diff --git a/parser/parser-dl_poly/dlPolyParser.py b/parser/parser-dl_poly/dlPolyParser.py
index 017069c17ab3c8201aca815216237f1a6d0a4668..3e4c0a0b3275232ea9094d463ea3f119c2fee03e 100644
--- a/parser/parser-dl_poly/dlPolyParser.py
+++ b/parser/parser-dl_poly/dlPolyParser.py
@@ -9,7 +9,7 @@ from nomadcore.local_meta_info import loadJsonFile, InfoKindEl
from nomadcore.parser_backend import JsonParseEventsWriterBackend
from contextlib import contextmanager
-from libDL_POLYParser import *
+from libDlPolyParser import *
try:
from momo import osio, endl, flush
@@ -39,48 +39,99 @@ def open_section(p, name):
yield
p.closeSection(name, gid)
+def push(jbe, terminal, key1, fct=lambda x: x.As(), key2=None):
+ if key2 == None: key2 = key1
+ value = fct(terminal[key2])
+ jbe.addValue(key1, value)
+ return value
def parse(output_file_name):
- p = JsonParseEventsWriterBackend(meta_info_env)
- o = open_section
- p.startedParsingSession(output_file_name, parser_info)
+ jbe = JsonParseEventsWriterBackend(meta_info_env)
+ jbe.startedParsingSession(output_file_name, parser_info)
- # PARSE CONTROLS
+ # PARSE CONTROLS ...
ctrl_file_name = 'CONTROL'
terminal_ctrls = DlPolyControls(osio)
- terminal_ctrls.ParseControls(ctrl_file_name)
-
- # PARSE OUTPUT / TOPOLOGY
+ terminal_ctrls.ParseControls(ctrl_file_name)
+ # PARSE OUTPUT / TOPOLOGY ...
output_file_name = 'OUTPUT'
terminal = DlPolyParser(osio)
- terminal.ParseOutput(output_file_name)
-
- # PARSE TRAJECTORY
+ terminal.ParseOutput(output_file_name)
+ # PARSE TRAJECTORY ...
cfg_file_name = 'CONFIG'
terminal_trj = DlPolyConfig(osio)
terminal_trj.ParseConfig(cfg_file_name)
-
- # SUMMARIZE KEY-TABLE DEFAULTS
+ # SUMMARIZE KEY-TABLE DEFAULTS ...
terminal.SummarizeKeyDefaults()
terminal.topology.SummarizeKeyDefaults()
terminal_ctrls.SummarizeKeyDefaults()
terminal_trj.SummarizeKeyDefaults()
+ # ABBREVIATE ...
+ ctr = terminal_ctrls
+ out = terminal
+ top = terminal.topology
+ trj = terminal_trj
- osio.okquit()
-
- with o(p, 'section_run'):
- p.addValue('program_name', 'DL_POLY')
-
- with o(p, 'section_topology'):
- pass
-
- with o(p, 'section_sampling_method'):
+ ofs = open('keys.log', 'w')
+ terminals = [ctr, out, top, trj]
+ for t in terminals:
+ keys = sorted(t.data.keys())
+ for key in keys:
+ ofs.write('[%s] %s\n' % (t.logtag, key))
+ ofs.write('\n')
+ ofs.close()
+
+ # PUSH TO BACKEND
+ with open_section(jbe, 'section_run'):
+ push(jbe, out, 'program_name')
+ push(jbe, out, 'program_version')
+ push(jbe, out, 'program_info', key2='program_version_date')
+
+ with open_section(jbe, 'section_topology'):
+ push(jbe, top, 'number_of_topology_molecules', lambda s: s.As(int))
+ push(jbe, top, 'number_of_topology_atoms', lambda s: s.As(int))
+ # Molecule types
+ for mol in top.molecules:
+ with open_section(jbe, 'section_molecule_type'):
+ push(jbe, mol, 'molecule_type_name')
+ push(jbe, mol, 'number_of_atoms_in_molecule', lambda s: s.As(int))
+ # TODO settings_atom_... is abstract type => set atom_in_molecule_charge via list,
+ # TODO same for atom_in_molecule_name
+ # TODO atom_to_molecule, molecule_to_molecule_type, atom_in_molecule_to_atom_type_ref
+ for atom in mol.atoms:
+ with open_section(jbe, 'settings_atom_in_molecule'):
+ push(jbe, atom, 'atom_in_molecule_charge', lambda s: s.As(float), 'atom_charge')
+ push(jbe, atom, 'atom_in_molecule_name', lambda s: s.As(), 'atom_name')
+ # Atom types
+ for mol in top.molecules:
+ for atom in mol.atoms:
+ with open_section(jbe, 'section_atom_type'):
+ push(jbe, atom, 'atom_type_name', lambda s: s.As(), 'atom_name')
+ push(jbe, atom, 'atom_type_mass', lambda s: s.As(float), 'atom_mass')
+ push(jbe, atom, 'atom_type_charge', lambda s: s.As(float), 'atom_charge')
+
+
+ with open_section(jbe, 'section_sampling_method'):
+ # Ensemble
+ ensemble = push(jbe, out, 'ensemble_type', lambda s: s.As().split()[0].upper())
+ # Method
+ push(jbe, out, 'sampling_method')
+ push(jbe, out, 'integrator_type')
+ push(jbe, out, 'integrator_dt', lambda s: s.As(float))
+ push(jbe, out, 'number_of_steps_requested', lambda s: s.As(int))
+ # Coupling
+ if 'T' in ensemble:
+ push(jbe, out, 'thermostat_target_temperature', lambda s: s.As(float))
+ push(jbe, out, 'thermostat_tau', lambda s: s.As(float))
