-
Notifications
You must be signed in to change notification settings - Fork 0
/
cli.py
361 lines (291 loc) · 14 KB
/
cli.py
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
from ase.io import read
from ase.md.verlet import VelocityVerlet
from ase import units
from ase.vibrations import Vibrations
import random
import argparse
import numpy as np
import os
from initialSampling import initialSampling
# Try importing psi4
try:
from psi4calc import psi4calculator
except ImportError:
print("WARNING: psi4 has not been loaded ... it will not be available for initial sampling")
# Try importing NWChemEx
try:
from nwchemexcalc import nwchemexcalculator
except ImportError:
print("WARNING: NWChemEx has not been loaded ... it will not be available for initial sampling")
# Try importing QCEngine/GAMESS
try:
from qcengineGAMESScalc import qcengineGAMESScalculator
except ImportError:
print("WARNING: QCEngine/GAMESS has not been loaded ... it will not be available for initial sampling")
# Try importing sGDML
try:
from sgdml.intf.ase_calc import SGDMLCalculator
except ImportError:
print("WARNING: sGDML has not been loaded ... it will not be available for initial sampling")
# Try importing Schnet
try:
import schnetpack as spk
import torch
except ImportError:
print("WARNING: Schnet has not been loaded ... it will not be available for initial sampling")
###################################################
# Define global constants up here in the correct
# units so that internally, everything uses:
# Energy: eV
# Distance: Angstrom
# Mass: Dalton
global r2threshold
###################################################
parser = argparse.ArgumentParser(description="Do a single MD trajectory using a initial geometry (and momenta) and a sGDML model",formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument("initialGeometryFile", type=str, help="XYZ file with initial geometry; if initial conditions are sampled in the script, then this argument is required but is just an example XYZ")
parser.add_argument("PESinputFile", type=str, help="PES input file (may be a psi4 input file or a sGDML .npz model)")
parser.add_argument("outputDir", type=str, help="Directory to output stuff in")
parser.add_argument("--isotopeMassesFile", type=str, help="Change masses of specific atoms e.g. like isotopic substitution", default=None)
parser.add_argument("--initialMomentaFile", type=str, help="XYZ file with initial momenta")
parser.add_argument("--atomsInFirstGroup", type=str, help="String with atoms which are in first group of atoms, separated by spaces")
parser.add_argument("--collisionEnergy", type=float, help="Collision energy in kcal/mol")
parser.add_argument("--impactParameter", type=float, help="Impact parameter in Angstrom")
parser.add_argument("--centerOfMassDistance", type=float, help="Distance between the two molecules' centers of mass in Angstrom")
parser.add_argument('--optimize', action=argparse.BooleanOptionalAction, default=True)
parser.add_argument("--production", type=int, help="Supply number of steps for a production run")
parser.add_argument("--interval", type=int, help="How often to print out the energy")
parser.add_argument("--time_step", type=float, help="The time step in fs for a production run")
parser.add_argument("--n_threads", type=int, help="The number of threads to ask psi4 to use")
parser.add_argument("--INITQPa", type=str, help="Initial sampling method for atoms in first group ('semiclassical', 'thermal', or None)", default=None)
parser.add_argument("--NVIBa", type=int, help="Vibrational quantum number of atoms in first group (supply if using the 'semiclassical' initial sampling)")
parser.add_argument("--NROTa", type=int, help="Rotational quantum number of atoms in first group (supply if using the 'semiclassical' initial sampling)")
parser.add_argument("--TVIBa", type=float, help="Vibrational temperature of atoms in first group (supply if using the 'thermal' initial sampling)")
parser.add_argument("--TROTa", type=float, help="Rotational temperature of atoms in first group (supply if using the 'thermal' initial sampling)")
parser.add_argument("--INITQPb", type=str, help="Initial sampling method for atoms in second group ('semiclassical', 'thermal', or None)", default=None)
parser.add_argument("--NVIBb", type=int, help="Vibrational quantum number of atoms in second group (supply if using the 'semiclassical' initial sampling)")
parser.add_argument("--NROTb", type=int, help="Rotational quantum number of atoms in second group (supply if using the 'semiclassical' initial sampling)")
