + 0.075145 -0.022558 + 0.030287 0.000345 + + Atomic covalent radius [Angstrom]: 0.770 + + Atomic van der Waals radius [Angstrom]: 1.700 + + GTH Potential information for GTH-PBE-q4 + + Description: Goedecker-Teter-Hutter pseudopotential + Goedecker et al., PRB 54, 1703 (1996) + Hartwigsen et al., PRB 58, 3641 (1998) + Krack, TCA 114, 145 (2005) + + Gaussian exponent of the core charge distribution: 4.364419 + Electronic configuration (s p d ...): 2 2 + + Parameters of the local part of the GTH pseudopotential: + + rloc C1 C2 C3 C4 + 0.338471 -8.803674 1.339211 + + Parameters of the non-local part of the GTH pseudopotential: + + l r(l) h(i,j,l) + + 0 0.302576 9.622487 + 1 0.291507 + + 2. Atomic kind: H Number of atoms: 4 + + Orbital Basis Set TZV2P-MOLOPT-GTH + + Number of orbital shell sets: 1 + Number of orbital shells: 5 + Number of primitive Cartesian functions: 7 + Number of Cartesian basis functions: 9 + Number of spherical basis functions: 9 + Norm type: 2 + + Normalised Cartesian orbitals: + + Set Shell Orbital Exponent Coefficient + + 1 1 2s 11.478000 0.129129 + 3.700759 0.177012 + 1.446884 0.141285 + 0.716815 0.245670 + 0.247919 0.094768 + 0.066918 0.004062 + 0.021708 -0.000053 + + 1 2 3s 11.478000 -0.079256 + 3.700759 -0.152992 + 1.446884 0.015066 + 0.716815 -0.331234 + 0.247919 0.210690 + 0.066918 0.058630 + 0.021708 -0.003429 + + 1 3 4s 11.478000 -0.246880 + 3.700759 0.023016 + 1.446884 -1.109374 + 0.716815 1.524652 + 0.247919 -0.227968 + 0.066918 -0.037343 + 0.021708 0.005696 + + 1 4 3px 11.478000 0.325290 + 3.700759 0.187466 + 1.446884 0.443300 + 0.716815 0.267738 + 0.247919 0.088285 + 0.066918 0.019092 + 0.021708 0.000629 + 1 4 3py 11.478000 0.325290 + 3.700759 0.187466 + 1.446884 0.443300 + 0.716815 0.267738 + 0.247919 0.088285 + 0.066918 0.019092 + 0.021708 0.000629 + 1 4 3pz 11.478000 0.325290 + 3.700759 0.187466 + 1.446884 0.443300 + 0.716815 0.267738 + 0.247919 0.088285 + 0.066918 0.019092 + 0.021708 0.000629 + + 1 5 4px 11.478000 -1.727188 + 3.700759 -0.598393 + 1.446884 -3.813128 + 0.716815 1.901151 + 0.247919 -0.262425 + 0.066918 0.006339 + 0.021708 0.007345 + 1 5 4py 11.478000 -1.727188 + 3.700759 -0.598393 + 1.446884 -3.813128 + 0.716815 1.901151 + 0.247919 -0.262425 + 0.066918 0.006339 + 0.021708 0.007345 + 1 5 4pz 11.478000 -1.727188 + 3.700759 -0.598393 + 1.446884 -3.813128 + 0.716815 1.901151 + 0.247919 -0.262425 + 0.066918 0.006339 + 0.021708 0.007345 + + Atomic covalent radius [Angstrom]: 0.320 + + Atomic van der Waals radius [Angstrom]: 1.090 + + GTH Potential information for GTH-PBE-q1 + + Description: Goedecker-Teter-Hutter pseudopotential + Goedecker et al., PRB 54, 1703 (1996) + Hartwigsen et al., PRB 58, 3641 (1998) + Krack, TCA 114, 145 (2005) + + Gaussian exponent of the core charge distribution: 12.500000 + Electronic configuration (s p d ...): 1 + + Parameters of the local part of the GTH pseudopotential: + + rloc C1 C2 C3 C4 + 0.200000 -4.178900 0.724463 + + + MOLECULE KIND INFORMATION + + + All atoms are their own molecule, skipping detailed information + + + TOTAL NUMBERS AND MAXIMUM NUMBERS + + Total number of - Atomic kinds: 2 + - Atoms: 6 + - Shell sets: 6 + - Shells: 36 + - Primitive Cartesian functions: 42 + - Cartesian basis functions: 84 + - Spherical basis functions: 80 + + Maximum angular momentum of- Orbital basis functions: 2 + - Local part of the GTH pseudopotential: 2 + - Non-local part of the GTH pseudopotential: 0 + + + MODULE QUICKSTEP: ATOMIC COORDINATES IN angstrom + + Atom Kind Element X Y Z Z(eff) Mass + 1 1 C 6 6.877573 5.937481 5.000001 4.0000 12.0107 + 2 1 C 6 5.546581 5.937481 5.000002 4.0000 12.0107 + 3 2 H 1 7.424154 6.874961 5.000004 1.0000 1.0079 + 4 2 H 1 7.424153 5.000000 5.000000 1.0000 1.0079 + 5 2 H 1 5.000000 6.874962 5.000000 1.0000 1.0079 + 6 2 H 1 5.000000 5.000000 5.000004 1.0000 1.0079 + + + + + SCF PARAMETERS Density guess: RESTART + -------------------------------------------------------- + max_scf: 40 + max_scf_history: 0 + max_diis: 4 + -------------------------------------------------------- + eps_scf: 1.00E-06 + eps_scf_history: 0.00E+00 + eps_diis: 1.00E-01 + eps_eigval: 1.00E-05 + -------------------------------------------------------- + level_shift [a.u.]: 0.00 + -------------------------------------------------------- + Outer loop SCF in use + No variables optimised in outer loop + eps_scf 1.00E-06 + max_scf 50 + No outer loop optimization + step_size 5.00E-01 + + PW_GRID| Information for grid number 1 + PW_GRID| Grid distributed over 2 processors + PW_GRID| Real space group dimensions 2 1 + PW_GRID| the grid is blocked: NO + PW_GRID| Cutoff [a.u.] 300.0 + PW_GRID| spherical cutoff: NO + PW_GRID| Bounds 1 -94 94 Points: 189 + PW_GRID| Bounds 2 -87 87 Points: 175 + PW_GRID| Bounds 3 -75 74 Points: 150 + PW_GRID| Volume element (a.u.^3) 0.2007E-02 Volume (a.u.^3) 9956.2508 + PW_GRID| Grid span FULLSPACE + PW_GRID| Distribution Average Max Min + PW_GRID| G-Vectors 2480625.0 2480625 2480625 + PW_GRID| G-Rays 13125.0 13125 13125 + PW_GRID| Real Space Points 2480625.0 2493750 2467500 + + PW_GRID| Information for grid number 2 + PW_GRID| Number of the reference grid 1 + PW_GRID| Grid distributed over 2 processors + PW_GRID| Real space group dimensions 2 1 + PW_GRID| the grid is blocked: NO + PW_GRID| Cutoff [a.u.] 100.0 + PW_GRID| spherical cutoff: NO + PW_GRID| Bounds 1 -52 52 Points: 105 + PW_GRID| Bounds 2 -52 52 Points: 105 + PW_GRID| Bounds 3 -44 43 Points: 88 + PW_GRID| Volume element (a.u.^3) 0.1026E-01 Volume (a.u.^3) 9956.2508 + PW_GRID| Grid span FULLSPACE + PW_GRID| Distribution Average Max Min + PW_GRID| G-Vectors 485100.0 485205 484995 + PW_GRID| G-Rays 4620.0 4621 4619 + PW_GRID| Real Space Points 485100.0 489720 480480 + + PW_GRID| Information for grid number 3 + PW_GRID| Number of the reference grid 1 + PW_GRID| Grid distributed over 2 processors + PW_GRID| Real space group dimensions 2 1 + PW_GRID| the grid is blocked: NO + PW_GRID| Cutoff [a.u.] 33.3 + PW_GRID| spherical cutoff: NO + PW_GRID| Bounds 1 -31 31 Points: 63 + PW_GRID| Bounds 2 -30 29 Points: 60 + PW_GRID| Bounds 3 -25 24 Points: 50 + PW_GRID| Volume element (a.u.^3) 0.5268E-01 Volume (a.u.^3) 9956.2508 + PW_GRID| Grid span FULLSPACE + PW_GRID| Distribution Average Max Min + PW_GRID| G-Vectors 94500.0 94500 94500 + PW_GRID| G-Rays 1500.0 1500 1500 + PW_GRID| Real Space Points 94500.0 96000 93000 + + PW_GRID| Information for grid number 4 + PW_GRID| Number of the reference grid 1 + PW_GRID| Grid distributed over 2 processors + PW_GRID| Real space group dimensions 2 1 + PW_GRID| the grid is blocked: NO + PW_GRID| Cutoff [a.u.] 11.1 + PW_GRID| spherical cutoff: NO + PW_GRID| Bounds 1 -17 17 Points: 35 + PW_GRID| Bounds 2 -16 16 Points: 33 + PW_GRID| Bounds 3 -15 14 Points: 30 + PW_GRID| Volume element (a.u.^3) 0.2873 Volume (a.u.^3) 9956.2508 + PW_GRID| Grid span FULLSPACE + PW_GRID| Distribution Average Max Min + PW_GRID| G-Vectors 17325.0 17360 17290 + PW_GRID| G-Rays 495.0 496 494 + PW_GRID| Real Space Points 17325.0 17820 16830 + + PW_GRID| Information for grid number 5 + PW_GRID| Number of the reference grid 1 + PW_GRID| Grid distributed over 2 processors + PW_GRID| Real space group dimensions 2 1 + PW_GRID| the grid is blocked: NO + PW_GRID| Cutoff [a.u.] 3.7 + PW_GRID| spherical cutoff: NO + PW_GRID| Bounds 1 -10 10 Points: 21 + PW_GRID| Bounds 2 -10 9 Points: 20 + PW_GRID| Bounds 3 -9 8 Points: 18 + PW_GRID| Volume element (a.u.^3) 1.317 Volume (a.u.