def energy_and_gradient(xyzs, *args): # argmuent of image
if len(args) != 0:
dijk, number = args
name = os.path.join('./Input_Files', 'ammonia_image_' + str(number))
else:
name = os.path.join('./Input_Files', 'ammonia')
in_file = qc.input_classes.inputfile()
geo = qc.input_classes.cartesian(atom_list=[[
"N", str(xyzs[0]), str(xyzs[1]),
str(xyzs[2])
], ["H", str(xyzs[3]), str(xyzs[4]),
str(xyzs[5])], [
"H", str(xyzs[6]), str(xyzs[7]),
str(xyzs[8])
], ["H", str(xyzs[9]), str(xyzs[10]),
str(xyzs[11])]])
in_file.add(geo)
in_file.add(rem)
if os.path.isfile(
os.path.join(scratch_path, name + '.dir',
str(53) + '.' + str(0))):
rem.add("SCF_GUESS", "READ")
in_file.run(name=name + '.in')
try:
out_file = qc.read(name + ".out", silent=True)
energy = out_file.general.energy
if energy == 'undefined' or energy == None:
print('Error in SCF calculation. Retrying from GWH guess')
in_file = qc.input_classes.inputfile()
rem.remove('SCF_GUESS')
rem.add('SCF_GUESS', 'GHW')
in_file.add(geo)
in_file.add(rem)
in_file.run(name=name + '.in')
out_file = qc.read(name + ".out", silent=True)
energy = out_file.general.energy
if energy == 'undefined' or energy == None:
out_file.general.info()
raise ValueError('No SCF convergence achieved')
except IOError:
print('energy error occurred')
if out_file.force.gradient_vector is None:
gradient = np.array([np.NAN] * 9).reshape(-1, 1)
else:
try:
gradient = out_file.force.gradient_vector.T.flatten()
gradient = gradient * (
1 / 0.52917721067
) # https://de.wikipedia.org/wiki/Bohrscher_Radius
except:
print("gradient error occurred")
scf_guess = None
return energy, gradient, scf_guess # out_file.opt.energies[0], out_file.opt.gradient_vector[0]
def test_h2(self):
""" Hard TestCase as the large numerical values in
the gradient are more difficult to parse. """
# Test for QChem version 5.0
job = qc.read(join(self.path, "force_h2_5.0.out"))
self.assertEqual(job.force.gradient, self._expected_grad_h2)
_np.testing.assert_array_equal(job.force.gradient_vector,
self._expected_grad_vec_h2)
def test_ethane(self):
""" Simple TestCase to ensure correct handling of the
somewhat strange printing format of QChem gradients"""
# Test for QChem version 5.0
job = qc.read(join(self.path, "force_c2h6_5.0.out"))
self.assertEqual(job.force.gradient, self._expected_grad_c2h6)
_np.testing.assert_array_equal(job.force.gradient_vector,
self._expected_grad_vec_c2h6)
def test_h2(self):
""" Hard TestCase as the large numerical values in
the gradient are more difficult to parse. """
# Test for QChem version 5.0
job = qc.read(join(self.path, "force_h2_5.0.out"))
self.assertEqual(job.force.gradient,
self._expected_grad_h2)
_np.testing.assert_array_equal(job.force.gradient_vector,
self._expected_grad_vec_h2)
def test_ethane(self):
""" Simple TestCase to ensure correct handling of the
somewhat strange printing format of QChem gradients"""
# Test for QChem version 5.0
job = qc.read(join(self.path, "force_c2h6_5.0.out"))
self.assertEqual(job.force.gradient,
self._expected_grad_c2h6)
_np.testing.assert_array_equal(job.force.gradient_vector,
self._expected_grad_vec_c2h6)
def energy_and_gradient(xyzs, *args): # argmuent of image
if len(args) != 0:
dijk, number = args
name = os.path.join('./Input_Files', 'Ethane_image_' + str(number))
else:
name = os.path.join('./Input_Files', 'Ethane')
in_file = qc.input_classes.inputfile()
geo = qc.input_classes.cartesian(atom_list=[
["H", str(xyzs[0]), str(xyzs[1]),
str(xyzs[2])], ["H", str(xyzs[3]),
str(xyzs[4]),
str(xyzs[5])],
["H", str(xyzs[6]), str(xyzs[7]),
str(xyzs[8])], ["C", str(xyzs[9]),
str(xyzs[10]),
str(xyzs[11])],
["C", str(xyzs[12]), str(xyzs[13]),
str(xyzs[14])], [
"H", str(xyzs[15]),
str(xyzs[16]), str(xyzs[17])
], ["H", str(xyzs[18]),
str(xyzs[19]), str(xyzs[20])],
["H", str(xyzs[21]), str(xyzs[22]),
str(xyzs[23])]
])
if os.path.isfile(
os.path.join(scratch_path, name + '.dir',
str(53) + '.' + str(0))):
rem.add("SCF_GUESS", "READ")
in_file.add(geo)
in_file.add(rem)
in_file.run(name=name + '.in')
out_file = qc.read(name + ".out", silent=True)
if out_file.force.gradient_vector is None:
gradient = np.array([np.NAN] * 24).reshape(-1, 1)
else:
try:
gradient = out_file.force.gradient_vector.T.flatten()
gradient = gradient * (
1 / 0.52917721067
) # https://de.wikipedia.org/wiki/Bohrscher_Radius
except:
print("gradient error occurred")
if out_file.general.energy is None:
energy = np.NAN
else:
try:
energy = out_file.general.energy
except:
print('energy error occurred')
scf_guess = None
return energy, gradient, scf_guess # out_file.opt.energies[0], out_file.opt.gradient_vector[0]
#
# This sample file generates center-of-mass displaced water molecules from the standard water dimer
# and loops through different multiplicative displacements
#
# MBG (02/2014)
#
import pyqchem as qc
from pylab import *
# load some sample inputs - here the first and second monomers of the water dimer
a = qc.read("../../databases/s22/Water-dimer_mono1.xyz")
a.name = "water-dimer_mono1"
b = qc.read("../../databases/s22/Water-dimer_mono2.xyz")
b.name = "water-dimer_mono2"
# Save direction and magnitude
d = b.com - a.com
# Translate both to origin
a.move(-a.com)
b.move(-b.com)
# loop over a multiplicative factor for center of mass distance and generate jobs
for i in arange(.9, 2.01, .1):
# translate to new coordinates
a.move(-i * d / 2)
b.move(i * d / 2)
# form new dimer
c = a + b
rem1 = qc.rem_array()
rem1.basis("6-31++G**")
rem1.exchange("hf")
rem1.thresh("14")
rem1.scf_convergence("10")
from copy import deepcopy
rem2 = deepcopy(rem1)
rem2.scf_guess("fragmo")
#make a rem_frgm array
rem_frgm = qc.rem_frgm_array()
rem_frgm.thresh("7")
rem_frgm.scf_convergence("3")
#make objects for holding the molecular geometries
xyz = qc.read("4water.xyz")
frag = qc.fragment(atom_list=xyz.list_of_atoms)
#make molecule array from cartesian object
mol1 = qc.mol_array(xyz)
mol2 = qc.mol_array(frag)
#make input object and write to disk
job1 = qc.inputfile()
job1.add(rem1)
job1.add(mol1)
job2 = qc.inputfile()
job2.add(rem2)
job2.rem.scf_guess("fragmo")
job2.add(rem_frgm)
import pyqchem as qc
import os
#make a generic rem array
rem=qc.rem_array()
rem.basis("sto-3g")
rem.exchange("hf")
#make a list of jobs
job_list=[]
#for all xyzs in a database, create and append the job to the list
for i in os.popen("ls ../../databases/a24/*.xyz").read().splitlines():
#make the jobs
job=qc.inputfile()
#give job a name
job.runinfo.name=i.split('/')[-1].replace(".xyz","")
#read the xyz
xyz=qc.read(i)
#append the molecule and rem array
job.add(qc.mol_array(xyz))
job.add(rem)
job_list.append(job)
# run all jobs in list using 12 workers
qc.queue(job_list,num_workers=12)
rem = qc.rem_array()
rem.basis("6-31g")
rem.jobtype("sp")
rem.method("adc(2)")
rem.ee_singlets("[2,0,0,0,0,2,0,0]")
xyz = qc.cartesian()
xyz.add_atom()
xyz.add_atom("H", "0", "0", ".74")
molec = qc.mol_array(xyz)
job = qc.inputfile()
job.add(rem)
job.add(molec)
#run job with name "h2" making h2.in h2.sh, and h2.out
job.run(name="h2")
#read in output
out = qc.read("h2.out")
out.adc.info()
#let's compute the excitation energies between the excited states
print("\nExcitation energies between excited states:")
for i in range(0, len(out.adc.list_of_excited_states) - 1):
es1 = out.adc.list_of_excited_states[i]
for j in range(i + 1, len(out.adc.list_of_excited_states)):
es2 = out.adc.list_of_excited_states[j]
print(
("{0:10s} -> {1:10s}: {2:12.6f}".format(es1.term_symbol,
es2.term_symbol,
es2.energy - es1.energy)))
rem1=qc.rem_array()
rem1.basis("6-31++G**")
rem1.exchange("hf")
rem1.thresh("14")
rem1.scf_convergence("10")
from copy import deepcopy
rem2=deepcopy(rem1)
rem2.scf_guess("fragmo")
#make a rem_frgm array
rem_frgm=qc.rem_frgm_array()
rem_frgm.thresh("7")
rem_frgm.scf_convergence("3")
#make objects for holding the molecular geometries
xyz=qc.read("4water.xyz")
frag=qc.fragment(atom_list=xyz.list_of_atoms)
#make molecule array from cartesian object
mol1=qc.mol_array(xyz)
mol2=qc.mol_array(frag)
#make input object and write to disk
job1=qc.inputfile()
job1.add(rem1)
job1.add(mol1)
job2=qc.inputfile()
job2.add(rem2)
job2.rem.scf_guess("fragmo")
job2.add(rem_frgm)
rem=qc.rem_array()
rem.basis("sto-3g")
rem.jobtype("opt")
xyz=qc.cartesian()
xyz.add_atom()
xyz.add_atom("H","0","0",".74")
molec=qc.mol_array(xyz)
job=qc.inputfile()
job.add(rem)
job.add(molec)
#run job with name "h2" making h2.in h2.sh, and h2.out
job.run(name="h2")
#read in output
out=qc.read("h2.out")
out.opt.info()
#let's approximate how much this has changed
#grab first geometry
start=out.opt.geometries[0]
#grab last geometry
end=out.opt.geometries[-1]
#Print statistics for geometric distortions
print("\n\nApproximate change between starting and ending geometries by two metrics:\n")
print(qc.utilities.rmsd(start.xyzs,end.xyzs)," or ", qc.utilities.kabsch(start.xyzs,end.xyzs),"\n")
#Check for reordering (not necessary in this case) and print out sequential RMSDs
import pyqchem as qc
import os
#make a generic rem array
rem = qc.rem_array()
rem.basis("sto-3g")
rem.exchange("hf")
#make a list of jobs
job_list = []
#for all xyzs in a database, create and append the job to the list
for i in os.popen("ls ../../databases/a24/*.xyz").read().splitlines():
#make the jobs
job = qc.inputfile()
#give job a name
job.runinfo.name = i.split('/')[-1].replace(".xyz", "")
#read the xyz
xyz = qc.read(i)
#append the molecule and rem array
job.add(qc.mol_array(xyz))
job.add(rem)
job_list.append(job)
# run all jobs in list using 12 workers
qc.queue(job_list, num_workers=12)