From 3c13de10ccf5796e4958c464789e23bbc5639a5d Mon Sep 17 00:00:00 2001
From: pocar <cp605@cam.ac.uk>
Date: Thu, 27 Oct 2016 15:07:35 +0200
Subject: [PATCH] Method reference, custom units.
---
parser/parser-dl_poly/dlPolyParser.py | 85 ++++++++++++++++--------
parser/parser-dl_poly/libDlPolyParser.py | 26 +++++++-
2 files changed, 81 insertions(+), 30 deletions(-)
diff --git a/parser/parser-dl_poly/dlPolyParser.py b/parser/parser-dl_poly/dlPolyParser.py
index b9d1a56..3a9372f 100644
--- a/parser/parser-dl_poly/dlPolyParser.py
+++ b/parser/parser-dl_poly/dlPolyParser.py
@@ -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)
diff --git a/parser/parser-dl_poly/libDlPolyParser.py b/parser/parser-dl_poly/libDlPolyParser.py
index 6c06bed..66cdc78 100644
--- a/parser/parser-dl_poly/libDlPolyParser.py
+++ b/parser/parser-dl_poly/libDlPolyParser.py
@@ -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:
--
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