Amsterdam Modeling Suite
************************

PLAMS offers interfaces to the main programs of the Amsterdam Modeling
Suite.

All possible input keywords and options are covered, as well as
extraction of arbitrary data from binary files (called KF files)
produced by these programs.

Note:

  How do I run X using PLAMS?

  * ADF      : "AMSJob" with ADF engine

  * BAND     : "AMSJob" with BAND engine

  * DFTB     : "AMSJob" with DFTB engine

  * ReaxFF   : "AMSJob" with ReaxFF engine

  * MOPAC    : "AMSJob" with MOPAC engine

  * ForceField      : "AMSJob" with ForceField engine

  * ParAMS      : ParAMSJob

  * Densf    : "DensfJob"

  * FCF      : "FCFJob"

  * COSMO-RS : "CRSJob"

  * Zacros      : ZacrosJob

* AMS driver and engines

  * Preparing input

  * Preparing runscript

  * Molecule handling

    * Multiple molecules

  * AMSJob API

    * "AMSJob"

      * "AMSJob.__init__()"

      * "AMSJob.run()"

      * "AMSJob.get_input()"

      * "AMSJob.get_runscript()"

      * "AMSJob.check()"

      * "AMSJob.get_errormsg()"

      * "AMSJob.hash_input()"

      * "AMSJob.get_task()"

      * "AMSJob.load_external()"

      * "AMSJob.from_input()"

      * "AMSJob.from_inputfile()"

      * "AMSJob.settings_to_mol()"

  * AMSResults API

    * "AMSResults"

      * "AMSResults.collect()"

      * "AMSResults.refresh()"

      * "AMSResults.engine_names()"

      * "AMSResults.get_main_engine_name()"

      * "AMSResults.read_hybrid_term_rkf()"

      * "AMSResults.rkfpath()"

      * "AMSResults.readrkf()"

      * "AMSResults.read_rkf_section()"

      * "AMSResults.get_rkf_skeleton()"

      * "AMSResults.get_molecule()"

      * "AMSResults.get_system()"

      * "AMSResults.get_input_molecule()"

      * "AMSResults.get_input_system()"

      * "AMSResults.get_input_molecules()"

      * "AMSResults.get_main_molecule()"

      * "AMSResults.get_main_system()"

      * "AMSResults.get_main_ase_atoms()"

      * "AMSResults.get_history_molecule()"

      * "AMSResults.is_valid_stepnumber()"

      * "AMSResults.get_system_version()"

      * "AMSResults.get_history_variables()"

      * "AMSResults.get_history_length()"

      * "AMSResults.get_history_property()"

      * "AMSResults.get_property_at_step()"

      * "AMSResults.get_atomic_temperatures_at_step()"

      * "AMSResults.get_band_structure()"

      * "AMSResults.get_phonons_dos()"

      * "AMSResults.get_phonons_band_structure()"

      * "AMSResults.get_phonons_thermodynamic_properties()"

      * "AMSResults.get_engine_results()"

      * "AMSResults.get_engine_properties()"

      * "AMSResults.get_energy()"

      * "AMSResults.get_energy_uncertainty()"

      * "AMSResults.get_gradients()"

      * "AMSResults.get_gradients_uncertainty()"

      * "AMSResults.get_gradients_magnitude_uncertainty()"

      * "AMSResults.get_stresstensor()"

      * "AMSResults.get_hessian()"

      * "AMSResults.get_elastictensor()"

      * "AMSResults.get_frequencies()"

      * "AMSResults.get_frequency_spectrum()"

      * "AMSResults.get_force_constants()"

      * "AMSResults.get_pvdos()"

      * "AMSResults.get_reduced_masses()"

      * "AMSResults.get_normal_modes()"

      * "AMSResults.get_charges()"

      * "AMSResults.get_atom_types()"

      * "AMSResults.get_dipolemoment()"

      * "AMSResults.get_dipolegradients()"

      * "AMSResults.get_polarizability()"

      * "AMSResults.get_zero_point_energy()"

      * "AMSResults.get_ir_intensities()"

      * "AMSResults.get_raman_intensities()"

      * "AMSResults.get_vcd_rotational_strength()"

      * "AMSResults.get_ir_spectrum()"

      * "AMSResults.get_raman_spectrum()"

      * "AMSResults.get_vcd_spectrum()"

      * "AMSResults.get_n_spin()"

      * "AMSResults.get_orbital_energies()"

      * "AMSResults.get_orbital_occupations()"

      * "AMSResults.get_homo_energies()"

      * "AMSResults.get_lumo_energies()"

      * "AMSResults.get_smallest_homo_lumo_gap()"

      * "AMSResults.are_orbitals_fractionally_occupied()"

      * "AMSResults.get_timings()"

      * "AMSResults.get_forcefield_params()"

      * "AMSResults.get_exit_condition_message()"

      * "AMSResults.get_pesscan_results()"

      * "AMSResults.get_neb_results()"

      * "AMSResults.get_irc_results()"

      * "AMSResults.get_time_step()"

      * "AMSResults.get_velocity_acf()"

      * "AMSResults.get_dipole_derivatives_acf()"

      * "AMSResults.get_diffusion_coefficient_from_velocity_acf()"

      * "AMSResults.get_power_spectrum()"

      * "AMSResults.get_ir_spectrum_md()"

      * "AMSResults.get_green_kubo_viscosity()"

      * "AMSResults.get_density_along_axis()"

      * "AMSResults.get_work_function_results()"

      * "AMSResults.recreate_molecule()"

      * "AMSResults.recreate_settings()"

      * "AMSResults.ok()"

      * "AMSResults.get_errormsg()"

      * "AMSResults.name"

      * "AMSResults.get_energy_landscape()"

  * Other functions

    * "hybrid_committee_engine_settings()"

* AMS worker

  * AMSWorker API

    * "AMSWorker"

      * "AMSWorker.stop()"

      * "AMSWorker.SinglePoint()"

      * "AMSWorker.GeometryOptimization()"

      * "AMSWorker.ParseInput()"

  * AMSWorkerResults API

    * "AMSWorkerResults"

      * "AMSWorkerResults.name"

      * "AMSWorkerResults.ok()"

      * "AMSWorkerResults.get_errormsg()"

      * "AMSWorkerResults.get_energy()"

      * "AMSWorkerResults.get_gradients()"

      * "AMSWorkerResults.get_stresstensor()"

      * "AMSWorkerResults.get_hessian()"

      * "AMSWorkerResults.get_elastictensor()"

      * "AMSWorkerResults.get_charges()"

      * "AMSWorkerResults.get_dipolemoment()"

      * "AMSWorkerResults.get_dipolegradients()"

      * "AMSWorkerResults.get_input_molecule()"

      * "AMSWorkerResults.get_main_molecule()"

      * "AMSWorkerResults.get_main_ase_atoms()"

  * AMSWorkerPool API

    * "AMSWorkerPool"

      * "AMSWorkerPool.SinglePoints()"

      * "AMSWorkerPool.GeometryOptimizations()"

      * "AMSWorkerPool.stop()"

* ASE Calculator for AMS

  * Introduction

  * AMS settings

    * ASE results

    * Charge

  * AMS standalone and worker mode

  * Technical

  * AMSCalculator API

    * "AMSCalculator"

      * "AMSCalculator.__new__()"

      * "AMSCalculator.implemented_properties"

      * "AMSCalculator.calculate()"

      * "AMSCalculator.ensure_property()"

      * "AMSCalculator.stop_worker()"

      * "AMSCalculator.clean_exit()"

* Quick jobs

  * "preoptimize()"

  * "refine_density()"

  * "refine_lattice()"

  * "shakemd()"

* Analysis tools: Densf, FCF, analysis

  * "FCFJob"

    * "FCFJob.__init__()"

    * "FCFJob._serialize_mol()"

    * "FCFJob._remove_mol()"

  * "DensfJob"

    * "DensfJob.__init__()"

    * "DensfJob._serialize_mol()"

    * "DensfJob._remove_mol()"

    * "DensfJob.check()"

  * "AMSAnalysisJob"

