Skip to content
Snippets Groups Projects
Commit 3c13de10 authored by Carl Poelking's avatar Carl Poelking
Browse files

Method reference, custom units.

parent 5e6573e4
No related branches found
No related tags found
No related merge requests found
Hide whitespace changes
Inline Side-by-side
parser/parser-dl_poly/dlPolyParser.py
+ 58
− 27
View file @ 3c13de10
......@@ -42,24 +42,36 @@ def open_section(p, name):
yield gid
p.closeSection(name, gid)
def push(jbe, terminal, key1, fct=lambda x: x.As(), key2=None):
def push(jbe, terminal, key1, fct=lambda x: x.As(), key2=None, conv=None):
if key2 == None: key2 = key1
value = fct(terminal[key2])
jbe.addValue(key1, value)
if conv:
jbe.addValue(key1, value*conv)
else:
jbe.addValue(key1, value)
return value
def push_array(jbe, terminal, key1, fct=lambda x: x.As(), key2=None):
def push_array(jbe, terminal, key1, fct=lambda x: x.As(), key2=None, conv=None):
if key2 == None: key2 = key1
value = np.asarray(fct(terminal[key2]))
jbe.addArrayValues(key1, value)
if conv:
jbe.addArrayValues(key1, value*conv)
else:
jbe.addArrayValues(key1, value)
return value
def push_value(jbe, value, key):
jbe.addValue(key, value)
def push_value(jbe, value, key, conv=None):
if conv:
jbe.addValue(key, value*conv)
else:
jbe.addValue(key, value)
return value
def push_array_values(jbe, value, key):
jbe.addArrayValues(key, value)
def push_array_values(jbe, value, key, conv=None):
if conv:
jbe.addArrayValues(key, value*conv)
else:
jbe.addArrayValues(key, value)
return value
def parse(output_file_name):
......@@ -67,41 +79,54 @@ def parse(output_file_name):
jbe.startedParsingSession(output_file_name, parser_info)
base_dir = os.path.dirname(os.path.abspath(output_file_name))
# PARSE CONTROLS ...
ctrl_file_name = os.path.join(base_dir, 'CONTROL')
terminal_ctrls = DlPolyControls(osio)
terminal_ctrls.ParseControls(ctrl_file_name)
# PARSE OUTPUT / TOPOLOGY ...
output_file_name = os.path.join(base_dir, 'OUTPUT')
terminal = DlPolyParser(osio)
terminal.ParseOutput(output_file_name)
# PARSE CONFIG ...
cfg_file_name = os.path.join(base_dir, 'CONFIG')
terminal_cfg = DlPolyConfig(osio)
terminal_cfg.ParseConfig(cfg_file_name)
# PARSE TRAJECTORY
trj_file_name = os.path.join(base_dir, 'HISTORY')
terminal_trj = DlPolyTrajectory(osio)
terminal_trj.ParseTrajectory(trj_file_name, terminal.step_data, terminal.time_data)
# SUMMARIZE KEY-TABLE DEFAULTS ...
terminal.SummarizeKeyDefaults()
terminal.topology.SummarizeKeyDefaults()
terminal_ctrls.SummarizeKeyDefaults()
terminal_cfg.SummarizeKeyDefaults()
terminal_trj.SummarizeKeyDefaults()