^3) 9956.2508 + PW_GRID| Grid span FULLSPACE + PW_GRID| Distribution Average Max Min + PW_GRID| G-Vectors 3780.0 3780 3780 + PW_GRID| G-Rays 180.0 180 180 + PW_GRID| Real Space Points 3780.0 3960 3600 + + POISSON| Solver PERIODIC + POISSON| Periodicity XYZ + + RS_GRID| Information for grid number 1 + RS_GRID| Bounds 1 -94 94 Points: 189 + RS_GRID| Bounds 2 -87 87 Points: 175 + RS_GRID| Bounds 3 -75 74 Points: 150 + RS_GRID| Real space fully replicated + RS_GRID| Group size 1 + + RS_GRID| Information for grid number 2 + RS_GRID| Bounds 1 -52 52 Points: 105 + RS_GRID| Bounds 2 -52 52 Points: 105 + RS_GRID| Bounds 3 -44 43 Points: 88 + RS_GRID| Real space fully replicated + RS_GRID| Group size 1 + + RS_GRID| Information for grid number 3 + RS_GRID| Bounds 1 -31 31 Points: 63 + RS_GRID| Bounds 2 -30 29 Points: 60 + RS_GRID| Bounds 3 -25 24 Points: 50 + RS_GRID| Real space fully replicated + RS_GRID| Group size 1 + + RS_GRID| Information for grid number 4 + RS_GRID| Bounds 1 -17 17 Points: 35 + RS_GRID| Bounds 2 -16 16 Points: 33 + RS_GRID| Bounds 3 -15 14 Points: 30 + RS_GRID| Real space fully replicated + RS_GRID| Group size 1 + + RS_GRID| Information for grid number 5 + RS_GRID| Bounds 1 -10 10 Points: 21 + RS_GRID| Bounds 2 -10 9 Points: 20 + RS_GRID| Bounds 3 -9 8 Points: 18 + RS_GRID| Real space fully replicated + RS_GRID| Group size 1 + + BFGS| Use rational function optimization for step estimation: NO + BFGS| Use model Hessian for initial guess: YES + BFGS| Restart Hessian: NO + BFGS| Trust radius: 0.100 + + ******************************************************************************* + *** STARTING GEOMETRY OPTIMIZATION *** + *** BFGS *** + ******************************************************************************* + + Number of electrons: 12 + Number of occupied orbitals: 6 + Number of molecular orbitals: 6 + + Number of orbital functions: 80 + Number of independent orbital functions: 80 + + Extrapolation method: initial_guess + + *** WARNING in qs_initial_guess.F:309 :: User requested to restart the *** + *** wavefunction from the file named: ./parent_calc/aiida-RESTART.wfn. *** + *** This file does not exist. Please check the existence of the file or *** + *** change properly the value of the keyword WFN_RESTART_FILE_NAME. *** + *** Calculation continues using ATOMIC GUESS. *** + + + Atomic guess: The first density matrix is obtained in terms of atomic orbitals + and electronic configurations assigned to each atomic kind + + Guess for atomic kind: C + + Electronic structure + Total number of core electrons 2.00 + Total number of valence electrons 4.00 + Total number of electrons 6.00 + Multiplicity not specified + S [ 2.00] 2.00 + P 2.00 + + + ******************************************************************************* + Iteration Convergence Energy [au] + ******************************************************************************* + 1 0.106529 -5.270272483724 + 2 0.700070E-01 -5.275253796046 + 3 0.257977E-03 -5.278907327451 + 4 0.489006E-04 -5.278907347137 + 5 0.128506E-06 -5.278907348859 + + Energy components [Hartree] Total Energy :: -5.278907348859 + Band Energy :: -1.297504853113 + Kinetic Energy :: 3.437573111170 + Potential Energy :: -8.716480460029 + Virial (-V/T) :: 2.535649476576 + Core Energy :: -8.301868323195 + XC Energy :: -1.382083082551 + Coulomb Energy :: 4.405044056886 + Total Pseudopotential Energy :: -11.773288188249 + Local Pseudopotential Energy :: -12.379139771299 + Nonlocal Pseudopotential Energy :: 0.605851583050 + Confinement :: 0.338467538844 + + Orbital energies State L Occupation Energy[a.u.] Energy[eV] + + 1 0 2.000 -0.478379 -13.017346 + + 1 1 2.000 -0.170374 -4.636105 + + + Total Electron Density at R=0: 0.000341 + + Guess for atomic kind: H + + Electronic structure + Total number of core electrons 0.00 + Total number of valence electrons 1.00 + Total number of electrons 1.00 + Multiplicity not specified + S 1.00 + + + ******************************************************************************* + Iteration Convergence Energy [au] + ******************************************************************************* + 1 0.363633E-02 -0.424359639014 + 2 0.457201E-03 -0.424374328003 + 3 0.158035E-04 -0.424374562686 + 4 0.544881E-08 -0.424374562963 + + Energy components [Hartree] Total Energy :: -0.424374562963 + Band Energy :: -0.197817388557 + Kinetic Energy :: 0.463739149097 + Potential Energy :: -0.888113712060 + Virial (-V/T) :: 1.915114809241 + Core Energy :: -0.479953896523 + XC Energy :: -0.245504363650 + Coulomb Energy :: 0.301083697210 + Total Pseudopotential Energy :: -0.962570132454 + Local Pseudopotential Energy :: -0.962570132454 + Nonlocal Pseudopotential Energy :: 0.000000000000 + Confinement :: 0.188770868335 + + Orbital energies State L Occupation Energy[a.u.] Energy[eV] + + 1 0 1.000 -0.197817 -5.382885 + + + Total Electron Density at R=0: 0.235042 + Re-scaling the density matrix to get the right number of electrons + # Electrons Trace(P) Scaling factor + 12 12.000 1.000 + + + SCF WAVEFUNCTION OPTIMIZATION + + ----------------------------------- OT --------------------------------------- + Minimizer : CG : conjugate gradient + Preconditioner : FULL_SINGLE_INVERSE : inversion of + H + eS - 2*(Sc)(c^T*H*c+const)(Sc)^T + Precond_solver : DEFAULT + Line search : 2PNT : 2 energies, one gradient + stepsize : 0.08000000 energy_gap : 0.08000000 + eps_taylor : 0.10000E-15 max_taylor : 4 + ----------------------------------- OT --------------------------------------- + + Step Update method Time Convergence Total energy Change + ------------------------------------------------------------------------------ + 1 OT CG 0.80E-01 1.3 0.17512196 -12.5028932274 -1.25E+01 + 2 OT LS 0.11E+00 0.9 -13.2453329267 + 3 OT CG 0.11E+00 1.5 0.18341009 -13.2135556628 -7.11E-01 + 4 OT LS 0.40E-01 0.8 -12.7550925871 + 5 OT CG 0.40E-01 1.4 0.12115962 -13.4170797323 -2.04E-01 + 6 OT LS 0.69E-01 0.9 -13.6163466937 + 7 OT CG 0.69E-01 1.4 0.05205595 -13.6435520317 -2.26E-01 + 8 OT LS 0.86E-01 0.9 -13.6849570018 + 9 OT CG 0.86E-01 1.4 0.04097937 -13.6864314319 -4.29E-02 + 10 OT LS 0.56E-01 0.9 -13.7030296708 + 11 OT CG 0.56E-01 1.4 0.01793871 -13.7093395632 -2.29E-02 + 12 OT LS 0.12E+00 0.9 -13.7160026579 + 13 OT CG 0.12E+00 1.4 0.01365114 -13.7186417031 -9.30E-03 + 14 OT LS 0.11E+00 0.9 -13.7237671340 + 15 OT CG 0.11E+00 1.4 0.00799310 -13.7237818723 -5.14E-03 + 16 OT LS 0.77E-01 0.9 -13.7246631327 + 17 OT CG 0.77E-01 1.4 0.00402713 -13.7249554286 -1.17E-03 + 18 OT LS 0.12E+00 0.9 -13.7253552974 + 19 OT CG 0.12E+00 1.5 0.00296731 -13.7254079429 -4.53E-04 + 20 OT LS 0.81E-01 0.9 -13.7255469840 + 21 OT CG 0.81E-01 1.4 0.00158232 -13.7255792418 -1.71E-04 + 22 OT LS 0.12E+00 0.9 -13.7256424831 + 23 OT CG 0.12E+00 1.4 0.00109803 -13.7256486715 -6.94E-05 + 24 OT LS 0.95E-01 0.9 -13.7256747307 + 25 OT CG 0.95E-01 1.4 0.00053776 -13.7256760581 -2.74E-05 + 26 OT LS 0.10E+00 0.9 -13.7256830883 + 27 OT CG 0.10E+00 1.4 0.00040747 -13.7256831227 -7.06E-06 + 28 OT LS 0.95E-01 0.9 -13.7256869091 + 29 OT CG 0.95E-01 1.4 0.00025423 -13.7256869259 -3.80E-06 + 30 OT LS 0.93E-01 0.9 -13.7256883664 + 31 OT CG 0.93E-01 1.4 0.00010646 -13.7256883675 -1.44E-06 + 32 OT LS 0.16E+00 0.9 -13.7256887296 + 33 OT CG 0.16E+00 1.4 0.00010431 -13.7256888132 -4.46E-07 + 34 OT LS 0.71E-01 0.9 -13.7256886850 + 35 OT CG 0.71E-01 1.4 0.00005050 -13.7256889992 -1.86E-07 + 36 OT LS 0.12E+00 0.9 -13.7256890608 + 37 OT CG 0.12E+00 1.4 0.00002865 -13.7256890734 -7.42E-08 + 38 OT LS 0.13E+00 0.9 -13.7256890994 + 39 OT CG 0.13E+00 1.4 0.00002180 -13.7256890996 -2.62E-08 + 40 OT LS 0.68E-01 0.9 -13.7256891004 + + Leaving inner SCF loop after reaching 40 steps. + + + Electronic density on regular grids: -12.0000000000 0.0000000000 + Core density on regular grids: 12.0000000000 -0.0000000000 + Total charge density on r-space grids: -0.0000000000 + Total charge density g-space grids: -0.0000000000 + + Overlap energy of the core charge distribution: 0.00000236921509 + Self energy of the core charge distribution: -32.31191168900799 + Core Hamiltonian energy: 10.29782692709255 + Hartree energy: 13.16260376610867 + Exchange-correlation energy: -4.87374882251652 + Dispersion energy: -0.00046165125791 + + Total energy: -13.72568910036611 + + outer SCF iter = 1 RMS gradient = 0.22E-04 energy = -13.7256891004 + + ----------------------------------- OT --------------------------------------- + Minimizer : CG : conjugate gradient + Preconditioner : FULL_SINGLE_INVERSE : inversion of + H + eS - 2*(Sc)(c^T*H*c+const)(Sc)^T + Precond_solver : DEFAULT + Line search : 2PNT : 2 energies, one gradient + stepsize : 0.08000000 energy_gap : 0.08000000 + eps_taylor : 0.10000E-15 max_taylor : 4 + ----------------------------------- OT --------------------------------------- + + Step Update method Time Convergence Total energy Change + ------------------------------------------------------------------------------ + 1 OT CG 0.80E-01 2.3 0.00000955 -13.7256891074 -7.77E-09 + 2 OT LS 0.16E+00 0.9 -13.7256891100 + 3 OT CG 0.16E+00 1.4 0.00000524 -13.7256891108 -3.42E-09 + 4 OT LS 0.13E+00 0.9 -13.7256891116 + 5 OT CG 0.13E+00 1.4 0.00000134 -13.7256891116 -8.40E-10 + 6 OT LS 0.14E+00 0.9 -13.7256891117 + 7 OT CG 0.14E+00 1.4 0.00000042 -13.7256891117 -6.22E-11 + + *** SCF run converged in 7 steps *** + + + Electronic density on regular grids: -12.0000000000 -0.0000000000 + Core density on regular grids: 12.0000000000 -0.0000000000 + Total charge density on r-space grids: -0.0000000000 + Total charge density g-space grids: -0.0000000000 + + Overlap energy of the core charge distribution: 0.00000236921509 + Self energy of the core charge distribution: -32.31191168900799 + Core Hamiltonian energy: 10.29787686839921 + Hartree energy: 13.16256223742480 + Exchange-correlation energy: -4.87375724646832 + Dispersion energy: -0.00046165125791 + + Total energy: -13.72568911169511 + + outer SCF iter = 2 RMS gradient = 0.42E-06 energy = -13.7256891117 + outer SCF loop converged in 2 iterations or 47 steps + + + !-----------------------------------------------------------------------------! + Mulliken Population Analysis + + # Atom Element Kind Atomic population Net charge + 1 C 1 4.164086 -0.164086 + 2 C 1 4.164086 -0.164086 + 3 H 2 0.917957 0.082043 + 4 H 2 0.917957 0.082043 + 5 H 2 0.917957 0.082043 + 6 H 2 0.917957 0.082043 + # Total charge 12.000000 -0.000000 + + !-----------------------------------------------------------------------------! + + !-----------------------------------------------------------------------------! + Hirshfeld Charges + + #Atom Element Kind Ref Charge Population Net charge + 1 C 1 4.000 4.896 -0.896 + 2 C 1 4.000 4.896 -0.896 + 3 H 2 1.000 0.549 0.451 + 4 H 2 1.000 0.549 0.451 + 5 H 2 1.000 0.549 0.451 + 6 H 2 1.000 0.549 0.451 + + Total Charge 0.014 + !-----------------------------------------------------------------------------! + + ENERGY| Total FORCE_EVAL ( QS ) energy [a.u.]: -13.725689111701854 + + -------- Informations at step = 0 ------------ + Optimization Method = BFGS + Total Energy = -13.7256891117 + Used time = 56.034 + --------------------------------------------------- + + -------------------------- + OPTIMIZATION STEP: 1 + -------------------------- + + Number of electrons: 12 + Number of occupied orbitals: 6 + Number of molecular orbitals: 6 + + Number of orbital functions: 80 + Number of independent orbital functions: 80 + + Parameters for the always stable predictor-corrector (ASPC) method: + + ASPC order: 0 + + B(1) = 1.000000 + + Extrapolation method: ASPC + + + SCF WAVEFUNCTION OPTIMIZATION + + ----------------------------------- OT --------------------------------------- + Minimizer : CG : conjugate gradient + Preconditioner : FULL_SINGLE_INVERSE : inversion of + H + eS - 2*(Sc)(c^T*H*c+const)(Sc)^T + Precond_solver : DEFAULT + Line search : 2PNT : 2 energies, one gradient + stepsize : 0.08000000 energy_gap : 0.08000000 + eps_taylor : 0.10000E-15 max_taylor : 4 + ----------------------------------- OT --------------------------------------- + + Step Update method Time Convergence Total energy Change + ------------------------------------------------------------------------------ + 1 OT CG 0.80E-01 1.2 0.00101148 -13.7260965450 -1.37E+01 + 2 OT LS 0.20E+00 0.9 -13.7261281142 + 3 OT CG 0.20E+00 1.4 0.00030205 -13.7261465312 -5.00E-05 + 4 OT LS 0.14E+00 0.9 -13.7261487233 + 5 OT CG 0.14E+00 1.4 0.00008172 -13.7261494859 -2.95E-06 + 6 OT LS 0.14E+00 0.9 -13.7261497044 + 7 OT CG 0.14E+00 1.4 0.00001960 -13.7261497044 -2.19E-07 + 8 OT LS 0.19E+00 0.9 -13.7261497205 + 9 OT CG 0.19E+00 1.5 0.00000383 -13.7261497219 -1.75E-08 + 10 OT LS 0.20E+00 0.9 -13.7261497226 + 11 OT CG 0.20E+00 1.4 0.00000087 -13.7261497226 -7.20E-10 + + *** SCF run converged in 11 steps *** + + + Electronic density on regular grids: -12.0000000000 -0.0000000000 + Core density on regular grids: 12.0000000000 -0.0000000000 + Total charge density on r-space grids: -0.0000000000 + Total charge density g-space grids: -0.0000000000 + + Overlap energy of the core charge distribution: 0.00000221816287 + Self energy of the core charge distribution: -32.31191168900799 + Core Hamiltonian energy: 10.27764059005538 + Hartree energy: 13.17625315518391 + Exchange-correlation energy: -4.86766614432493 + Dispersion energy: -0.00046785269957 + + Total energy: -13.72614972263033 + + outer SCF iter = 1 RMS gradient = 0.87E-06 energy = -13.7261497226 + outer SCF loop converged in 1 iterations or 11 steps + + + !-----------------------------------------------------------------------------! + Mulliken Population Analysis + + # Atom Element Kind Atomic population Net charge + 1 C 1 4.163747 -0.163747 + 2 C 1 4.163747 -0.163747 + 3 H 2 0.918127 0.081873 + 4 H 2 0.918127 0.081873 + 5 H 2 0.918127 0.081873 + 6 H 2 0.918127 0.081873 + # Total charge 12.000000 -0.000000 + + !-----------------------------------------------------------------------------! + + !-----------------------------------------------------------------------------! + Hirshfeld Charges + + #Atom Element Kind Ref Charge Population Net charge + 1 C 1 4.000 4.896 -0.896 + 2 C 1 4.000 4.896 -0.896 + 3 H 2 1.000 0.549 0.451 + 4 H 2 1.000 0.549 0.451 + 5 H 2 1.000 0.549 0.451 + 6 H 2 1.000 0.549 0.451 + + Total Charge 0.014 + !-----------------------------------------------------------------------------! + + ENERGY| Total FORCE_EVAL ( QS ) energy [a.u.]: -13.726149722666982 + + -------- Informations at step = 1 ------------ + Optimization Method = BFGS + Total Energy = -13.7261497227 + Real energy change = -0.0004606110 + Predicted change in energy = -0.0003565862 + Scaling factor = 0.0000000000 + Step size = 0.0376199092 + Trust radius = 0.1000000000 + Decrease in energy = YES + Used time = 14.633 + + Convergence check : + Max. step size = 0.0376199092 + Conv. limit for step size = 0.0030000000 + Convergence in step size = NO + RMS step size = 0.0189431999 + Conv. limit for RMS step = 0.0015000000 + Convergence in RMS step = NO + Max. gradient = 0.0015528294 + Conv. limit for gradients = 0.0004500000 + Conv. for gradients = NO + RMS gradient = 0.0007719361 + Conv. limit for RMS grad. = 0.0003000000 + Conv. for gradients = NO + --------------------------------------------------- + + -------------------------- + OPTIMIZATION STEP: 2 + -------------------------- + + Number of electrons: 12 + Number of occupied orbitals: 6 + Number of molecular orbitals: 6 + + Number of orbital functions: 80 + Number of independent orbital functions: 80 + + Parameters for the always stable predictor-corrector (ASPC) method: + + ASPC order: 0 + + B(1) = 2.000000 + B(2) = -1.000000 + + Extrapolation method: ASPC + + + SCF WAVEFUNCTION OPTIMIZATION + + ----------------------------------- OT --------------------------------------- + Minimizer : CG : conjugate gradient + Preconditioner : FULL_SINGLE_INVERSE : inversion of + H + eS - 2*(Sc)(c^T*H*c+const)(Sc)^T + Precond_solver : DEFAULT + Line search : 2PNT : 2 energies, one gradient + stepsize : 0.08000000 energy_gap : 0.08000000 + eps_taylor : 0.10000E-15 max_taylor : 4 + ----------------------------------- OT --------------------------------------- + + Step Update method Time Convergence Total energy Change + ------------------------------------------------------------------------------ + 1 OT CG 0.80E-01 1.2 0.00061049 -13.7261733873 -1.37E+01 + 2 OT LS 0.21E+00 0.9 -13.7261850037 + 3 OT CG 0.21E+00 1.4 0.00015176 -13.7261923873 -1.90E-05 + 4 OT LS 0.15E+00 0.9 -13.7261930827 + 5 OT CG 0.15E+00 1.4 0.00003549 -13.7261932214 -8.34E-07 + 6 OT LS 0.13E+00 0.9 -13.7261932609 + 7 OT CG 0.13E+00 1.4 0.00001187 -13.7261932617 -4.02E-08 + 8 OT LS 0.17E+00 0.9 -13.7261932672 + 9 OT CG 0.17E+00 1.4 0.00000235 -13.7261932675 -5.82E-09 + 10 OT LS 0.20E+00 0.9 -13.7261932677 + 11 OT CG 0.20E+00 1.4 0.00000052 -13.7261932677 -2.68E-10 + + *** SCF run converged in 11 steps *** + + + Electronic density on regular grids: -12.0000000000 0.0000000000 + Core density on regular grids: 12.0000000000 -0.0000000000 + Total charge density on r-space grids: -0.0000000000 + Total charge density g-space grids: -0.0000000000 + + Overlap energy of the core charge distribution: 0.00000212715790 + Self energy of the core charge distribution: -32.31191168900799 + Core Hamiltonian energy: 10.26566042899938 + Hartree energy: 13.18454564196607 + Exchange-correlation energy: -4.86401939924276 + Dispersion energy: -0.00047037761700 + + Total energy: -13.72619326774439 + + outer SCF iter = 1 RMS gradient = 0.52E-06 energy = -13.7261932677 + outer SCF loop converged in 1 iterations or 11 steps + + + !