Index

A

add_bonds() (in module dpti.lib.water) add_module_subparsers() (in module dpti.equi) (in module dpti.gdi) (in module dpti.hti) (in module dpti.hti_ice) (in module dpti.hti_liq) (in module dpti.hti_water) (in module dpti.mti) (in module dpti.ti) (in module dpti.ti_water)

add_subparsers() (in module dpti.equi) (in module dpti.hti_ice) (in module dpti.hti_water) (in module dpti.mti) (in module dpti.ti_water)

B

block_avg() (in module dpti.lib.utils) block_call() (dpti.lib.RemoteJob.RemoteJob method)

block_checkcall() (dpti.lib.RemoteJob.RemoteJob method) box2dumpbox() (in module dpti.lib.dump) box2lmpbox() (in module dpti.lib.lmp)

C

check_status() (dpti.lib.RemoteJob.CloudMachineJob method) (dpti.lib.RemoteJob.PBSJob method) (dpti.lib.RemoteJob.SlurmJob method) clean() (dpti.lib.RemoteJob.RemoteJob method) close() (dpti.lib.RemoteJob.SSHSession method) CloudMachineJob (class in dpti.lib.RemoteJob) compute_bonds() (in module dpti.lib.water) compute_ideal_mol() (in module dpti.hti_water) compute_lambda() (in module dpti.einstein) compute_nrefine() (in module dpti.lib.utils)

compute_spring() (in module dpti.einstein) compute_task() (in module dpti.hti) (in module dpti.hti_liq) (in module dpti.ti) copy_file_list() (in module dpti.lib.utils) create_dict_not_empty_key() (in module dpti.lib.utils) create_loop_dag() (dpti.dags.dp_ti_gdi.GDIDAGFactory method) create_main_dag() (dpti.dags.dp_ti_gdi.GDIDAGFactory method) create_parser() (in module dpti.main) create_path() (in module dpti.lib.utils) cvt_conf() (in module dpti.lib.utils)

D

dagargs (dpti.dags.dp_ti_gdi.GDIDAGFactory attribute) default_args (dpti.dags.dp_ti_gdi.GDIDAGFactory attribute) dist_via_oh_list() (in module dpti.lib.water) download() (dpti.lib.RemoteJob.RemoteJob method) dpti module dpti.dags module dpti.dags.dp_ti_gdi module dpti.dags.utils module dpti.einstein module dpti.equi module dpti.gdi module dpti.hti module dpti.hti_ice module dpti.hti_liq module dpti.hti_water module dpti.lib module

dpti.lib.dump module dpti.lib.lammps module dpti.lib.lmp module dpti.lib.output module dpti.lib.RemoteJob module dpti.lib.utils module dpti.lib.vasp module dpti.lib.water module dpti.main module dpti.mti module dpti.old_equi module dpti.ti module dpti.ti_water module dumpbox2box() (in module dpti.lib.dump)

E

exec_args() (in module dpti.equi) (in module dpti.hti_ice) (in module dpti.hti_water) (in module dpti.mti) (in module dpti.ti_water)

extract() (in module dpti.equi) (in module dpti.old_equi)

F

finished (dpti.lib.RemoteJob.JobStatus attribute) format_refine_summary() (in module dpti.hti)

free_energy() (in module dpti.einstein) frenkel() (in module dpti.einstein) from_system_data() (in module dpti.lib.lmp)

G

gdi_main_loop() (in module dpti.gdi) GDIDAGFactory (class in dpti.dags.dp_ti_gdi) GDIWorkflow (class in dpti.dags.dp_ti_gdi) gen_equi_dump_settings() (in module dpti.equi) gen_equi_ensemble_settings() (in module dpti.equi) gen_equi_force_field() (in module dpti.equi) gen_equi_header() (in module dpti.equi) gen_equi_lammps_input() (in module dpti.equi) gen_equi_thermo_settings() (in module dpti.equi) get_atoms() (in module dpti.lib.lmp) get_atype() (in module dpti.lib.dump) (in module dpti.lib.lmp) get_dag_run_state() (dpti.dags.dp_ti_gdi.GDIWorkflow method) get_dumpbox() (in module dpti.lib.dump) get_empty_submission() (in module dpti.dags.utils) get_file_md5() (in module dpti.lib.utils) get_first_matched_key_from_dict() (in module dpti.lib.utils) get_id() (in module dpti.lib.lmp)

get_job_root() (dpti.lib.RemoteJob.RemoteJob method) get_last_dump() (in module dpti.lib.lammps) get_lmpbox() (in module dpti.lib.lmp) get_natoms() (in module dpti.lib.dump) (in module dpti.lib.lammps) (in module dpti.lib.lmp) get_natoms_vec() (in module dpti.lib.dump) (in module dpti.lib.lmp) get_natomtypes() (in module dpti.lib.dump) (in module dpti.lib.lmp) get_npt_anchor_state() (in module dpti.hti) get_posi() (in module dpti.lib.dump) (in module dpti.lib.lmp) get_session_root() (dpti.lib.RemoteJob.SSHSession method) get_ssh_client() (dpti.lib.RemoteJob.SSHSession method) get_task_file_abspath() (in module dpti.lib.utils) get_thermo() (in module dpti.lib.lammps) get_thermo_old() (in module dpti.lib.lammps) GibbsDuhemFunc (class in dpti.gdi)

H

handle_compute() (in module dpti.equi) (in module dpti.hti) (in module dpti.hti_ice) (in module dpti.hti_liq) (in module dpti.hti_water) (in module dpti.mti) (in module dpti.ti) (in module dpti.ti_water) handle_extract() (in module dpti.equi) handle_gdi() (in module dpti.gdi) handle_gen() (in module dpti.equi) (in module dpti.hti) (in module dpti.hti_ice) (in module dpti.hti_liq) (in module dpti.hti_water) (in module dpti.mti) (in module dpti.ti) (in module dpti.ti_water)

handle_refine() (in module dpti.hti) (in module dpti.hti_ice) (in module dpti.hti_liq) (in module dpti.hti_water) (in module dpti.ti) (in module dpti.ti_water) handle_run() (in module dpti.equi) (in module dpti.hti) (in module dpti.hti_ice) (in module dpti.hti_liq) (in module dpti.hti_water) (in module dpti.mti) (in module dpti.ti) (in module dpti.ti_water) handle_stat_bond() (in module dpti.equi) hti_phase_trans_analyze() (in module dpti.hti)

I

ideal_gas_fe() (in module dpti.einstein) integrate() (in module dpti.lib.utils) integrate_range() (in module dpti.lib.utils) integrate_range_hti() (in module dpti.lib.utils) integrate_range_simpson() (in module dpti.lib.utils) integrate_range_trapezoidal() (in module dpti.lib.utils)

integrate_simpson() (in module dpti.lib.utils) integrate_simpson_nonuniform() (in module dpti.lib.utils) integrate_sys_err() (in module dpti.lib.utils) integrate_sys_err_simpson() (in module dpti.lib.utils) integrate_sys_err_trapezoidal() (in module dpti.lib.utils) integrate_trapezoidal() (in module dpti.lib.utils) interval_sys_err_trapezoidal() (in module dpti.lib.utils)

J

JobStatus (class in dpti.lib.RemoteJob)

L

link_file_in_dict() (in module dpti.lib.utils)

lmpbox2box() (in module dpti.lib.lmp)

M

main() (in module dpti.main) make_dpdt() (in module dpti.gdi) make_iter_name() (in module dpti.hti) (in module dpti.hti_liq) (in module dpti.lib.utils) (in module dpti.ti) make_task() (in module dpti.equi) (in module dpti.old_equi) make_tasks() (in module dpti.hti) (in module dpti.hti_liq) (in module dpti.hti_water) (in module dpti.mti) (in module dpti.ti) min_ho() (in module dpti.lib.water) min_oh_list() (in module dpti.lib.water) min_oho() (in module dpti.lib.water) min_oo() (in module dpti.lib.water) module dpti dpti.dags dpti.dags.dp_ti_gdi dpti.dags.utils dpti.einstein dpti.equi dpti.gdi dpti.hti dpti.hti_ice dpti.hti_liq dpti.hti_water dpti.lib dpti.lib.dump dpti.lib.lammps dpti.lib.lmp dpti.lib.output dpti.lib.RemoteJob dpti.lib.utils dpti.lib.vasp dpti.lib.water dpti.main dpti.mti dpti.old_equi dpti.ti dpti.ti_water

N

npt_equi_conf() (in module dpti.equi) (in module dpti.old_equi)

P

parse_lj_sigma_epsilon() (in module dpti.hti_liq) parse_seq() (in module dpti.lib.utils) parse_seq_ginv() (in module dpti.ti) PBSJob (class in dpti.lib.RemoteJob) perturb_xz() (in module dpti.lib.vasp) poscar_natoms() (in module dpti.lib.vasp) poscar_scale() (in module dpti.lib.vasp) poscar_vol() (in module dpti.lib.vasp) posi_diff() (in module dpti.lib.water) posi_shift() (in module dpti.lib.water)

post_task() (in module dpti.equi) (in module dpti.old_equi) post_tasks() (in module dpti.hti) (in module dpti.hti_liq) (in module dpti.hti_water) (in module dpti.mti) (in module dpti.ti) post_tasks_mbar() (in module dpti.ti) print_refine_summary() (in module dpti.hti) print_thermo_info() (in module dpti.hti)

R

reciprocal_box() (in module dpti.lib.vasp) refine_task() (in module dpti.hti) (in module dpti.ti) refine_tasks() (in module dpti.hti_ice) (in module dpti.hti_liq) (in module dpti.hti_water) regulate_poscar() (in module dpti.lib.vasp)

relative_link_file() (in module dpti.lib.utils) RemoteJob (class in dpti.lib.RemoteJob) run_task() (in module dpti.equi) (in module dpti.hti) (in module dpti.mti) (in module dpti.ti) running (dpti.lib.RemoteJob.JobStatus attribute)

S

SlurmJob (class in dpti.lib.RemoteJob) sort_poscar() (in module dpti.lib.vasp) split_traj() (in module dpti.lib.dump) spring_inte() (in module dpti.hti_water) SSHSession (class in dpti.lib.RemoteJob)

submit() (dpti.lib.RemoteJob.CloudMachineJob method) (dpti.lib.RemoteJob.PBSJob method) (dpti.lib.RemoteJob.SlurmJob method) system_data() (in module dpti.lib.dump) (in module dpti.lib.lmp)

T

tee_stdout() (in module dpti.lib.output) terminated (dpti.lib.RemoteJob.JobStatus attribute)

to_system_data() (in module dpti.lib.lmp) trigger_loop() (dpti.dags.dp_ti_gdi.GDIWorkflow method)

U

unknow (dpti.lib.RemoteJob.JobStatus attribute)

unsubmitted (dpti.lib.RemoteJob.JobStatus attribute) upload() (dpti.lib.RemoteJob.RemoteJob method)

W

wait_until_end() (dpti.dags.dp_ti_gdi.GDIWorkflow method) waiting (dpti.lib.RemoteJob.JobStatus attribute)

water_bond() (in module dpti.equi) (in module dpti.old_equi)