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* Add Eigen -> std::vector conversion * Allow negative print_level for complete silence * Add json property output * Add OrbitalEnergies property * Revert mrchem_parsed.json intermediate Now mrchem.json contains both the parsed input and the json output. It's still possible to give user input as JSON, but file name should still be mrchem.inp for this. * Add missing license headers * Add json SCF output * Compute dipole moment by default * Add json RSP output * Remove GTO rsp initial guess * Add schema for program input * Make Response.localize default to SCF.localize * Only MPI grand master dumps JSON * Improve JSON output * Add schema for program output * Occupancy -> occupation * Polarizability and NMR json list -> dict * Flush very small property values to zero * Tweak NMR output * Update to nlohmann::json-3.6.1 * Make use of json.contains() * Cleanup JSON output * Fix schemas * Remove orbital_energies input keyword * Update test refs * Require full basis name (legendre/interpolating) * Make default constructors for properties * Cleanup Molecule's handling of properties * Geometry derivative -> geometric derivative * Move eigen_to_vector to print_utils * Define PropertyMap * Move calculation of dia properties to RSP part * Fix printing
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| Original file line number | Diff line number | Diff line change |
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| "output": { | ||
| "properties": { # Collection of final properties | ||
| "charge": int, # Total molecular charge | ||
| "multiplicity": int, # Total spin multiplicity | ||
| "center_of_mass": array[float], # Center of mass coordinate | ||
| "geometry": array[ # Array of atoms | ||
| { # (one entry per atom) | ||
| "symbol": string, # Atomic symbol | ||
| "xyz": array[float] # Cartesian coordinate | ||
| } | ||
| ], | ||
| "orbital_energies": { # Collection of orbital energies | ||
| "spin": array[string], # Array of spins ('p', 'a' or 'b') | ||
| "energy": array[float], # Array of energies | ||
| "occupation": array[int], # Array of orbital occupations | ||
| "sum_occupied": float # \sum_i occupation[i]*energy[i] | ||
| }, | ||
| "scf_energy": { # Collection of energy contributions | ||
| "E_kin": float, # Kinetic energy | ||
| "E_nn": float, # Classical nuclear-nuclear interaction | ||
| "E_en": float, # Classical electron-nuclear interaction | ||
| "E_ee": float, # Classical electron-electron interaction | ||
| "E_next": float, # Classical nuclear-external field interaction | ||
| "E_eext": float, # Classical electron-external field interaction | ||
| "E_x": float, # Hartree-Fock exact exchange energy | ||
| "E_xc": float, # DFT exchange-correlation energy | ||
| "E_el": float, # Sum of electronic contributions | ||
| "E_nuc": float, # Sum of nuclear contributions | ||
| "E_tot": float # Sum of all contributions | ||
| }, | ||
| "dipole_moment": { # Collection of electric dipole moments | ||
| id (string): { # Unique identifier, default 'dip-1' | ||
| "r_O": array[float], # Gauge origin vector | ||
| "vector": array[float], # Total dipole vector | ||
| "vector_el": array[float], # Electronic dipole vector | ||
| "vector_nuc": array[float], # Nuclear dipole vector | ||
| "magnitude": float # Magnitude of total vector | ||
| } | ||
| }, | ||
| "quadrupole_moment": { # Collection of electric quadrupole moments | ||
| id (string): { # Unique identifier, default 'quad-1' | ||
| "r_O": array[float], # Gauge origin vector | ||
| "tensor": array[float], # Total quadrupole tensor | ||
| "tensor_el": array[float], # Electronic quadrupole tensor | ||
| "tensor_nuc": array[float] # Nuclear quadrupole tensor | ||
| } | ||
| }, | ||
| "polarizability": { # Collection of polarizabilities | ||
| id (string): { # Unique identifier, default 'pol-${frequency}' | ||
| "frequency": float, # Perturbation frequency | ||
| "r_O": array[float], # Gauge origin vector | ||
| "tensor": array[float], # Full polarizability tensor | ||
| "isotropic_average": float # Diagonal average | ||
| } | ||
| }, | ||
| "magnetizability": { # Collection of magnetizability | ||
| id (string): { # Unique identifier, default 'mag-${frequency}' | ||
| "frequency": float, # Perturbation frequency | ||
| "r_O": array[float], # Gauge origin vector | ||
| "tensor": array[float], # Full magnetizability tensor | ||
| "tensor_dia": array[float], # Diamagnetic tensor | ||
| "tensor_para": array[float], # Paramagnetic tensor | ||