# ABBREVIATE ...
ctr = terminal_ctrls
out = terminal
top = terminal.topology
cfg = terminal_cfg
trj = terminal_trj
ofs = open('parser.keys.log', 'w')
terminals = [ctr, out, top, cfg, trj]
# ESTABLISH (ENERGY) UNITS
unit_energy = top['energy_units'].As(str).lower().replace(' ','').replace('/','_').replace('(','_').replace(')','')
UNITCONV_DLPOLY_TO_SI['energy'] = UNITCONV_DLPOLY_CUSTOM_TO_SI['energy_%s' % unit_energy]
ofs = open('parser.keys.log', 'w')
for quantity, conv in UNITCONV_DLPOLY_TO_SI.items():
ofs.write('Unit [%s] = %e SI\n' % (quantity, conv))
ofs.write('\n')
for t in terminals:
keys = sorted(t.data.keys())
for key in keys:
ofs.write('[%s] %s\n' % (t.logtag, key))
ofs.write('[%s] %s = %s\n' % (t.logtag, key, t[key].As(str)))
ofs.write('\n')
ofs.close()
......@@ -130,8 +155,8 @@ def parse(output_file_name):
atom_id = atom['atom_id'].As(int)
mol_type_atom_type_id_to_atom_type_gid[mol_name][atom_id] = gid_atom
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')
push(jbe, atom, 'atom_type_mass', lambda s: s.As(float), 'atom_mass', conv=UNITCONV_DLPOLY_TO_SI['mass'])
push(jbe, atom, 'atom_type_charge', lambda s: s.As(float), 'atom_charge', conv=UNITCONV_DLPOLY_TO_SI['charge'])
# Molecule types
molecule_type_name_to_type_gid = {}
for mol in top.molecules:
......@@ -149,7 +174,7 @@ def parse(output_file_name):
push(jbe, mol, 'number_of_atoms_in_molecule', lambda s: s.As(int))
push_array(jbe, mol, 'atom_in_molecule_name')
push_array(jbe, mol, 'atom_in_molecule_charge')
push_array(jbe, mol, 'atom_in_molecule_charge', conv=UNITCONV_DLPOLY_TO_SI['charge'])
push_array_values(jbe, np.asarray(atom_gid_list), 'atom_in_molecule_to_atom_type_ref')
# Global molecule type map
molecule_to_molecule_type = []
......@@ -188,18 +213,23 @@ def parse(output_file_name):
push(jbe, out, 'x_dl_poly_number_of_steps_requested', lambda s: s.As(int))
# Coupling
if 'T' in ensemble:
push(jbe, out, 'x_dl_poly_thermostat_target_temperature', lambda s: s.As(float))
push(jbe, out, 'x_dl_poly_thermostat_target_temperature', lambda s: s.As(float), conv=UNITCONV_DLPOLY_TO_SI['temperature'])
push(jbe, out, 'x_dl_poly_thermostat_tau', lambda s: s.As(float))
pass
if 'P' in ensemble:
push(jbe, out, 'x_dl_poly_barostat_target_pressure', lambda s: s.As(float))
push(jbe, out, 'x_dl_poly_barostat_tau', lambda s: s.As(float))
push(jbe, out, 'x_dl_poly_barostat_target_pressure', lambda s: s.As(float), conv=UNITCONV_DLPOLY_TO_SI['pressure_katm'])
push(jbe, out, 'x_dl_poly_barostat_tau', lambda s: s.As(float), conv=UNITCONV_DLPOLY_TO_SI['time'])
pass
pass
# METHOD SECTION
sec_method_ref = None
with open_section(jbe, 'section_method') as gid_sec_method:
sec_method_ref = gid_sec_method
push_value(jbe, 'force_field', 'calculation_method')
# TODO Store state variables in frames/system description (temperature, pressure)
# TODO Store interactions
# TODO Add section_method (!= section_sampling_method)
# SYSTEM DESCRIPTION
refs_system_description = []
......@@ -210,13 +240,13 @@ def parse(output_file_name):
# Configuration core
atom_labels = np.array([ atom['atom_name'].As() for atom in frame.atoms ])
push_array_values(jbe, atom_labels, 'atom_labels')
push_array_values(jbe, frame.position_matrix, 'atom_positions')
push_array_values(jbe, frame.box_matrix, 'simulation_cell')
push_array_values(jbe, frame.position_matrix, 'atom_positions', conv=UNITCONV_DLPOLY_TO_SI['length'])
push_array_values(jbe, frame.box_matrix, 'simulation_cell', conv=UNITCONV_DLPOLY_TO_SI['length'])
push_array_values(jbe, frame.pbc_booleans, 'configuration_periodic_dimensions')
if frame.has_velocities:
push_array_values(jbe, frame.velocity_matrix, 'atom_velocities')
push_array_values(jbe, frame.velocity_matrix, 'atom_velocities', conv=UNITCONV_DLPOLY_TO_SI['length']/UNITCONV_DLPOLY_TO_SI['time'])
if frame.has_forces:
# TODO Wouldn't it be nicer if forces were added here?
# TODO Wouldn't it be simpler if forces were added here?
pass
pass
......@@ -232,11 +262,12 @@ def parse(output_file_name):
push_value(jbe, ref_system, 'single_configuration_calculation_to_system_ref')
# Energy total
if frame.has_energy_total:
push_value(jbe, frame.energy_total, 'energy_total')
push_value(jbe, frame.energy_total, 'energy_total', conv=UNITCONV_DLPOLY_TO_SI['energy'])
# Forces
if frame.has_forces:
push_array_values(jbe, frame.force_matrix, 'atom_forces')
# TODO Set section_method reference
push_array_values(jbe, frame.force_matrix, 'atom_forces', conv=UNITCONV_DLPOLY_TO_SI['mass']*UNITCONV_DLPOLY_TO_SI['length']/UNITCONV_DLPOLY_TO_SI['time']**2)
# Method reference
push_value(jbe, sec_method_ref, 'single_configuration_to_calculation_method_ref')
pass
# FRAME-SEQUENCE SECTION
......@@ -246,8 +277,8 @@ def parse(output_file_name):
push_value(jbe, sec_sampling_method_ref, 'frame_sequence_to_sampling_ref')
refs_config = np.array(refs_single_configuration)
push_array_values(jbe, refs_config, 'frame_sequence_local_frames_ref')
# TODO Push this to frame_sequence_time
time_values = [ frame['time_value'].As(float) for frame in trj.frames ]
time_values = np.array([ frame['time_value'].As(float)*UNITCONV_DLPOLY_TO_SI['time'] for frame in trj.frames ])
push_array_values(jbe, time_values, 'frame_sequence_time')
pass
jbe.finishedParsingSession("ParseSuccess", None)
......
parser/parser-dl_poly/libDlPolyParser.py
+ 23
− 3
View file @ 3c13de10
......@@ -14,7 +14,27 @@ import numpy as np
# TODO - Pressure
# TODO Check sampling_method
UNITCONV_DLPOLY_TO_SI = {
'time' : 1e-12, # ps to s
'length' : 1e-10, # AA to m
'mass' : 1.6605402e-27, # u to kg
'charge' : 1.6021733e-19, # e to C
'energy' : 1.6605402e-23, # 10*J/mol to J
'pressure' : 1.6605402e+7, # 163.88 atm to Pa
'pressure_katm' : 1.01325000e+8, # katm to Pa
'temperature' : 1. # K to K
}
UNITCONV_DLPOLY_CUSTOM_TO_SI = {
'energy_kj_mol' : 1.6605402e-21, # kJ/mol to J
'energy_kj' : 1.6605402e-21, # kJ/mol to J
'energy_ev' : 1.6021733e-19, # eV to J
'energy_kcal_mol' : 4.184*1.6605402e-21, # kcal/mol to J
'energy_kcal' : 4.184*1.6605402e-21, # kcal/mol to J
'energy_kelvin_boltzmann' : None,
'energy_k' : None,
'energy_dl_polyinternalunits_10j_mol' : 1.6605402e-23 # 10*J/mol to J
}
# =================
# TRANSLATION RULES
......@@ -203,8 +223,8 @@ class FileStream(object):
self.ifs.close()
def nextline(self):
while True:
ln = self.ifs.readline()
if ln.strip() != '':
ln = self.ifs.readline().replace('\n','').strip()
if ln != '':
return ln
else: pass
if self.all_read(): break
......@@ -459,7 +479,7 @@ class DlPolyControls(DlPolyParser):
ifs = FileStream(ctrl_file)
while not ifs.all_read():
ln = ifs.ln()
if ln[0:1] == '#': continue
if ln == '' or ln[0:1] == '#': continue
sp = ln.split()
key = sp[0]
try:
......
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment