dpti package

Subpackages

Submodules

dpti.einstein module

dpti.einstein.compute_lambda(temp, mass)[source]
dpti.einstein.compute_spring(temp, spring_k)[source]
dpti.einstein.free_energy(job)[source]
dpti.einstein.frenkel(job)[source]
dpti.einstein.ideal_gas_fe(job)[source]

dpti.equi module

dpti.equi.add_module_subparsers(main_subparsers)[source]
dpti.equi.add_subparsers(module_subparsers)[source]
dpti.equi.exec_args(args, parser)[source]
dpti.equi.extract(job_dir, output)[source]
dpti.equi.gen_equi_dump_settings(if_dump_avg_posi)[source]
dpti.equi.gen_equi_ensemble_settings(ens)[source]
dpti.equi.gen_equi_force_field(model, if_meam=False, meam_model=None)[source]
dpti.equi.gen_equi_header(nsteps, thermo_freq, dump_freq, mass_map, temp, tau_t, tau_p, equi_conf, pres=None)[source]
dpti.equi.gen_equi_lammps_input(nsteps, thermo_freq, dump_freq, mass_map, temp, tau_t, tau_p, equi_conf, model, timestep, if_dump_avg_posi, ens, pres=None, if_meam=False, meam_model=None)[source]
dpti.equi.gen_equi_thermo_settings(timestep)[source]
dpti.equi.handle_compute(args)[source]
dpti.equi.handle_extract(args)[source]
dpti.equi.handle_gen(args)[source]
dpti.equi.handle_run(args)[source]
dpti.equi.handle_stat_bond(args)[source]
dpti.equi.make_task(iter_name, jdata, ens=None, temp=None, pres=None, if_dump_avg_posi=None, npt_dir=None)[source]
dpti.equi.npt_equi_conf(npt_dir)[source]
dpti.equi.post_task(iter_name, natoms=None, is_water=None)[source]
dpti.equi.run_task(task_name, machine_file)[source]
dpti.equi.water_bond(iter_name, skip=1)[source]

dpti.gdi module

class dpti.gdi.GibbsDuhemFunc(jdata, mdata, task_path, inte_dir, pref=1.0, natoms=None, shift=[0, 0], verbose=False, if_meam=False, meam_model=None, workflow=None)[source]

Bases: object

Methods

__call__(x, y)

Call self as a function.

dpti.gdi.add_module_subparsers(main_subparsers)[source]
dpti.gdi.gdi_main_loop(jdata, mdata, gdidata_dict={}, gdidata_cli={}, workflow=None)[source]
dpti.gdi.handle_gdi(args)[source]
dpti.gdi.make_dpdt(temp, pres, inte_dir, task_path, mdata, natoms=None, shift=[0, 0], verbose=False, if_meam=False, meam_model=None, workflow=None)[source]

dpti.hti module

dpti.hti.add_module_subparsers(main_subparsers)[source]
dpti.hti.compute_task(job, free_energy_type='helmholtz', method='inte', scheme='simpson', manual_pv=None, manual_pv_err=None)[source]
dpti.hti.handle_compute(args)[source]
dpti.hti.handle_gen(args)[source]
dpti.hti.handle_run(args)[source]
dpti.hti.hti_phase_trans_analyze(job, jdata=None)[source]
dpti.hti.make_iter_name(iter_index)[source]
dpti.hti.make_tasks(iter_name, jdata, ref='einstein', switch='one-step', if_meam=None)[source]
dpti.hti.post_tasks(iter_name, jdata, natoms=None, method='inte', scheme='s')[source]
dpti.hti.print_thermo_info(info)[source]
dpti.hti.refine_task(from_task, to_task, err, print_ref=False, if_meam=None, meam_model=None)[source]
dpti.hti.run_task(task_dir, machine_file, task_name, no_dp=False)[source]

dpti.hti_ice module

dpti.hti_ice.add_module_subparsers(main_subparsers)[source]
dpti.hti_ice.add_subparsers(module_subparsers)[source]
dpti.hti_ice.exec_args(args, parser)[source]
dpti.hti_ice.handle_compute(args)[source]
dpti.hti_ice.handle_gen(args)[source]
dpti.hti_ice.handle_refine(args)[source]
dpti.hti_ice.handle_run(args)[source]

dpti.hti_liq module

dpti.hti_liq.add_module_subparsers(main_subparsers)[source]
dpti.hti_liq.compute_task(job, free_energy_type='helmholtz', scheme='simpson', manual_pv=None, manual_pv_err=None)[source]
dpti.hti_liq.handle_compute(args)[source]
dpti.hti_liq.handle_gen(args)[source]
dpti.hti_liq.handle_run(args)[source]
dpti.hti_liq.make_iter_name(iter_index)[source]
dpti.hti_liq.make_tasks(iter_name, jdata, if_meam=None)[source]
dpti.hti_liq.post_tasks(iter_name, natoms)[source]

dpti.hti_water module

dpti.hti_water.add_module_subparsers(main_subparsers)[source]
dpti.hti_water.add_subparsers(module_subparsers)[source]
dpti.hti_water.compute_ideal_mol(iter_name)[source]
dpti.hti_water.exec_args(args, parser)[source]
dpti.hti_water.handle_compute(args)[source]
dpti.hti_water.handle_gen(args)[source]
dpti.hti_water.handle_refine(args)[source]
dpti.hti_water.handle_run(args)[source]
dpti.hti_water.make_tasks(iter_name, jdata)[source]
dpti.hti_water.post_tasks(iter_name, natoms, method='inte', scheme='s')[source]
dpti.hti_water.refine_tasks(from_task, to_task, err)[source]
dpti.hti_water.spring_inte(temp, kk, r0)[source]

dpti.main module

dpti.main.create_parser()[source]
dpti.main.main()[source]

dpti.old_equi module

dpti.old_equi.extract(job_dir, output)[source]
dpti.old_equi.make_task(iter_name, jdata, ens=None, temp=None, pres=None, avg_posi=None, npt_conf=None, if_meam=None)[source]
dpti.old_equi.npt_equi_conf(npt_name)[source]
dpti.old_equi.post_task(iter_name, natoms=None, is_water=False)[source]
dpti.old_equi.water_bond(iter_name, skip=1)[source]

dpti.relax module

dpti.ti module

dpti.ti.add_module_subparsers(main_subparsers)[source]
dpti.ti.compute_task(job, inte_method, Eo, Eo_err, To, scheme='simpson')[source]
dpti.ti.handle_compute(args)[source]
dpti.ti.handle_gen(args)[source]
dpti.ti.handle_refine(args)[source]
dpti.ti.handle_run(args)[source]
dpti.ti.make_iter_name(iter_index)[source]
dpti.ti.make_tasks(iter_name, jdata, if_meam=None)[source]
dpti.ti.parse_seq_ginv(seq)[source]
dpti.ti.post_tasks(iter_name, jdata, Eo, Eo_err=0, To=None, natoms=None, scheme='simpson', shift=0.0)[source]
dpti.ti.post_tasks_mbar(iter_name, jdata, Eo, natoms=None)[source]
dpti.ti.refine_task(from_task, to_task, err)[source]
dpti.ti.run_task(task_name, machine_file)[source]

dpti.ti_water module

dpti.ti_water.add_module_subparsers(main_subparsers)[source]
dpti.ti_water.add_subparsers(module_subparsers)[source]
dpti.ti_water.exec_args(args, parser)[source]
dpti.ti_water.handle_compute(args)[source]
dpti.ti_water.handle_gen(args)[source]
dpti.ti_water.handle_refine(args)[source]
dpti.ti_water.handle_run(args)[source]