Add ase_interface with support for optimization and md

Data_Mechanics_Integrated_Scientific_Computing/application_configs/calculator/ase.yaml

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+_target_: ppmat.calculator.ase.ASECalculator
+type: ase

Data_Mechanics_Integrated_Scientific_Computing/application_configs/logger/default.yaml

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+log_file: out.log           # Resolved to ${hydra:run.dir}/out.log
+log_level: INFO             # Logging level
+# use_visualdl: False         # Use VisualDL
+# use_wandb: False            # Use Weights & Biases (wandb)
+# use_tensorboard: False      # Use TensorBoard

Data_Mechanics_Integrated_Scientific_Computing/application_configs/md_ase.yaml

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+# @package _global_
+
+# To run the script, use the following command:
+# Option A:
+# python applications/main.py --config-name md_ase \
+#            model.model_name=chgnet_mptrj \
+#
+# Option B:
+# python applications/main.py --config-name md_ase \
+#            model.config_path=output/chgnet_mptrj/chgnet_mptrj.yaml \
+#            model.checkpoint_path=output/chgnet_mptrj/checkpoints/best.pdparams
+
+
+device: cuda
+seed: null
+
+defaults:
+  - _self_
+  - run: default
+  - logger: default
+  - model: load_model
+  - system: load_system                   # load_system, ase_create
+  - task: md                              # opt, md
+  - calculator: ase
+  - override hydra/job_logging: disabled
+
+hydra:
+  job:
+    name: md_ase
+    chdir: True                           # change working directory to run.dir
+  run:
+    dir: ./out_${hydra:job.name}/${now:%Y%m%d_%H%M%S}  # output directory
+
+# To convert the trajectory (.traj) file to XYZ format, run:
+# ase convert <trajectory_file>.traj <output_file>.xyz

Data_Mechanics_Integrated_Scientific_Computing/application_configs/model/load_model.yaml

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+model_name: null
+config_path: null
+weights_name: null
+checkpoint_path: null

Data_Mechanics_Integrated_Scientific_Computing/application_configs/optimizer_ase.yaml

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+# @package _global_
+
+# To run the script, use the following command:
+# Option A:
+# python applications/main.py --config-name optimizer_ase \
+#            model.model_name=chgnet_mptrj \
+#
+# Option B:
+# python applications/main.py --config-name optimizer_ase \
+#            model.config_path=output/chgnet_mptrj/chgnet_mptrj.yaml \
+#            model.checkpoint_path=output/chgnet_mptrj/checkpoints/best.pdparams
+
+device: cuda
+seed: null
+
+defaults:
+  - _self_
+  - run: default
+  - logger: default
+  - model: load_model
+  - system: ase_create                   # load_system, ase_create
+  - task: opt                            # opt, md
+  - calculator: ase
+  - override hydra/job_logging: disabled
+
+hydra:
+  job:
+    name: optimizer_ase
+    chdir: True                          # change working directory to run.dir
+  run:
+    dir: ./out_${hydra:job.name}/${now:%Y%m%d_%H%M%S}  # output directory
+
+# To convert the trajectory (.traj) file to XYZ format, run:
+# ase convert <trajectory_file>.traj <output_file>.xyz

Data_Mechanics_Integrated_Scientific_Computing/application_configs/potential.yaml

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+# @package _global_
+
+# To run the script, use the following command:
+
+# Option A:
+# python applications/main.py --config-name potential \
+#            model.model_name=chgnet_mptrj \
+#
+# Option B:
+# python applications/main.py --config-name potential \
+#            model.model_name=chgnet_mptrj \
+#            system.file_path=./interatomic_potentials/example_data/cifs/
+#
+# Option C:
+# python applications/main.py --config-name potential \
+#            model.config_path=output/chgnet_mptrj/chgnet_mptrj.yaml \
+#            model.checkpoint_path=output/chgnet_mptrj/checkpoints/best.pdparams
+#            system.file_path=./interatomic_potentials/example_data/cifs/
+
+device: cuda
+seed: null
+
+defaults:
+  - _self_
+  - run: default
+  - logger: default
+  - model: load_model
+  - system: load_system                   # load_system, ase_create
+  - override hydra/job_logging: disabled
+
+hydra:
+  job:
+    name: potential
+    chdir: True                           # change working directory to run.dir
+  run:
+    dir: ./out_${hydra:job.name}/${now:%Y%m%d_%H%M%S}  # output directory
+
+# To convert the trajectory (.traj) file to XYZ format, run:
+# ase convert <trajectory_file>.traj <output_file>.xyz

