def write_lammps_trajectory(filename, structure):
if isinstance(filename,str):
f = open(filename,'w')
else:
f = filename
f.write("ITEM: TIMESTEP\n0\nITEM: NUMBER OF ATOMS\n")
atoms = AseAtomsAdaptor.get_atoms(structure)
f.write("{0}\n".format(len(atoms)))
f.write("ITEM: BOX BOUNDS ")
pbc = atoms.get_pbc()
for bound in pbc:
if bound:
f.write("pp ")
else:
f.write("s ")
f.write("\n")
p = prism(atoms.get_cell())
xhi, yhi, zhi, xy, xz, yz = p.get_lammps_prism_str()
f.write('0.0 {0}\n'.format(xhi))
f.write('0.0 {0}\n'.format(yhi))
f.write('0.0 {0}\n'.format(zhi))
if p.is_skewed():
f.write('%s %s %s\n' % (xy, xz, yz))
f.write('ITEM: ATOMS id type x y z vx vy vz fx fy fz\n')
syms = sorted(list(set(atoms.get_chemical_symbols())))
symlist = [one for one in enumerate(syms)]
for idx in range(len(atoms)):
type = [ty+1 for ty,sym in symlist if sym==atoms[idx].symbol][0]
f.write('{0} {1} {2}'.format(idx+1,type, ' '.join([repr(x) for x in atoms[0].position])))
f.write('0 0 0 0 0 0\n')
f.close()
return
def write_lammps_trajectory(filename, structure):
if isinstance(filename, str):
f = open(filename, 'w')
else:
f = filename
f.write("ITEM: TIMESTEP\n0\nITEM: NUMBER OF ATOMS\n")
atoms = AseAtomsAdaptor.get_atoms(structure)
f.write("{0}\n".format(len(atoms)))
f.write("ITEM: BOX BOUNDS ")
pbc = atoms.get_pbc()
for bound in pbc:
if bound:
f.write("pp ")
else:
f.write("s ")
f.write("\n")
p = prism(atoms.get_cell())
xhi, yhi, zhi, xy, xz, yz = p.get_lammps_prism_str()
f.write('0.0 {0}\n'.format(xhi))
f.write('0.0 {0}\n'.format(yhi))
f.write('0.0 {0}\n'.format(zhi))
if p.is_skewed():
f.write('%s %s %s\n' % (xy, xz, yz))
f.write('ITEM: ATOMS id type x y z vx vy vz fx fy fz\n')
syms = sorted(list(set(atoms.get_chemical_symbols())))
symlist = [one for one in enumerate(syms)]
for idx in range(len(atoms)):
type = [ty + 1 for ty, sym in symlist if sym == atoms[idx].symbol][0]
f.write('{0} {1} {2}'.format(
idx + 1, type, ' '.join([repr(x) for x in atoms[0].position])))
f.write('0 0 0 0 0 0\n')
f.close()
return
def forward_final_structure_file(self, childpath, newname="DATA"):
"""Forward the final structure.
For LAMMPS, this is the Trajectory.
Args:
childpath <str>: Path of child ingredient
newname <str>: new name (default 'POSCAR')
"""
trajstruct = self.get_structure_from_file("TRAJECTORY")
trajatoms = AseAtomsAdaptor.get_atoms(trajstruct)
write_lammps_data("FINAL", trajatoms)
self.copy_a_file(childpath, "FINAL", newname)
self.copy_a_file(childpath, "atom_symbols", "atom_symbols")
def forward_final_structure_file(self, childpath, newname="DATA"):
"""Forward the final structure.
For LAMMPS, this is the Trajectory.