-----------------------------------------------------------------------------! + Mulliken Population Analysis + + # Atom Element Kind Atomic population Net charge + 1 C 1 4.163480 -0.163480 + 2 C 1 4.163480 -0.163480 + 3 H 2 0.918260 0.081740 + 4 H 2 0.918260 0.081740 + 5 H 2 0.918260 0.081740 + 6 H 2 0.918260 0.081740 + # Total charge 12.000000 0.000000 + + !-----------------------------------------------------------------------------! + + !-----------------------------------------------------------------------------! + Hirshfeld Charges + + #Atom Element Kind Ref Charge Population Net charge + 1 C 1 4.000 4.896 -0.896 + 2 C 1 4.000 4.896 -0.896 + 3 H 2 1.000 0.549 0.451 + 4 H 2 1.000 0.549 0.451 + 5 H 2 1.000 0.549 0.451 + 6 H 2 1.000 0.549 0.451 + + Total Charge 0.014 + !-----------------------------------------------------------------------------! + + ENERGY| Total FORCE_EVAL ( QS ) energy [a.u.]: -13.726193267757822 + + -------- Informations at step = 2 ------------ + Optimization Method = BFGS + Total Energy = -13.7261932678 + Real energy change = -0.0000435451 + Predicted change in energy = -0.0000436237 + Scaling factor = 0.0000000000 + Step size = 0.0155526726 + Trust radius = 0.1000000000 + Decrease in energy = YES + Used time = 14.588 + + Convergence check : + Max. step size = 0.0155526726 + Conv. limit for step size = 0.0030000000 + Convergence in step size = NO + RMS step size = 0.0076510487 + Conv. limit for RMS step = 0.0015000000 + Convergence in RMS step = NO + Max. gradient = 0.0003036618 + Conv. limit for gradients = 0.0004500000 + Conv. in gradients = YES + RMS gradient = 0.0001078140 + Conv. limit for RMS grad. = 0.0003000000 + Conv. in RMS gradients = YES + --------------------------------------------------- + + -------------------------- + OPTIMIZATION STEP: 3 + -------------------------- + + Number of electrons: 12 + Number of occupied orbitals: 6 + Number of molecular orbitals: 6 + + Number of orbital functions: 80 + Number of independent orbital functions: 80 + + Parameters for the always stable predictor-corrector (ASPC) method: + + ASPC order: 1 + + B(1) = 2.500000 + B(2) = -2.000000 + B(3) = 0.500000 + + Extrapolation method: ASPC + + + SCF WAVEFUNCTION OPTIMIZATION + + ----------------------------------- OT --------------------------------------- + Minimizer : CG : conjugate gradient + Preconditioner : FULL_SINGLE_INVERSE : inversion of + H + eS - 2*(Sc)(c^T*H*c+const)(Sc)^T + Precond_solver : DEFAULT + Line search : 2PNT : 2 energies, one gradient + stepsize : 0.08000000 energy_gap : 0.08000000 + eps_taylor : 0.10000E-15 max_taylor : 4 + ----------------------------------- OT --------------------------------------- + + Step Update method Time Convergence Total energy Change + ------------------------------------------------------------------------------ + 1 OT CG 0.80E-01 1.2 0.00017484 -13.7261921885 -1.37E+01 + 2 OT LS 0.15E+00 0.9 -13.7261930449 + 3 OT CG 0.15E+00 1.4 0.00006751 -13.7261932739 -1.09E-06 + 4 OT LS 0.14E+00 0.9 -13.7261934271 + 5 OT CG 0.14E+00 1.4 0.00001289 -13.7261934275 -1.54E-07 + 6 OT LS 0.18E+00 0.9 -13.7261934343 + 7 OT CG 0.18E+00 1.5 0.00000255 -13.7261934346 -7.06E-09 + 8 OT LS 0.17E+00 0.9 -13.7261934349 + 9 OT CG 0.17E+00 1.4 0.00000043 -13.7261934349 -2.72E-10 + + *** SCF run converged in 9 steps *** + + + Electronic density on regular grids: -12.0000000000 0.0000000000 + Core density on regular grids: 12.0000000000 -0.0000000000 + Total charge density on r-space grids: -0.0000000000 + Total charge density g-space grids: -0.0000000000 + + Overlap energy of the core charge distribution: 0.00000212008668 + Self energy of the core charge distribution: -32.31191168900799 + Core Hamiltonian energy: 10.26484863922778 + Hartree energy: 13.18511914217061 + Exchange-correlation energy: -4.86378114738674 + Dispersion energy: -0.00047049995296 + + Total energy: -13.72619343486261 + + outer SCF iter = 1 RMS gradient = 0.43E-06 energy = -13.7261934349 + outer SCF loop converged in 1 iterations or 9 steps + + + !-----------------------------------------------------------------------------! + Mulliken Population Analysis + + # Atom Element Kind Atomic population Net charge + 1 C 1 4.163453 -0.163453 + 2 C 1 4.163453 -0.163453 + 3 H 2 0.918274 0.081726 + 4 H 2 0.918274 0.081726 + 5 H 2 0.918273 0.081727 + 6 H 2 0.918273 0.081727 + # Total charge 12.000000 0.000000 + + !-----------------------------------------------------------------------------! + + !-----------------------------------------------------------------------------! + Hirshfeld Charges + + #Atom Element Kind Ref Charge Population Net charge + 1 C 1 4.000 4.896 -0.896 + 2 C 1 4.000 4.896 -0.896 + 3 H 2 1.000 0.549 0.451 + 4 H 2 1.000 0.549 0.451 + 5 H 2 1.000 0.549 0.451 + 6 H 2 1.000 0.549 0.451 + + Total Charge 0.014 + !-----------------------------------------------------------------------------! + + ENERGY| Total FORCE_EVAL ( QS ) energy [a.u.]: -13.726193434870883 + + -------- Informations at step = 3 ------------ + Optimization Method = BFGS + Total Energy = -13.7261934349 + Real energy change = -0.0000001671 + Predicted change in energy = -0.0000001203 + Scaling factor = 0.0000000000 + Step size = 0.0003463701 + Trust radius = 0.1000000000 + Decrease in energy = YES + Used time = 12.346 + + Convergence check : + Max. step size = 0.0003463701 + Conv. limit for step size = 0.0030000000 + Convergence in step size = YES + RMS step size = 0.0001827720 + Conv. limit for RMS step = 0.0015000000 + Convergence in RMS step = YES + Max. gradient = 0.0000728782 + Conv. limit for gradients = 0.0004500000 + Conv. in gradients = YES + RMS gradient = 0.0000258819 + Conv. limit for RMS grad. = 0.0003000000 + Conv. in RMS gradients = YES + --------------------------------------------------- + + ******************************************************************************* + *** GEOMETRY OPTIMIZATION COMPLETED *** + ******************************************************************************* + + Reevaluating energy at the minimum + + Number of electrons: 12 + Number of occupied orbitals: 6 + Number of molecular orbitals: 6 + + Number of orbital functions: 80 + Number of independent orbital functions: 80 + + Parameters for the always stable predictor-corrector (ASPC) method: + + ASPC order: 2 + + B(1) = 2.800000 + B(2) = -2.800000 + B(3) = 1.200000 + B(4) = -0.200000 + + Extrapolation method: ASPC + + + SCF WAVEFUNCTION OPTIMIZATION + + ----------------------------------- OT --------------------------------------- + Minimizer : CG : conjugate gradient + Preconditioner : FULL_SINGLE_INVERSE : inversion of + H + eS - 2*(Sc)(c^T*H*c+const)(Sc)^T + Precond_solver : DEFAULT + Line search : 2PNT : 2 energies, one gradient + stepsize : 0.08000000 energy_gap : 0.08000000 + eps_taylor : 0.10000E-15 max_taylor : 4 + ----------------------------------- OT --------------------------------------- + + Step Update method Time Convergence Total energy Change + ------------------------------------------------------------------------------ + 1 OT CG 0.80E-01 1.2 0.00022600 -13.7261909453 -1.37E+01 + 2 OT LS 0.18E+00 0.9 -13.7261924800 + 3 OT CG 0.18E+00 1.4 0.00008436 -13.7261931992 -2.25E-06 + 4 OT LS 0.13E+00 0.9 -13.7261933785 + 5 OT CG 0.13E+00 1.4 0.00002003 -13.7261934190 -2.20E-07 + 6 OT LS 0.16E+00 0.9 -13.7261934335 + 7 OT CG 0.16E+00 1.4 0.00000429 -13.7261934340 -1.50E-08 + 8 OT LS 0.19E+00 0.9 -13.7261934348 + 9 OT CG 0.19E+00 1.4 0.00000086 -13.7261934348 -8.28E-10 + + *** SCF run converged in 9 steps *** + + + Electronic density on regular grids: -12.0000000000 -0.0000000000 + Core density on regular grids: 12.0000000000 -0.0000000000 + Total charge density on r-space grids: -0.0000000000 + Total charge density g-space grids: -0.0000000000 + + Overlap energy of the core charge distribution: 0.00000212008668 + Self energy of the core charge distribution: -32.31191168900799 + Core Hamiltonian energy: 10.26485101545395 + Hartree energy: 13.18511786814852 + Exchange-correlation energy: -4.86378224956177 + Dispersion energy: -0.00047049995296 + + Total energy: -13.72619343483357 + + outer SCF iter = 1 RMS gradient = 0.86E-06 energy = -13.7261934348 + outer SCF loop converged in 1 iterations or 9 steps + + + The electron density is written in cube file format to the file: + + aiida-ELECTRON_DENSITY-1_3.cube + + !