Data_Mechanics_Integrated_Scientific_Computing/application_configs/property.yaml

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+# @package _global_
+
+# To run the script, use the following command:
+# Option A:
+# python applications/main.py --config-name property \
+#            model.model_name=megnet_mp2018_train_60k_e_form \
+#            system.file_path=./property_prediction/example_data/cifs/
+#
+# Option B:
+# python applications/main.py --config-name property \
+#            model.config_path=output/megnet_mp2018_train_60k_e_form/megnet_mp2018_train_60k_e_form.yaml \
+#            model.checkpoint_path=output/megnet_mp2018_train_60k_e_form/checkpoints/best.pdparams
+
+device: cuda
+seed: null
+
+defaults:
+  - _self_
+  - run: default
+  - logger: default
+  - model: load_model
+  - system: ase_create                   # load_system, ase_create
+  - override hydra/job_logging: disabled
+
+hydra:
+  job:
+    name: property
+    chdir: True                          # change working directory to run.dir
+  run:
+    dir: ./out_${hydra:job.name}/${now:%Y%m%d_%H%M%S}  # output directory
+
+# To convert the trajectory (.traj) file to XYZ format, run:
+# ase convert <trajectory_file>.traj <output_file>.xyz

Data_Mechanics_Integrated_Scientific_Computing/application_configs/run/default.yaml

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+experiment: null
+work_dir: ${hydra:runtime.cwd}
+
+# data_dir: ${run.work_dir}/data
+# path: ${run.work_dir}/runs
+# id: ${uuid:1}
+# ckpt_path: null

Data_Mechanics_Integrated_Scientific_Computing/application_configs/sample.yaml

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+# @package _global_
+
+# To run the script, use the following command:
+# Option A:
+# python applications/main.py --config-name property \
+#            model.model_name=megnet_mp2018_train_60k_e_form \
+#            system.file_path=./property_prediction/example_data/cifs/
+#
+# Option B:
+# python applications/main.py --config-name property \
+#            model.config_path=output/megnet_mp2018_train_60k_e_form/megnet_mp2018_train_60k_e_form.yaml \
+#            model.checkpoint_path=output/megnet_mp2018_train_60k_e_form/checkpoints/best.pdparams
+
+device: cuda
+seed: null
+
+defaults:
+  - _self_
+  - run: default
+  - logger: default
+  - model: load_model
+  - sample: ???           # Option: compute_metric, by_chemical_formula, by_num_atoms, by_dataloader
+  - override hydra/job_logging: disabled
+
+hydra:
+  job:
+    name: sample
+    chdir: True                          # change working directory to run.dir
+  run:
+    dir: ./out_${hydra:job.name}/${now:%Y%m%d_%H%M%S}  # output directory
+
+# To convert the trajectory (.traj) file to XYZ format, run:
+# ase convert <trajectory_file>.traj <output_file>.xyz

Data_Mechanics_Integrated_Scientific_Computing/application_configs/sample/by_chemical_formula.yaml

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+name: by_chemical_formula
+chemical_formula: ???

Data_Mechanics_Integrated_Scientific_Computing/application_configs/sample/by_dataloader.yaml

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+name: by_dataloader

Data_Mechanics_Integrated_Scientific_Computing/application_configs/sample/by_num_atoms.yaml

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+name: by_num_atoms
+num_atoms: ???

Data_Mechanics_Integrated_Scientific_Computing/application_configs/sample/compute_metric.yaml

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+name: compute_metric

Data_Mechanics_Integrated_Scientific_Computing/application_configs/system/ase_create.yaml

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+interface: ase
+structures:
+  - element: Fe
+  - element: Cu
+  - element: Mg
+    type: fcc
+    repeat: [4, 4, 4]

Data_Mechanics_Integrated_Scientific_Computing/application_configs/system/load_system.yaml

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+interface: load_file
+file_path: applications/example_data/cifs
+# position_unit_input: Angstrom
+# mass_unit_input: 1.0

Data_Mechanics_Integrated_Scientific_Computing/application_configs/task/md.yaml

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+_target_: ppmat.calculator.ase.MDSimulationTask
+
+temperature: 300  # Temperature in Kelvin
+timestep: 0.1     # Timestep for MD simulation in fs
+steps: 1000       # Number of MD steps
+interval: 1       # Interval to save trajectory