+ if 'P' in ensemble:
+ push(jbe, out, 'barostat_target_pressure', lambda s: s.As(float))
+ push(jbe, out, 'barostat_tau', lambda s: s.As(float))
pass
- with o(p, 'section_frame_sequence'):
+ with open_section(jbe, 'section_frame_sequence'):
pass
- p.finishedParsingSession("ParseSuccess", None)
+ jbe.finishedParsingSession("ParseSuccess", None)
return
if __name__ == '__main__':
diff --git a/parser/parser-dl_poly/libDlPolyParser.py b/parser/parser-dl_poly/libDlPolyParser.py
index 9eefc69b808c61a2d182ef463c549123b61a9d0d..2e0db546f47156707a3200eb11b5b28e7f122e4c 100644
--- a/parser/parser-dl_poly/libDlPolyParser.py
+++ b/parser/parser-dl_poly/libDlPolyParser.py
@@ -2,19 +2,26 @@ import os
import sys
import re
+# TODO Distinguish: number_of_steps vs number_of_steps_equilibration
+# TODO Check units and install conversions
+# TODO - Pressure
+# TODO Check sampling_method
+
+
+
# =================
# TRANSLATION RULES
# =================
KEY_TRANSFORM_SIM_CTRL = {
-'simulation_temperature_k' : 'thermostat_T',
-'simulation_pressure_katms' : 'barostat_P',
-'integration' : 'integrator',
-'ensemble' : None,
+'simulation_temperature_k' : 'thermostat_target_temperature',
+'simulation_pressure_katms' : 'barostat_target_pressure',
+'integration' : 'integrator_type',
+'ensemble' : 'ensemble_type',
'thermostat_relaxation_time_ps' : 'thermostat_tau',
'barostat_relaxation_time_ps' : 'barostat_tau',
-'selected_number_of_timesteps' : 'n_steps',
-'equilibration_period_steps' : 'n_steps_equ',
+'selected_number_of_timesteps' : 'number_of_steps_requested',
+'equilibration_period_steps' : 'number_of_steps_equil_requested',
'temperature_scaling_on_during' : None,
'temperature_scaling_interval' : None,
'equilibration_included_in_overall' : None,
@@ -29,7 +36,7 @@ KEY_TRANSFORM_SIM_CTRL = {
'extended_coulombic_exclusion' : None,
'cutoff_padding_reset_to_angs' : None,
'vdw_cutoff_reset_to_angs' : None,
-'fixed_simulation_timestep_ps' : None,
+'fixed_simulation_timestep_ps' : 'integrator_dt',
'data_dumping_interval_steps' : None,
'allocated_job_run_time_s' : None,
'allocated_job_close_time_s' : None
@@ -43,7 +50,7 @@ KEY_TRANSFORM_SYS_SPEC = {
KEY_TRANSFORM_MOL_GLOBAL = {
'molecular_species_type' : 'molecule_type_id',
'name_of_species' : 'molecule_type_name',
-'number_of_molecules' : 'n_instances_molecule_type'
+'number_of_molecules' : 'number_of_molecules'
}
KEY_RULES_CONTROLS = {
@@ -347,10 +354,12 @@ class DlPolyParser(object):
self.log << self.log.mg << "Start simulation method ..." << self.log.endl
ifs = FileStream(output_file)
+ self.Set('program_name', 'DL_POLY')
+ self.Set('sampling_method', 'molecular_dynamics')
# HEADER & NODE STRUCTURE
ln = ifs.SkipTo('** DL_POLY **')
- self.SearchMapKeys('version:\s*(\d+.\d+)\s*/\s*(\w+\s*\d+)', ifs.ln(), ['version', 'version_date'])
+ self.SearchMapKeys('version:\s*(\d+.\d+)\s*/\s*(\w+\s*\d+)', ifs.ln(), ['program_version', 'program_version_date'])
self.SearchMapKeys('execution on\s*(\d+)\s*node', ifs.ln(), ['n_nodes'])
ln = ifs.SkipTo('node/domain decomposition')
self.Set('domain_decomposition', map(int, ln.split()[-3:]))
@@ -487,7 +496,18 @@ class DlPolyTopology(DlPolyParser):
self.molecules = []
for block_mol in block_mols:
if self.log: self.log << self.log.mg << "Start molecule ..." << self.log.endl
- new_mol = DlPolyMolecule(block_mol, self)
+ new_mol = DlPolyMolecule(block_mol, self)
+ self.molecules.append(new_mol)
+
+ n_atoms_total = 0
+ n_molecules_total = 0
+ for mol in self.molecules:
+ n_mol = mol['number_of_molecules'].As(int)
+ n_atoms = mol['number_of_atoms_in_molecule'].As(int)
+ n_atoms_total += n_mol*n_atoms
+ n_molecules_total += n_mol
+ self.Set('number_of_topology_atoms', n_atoms_total)
+ self.Set('number_of_topology_molecules', n_molecules_total)
return
@@ -526,7 +546,7 @@ class DlPolyMolecule(DlPolyParser):
if self.log: self.log << self.log.mg << "Start atoms ..." << self.log.endl
block = blocks[expr_atoms][0]
n_atoms = int(block.ln().split()[-1])
- self.Set('n_atoms_in_molecule', n_atoms)
+ self.Set('number_of_atoms_in_molecule', n_atoms)
assert 'atomic characteristics' in block.ln()
# Determine atom properties
atom_property_labels = block.ln().split()