-----------------------------------------------------------------------------! + Mulliken Population Analysis + + # Atom Element Kind Atomic population Net charge + 1 C 1 4.163454 -0.163454 + 2 C 1 4.163452 -0.163452 + 3 H 2 0.918274 0.081726 + 4 H 2 0.918274 0.081726 + 5 H 2 0.918274 0.081726 + 6 H 2 0.918274 0.081726 + # Total charge 12.000000 0.000000 + + !-----------------------------------------------------------------------------! + + !-----------------------------------------------------------------------------! + Hirshfeld Charges + + #Atom Element Kind Ref Charge Population Net charge + 1 C 1 4.000 4.896 -0.896 + 2 C 1 4.000 4.896 -0.896 + 3 H 2 1.000 0.549 0.451 + 4 H 2 1.000 0.549 0.451 + 5 H 2 1.000 0.549 0.451 + 6 H 2 1.000 0.549 0.451 + + Total Charge 0.014 + !-----------------------------------------------------------------------------! + + Eigenvalues of the occupied subspace spin 1 + --------------------------------------------- + -0.68412780 -0.51657878 -0.41454219 -0.36888136 + -0.30660434 -0.24103549 + Fermi Energy [eV] : -6.558909 + + Lowest Eigenvalues of the unoccupied subspace spin 1 + ----------------------------------------------------- + OT| Eigensolver reached convergence in 53 iterations + -0.02897857 + + HOMO - LUMO gap [eV] : 5.770362 + + ENERGY| Total FORCE_EVAL ( QS ) energy [a.u.]: -13.726193434833574 + + ------------------------------------------------------------------------------- + - - + - DBCSR STATISTICS - + - - + ------------------------------------------------------------------------------- + COUNTER TOTAL BLAS SMM ACC + flops 6 x 1 x 6 144 100.0% 0.0% 0.0% + flops 6 x 1 x 40 1920 100.0% 0.0% 0.0% + flops 40 x 1 x 6 1920 100.0% 0.0% 0.0% + flops 7 x 1 x 7 2646 100.0% 0.0% 0.0% + flops 9 x 6 x 6 15552 100.0% 0.0% 0.0% + flops 7 x 7 x 40 15680 100.0% 0.0% 0.0% + flops 1 x 1 x 40 16480 100.0% 0.0% 0.0% + flops 22 x 6 x 6 19008 100.0% 0.0% 0.0% + flops 7 x 1 x 40 30240 100.0% 0.0% 0.0% + flops 40 x 1 x 7 30240 100.0% 0.0% 0.0% + flops 6 x 6 x 6 151200 100.0% 0.0% 0.0% + flops 40 x 7 x 40 179200 100.0% 0.0% 0.0% + flops 9 x 1 x 9 282528 100.0% 0.0% 0.0% + flops 22 x 1 x 9 345312 100.0% 0.0% 0.0% + flops 9 x 1 x 22 345312 100.0% 0.0% 0.0% + flops 40 x 1 x 40 345600 100.0% 0.0% 0.0% + flops 22 x 1 x 22 422048 100.0% 0.0% 0.0% + flops 22 x 9 x 6 969408 100.0% 0.0% 0.0% + flops 9 x 22 x 6 969408 100.0% 0.0% 0.0% + flops 9 x 9 x 6 991440 100.0% 0.0% 0.0% + flops 6 x 6 x 40 1307520 100.0% 0.0% 0.0% + flops 40 x 6 x 6 1762560 100.0% 0.0% 0.0% + flops 22 x 22 x 6 1777248 100.0% 0.0% 0.0% + flops 9 x 6 x 9 2674944 100.0% 0.0% 0.0% + flops 22 x 6 x 9 3269376 100.0% 0.0% 0.0% + flops 9 x 6 x 22 3269376 100.0% 0.0% 0.0% + flops 40 x 6 x 40 3993600 100.0% 0.0% 0.0% + flops 22 x 6 x 22 3995904 100.0% 0.0% 0.0% + flops inhomo. stacks 26194 100.0% 0.0% 0.0% + flops total 27.212008E+06 100.0% 0.0% 0.0% + flops max/rank 14.665424E+06 100.0% 0.0% 0.0% + matmuls inhomo. stacks 617 100.0% 0.0% 0.0% + matmuls total 15006 100.0% 0.0% 0.0% + number of processed stacks 8048 100.0% 0.0% 0.0% + average stack size 1.9 0.0 0.0 + marketing flops 30.373304E+06 + ------------------------------------------------------------------------------- + # multiplications 2012 + max memory usage/rank 1.061261E+09 + # max total images/rank 2 + # max 3D layers 1 + # MPI messages exchanged 4024 + MPI messages size (bytes): + total size 2.510504E+06 + min size 0.000000E+00 + max size 3.840000E+03 + average size 623.882690E+00 + MPI breakdown and total messages size (bytes): + size <= 128 1814 6888 + 128 < size <= 8192 2210 2503616 + 8192 < size <= 32768 0 0 + 32768 < size <= 131072 0 0 + 131072 < size <= 4194304 0 0 + 4194304 < size <= 16777216 0 0 + 16777216 < size 0 0 + ------------------------------------------------------------------------------- + + *** WARNING in dbcsr_mm.F:294 :: Using a non-square number of MPI ranks *** + *** might lead to poor performance. Used ranks: 2 Suggested: 1 4 *** + + ------------------------------------------------------------------------------- + - - + - DBCSR MESSAGE PASSING PERFORMANCE - + - - + ------------------------------------------------------------------------------- + ROUTINE CALLS AVE VOLUME [Bytes] + MP_Bcast 29 12. + MP_Allreduce 10079 8. + MP_Alltoall 7695 393. + MP_ISend 12770 435. + MP_IRecv 13696 337. + ------------------------------------------------------------------------------- + + ------------------------------------------------------------------------------- + - - + - GRID STATISTICS - + - - + ------------------------------------------------------------------------------- + LP KERNEL BACKEND COUNT PERCENT + 2 collocate ortho REF 244132 32.65% + 3 collocate ortho REF 178848 23.92% + 2 integrate ortho REF 122052 16.32% + 3 integrate ortho REF 100044 13.38% + 4 collocate ortho REF 61364 8.21% + 4 integrate ortho REF 38458 5.14% + 5 integrate ortho REF 2668 0.36% + 0 collocate general REF 60 0.01% + 1 collocate ortho REF 56 0.01% + 0 integrate general REF 30 0.00% + 1 integrate general REF 24 0.00% + ------------------------------------------------------------------------------- + + MEMORY| Estimated peak process memory [MiB] 1013 + + ------------------------------------------------------------------------------- + ---- MULTIGRID INFO ---- + ------------------------------------------------------------------------------- + count for grid 1: 26688 cutoff [a.u.] 300.00 + count for grid 2: 23357 cutoff [a.u.] 100.00 + count for grid 3: 23211 cutoff [a.u.] 33.33 + count for grid 4: 18619 cutoff [a.u.] 11.11 + count for grid 5: 18346 cutoff [a.u.] 3.70 + total gridlevel count : 110221 + + ------------------------------------------------------------------------------- + - - + - MESSAGE PASSING PERFORMANCE - + - - + ------------------------------------------------------------------------------- + + ROUTINE CALLS AVE VOLUME [Bytes] + MP_Group 5 + MP_Bcast 1675 209094. + MP_Allreduce 5015 255. + MP_Sync 91 + MP_Alltoall 1342 95007402. + MP_SendRecv 16 132. + MP_ISendRecv 739 5347348. + MP_Wait 739 + MP_Recv 3 1296. + MP_Write_All 4 2351184. + ------------------------------------------------------------------------------- + + + ------------------------------------------------------------------------------- + - - + - R E F E R E N C E S - + - - + ------------------------------------------------------------------------------- + + CP2K version 9.1, the CP2K developers group (2021). + CP2K is freely available from https://www.cp2k.org/ . + + Kuehne,Thomas D.; Iannuzzi,Marcella; Del Ben,Mauro; + Rybkin,Vladimir V.; Seewald,Patrick; Stein,Frederick; Laino,Teodoro; + Khaliullin,Rustam Z.; Schuett,Ole; Schiffmann,Florian; Golze,Dorothea; + Wilhelm,Jan; Chulkov,Sergey; Bani-Hashemian,Mohammad Hossein; + Weber,Valery; Borstnik,Urban; Taillefumier,Mathieu; + Jakobovits,Alice Shoshana; Lazzaro,Alfio; Pabst,Hans; Mueller,Tiziano; + Schade,Robert; Guidon,Manuel; Andermatt,Samuel; Holmberg,Nico; + Schenter,Gregory K.; Hehn,Anna; Bussy,Augustin; Belleflamme,Fabian; + Tabacchi,Gloria; Gloess,Andreas; Lass,Michael; Bethune,Iain; + Mundy,Christopher J.; Plessl,Christian; Watkins,Matt; + VandeVondele,Joost; Krack,Matthias; Hutter,Juerg. + The Journal of Chemical Physics, 152 (19), (2020). + CP2K: An electronic structure and molecular dynamics software package - + Quickstep: Efficient and accurate electronic structure calculations. + https://doi.org/10.1063/5.0007045 + + Goerigk, Lars; Hansen, Andreas; Bauer, Christoph; Ehrlich, Stephan; + Najibi, Asim; Grimme, Stefan. , 19 (48), (2017). + A look at the density functional theory zoo with the advanced GMTKN55 database + for general main group thermochemistry, kinetics and noncovalent