parser.add_argument("--TVIBb", type=float, help="Vibrational temperature of atoms in second group (supply if using the 'thermal' initial sampling)")
parser.add_argument("--TROTb", type=float, help="Rotational temperature of atoms in second group (supply if using the 'thermal' initial sampling)")
args = vars(parser.parse_args())
########################################################################################
# A function to print the potential, kinetic and total energy
def printenergy(a):
epot = a.get_potential_energy() / (units.kcal/units.mol)
ekin = a.get_kinetic_energy() / (units.kcal/units.mol)
print('@Epot = %.3f Ekin = %.3f (T=%3.0fK) '
'Etot = %.3f kcal/mol' % (epot, ekin, ekin / (len(a) * 1.5 * 8.617281e-5), epot + ekin))
########################################################################################
# Get the various arguments
Qfile = args["initialGeometryFile"]
input_path = args["PESinputFile"]
output_path = args["outputDir"]
Pfile = args["initialMomentaFile"]
atomsInFirstGroup = args["atomsInFirstGroup"]
ce = args["collisionEnergy"]
b = args["impactParameter"]
dCM = args["centerOfMassDistance"]
isotopeMassesFile = args["isotopeMassesFile"]
Nsteps = args["production"]
Nprint = args["interval"]
dt = args["time_step"]
optimize_flag = args["optimize"]
if ((Nsteps is None) or (Nprint is None) or (dt is None)):
raise ValueError("For MD, need to specify these three: --production --interval --time_step")
n_threads = args["n_threads"]
if (n_threads is None): n_threads = 1
samplingMethod = [ args["INITQPa"], args["INITQPb"] ]
vibrationSampling = []
rotationSampling = []
if (samplingMethod[0] == "semiclassical"):
vibrationSampling.append(args["NVIBa"])
rotationSampling.append(args["NROTa"])
else:
vibrationSampling.append(args["TVIBa"])
rotationSampling.append(args["TROTa"])
if (samplingMethod[1] == "semiclassical"):
vibrationSampling.append(args["NVIBb"])
rotationSampling.append(args["NROTb"])
else:
vibrationSampling.append(args["TVIBb"])
rotationSampling.append(args["TROTb"])
# Note:
# Right now, all arguments are mandatory (even though this does
# not raise a warning) except for isotopeMassesFile
# Adjust the maximum interatomic distance allowed
# for the simulation
r2threshold = 24.0*24.0
if ((b is not None) and (dCM is not None) and (1.2*(b**2 + dCM**2) > r2threshold)):
r2threshold = 1.2*(b**2 + dCM**2)
########################################################################################
# Look at the input file name to guess its identity
try_psi4 = False
try_nwchemex = False
try_qcenginegamess = False
try_sgdml = False
try_schnet = False
if (input_path.endswith(('.npz',))):
print("Input file '"+input_path+"' looks like a sGDML file so will attempt to read it in as such...")
try:
calc = SGDMLCalculator(input_path)
try_sgdml = True
# try_psi4 = False
except:
print(" Could not load file '"+input_path+"' as a sGDML model!")
try_psi4 = True
elif (input_path.endswith(('.psi4',))):
try_psi4 = True
elif (input_path.endswith(('.gamess.qcengine',))):
try_qcenginegamess = True
elif (input_path.endswith(('.nwchemex',))):
try_nwchemex = True
else:
try_schnet = True
# Initialize the ML ase interface
schnet_model = torch.load(input_path, map_location="cpu")
schnet_model.requires_stress = False
for athing in schnet_model.output_modules:
athing.stress = None
# To accomodate for the older versions of numpy used in Schnet==1.0
np.int = np.int32
np.float = np.float64
np.bool = np.bool_
calc = spk.interfaces.SpkCalculator(
schnet_model,
device="cpu",
energy="energy", # Name of energies
forces="forces", # Name of forces
energy_units="kcal/mol",
forces_units="kcal/mol/A",
environment_provider=spk.environment.SimpleEnvironmentProvider(),
)
if (try_psi4):
print("Reading input file '"+input_path+"' as a psi4 input file...")
calc = psi4calculator(input_path,n_threads=n_threads)
# To conform to VENUS, we are going to keep the units
# in kcal/mol and Angstroms (which the model was
# originally trained on)
calc.E_to_eV = units.Ha
calc.Ang_to_R = units.Ang
calc.F_to_eV_Ang = (units.Ha / units.Bohr)
if (try_qcenginegamess):
print("Reading input file '"+input_path+"' as a QCEngine/GAMESS input file...")
calc = qcengineGAMESScalculator(input_path,n_threads=n_threads)
# To conform to VENUS, we are going to keep the units
# in kcal/mol and Angstroms (which the model was
# originally trained on)
calc.E_to_eV = units.Ha
calc.Ang_to_R = (units.Ang / units.Bohr)
calc.F_to_eV_Ang = (units.Ha / units.Bohr)
if (try_nwchemex):
print("Reading input file '"+input_path+"' as a NWChemEx input file...")