Args:
childpath <str>: Path of child ingredient
newname <str>: new name (default 'POSCAR')
"""
trajstruct = self.get_structure_from_file("TRAJECTORY")
trajatoms = AseAtomsAdaptor.get_atoms(trajstruct)
write_lammps_data("FINAL",trajatoms)
self.copy_a_file(childpath, "FINAL", newname)
self.copy_a_file(childpath, "atom_symbols", "atom_symbols")
def read_xyz(fileobj,n=-1,data=False):
"""
Function to read multi-atom xyz file with data
Inputs:
fileobj = String containing file name or file object
n = Integer indicating number for structure from xyz file
to read. Default is last structure in file.
Or String=='All' which will output all structures in file
data = True/False boolean indicating whether or not to output
any data strings read from xyz file
Outputs:
atmslist = ASE Atoms class object containing structure from file
or list of Atoms objects if n=='All'
datalist(Optional) = String of data read from xyz file or list
of data strings read from xyz file
"""
try:
from pymatgen.io.vaspio import Poscar
mystructure = Poscar.from_file(fileobj).structure
from pymatgen.io.aseio import AseAtomsAdaptor
myatoms = AseAtomsAdaptor.get_atoms(mystructure)
return myatoms
except:
if isinstance(fileobj, str):
fileobj = open(fileobj,'r')
lines = fileobj.readlines()
atmslist = []
datalist = []
while len(lines)>0:
natoms = int(lines[0])
datalist.append(lines[1])
atm1 = Atoms()
i =- 1
for i in range(natoms):
a = lines[i+2].split()
sym = a[0]
position = [float(a[1]),float(a[2]),float(a[3])]
atm1.append(Atom(symbol=sym,position=position))
atmslist.append(atm1)
lines = lines[i+3::]
if n == 'All':
if data == True:
return atmslist, datalist
else:
return atmslist
else:
if data == True:
return atmslist[n],datalist[n]
else:
return atmslist[n]
def _lammps_data_setup(self):
"""Set up the DATA file for a single LAMMPS run.
"""
name = self.keywords['name']
datapath = os.path.join(name, "DATA")
if os.path.isfile(datapath):
my_data_structure = self.get_structure_from_file(datapath)
#parent should have given a structure
else: #this is an originating run; mast should give it a structure
my_data_structure = self.keywords['structure']
self.logger.info("No DATA file found from a parent; base structure used for %s" % self.keywords['name'])
if 'mast_coordinates' in self.keywords['program_keys'].keys():
sxtend = StructureExtensions(struc_work1=my_data_structure, name=self.keywords['name'])
coordstrucs=self.get_coordinates_only_structure_from_input()
newstruc = sxtend.graft_coordinates_onto_structure(coordstrucs[0])
my_data_structure=newstruc.copy()
#dirutil.lock_directory(name)
my_data_atoms = AseAtomsAdaptor.get_atoms(my_data_structure)
write_lammps_data(datapath, my_data_atoms)
#dirutil.unlock_directory(name)
return datapath
def _lammps_data_setup(self):
"""Set up the DATA file for a single LAMMPS run.