interactions. + https://doi.org/10.1039/C7CP04913G + + Schuett, Ole; Messmer, Peter; Hutter, Juerg; VandeVondele, Joost. + Electronic Structure Calculations on Graphics Processing Units, John + Wiley & Sons, Ltd, 173-190 (2016). + GPU-Accelerated Sparse Matrix-Matrix Multiplication for + Linear Scaling Density Functional Theory. + https://doi.org/10.1002/9781118670712.ch8 + + Borstnik, U; VandeVondele, J; Weber, V; Hutter, J. + PARALLEL COMPUTING, 40 (5-6), 47-58 (2014). + Sparse matrix multiplication: The distributed block-compressed sparse + row library. + https://doi.org/10.1016/j.parco.2014.03.012 + + Hutter, J; Iannuzzi, M; Schiffmann, F; VandeVondele, J. + WIREs Comput Mol Sci., 4 (1), 15-25 (2014). + CP2K: atomistic simulations of condensed matter systems. + https://doi.org/10.1002/wcms.1159 + + Marek, A; Blum, V; Johanni, R; Havu, V; Lang, B; Auckenthaler, T; + Heinecke, A; Bungartz, H; Lederer, H. + Journal of Physics: Condensed Matter, 26 (21), (2014). + The ELPA library: scalable parallel eigenvalue solutions for + electronic structure + theory and computational science. + https://doi.org/10.1088/0953-8984/26/21/213201 + + Grimme, S; Ehrlich, S; Goerigk, L. + JOURNAL OF COMPUTATIONAL CHEMISTRY, 32, 1456 (2011). + Effect of the damping function in dispersion corrected density functional theory. + https://doi.org/10.1002/jcc.21759 + + Grimme, S; Antony, J; Ehrlich, S; Krieg, H. + JOURNAL OF CHEMICAL PHYSICS, 132 (15), 154104 (2010). + A consistent and accurate ab initio parametrization of density + functional dispersion correction (DFT-D) for the 94 elements H-Pu. + https://doi.org/10.1063/1.3382344 + + VandeVondele, J; Hutter, J. + JOURNAL OF CHEMICAL PHYSICS, 127 (11), 114105 (2007). + Gaussian basis sets for accurate calculations on molecular systems in + gas and condensed phases. + https://doi.org/10.1063/1.2770708 + + Kuhne, TD; Krack, M; Mohamed, FR; Parrinello, M. + PHYSICAL REVIEW LETTERS, 98 (6), 066401 (2007). + Efficient and accurate Car-Parrinello-like approach to + Born-Oppenheimer molecular dynamics. + https://doi.org/10.1103/PhysRevLett.98.066401 + + Krack, M. + THEORETICAL CHEMISTRY ACCOUNTS, 114 (1-3), 145-152 (2005). + Pseudopotentials for H to Kr optimized for gradient-corrected + exchange-correlation functionals. + https://doi.org/10.1007/s00214-005-0655-y + + VandeVondele, J; Krack, M; Mohamed, F; Parrinello, M; Chassaing, T; + Hutter, J. COMPUTER PHYSICS COMMUNICATIONS, 167 (2), 103-128 (2005). + QUICKSTEP: Fast and accurate density functional calculations using a + mixed Gaussian and plane waves approach. + https://doi.org/10.1016/j.cpc.2004.12.014 + + Frigo, M; Johnson, SG. + PROCEEDINGS OF THE IEEE, 93 (2), 216-231 (2005). + The design and implementation of FFTW3. + https://doi.org/10.1109/JPROC.2004.840301 + + Kolafa, J. + JOURNAL OF COMPUTATIONAL CHEMISTRY, 25 (3), 335-342 (2004). + Time-reversible always stable predictor-corrector method for + molecular dynamics of polarizable molecules. + https://doi.org/10.1002/jcc.10385 + + VandeVondele, J; Hutter, J. + JOURNAL OF CHEMICAL PHYSICS, 118 (10), 4365-4369 (2003). + An efficient orbital transformation method for electronic structure + calculations. + https://doi.org/10.1063/1.1543154 + + Hartwigsen, C; Goedecker, S; Hutter, J. + PHYSICAL REVIEW B, 58 (7), 3641-3662 (1998). + Relativistic separable dual-space Gaussian pseudopotentials from H to Rn. + https://doi.org/10.1103/PhysRevB.58.3641 + + Lippert, G; Hutter, J; Parrinello, M. + MOLECULAR PHYSICS, 92 (3), 477-487 (1997). + A hybrid Gaussian and plane wave density functional scheme. + https://doi.org/10.1080/002689797170220 + + Perdew, JP; Burke, K; Ernzerhof, M. + PHYSICAL REVIEW LETTERS, 77 (18), 3865-3868 (1996). + Generalized gradient approximation made simple. + https://doi.org/10.1103/PhysRevLett.77.3865 + + Goedecker, S; Teter, M; Hutter, J. + PHYSICAL REVIEW B, 54 (3), 1703-1710 (1996). + Separable dual-space Gaussian pseudopotentials. + https://doi.org/10.1103/PhysRevB.54.1703 + + + ------------------------------------------------------------------------------- + - - + - T I M I N G - + - - + ------------------------------------------------------------------------------- + SUBROUTINE CALLS ASD SELF TIME TOTAL TIME + MAXIMUM AVERAGE MAXIMUM AVERAGE MAXIMUM + CP2K 1 1.0 0.007 0.008 110.059 110.060 + cp_geo_opt 1 2.0 0.000 0.000 109.633 109.633 + geoopt_bfgs 1 3.0 0.001 0.001 109.633 109.633 + cp_eval_at 5 4.0 0.000 0.000 109.624 109.624 + qs_energies 5 5.8 0.001 0.001 104.612 104.612 + scf_env_do_scf 5 6.8 0.000 0.000 101.269 101.269 + qs_forces 4 5.0 0.001 0.001 97.592 97.592 + scf_env_do_scf_inner_loop 87 7.9 0.002 0.003 94.021 94.021 + rebuild_ks_matrix 91 9.8 0.000 0.000 84.819 84.819 + qs_ks_build_kohn_sham_matrix 91 10.8 0.009 0.010 84.819 84.819 + qs_ks_update_qs_env 93 8.9 0.000 0.000 79.962 79.962 + qs_vxc_create 91 11.8 0.001 0.001 69.039 69.152 + xc_rho_set_and_dset_create 91 13.8 0.165 0.165 53.062 53.369 + pw_transfer 1524 13.2 0.042 0.043 51.542 51.669 + fft_wrap_pw1pw2 1342 14.2 0.006 0.006 51.019 51.145 + fft_wrap_pw1pw2_300 766 15.5 2.320 2.366 49.252 49.395 + xc_vxc_pw_create 50 12.7 0.962 0.986 44.824 44.937 + fft3d_ps 1342 16.2 26.437 27.328 35.037 35.161 + xc_functional_eval 91 14.8 0.001 0.001 34.107 34.338 + pbe_lda_eval 91 15.8 34.107 34.337 34.107 34.337 + xc_exc_calc 41 12.9 0.378 0.381 24.214 24.214 + qs_rho_update_rho 92 8.9 0.000 0.000 22.264 22.264 + calculate_rho_elec 92 9.9 0.858 0.865 22.263 22.263 + density_rs2pw 92 10.9 0.003 0.003 15.476 15.648 + sum_up_and_integrate 50 11.7 0.071 0.071 9.530 9.794 + integrate_v_rspace 50 12.7 0.001 0.001 9.459 9.723 + init_scf_loop 6 7.8 0.000 0.000 7.247 7.247 + pw_gather_p 675 15.5 6.933 6.959 6.933 6.959 + pw_scatter_p 667 17.0 6.618 6.688 6.618 6.688 + mp_alltoall_z22v 1342 18.2 5.754 6.529 5.754 6.529 + grid_collocate_task_list 92 10.9 5.745 6.093 5.745 6.093 + x_to_yz 667 18.0 1.811 1.821 5.209 5.711 + potential_pw2rs 50 13.7 0.014 0.014 4.899 4.899 + qs_ks_update_qs_env_forces 4 6.0 0.000 0.000 4.860 4.860 + grid_integrate_task_list 50 13.7 4.560 4.824 4.560 4.824 + yz_to_x 675 16.5 1.018 1.022 3.374 3.640 + rs_pw_transfer 739 12.8 0.004 0.004 3.208 3.560 + rs_pw_transfer_RS2PW_300 104 12.7 1.120 1.122 1.995 2.346 + pw_poisson_solve 91 11.8 0.606 0.610 2.317 2.317 + ------------------------------------------------------------------------------- + + The number of warnings for this run is : 2 + + ------------------------------------------------------------------------------- + **** **** ****** ** PROGRAM ENDED AT 2025-01-22 08:39:15.778 + ***** ** *** *** ** PROGRAM RAN ON 4d88af77387d + ** **** ****** PROGRAM RAN BY + ***** ** ** ** ** PROGRAM PROCESS ID 4189 + **** ** ******* ** PROGRAM STOPPED IN /home/jovyan/aiida_run/27/dc/845f-632 + 3-402a-8e1d-7a53a3cd164d diff --git a/test/test_parser.py b/test/test_parser.py index 7aa7f0b9..4fe4e6e8 100644 --- a/test/test_parser.py +++ b/test/test_parser.py @@ -266,6 +266,59 @@ def test_cp2k_output_parser(output_file, reference_dict): } +geo_opt_v9_1_out_advanced_result = { + "exceeded_walltime": False, + "cp2k_version": 9.1, + "run_type": "GEO_OPT", + "motion_opt_converged": True, + "motion_step_info": { + "step": [0, 1, 2, 3], + "energy_au": [-13.725689111701854, -13.726149722666982, -13.726193267757822, -13.726193434870883], + "dispersion_energy_au": [-0.00046165125791, -0.00046785269957, -0.000470377617, -0.00047049995296], + "pressure_bar": [None, None, None, None], + "cell_vol_angs3": [1475.364128, 1475.364128, 1475.364128, 1475.364128], + "cell_a_angs": [12.424154, 12.424154, 12.424154, 12.424154], + "cell_b_angs": [11.874962, 11.874962, 11.874962, 11.874962], + "cell_c_angs": [10.000004, 10.000004, 10.000004, 10.000004], + "cell_alp_deg": [90.0, 90.0, 90.0, 90.0], + "cell_bet_deg": [90.0, 90.0, 90.0, 90.0], + "cell_gam_deg": [90.0, 90.0, 90.0, 90.0], + "max_step_au": [None, 0.0376199092, 0.0155526726, 0.0003463701], + "rms_step_au": [None, 0.0189431999, 0.0076510487, 0.000182772], + "max_grad_au": [None, 0.0015528294, 0.0003036618, 7.28782e-05], + "rms_grad_au": [None, 0.0007719361, 0.000107814, 2.58819e-05], + "edens_rspace": [-0.0, -0.0, -0.0, -0.0], + "scf_converged": [True, True, True, True], + }, + +} + +geo_opt_v2024_3_out_advanced_result = { + "exceeded_walltime": False, + "cp2k_version": 2024.3, + "run_type": "GEO_OPT", + "motion_opt_converged": True, + "motion_step_info": { + "step": [0, 1, 2, 3], + "energy_au": [-13.725689111701852, -13.726149722666458, -13.726193267757864, -13.726193434870929], + "dispersion_energy_au": [-0.00046165125791, -0.00046785269954, -0.00047037761701, -0.00047049995297], + "pressure_bar": [None, None, None, None], + "cell_vol_angs3": [1475.364128, 1475.364128, 1475.364128, 1475.364128], + "cell_a_angs": [12.424154, 12.424154, 12.424154, 12.424154], + "cell_b_angs": [11.874962, 11.874962, 11.874962, 11.874962], + "cell_c_angs": [10.000004, 10.000004, 10.000004, 10.000004], + "cell_alp_deg": [90.0, 90.0, 90.0, 90.0], + "cell_bet_deg": [90.0, 90.0, 90.0, 90.0], + "cell_gam_deg": [90.0, 90.0, 90.0, 90.0], + "max_step_au": [None, 0.037619909, 0.0155526727, 0.0003463702], + "rms_step_au": [None, 0.0189431999, 0.0076510488, 0.000182772], + "max_grad_au": [None, 0.0015528293, 0.0003036619, 7.28784e-05], + "rms_grad_au": [None, 0.0007719361, 0.000107814, 2.58819e-05], + "edens_rspace": [-0.0, -0.0, -0.0, -0.0], + "scf_converged": [True, True, True, True], + }, +} + @pytest.mark.parametrize( "output_file, reference_dict", [ @@ -274,6 +327,8 @@ def test_cp2k_output_parser(output_file, reference_dict): ("BSSE_output_v5.1_.out", bsse_output_v5_1_out_advanced_result), ("cdft_dos_cp2k_6.0.out", cdft_dos_cp2k_6_0_out_advanced_result), ("OT_v9.1.out", ot_v9_1_out_advanced_result), + ("GEO_OPT_v9.1.out", geo_opt_v9_1_out_advanced_result), + ("GEO_OPT_v2024.3.out", geo_opt_v2024_3_out_advanced_result), ], ) def test_cp2k_output_advanced(output_file, reference_dict): @@ -301,5 +356,4 @@ def test_trajectory_parser_pbc(): with open(OUTPUTS_DIR / file) as fobj: content = fobj.read() structure_data = parse_cp2k_trajectory(content) - assert structure_data["pbc"] == boundary_cond From c30932f7e13d9c096274d3ad7477331d015a1345 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Tue, 28 Jan 2025 09:22:04 +0000 Subject: [PATCH 07/12] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- test/test_parser.py | 30 +++++++++++++++++++++++++----- 1 file changed, 25 insertions(+), 5 deletions(-) diff --git a/test/test_parser.py b/test/test_parser.py index 4fe4e6e8..eff3867d 100644 --- a/test/test_parser.py +++ b/test/test_parser.py @@ -273,8 +273,18 @@ def test_cp2k_output_parser(output_file, reference_dict): "motion_opt_converged": True, "motion_step_info": { "step": [0, 1, 2, 3], - "energy_au": [-13.725689111701854, -13.726149722666982, -13.726193267757822, -13.726193434870883], - "dispersion_energy_au": [-0.00046165125791, -0.00046785269957, -0.000470377617, -0.00047049995296], + "energy_au": [ + -13.725689111701854, + -13.726149722666982, + -13.726193267757822, + -13.726193434870883, + ], + "dispersion_energy_au": [ + -0.00046165125791, + -0.00046785269957, + -0.000470377617, + -0.00047049995296, + ], "pressure_bar": [None, None, None, None], "cell_vol_angs3": [1475.364128, 1475.364128, 1475.364128, 1475.364128], "cell_a_angs": [12.424154, 12.424154, 12.424154, 12.424154], @@ -290,7 +300,6 @@ def test_cp2k_output_parser(output_file, reference_dict): "edens_rspace": [-0.0, -0.0, -0.0, -0.0], "scf_converged": [True, True, True, True], }, - } geo_opt_v2024_3_out_advanced_result = { @@ -300,8 +309,18 @@ def test_cp2k_output_parser(output_file, reference_dict): "motion_opt_converged": True, "motion_step_info": { "step": [0, 1, 2, 3], - "energy_au": [-13.725689111701852, -13.726149722666458, -13.726193267757864, -13.726193434870929], - "dispersion_energy_au": [-0.00046165125791, -0.00046785269954, -0.00047037761701, -0.00047049995297], + "energy_au": [ + -13.725689111701852, + -13.726149722666458, + -13.726193267757864, + -13.726193434870929, + ], + "dispersion_energy_au": [ + -0.00046165125791, + -0.00046785269954, + -0.00047037761701, + -0.00047049995297, + ], "pressure_bar": [None, None, None, None], "cell_vol_angs3": [1475.364128, 1475.364128, 1475.364128, 1475.364128], "cell_a_angs": [12.424154, 12.424154, 12.424154, 12.424154], @@ -319,6 +338,7 @@ def test_cp2k_output_parser(output_file, reference_dict): }, } + @pytest.mark.parametrize( "output_file, reference_dict", [ From 6c56102ad5881d5f0c3e5f53b61b01f3476720f3 Mon Sep 17 00:00:00 2001 From: Aliaksandr Yakutovich Date: Tue, 28 Jan 2025 09:36:24 +0000 Subject: [PATCH 08/12] Add an example run for an advanced parser. --- .../example_geopt_advanced_parser.py | 153 ++++++++++++++++++ 1 file changed, 153 insertions(+) create mode 100644 examples/single_calculations/example_geopt_advanced_parser.py diff --git a/examples/single_calculations/example_geopt_advanced_parser.py b/examples/single_calculations/example_geopt_advanced_parser.py new file mode 100644 index 00000000..81b44a17 --- /dev/null +++ b/examples/single_calculations/example_geopt_advanced_parser.py @@ -0,0 +1,153 @@ +############################################################################### +# Copyright (c), The AiiDA-CP2K authors. # +# SPDX-License-Identifier: MIT # +# AiiDA-CP2K is hosted on GitHub at https://github.com/aiidateam/aiida-cp2k # +# For further information on the license, see the LICENSE.txt file. # +############################################################################### +"""Run DFT geometry optimization.""" + +import os +import sys + +import ase.io +import click +from aiida.common import NotExistent +from aiida.engine import run +from aiida.orm import Dict, SinglefileData, load_code +from aiida.plugins import DataFactory + +StructureData = DataFactory("core.structure") + + +def example_geopt(cp2k_code): + """Run DFT geometry optimization.""" + + print("Testing CP2K GEO_OPT on H2O (DFT)...") + + thisdir = os.path.dirname(os.path.realpath(__file__)) + + # Structure. + structure = StructureData( + ase=ase.io.read(os.path.join(thisdir, "..", "files", "h2.xyz")) + ) + + # Basis set. + basis_file = SinglefileData( + file=os.path.join(thisdir, "..", "files", "BASIS_MOLOPT") + ) + + # Pseudopotentials. + pseudo_file = SinglefileData( + file=os.path.join(thisdir, "..", "files", "GTH_POTENTIALS") + ) + + # Parameters. + parameters = Dict( + { + "GLOBAL": { + "RUN_TYPE": "GEO_OPT", + }, + "FORCE_EVAL": { + "METHOD": "Quickstep", + "DFT": { + "BASIS_SET_FILE_NAME": "BASIS_MOLOPT", + "POTENTIAL_FILE_NAME": "GTH_POTENTIALS", + "QS": { + "EPS_DEFAULT": 1.0e-12, + "WF_INTERPOLATION": "ps", + "EXTRAPOLATION_ORDER": 3, + }, + "MGRID": { + "NGRIDS": 4, + "CUTOFF": 280, + "REL_CUTOFF": 30, + }, + "XC": { + "XC_FUNCTIONAL": { + "_": "PBE", + }, + }, + "POISSON": { + "PERIODIC": "none", + "PSOLVER": "MT", + }, + }, + "SUBSYS": { + "KIND": [ + { + "_": "O", + "BASIS_SET": "DZVP-MOLOPT-SR-GTH", + "POTENTIAL": "GTH-PBE-q6", + }, + { + "_": "H", + "BASIS_SET": "DZVP-MOLOPT-SR-GTH", + "POTENTIAL": "GTH-PBE-q1", + }, + ], + }, + }, + } + ) + + # Construct process builder. + builder = cp2k_code.get_builder() + builder.structure = structure + builder.parameters = parameters + builder.code = cp2k_code + builder.file = { + "basis": basis_file, + "pseudo": pseudo_file, + } + builder.metadata.options.resources = { + "num_machines": 1, + "num_mpiprocs_per_machine": 1, + } + builder.metadata.options.max_wallclock_seconds = 1 * 3 * 60 + builder.metadata.options.parser_name = "cp2k_advanced_parser" + + print("Submitted calculation...") + calc = run(builder) + + # Check walltime not exceeded. + assert calc["output_parameters"]["exceeded_walltime"] is False + + # Check energy. + expected_energy = -1.17212345935 + if abs(calc["output_parameters"]["energy"] - expected_energy) < 1e-10: + print("OK, energy has the expected value.") + else: + print("ERROR!") + print(f"Expected energy value: {expected_energy}") + print(f"Actual energy value: {calc['output_parameters']['energy']}") + sys.exit(3) + + # Check geometry. + expected_dist = 0.732594809575 + dist = calc["output_structure"].get_ase().get_distance(0, 1) + if abs(dist - expected_dist) < 1e-7: + print("OK, H-H distance has the expected value.") + else: + print("ERROR!") + print(f"Expected dist value: {expected_dist}") + print(f"Actual dist value: {dist}") + sys.exit(3) + + # Check motion step information. + assert