    * "AMSAnalysisJob.__init__()"

    * "AMSAnalysisJob._serialize_mol()"

    * "AMSAnalysisJob._remove_mol()"

    * "AMSAnalysisJob._atom_suffix()"

    * "AMSAnalysisJob.check()"

* KF files

  * "KFFile"

    * "KFFile.__init__()"

    * "KFFile.read()"

    * "KFFile.read_int()"

    * "KFFile.read_ints()"

    * "KFFile.read_real()"

    * "KFFile.read_reals()"

    * "KFFile.read_logical()"

    * "KFFile.read_logicals()"

    * "KFFile.read_string()"

    * "KFFile.write()"

    * "KFFile.save()"

    * "KFFile.delete_section()"

    * "KFFile.sections()"

    * "KFFile.read_section()"

    * "KFFile.keys()"

    * "KFFile.get_skeleton()"

    * "KFFile._variable_type_equals()"

    * "KFFile.__getitem__()"

    * "KFFile.__setitem__()"

    * "KFFile.__iter__()"

    * "KFFile.__contains__()"

    * "KFFile._split()"

    * "KFFile._str()"

  * "KFReader"

    * "KFReader.__init__()"

    * "KFReader.read()"

    * "KFReader.variable_type()"

    * "KFReader.__iter__()"

    * "KFReader._autodetect()"

    * "KFReader._read_block()"

    * "KFReader._parse()"

    * "KFReader._get_data()"

    * "KFReader._create_index()"

    * "KFReader._datablocks()"

  * "KFHistory"

    * "KFHistory.__init__()"

    * "KFHistory.read_all()"

    * "KFHistory.iter()"

    * "KFHistory.iter_optional()"

* COSMO-RS

  * Settings

  * Settings with multiple compounds

  * ADF and CRSJob

  * COSMO-RS Parameters

  * Data analyses and plotting

  * API

    * "CRSJob"

      * "CRSJob._result_type"

      * "CRSJob.__init__()"

      * "CRSJob.cos_to_coskf()"

    * "CRSResults"

      * "CRSResults.get_energy()"

      * "CRSResults.get_activity_coefficient()"

      * "CRSResults.get_sigma_profile()"

      * "CRSResults.get_sigma_potential()"

      * "CRSResults.get_prop_names()"

      * "CRSResults.get_results()"

      * "CRSResults.get_multispecies_dist()"

      * "CRSResults.get_structure_energy()"

      * "CRSResults.plot()"

      * "CRSResults._get_array_dict()"

      * "CRSResults._construct_array_dict()"

      * "CRSResults._dict_to_df()"

* ParAMS, Simple Active Learning

* Conformers

  * ConformersJob

    * "ConformersJob"

      * "ConformersJob._result_type"

      * "ConformersJob.__init__()"

      * "ConformersJob.check()"

      * "ConformersJob.get_input()"

      * "ConformersJob.get_runscript()"

      * "ConformersJob.load_external()"

    * "ConformersResults"

      * "ConformersResults.__init__()"

      * "ConformersResults.rkfpath()"

      * "ConformersResults.get_lowest_conformer()"

      * "ConformersResults.get_conformers()"

      * "ConformersResults.get_relative_energies()"

      * "ConformersResults.get_energies()"

      * "ConformersResults.get_lowest_energy()"

      * "ConformersResults.get_boltzmann_distribution()"

      * "ConformersResults.__str__()"

      * "ConformersResults.collect()"

    * "plot_conformers()"

* Recipes

  * COSMO-RS Compound

    * Overview

    * API

    * Code

  * COSMO-RS Conformers

    * Overview

    * API

    * Code

  * MD Jobs

    * Overview

    * API

    * Code

  * ADF Fragment

    * Overview

    * API

    * Code

  * BAND Fragment

    * Overview

    * API

    * Code

  * Reorganization Energy

    * Overview

    * API

    * Code

  * ADFNBO

    * Overview

    * API

    * Code

  * pyAHFCDOS

    * Overview

    * API

    * Code

  * ADFVibronicDOS

    * Overview

    * API

    * Code

* Reactions Discovery

* Zacros