calc = nwchemexcalculator(input_path,output_path=output_path,n_threads=n_threads)
# To conform to VENUS, we are going to keep the units
# in kcal/mol and Angstroms (which the model was
# originally trained on)
calc.E_to_eV = units.Ha
calc.Ang_to_R = (units.Ang / units.Bohr)
calc.F_to_eV_Ang = (units.Ha / units.Bohr)
# Read in the geometry; set it in the "calculator"
mol = read(Qfile)
mol.set_calculator(calc)
mol.calc = calc
mol._calc = calc
# Get the output trajectory file ready
trajfile = os.path.join(output_path, "production.traj")
# If the masses are given, update the masses
# Note: this must be done BEFORE setting the momenta
if not (isotopeMassesFile is None):
massFile = open(isotopeMassesFile,"r")
newMasses = massFile.readlines()
massFile.close()
if (len(newMasses) != len(mol)): #.masses)):
raise ValueError("Number of masses provided in the isotope mass file does not match the input XYZ")
mol.set_masses([float(i) for i in newMasses])
# If a momenta file is given, read in the momenta
# Read it in as a geometry, and then set it into the molecule
if not (Pfile is None):
frame = read(Pfile)
p = [atom.position for atom in frame]
mol.set_momenta(p)
masses=mol.get_masses()
v = [p[i]/masses[i] for i in range(len(p))]
mol.set_velocities(v)
# If there is no momenta file, then do initial sampling
else:
Natoms = len(mol)
# If no atoms are specified to be in the first group,
# assume that this is a unimolecular sampling
if (atomsInFirstGroup is None):
atomsInFirstGroup = range(Natoms)
atomsInFirstGroup = [int(i)-1 for i in atomsInFirstGroup.split()]
atomsInSecondGroup = []
for i in range(Natoms):
if (i not in atomsInFirstGroup): atomsInSecondGroup.append(i)
if ((len(atomsInFirstGroup) > 0) and (len(atomsInSecondGroup) > 0)):
bimolecular_flag = True
if ((ce is None) or (b is None) or (dCM is None)):
raise ValueError("Lacking an argument for bimolecular sampling (collision energy, impact parameter, of center of mass distance)")
else:
bimolecular_flag = False
print("")
print("GEOMETRY INPUT")
print(" Input geometry file: ", Qfile)
print("Atoms in first group: ", atomsInFirstGroup)
print("Atoms in second group: ", atomsInSecondGroup)
print("SAMPLING INPUT")
print(" Input momenta file: ", Pfile)
if (Pfile is None):
print(" Optimize molecules? ", optimize_flag)
print(" Group A sampling method: ", samplingMethod[0])
print(" Group A vibration: ", vibrationSampling[0])
print(" Group A rotation: ", rotationSampling[0])
print(" Group B sampling method: ", samplingMethod[1])
print(" Group B vibration: ", vibrationSampling[1])
print(" Group B rotation: ", rotationSampling[1])
print(" Impact parameter (A): ", b)
print(" Initial separation (A): ", dCM)
print(" Collsion energy (kcal/mol): ", ce)
else:
print(" Input momenta file: ", Pfile)
print("##############################################################")
print("")
# Sample the internal positions and momenta of each of
# the two molecules
sampler = initialSampling(mol,atomsInFirstGroup,optimize=optimize_flag,
optimization_file=os.path.join(output_path, "optimization.traj"),
samplingMethodA=samplingMethod[0],vibrationalSampleA=vibrationSampling[0],rotationalSampleA=rotationSampling[0],
samplingMethodB=samplingMethod[1],vibrationalSampleB=vibrationSampling[1],rotationalSampleB=rotationSampling[1])
print("Sampling internal degrees of freedom...")
sampler.sampleRelativeQP()
if (bimolecular_flag):
print("Sampling relative degrees of freedom...")
sampler.sampleAbsoluteQP(ce,dCM=dCM,b=b)
########################################################################################
# Run MD with constant energy using the velocity verlet algorithm
dyn = VelocityVerlet(mol, dt * units.fs, trajectory=trajfile)
# A function to see if any interatomic distance is > 20
def checkGeneralReactionProgress(a):
Natoms = len(a)
stop_flag = False
for i1 in range(1,Natoms):
for i2 in range(0,Natoms-1):
# Check the squared interatomic distances if any
# are greater than r2threshold (default is 20^2 = 400)
r = sum([(a.positions[i1][i] -
a.positions[i2][i])**2 for i in range(3)])
if (r > r2threshold):
stop_flag = True
break
return stop_flag
# If movecs, Q, and P restarting is available, start it now:
if try_nwchemex:
if (calc.save_movecs_interval):
# calc.save_movecs_count = calc.save_movecs_interval # Save once at the start
calc.save_movecs_count = 0 # Save only once every "save_movecs_interval"
# Now run the dynamics
printenergy(mol)
for i in range(Nsteps):
dyn.run(Nprint)
printenergy(mol)
stop_flag = checkGeneralReactionProgress(mol)
if (stop_flag): break