calc['output_parameters']['motion_step_info']['step'] == [0, 1, 2], "ERROR: motion step info is incorrect" + assert calc['output_parameters']['motion_step_info']['cell_a_angs'] == [4.0, 4.0, 4.0], "ERROR: motion step info is incorrect" + +@click.command("cli") +@click.argument("codelabel") +def cli(codelabel): + """Click interface.""" + try: + code = load_code(codelabel) + except NotExistent: + print(f"The code '{codelabel}' does not exist.") + sys.exit(1) + example_geopt(code) + + +if __name__ == "__main__": + cli() From 0fb560264d4ff7300de571d9565f87c1dc723a2d Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Tue, 28 Jan 2025 09:36:39 +0000 Subject: [PATCH 09/12] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- .../example_geopt_advanced_parser.py | 15 ++++++++++++--- 1 file changed, 12 insertions(+), 3 deletions(-) diff --git a/examples/single_calculations/example_geopt_advanced_parser.py b/examples/single_calculations/example_geopt_advanced_parser.py index 81b44a17..7a069916 100644 --- a/examples/single_calculations/example_geopt_advanced_parser.py +++ b/examples/single_calculations/example_geopt_advanced_parser.py @@ -132,10 +132,19 @@ def example_geopt(cp2k_code): print(f"Expected dist value: {expected_dist}") print(f"Actual dist value: {dist}") sys.exit(3) - + # Check motion step information. - assert calc['output_parameters']['motion_step_info']['step'] == [0, 1, 2], "ERROR: motion step info is incorrect" - assert calc['output_parameters']['motion_step_info']['cell_a_angs'] == [4.0, 4.0, 4.0], "ERROR: motion step info is incorrect" + assert calc["output_parameters"]["motion_step_info"]["step"] == [ + 0, + 1, + 2, + ], "ERROR: motion step info is incorrect" + assert calc["output_parameters"]["motion_step_info"]["cell_a_angs"] == [ + 4.0, + 4.0, + 4.0, + ], "ERROR: motion step info is incorrect" + @click.command("cli") @click.argument("codelabel") From d9c01a55ef1ad96255d3a1d1ac8b7f3209cf3887 Mon Sep 17 00:00:00 2001 From: Aliaksandr Yakutovich Date: Tue, 28 Jan 2025 10:20:18 +0000 Subject: [PATCH 10/12] Improve regexes for getting step info. --- aiida_cp2k/utils/parser.py | 45 +++++++++++++++++++------------------- 1 file changed, 23 insertions(+), 22 deletions(-) diff --git a/aiida_cp2k/utils/parser.py b/aiida_cp2k/utils/parser.py index cb2886fa..4245bed2 100644 --- a/aiida_cp2k/utils/parser.py +++ b/aiida_cp2k/utils/parser.py @@ -211,39 +211,40 @@ def parse_cp2k_output_advanced( print_now = True if result_dict["run_type"] in ["GEO_OPT", "CELL_OPT"]: # Note: with CELL_OPT/LBFGS there is no "STEP 0", while there is with CELL_OPT/BFGS + + # Getting the step number. if re.search(r"Informations at step", line): step = int(data[5]) - # Note fixes v2024.3 - if re.search(r"OPT\| Step number ", line): - step = int(data[3]) + elif re.search( + r"OPT\| Step number ", line + ): # Fix for new CP2K versions. + step = int(data[-1]) + + # Getting the maximum step size. if re.search( - r"Maximum step size ", - line, - ): - max_step = float(data[-1]) - if re.search(r"Max. step size =", line): + r"OPT\| Maximum step size\s*[-+]?\d*\.?\d+", line + ) or re.search(r"Max. step size\s+=", line): max_step = float(data[-1]) + + # Getting the RMS step size. if re.search( - r"RMS step size ", - line, - ): - rms_step = float(data[-1]) - if re.search(r"RMS step size =", line): + r"OPT\| RMS step size\s*[-+]?\d*\.?\d+", line + ) or re.search(r"RMS step size\s+=", line): rms_step = float(data[-1]) + + # Getting the maximum gradient. if re.search( - r"Maximum gradient ", - line, - ): - max_grad = float(data[-1]) - if re.search(r"Max. gradient =", line): + r"OPT\| Maximum gradient\s*[-+]?\d*\.?\d+", line + ) or re.search(r"Max. gradient\s+=", line): max_grad = float(data[-1]) + + # Getting the RMS gradient. if re.search( - r"RMS gradient ", + r"OPT\| RMS gradient\s*[-+]?\d*\.?\d+", line, - ): - rms_grad = float(data[-1]) - if re.search(r"RMS gradient =", line): + ) or re.search(r"RMS gradient\s{3,}=", line): rms_grad = float(data[-1]) + if ( ( len(data) == 1 From 44a77a57a67712f1024ccee2e59376d2dcafdd0c Mon Sep 17 00:00:00 2001 From: Aliaksandr Yakutovich Date: Tue, 28 Jan 2025 10:34:06 +0000 Subject: [PATCH 11/12] Simplify reading end of step info --- aiida_cp2k/utils/parser.py | 27 +++++++++++---------------- 1 file changed, 11 insertions(+), 16 deletions(-) diff --git a/aiida_cp2k/utils/parser.py b/aiida_cp2k/utils/parser.py index 4245bed2..5430ad12 100644 --- a/aiida_cp2k/utils/parser.py +++ b/aiida_cp2k/utils/parser.py @@ -178,7 +178,7 @@ def parse_cp2k_output_advanced( edens_rspace = None scf_converged = True - print_now = False + dump_step_info = False data = line.split() # Parse general info if line.startswith(" CELL|"): @@ -208,7 +208,7 @@ def parse_cp2k_output_advanced( # Parse specific info if result_dict["run_type"] in ["ENERGY", "ENERGY_FORCE"]: if energy is not None and not result_dict["motion_step_info"]["step"]: - print_now = True + dump_step_info = True if result_dict["run_type"] in ["GEO_OPT", "CELL_OPT"]: # Note: with CELL_OPT/LBFGS there is no "STEP 0", while there is with CELL_OPT/BFGS @@ -246,15 +246,10 @@ def parse_cp2k_output_advanced( rms_grad = float(data[-1]) if ( - ( - len(data) == 1 - and data[0] - == "---------------------------------------------------" - ) - or (len(data) == 10 and data[0] == "OPT|" and data[2] == "peak") - or (len(data) == 7 and data[0] == "OPT|" and data[2] == "peak") - ): - print_now = True # 51('-') + len(data) == 1 + and data[0] == "---------------------------------------------------" + ) or re.search(r"OPT\| Estimated peak process memory", line): + dump_step_info = True # 51('-') if re.search( r"Reevaluating energy at the minimum", line ): # not clear why it is doing a last one... @@ -268,16 +263,16 @@ def parse_cp2k_output_advanced( step = int(data[3]) if re.search(r"INITIAL PRESSURE\[bar\]", line): pressure = float(data[3]) - print_now = True + dump_step_info = True if re.search(r"PRESSURE \[bar\]", line): pressure = float(data[3]) - print_now = True + dump_step_info = True if result_dict["run_type"] == "MD-NPT_F": if re.search(r"^ STEP NUMBER", line): step = int(data[3]) if re.search(r"^ INITIAL PRESSURE\[bar\]", line): pressure = float(data[3]) - print_now = True + dump_step_info = True if re.search(r"^ PRESSURE \[bar\]", line): pressure = float(data[3]) if re.search(r"^ VOLUME\[bohr\^3\]", line): @@ -290,9 +285,9 @@ def parse_cp2k_output_advanced( cell_alp = float(data[3]) cell_bet = float(data[4]) cell_gam = float(data[5]) - print_now = True + dump_step_info = True - if print_now and energy is not None: + if dump_step_info and energy is not None: result_dict["motion_step_info"]["step"].append(step) result_dict["motion_step_info"]["energy_au"].append(energy) result_dict["motion_step_info"]["dispersion_energy_au"].append( From a5ddaad5751b38c5c7a57e2260882bbe5ad6ef89 Mon Sep 17 00:00:00 2001 From: Aliaksandr Yakutovich Date: Tue, 28 Jan 2025 11:09:08 +0000 Subject: [PATCH 12/12] Base workchain: improve output parsing. --- aiida_cp2k/workchains/base.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/aiida_cp2k/workchains/base.py b/aiida_cp2k/workchains/base.py index 08b2159d..76cc312a 100644 --- a/aiida_cp2k/workchains/base.py +++ b/aiida_cp2k/workchains/base.py @@ -1,5 +1,7 @@ """Base work chain to run a CP2K calculation.""" +import re + from aiida import common, engine, orm, plugins from .. import utils @@ -85,7 +87,7 @@ def restart_incomplete_calculation(self, calc): content_string = calc.outputs.retrieved.base.repository.get_object_content(calc.base.attributes.get('output_filename')) # CP2K was updating geometry - continue with that. - restart_geometry_transformation = "Max. gradient =" in content_string or "OPT| Maximum gradient " in content_string or "MD| Step number" in content_string + restart_geometry_transformation = re.search(r"Max. gradient\s+=", content_string) or re.search(r"OPT\| Maximum gradient\s*[-+]?\d*\.?\d+", content_string) or "MD| Step number" in content_string end_inner_scf_loop = "Total energy: " in content_string # The message is written in the log file when the CP2K input parameter `LOG_PRINT_KEY` is set to True. if not (restart_geometry_transformation or end_inner_scf_loop or "Writing RESTART" in content_string):