"""
name = self.keywords['name']
datapath = os.path.join(name, "DATA")
if os.path.isfile(datapath):
my_data_structure = self.get_structure_from_file(datapath)
#parent should have given a structure
else: #this is an originating run; mast should give it a structure
my_data_structure = self.keywords['structure']
self.logger.info(
"No DATA file found from a parent; base structure used for %s"
% self.keywords['name'])
if 'mast_coordinates' in self.keywords['program_keys'].keys():
sxtend = StructureExtensions(struc_work1=my_data_structure,
name=self.keywords['name'])
coordstrucs = self.get_coordinates_only_structure_from_input()
newstruc = sxtend.graft_coordinates_onto_structure(coordstrucs[0])
my_data_structure = newstruc.copy()
#dirutil.lock_directory(name)
my_data_atoms = AseAtomsAdaptor.get_atoms(my_data_structure)
write_lammps_data(datapath, my_data_atoms)
#dirutil.unlock_directory(name)
return datapath
def readable_lammps_parameters(parameters, structure):
atoms = AseAtomsAdaptor.get_atoms(structure)
atomlist = sorted(list(set(atoms.get_chemical_symbols())))
masslist = [Atom(sym).mass for sym in atomlist]
if 'potential_file' in parameters:
if parameters['potential_file']:
parameters['pot_file'] = os.path.basename(
parameters['potential_file'])
if parameters['pair_style'] == 'tersoff':
parcoff = '* * {0}'.format(parameters['pot_file'])
for one in atomlist:
parcoff += ' {0}'.format(one[0])
parameters['pair_coeff'] = [parcoff]
mass = ['1 {0}'.format(masslist[0])]
if len(masslist) > 1:
for i in range(len(masslist) - 1):
mass.append('{0} {1}'.format(i + 2, masslist[i + 1]))
parameters['mass'] = mass
elif parameters['pair_style'] == 'eam':
pair_coeff = ['* * {0}'.format(parameters['pot_file'])]
parameters['pair_coeff'] = pair_coeff
elif parameters['pair_style'] == 'eam/fs':
parcoff = '* * {0}'.format(parameters['pot_file'])
for one in atomlist:
parcoff += ' {0}'.format(one[0])
parameters['pair_coeff'] = [parcoff]
mass = ['1 {0}'.format(masslist[0])]
if len(masslist) > 1:
for i in range(len(masslist) - 1):
mass.append('{0} {1}'.format(i + 2, masslist[i + 1]))
elif parameters['pair_style'] == 'eam/cd':
parcoff = '* * {0}'.format(parameters['pot_file'])
for one in atomlist:
parcoff += ' {0}'.format(one[0])
parameters['pair_coeff'] = [parcoff]
elif parameters['pair_style'] == 'edip':
parcoff = '* * {0}'.format(parameters['pot_file'])
for one in atomlist:
parcoff += ' {0}'.format(one[0])
parameters['pair_coeff'] = [parcoff]
mass = ['1 {0}'.format(masslist[0])]
if len(masslist) > 1:
for i in range(len(masslist) - 1):
mass.append('{0} {1}'.format(i + 2, masslist[i + 1]))
parameters['mass'] = mass
parameters['newton'] = 'on'
elif parameters['pair_style'] == 'bop':
parcoff = '* * {0}'.format(parameters['pot_file'])
for one in atomlist:
parcoff += ' {0}'.format(one[0])
parcoff += '\ncommunicate single cutoff {0}'.format(
parameters['bopcutoff'])
parameters['pair_coeff'] = [parcoff]
mass = ['1 {0}'.format(masslist[0])]
if len(masslist) > 1:
for i in range(len(masslist) - 1):
mass.append('{0} {1}'.format(i + 2, masslist[i + 1]))
parameters['mass'] = mass
parameters['newton'] = 'on'
elif parameters['pair_style'] == 'buck':
pairstyle = '{0} {1}'.format(parametes['pair_style'],
parameters['buckcutoff'])
pair_coeff = parameters['buckparameters']
mass = ['1 {0}'.format(masslist[0])]
if len(masslist) > 1:
for i in range(len(masslist) - 1):
mass.append('{0} {1}'.format(i + 2, masslist[i + 1]))
parameters['pair_style'] = pairstyle
parameters['pair_coeff'] = pair_coeff