| "isotropic_average": float # Diagonal average | ||
| } | ||
| }, | ||
| "nmr_shielding": { # Collection of NMR shielding tensors | ||
| id (string): { # Unique identifier, default 'nmr-${index}+${symbol}' | ||
| "r_O": array[float], # Gauge origin vector | ||
| "r_K": array[float], # Nuclear coordinate vector | ||
| "tensor": array[float], # Full NMR shielding tensor | ||
| "tensor_dia": array[float], # Diamagnetic tensor | ||
| "tensor_para": array[float], # Paramagnetic tensor | ||
| "diagonalized_tensor": array[float], # Diagonalized tensor used for (an)isotropy | ||
| "isotropic_average": float, # Diagonal average | ||
| "anisotropy": float # Anisotropy of tensor | ||
| } | ||
| } | ||
| }, | ||
| "scf_calculation": { # Ground state SCF calculation | ||
| "success": bool, # SCF finished successfully | ||
| "initial_energy": { # Energy computed from initial orbitals | ||
| "E_kin": float, # Kinetic energy | ||
| "E_nn": float, # Classical nuclear-nuclear interaction | ||
| "E_en": float, # Classical electron-nuclear interaction | ||
| "E_ee": float, # Classical electron-electron interaction | ||
| "E_next": float, # Classical nuclear-external field interaction | ||
| "E_eext": float, # Classical electron-external field interaction | ||
| "E_x": float, # Hartree-Fock exact exchange energy | ||
| "E_xc": float, # DFT exchange-correlation energy | ||
| "E_el": float, # Sum of electronic contributions | ||
| "E_nuc": float, # Sum of nuclear contributions | ||
| "E_tot": float # Sum of all contributions | ||
| }, | ||
| "scf_solver": { # Details from SCF optimization | ||
| "converged": bool, # Optimization converged | ||
| "wall_time": float, # Wall time (sec) for SCF optimization | ||
| "cycles": array[ # Array of SCF cycles | ||
| { # (one entry per cycle) | ||
| "energy_total": float, # Current total energy | ||
| "energy_update": float, # Current energy update | ||
| "mo_residual": float, # Current orbital residual | ||
| "wall_time": float, # Wall time (sec) for SCF cycle | ||
| "energy_terms": { # Energy contributions | ||
| "E_kin": float, # Kinetic energy | ||
| "E_nn": float, # Classical nuclear-nuclear interaction | ||
| "E_en": float, # Classical electron-nuclear interaction | ||
| "E_ee": float, # Classical electron-electron interaction | ||
| "E_next": float, # Classical nuclear-external field interaction | ||
| "E_eext": float, # Classical electron-external field interaction | ||
| "E_x": float, # Hartree-Fock exact exchange energy | ||
| "E_xc": float, # DFT exchange-correlation energy | ||
| "E_el": float, # Sum of electronic contributions | ||
| "E_nuc": float, # Sum of nuclear contributions | ||
| "E_tot": float # Sum of all contributions | ||
| } | ||
| } | ||
| ] | ||
| } | ||
| }, | ||
| "rsp_calculations": { # Collection of response calculations | ||
| id (string): { # Response identifier, e.g. 'ext_el-${frequency}' | ||
| "success": bool, # Response finished successfully | ||
| "frequency": float, # Frequency of perturbation | ||
| "perturbation": string, # Name of perturbation operator | ||
| "components": array[ # Array of operator components | ||
| { # (one entry per Cartesian direction) | ||
| "rsp_solver": { # Details from response optimization | ||
| "wall_time": float, # Wall time (sec) for response calculation | ||
| "converged": bool, # Optimization converged | ||
| "cycles": array[ # Array of response cycles | ||
| { # (one entry per cycle) | ||
| "symmetric_property": float, # Property computed from perturbation operator | ||
| "property_update": float, # Current symmetric property update | ||
| "mo_residual": float, # Current orbital residual | ||
| "wall_time": float # Wall time (sec) for response cycle | ||
| } | ||
| ] | ||
| } | ||
| } | ||
| ] | ||
| } | ||
| } | ||
| } | ||
|
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| ----------------------------- | ||
| The program input/output file | ||
| ----------------------------- | ||
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| Input schema | ||
| ------------ | ||
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| .. literalinclude:: schema_input.json | ||
| :language: JSON | ||
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| Output schema | ||
| ------------- | ||
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| .. literalinclude:: schema_output.json | ||
| :language: JSON |
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| ---------------- | ||
| User output file | ||
| ---------------- | ||
|
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