Data_Mechanics_Integrated_Scientific_Computing/application_configs/task/opt.yaml

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+_target_: ppmat.calculator.ase.OptimizationTask
+
+optimizer: LBFGS            # Optimizer name
+filter: FrechetCellFilter   # Filter name
+fmax: 0.05                  # Maximum force tolerance
+steps: 100                  # Number of steps

Data_Mechanics_Integrated_Scientific_Computing/example_data/cifs/Al.cif

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+# generated using pymatgen
+data_Al
+_symmetry_space_group_name_H-M   'P 1'
+_cell_length_a   4.03892969
+_cell_length_b   4.03892969
+_cell_length_c   4.03892969
+_cell_angle_alpha   90.00000000
+_cell_angle_beta   90.00000000
+_cell_angle_gamma   90.00000000
+_symmetry_Int_Tables_number   1
+_chemical_formula_structural   Al
+_chemical_formula_sum   Al4
+_cell_volume   65.88687052
+_cell_formula_units_Z   4
+loop_
+ _symmetry_equiv_pos_site_id
+ _symmetry_equiv_pos_as_xyz
+  1  'x, y, z'
+loop_
+ _atom_type_symbol
+ _atom_type_oxidation_number
+  Al0+  0.0
+loop_
+ _atom_site_type_symbol
+ _atom_site_label
+ _atom_site_symmetry_multiplicity
+ _atom_site_fract_x
+ _atom_site_fract_y
+ _atom_site_fract_z
+ _atom_site_occupancy
+  Al0+  Al0  1  0.00000000  0.00000000  0.00000000  1
+  Al0+  Al1  1  0.00000000  0.50000000  0.50000000  1
+  Al0+  Al2  1  0.50000000  0.00000000  0.50000000  1
+  Al0+  Al3  1  0.50000000  0.50000000  0.00000000  1

Data_Mechanics_Integrated_Scientific_Computing/example_data/cifs/AlCu.cif

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+# generated using pymatgen
+data_AlCu
+_symmetry_space_group_name_H-M   'P 1'
+_cell_length_a   4.05572184
+_cell_length_b   6.31517560
+_cell_length_c   6.32456864
+_cell_angle_alpha   65.48687748
+_cell_angle_beta   71.36152755
+_cell_angle_gamma   71.43809003
+_symmetry_Int_Tables_number   1
+_chemical_formula_structural   AlCu
+_chemical_formula_sum   'Al5 Cu5'
+_cell_volume   136.37894604
+_cell_formula_units_Z   5
+loop_
+ _symmetry_equiv_pos_site_id
+ _symmetry_equiv_pos_as_xyz
+  1  'x, y, z'
+loop_
+ _atom_site_type_symbol
+ _atom_site_label
+ _atom_site_symmetry_multiplicity
+ _atom_site_fract_x
+ _atom_site_fract_y
+ _atom_site_fract_z
+ _atom_site_occupancy
+  Al  Al0  1  0.50000000  0.50000000  0.50000000  1
+  Al  Al1  1  0.84514971  0.46048356  0.84957741  1
+  Al  Al2  1  0.15485029  0.53951644  0.15042259  1
+  Al  Al3  1  0.62316791  0.99377092  0.76059171  1
+  Al  Al4  1  0.37683209  0.00622908  0.23940829  1
+  Cu  Cu5  1  0.00000000  0.00000000  0.00000000  1
+  Cu  Cu6  1  0.73969721  0.24150696  0.27583163  1
+  Cu  Cu7  1  0.26030279  0.75849304  0.72416837  1
+  Cu  Cu8  1  0.89095358  0.77254544  0.44562536  1
+  Cu  Cu9  1  0.10904642  0.22745456  0.55437464  1

Data_Mechanics_Integrated_Scientific_Computing/example_data/cifs/mp-18767-LiMnO2.cif

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+# generated using pymatgen
+data_LiMnO2
+_symmetry_space_group_name_H-M   'P 1'
+_cell_length_a   2.86877900
+_cell_length_b   4.63447500
+_cell_length_c   5.83250700
+_cell_angle_alpha   90.00000000
+_cell_angle_beta   90.00000000
+_cell_angle_gamma   90.00000000
+_symmetry_Int_Tables_number   1
+_chemical_formula_structural   LiMnO2
+_chemical_formula_sum   'Li2 Mn2 O4'
+_cell_volume   77.54484024
+_cell_formula_units_Z   2
+loop_
+ _symmetry_equiv_pos_site_id
+ _symmetry_equiv_pos_as_xyz
+  1  'x, y, z'
+loop_
+ _atom_type_symbol
+ _atom_type_oxidation_number
+  Li+  1.0
+  Mn3+  3.0
+  O2-  -2.0
+loop_
+ _atom_site_type_symbol
+ _atom_site_label
+ _atom_site_symmetry_multiplicity
+ _atom_site_fract_x
+ _atom_site_fract_y
+ _atom_site_fract_z
+ _atom_site_occupancy
+  Li+  Li0  1  0.50000000  0.50000000  0.37975050  1
+  Li+  Li1  1  0.00000000  0.00000000  0.62024950  1
+  Mn3+  Mn2  1  0.50000000  0.50000000  0.86325250  1
+  Mn3+  Mn3  1  0.00000000  0.00000000  0.13674750  1
+  O2-  O4  1  0.50000000  0.00000000  0.36082450  1
+  O2-  O5  1  0.00000000  0.50000000  0.09851350  1
+  O2-  O6  1  0.50000000  0.00000000  0.90148650  1
+  O2-  O7  1  0.00000000  0.50000000  0.63917550  1

Data_Mechanics_Integrated_Scientific_Computing/example_data/cifs/results_pred_property.csv

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+file_name,energy_per_atom,force,stress,magmom
+property_prediction/example_data/cifs/Al.cif,[[-3.6643398]],"[[-1.4901161e-08  1.3858080e-06 -4.3120235e-07]
+ [-9.3132257e-10 -8.6519867e-07  1.0430813e-07]
+ [ 6.9150701e-07 -1.6763806e-08  1.2293458e-06]
+ [-6.6123903e-07 -4.8521906e-07 -9.0338290e-07]]","[[-1.2588882e-01  4.2487745e-06  8.6164600e-06]
+ [ 4.4294275e-06 -1.2588955e-01 -6.6498583e-06]
+ [ 8.8680017e-06 -6.6590051e-06 -1.2589219e-01]]","[[0.02061005]
+ [0.02061002]
+ [0.02060978]
+ [0.02060993]]"
+property_prediction/example_data/cifs/AlCu.cif,[[-4.118485]],"[[ 4.1117892e-07 -4.4133049e-07  2.0021107e-06]
+ [-5.2160695e-03  4.0400606e-03  1.6855899e-02]
+ [ 5.2174702e-03 -4.0380079e-03 -1.6858250e-02]
+ [-1.5204746e-02 -7.6037906e-03  5.5945456e-02]
+ [ 1.5203571e-02  7.6041333e-03 -5.5943772e-02]
+ [ 4.8428774e-08 -1.0426156e-06 -5.3364784e-07]
+ [ 3.8307473e-02 -9.5896043e-02 -6.1208583e-02]
+ [-3.8307074e-02  9.5897190e-02  6.1209716e-02]
+ [ 2.5706176e-02 -1.8066719e-02 -3.9052561e-02]
+ [-2.5707349e-02  1.8064771e-02  3.9050829e-02]]","[[-3.7951264   0.01920414  0.23555437]
+ [ 0.01920349 -2.4701474  -0.23675922]
+ [ 0.23555323 -0.23675986 -4.492184  ]]","[[0.00778838]
+ [0.01051749]
+ [0.01051739]
+ [0.01494901]
+ [0.01494877]
+ [0.01929218]
+ [0.01869392]
+ [0.01869386]
+ [0.01622796]
+ [0.01622802]]"
+property_prediction/example_data/cifs/mp-18767-LiMnO2.cif,[[-7.367691]],"[[-1.4901161e-08 -4.2142347e-08  2.3821428e-02]
+ [-2.9802322e-08  2.9685907e-08 -2.3822412e-02]
+ [ 2.6822090e-07 -1.3038516e-07  9.2583150e-02]
+ [ 1.1920929e-07  1.1175871e-08 -9.2581131e-02]
+ [-5.9604645e-08  2.3283064e-08 -2.4323463e-03]
+ [ 1.0132790e-06 -2.0703301e-06 -1.3078392e-02]
+ [-1.3113022e-06  2.0330772e-06  1.3077289e-02]
+ [-5.9604645e-08  5.3085387e-08  2.4323836e-03]]","[[-3.0404767e-01 -3.9735078e-06  1.2365246e-06]
+ [-3.2817538e-06  2.2306754e-01  6.0997813e-06]
+ [ 3.0538124e-06  6.8471963e-06 -1.0721654e-01]]","[[3.0493736e-03]
+ [3.0493736e-03]
+ [3.8694177e+00]
+ [3.8694177e+00]
+ [4.4135526e-02]
+ [3.8622051e-02]
+ [3.8622051e-02]
+ [4.4135392e-02]]"