parameters['mass'] = mass
parameters['potential_file'] = None
elif parameters['pair_style'] == 'other':
mass = ['1 {0}'.format(masslist[0])]
if len(masslist) > 1:
for i in range(len(masslist) - 1):
mass.append('{0} {1}'.format(i + 2, masslist[i + 1]))
if 'charges' in parameters:
cs = parameters['charges']
parameters['mass'][len(parameters['mass']) - 1] += cs[1]
parameters['newton'] += '\natom_style charge'
else:
parameters = {'potential_file': None}
print 'WARNING: No LAMMPS potential recognized. Assuming Lennard Jones Potential'
return parameters
def _lammps_input_setup(self,
lammps_input_file="INPUT",
lammps_data_file="DATA",
lammps_trajectory_file="TRAJECTORY"):
"""Function to write a lammps input file
Input:
lammps_input_file = file to write lammps input to
lammps_data_file = file to load lammps data from
lammps_trajectory_file = file to write lammps trajectory to
"""
if isinstance(lammps_input_file, str):
f = open(lammps_input_file, 'w')
else:
f = lammps_input_file
# Write file variable names
f.write('clear\n' +
('variable dump_file string "%s"\n' % lammps_trajectory_file) +
('variable data_file string "%s"\n' % lammps_data_file))
f.write('units metal \n')
#Write to specified log file
#logname = os.path.join(os.path.dirname(lammps_data_file),"LOG")
#f.write('log %s append\n' % logname)
#Get keyword parameters
parameters = dict()
parameters = self._lammps_input_get_non_mast_keywords()
#Copy potential file to current working directory
if 'potential_file' in parameters:
if parameters['potential_file']:
newlocation = os.path.join(
os.path.dirname(lammps_data_file),
os.path.basename(parameters['potential_file']))
shutil.copyfile(parameters['potential_file'], newlocation)
self.potential_file = newlocation
atoms = AseAtomsAdaptor.get_atoms(self.keywords['structure'])
pbc = atoms.get_pbc()
if ('boundary' in parameters):
f.write('boundary %s \n' % parameters['boundary'])
else:
f.write('boundary %c %c %c \n' % tuple('sp'[x] for x in pbc))
f.write('atom_modify sort 0 0.0 \n')
if ('neighbor' in parameters):
f.write('neighbor %s \n' % parameters['neighbor'])
if ('newton' in parameters):
f.write('newton %s \n' % parameters['newton'])
f.write('\n')
f.write('read_data %s\n' % lammps_data_file)
# Write pair potential information
f.write('\n### interactions \n')
if (('pair_style' in parameters) and ('pair_coeff' in parameters)):
pair_style = parameters['pair_style']
f.write('pair_style %s \n' % pair_style)
if not isinstance(parameters['pair_coeff'], list):
try:
parameters['pair_coeff'] = eval(parameters['pair_coeff'])
except:
parameters['pair_coeff'] = [parameters['pair_coeff']]
for pair_coeff in parameters['pair_coeff']:
f.write('pair_coeff %s \n' % pair_coeff)
if 'mass' in parameters:
if not isinstance(parameter['mass'], list):
try:
parameters['mass'] = eval(parameters['mass'])
except:
parameters['mass'] = [parameters['mass']]
for mass in parameters['mass']:
f.write('mass %s \n' % mass)
else: # Use simple leonnard jones calculation
f.write('pair_style lj/cut 2.5 \n' + 'pair_coeff * * 1 1 \n' +
'mass * 1.0 \n')
#Set up min_style if appropriate
if 'min_style' in parameters:
f.write('min_style %s \n' % parameters['min_style'])
#Write line for thermo arguments and stemps
thermo_args = [
'step', 'temp', 'press', 'cpu', 'pxx', 'pyy', 'pzz', 'pxy', 'pxz',
'pyz', 'ke', 'pe', 'etotal', 'vol', 'lx', 'ly', 'lz', 'atoms'
]
thermo_mark = ' '.join([x.capitalize() for x in thermo_args[0:3]])
if 'thermosteps' not in parameters:
parameters['thermosteps'] = '1'
f.write('\n### run\n' + 'fix fix_nve all nve\n' +
('dump dump_all all custom {0} {1}'.format(
parameters['thermosteps'], lammps_trajectory_file)) +
' id type x y z vx vy vz fx fy fz' + '\n')
f.write(('thermo_style custom %s\n' + 'thermo_modify flush yes\n' +
'thermo ' + repr(parameters['thermosteps']) + '\n') %
(' '.join(thermo_args)))
if 'minimize' in parameters:
f.write('minimize %s\n' % parameters['minimize'])
if 'run' in parameters:
f.write('run %s\n' % parameters['run'])
if not (('minimize' in parameters) or ('run' in parameters)):
f.write('run 0\n')
f.write('print "CALCULATION HAS FINISHED"\n')
f.write('log /dev/stdout\n') # Force LAMMPS to flush log
f.write('undump dump_all\n') # Force LAMMPS to flush trj
f.close()
return lammps_input_file
def readable_lammps_parameters(parameters, structure):
atoms = AseAtomsAdaptor.get_atoms(structure)
atomlist = sorted(list(set(atoms.get_chemical_symbols())))
masslist = [Atom(sym).mass for sym in atomlist]
if 'potential_file' in parameters:
if parameters['potential_file']:
parameters['pot_file'] = os.path.basename(parameters['potential_file'])
if parameters['pair_style']=='tersoff':
parcoff = '* * {0}'.format(parameters['pot_file'])
for one in atomlist:
parcoff+=' {0}'.format(one[0])
parameters['pair_coeff'] = [parcoff]
mass = ['1 {0}'.format(masslist[0])]
if len(masslist) > 1:
for i in range(len(masslist)-1):
mass.append('{0} {1}'.format(i+2,masslist[i+1]))
parameters['mass'] = mass
elif parameters['pair_style']=='eam':
pair_coeff = [ '* * {0}'.format(parameters['pot_file'])]
parameters['pair_coeff'] = pair_coeff
elif parameters['pair_style']=='eam/fs':
parcoff = '* * {0}'.format(parameters['pot_file'])
for one in atomlist:
parcoff+=' {0}'.format(one[0])
parameters['pair_coeff'] = [parcoff]
mass = ['1 {0}'.format(masslist[0])]
if len(masslist) > 1:
for i in range(len(masslist)-1):
mass.append('{0} {1}'.format(i+2,masslist[i+1]))
elif parameters['pair_style']=='eam/cd':
parcoff = '* * {0}'.format(parameters['pot_file'])
for one in atomlist:
parcoff+=' {0}'.format(one[0])
parameters['pair_coeff'] = [parcoff]
elif parameters['pair_style']=='edip':
parcoff = '* * {0}'.format(parameters['pot_file'])
for one in atomlist:
parcoff+=' {0}'.format(one[0])
parameters['pair_coeff'] = [parcoff]
mass = ['1 {0}'.format(masslist[0])]
if len(masslist) > 1:
for i in range(len(masslist)-1):
mass.append('{0} {1}'.format(i+2,masslist[i+1]))
parameters['mass'] = mass
parameters['newton'] = 'on'
elif parameters['pair_style']=='bop':
parcoff = '* * {0}'.format(parameters['pot_file'])
for one in atomlist:
parcoff+=' {0}'.format(one[0])
parcoff+='\ncommunicate single cutoff {0}'.format(parameters['bopcutoff'])
parameters['pair_coeff'] = [parcoff]
mass = ['1 {0}'.format(masslist[0])]
if len(masslist) > 1:
for i in range(len(masslist)-1):
mass.append('{0} {1}'.format(i+2,masslist[i+1]))
parameters['mass'] = mass
parameters['newton'] = 'on'
elif parameters['pair_style']=='buck':
pairstyle='{0} {1}'.format(parametes['pair_style'], parameters['buckcutoff'])
pair_coeff=parameters['buckparameters']
mass = ['1 {0}'.format(masslist[0])]
if len(masslist) > 1:
for i in range(len(masslist)-1):
mass.append('{0} {1}'.format(i+2, masslist[i+1]))
parameters['pair_style'] = pairstyle
parameters['pair_coeff'] = pair_coeff
parameters['mass'] = mass
parameters['potential_file'] = None
elif parameters['pair_style']=='other':
mass = ['1 {0}'.format(masslist[0])]
if len(masslist) > 1:
for i in range(len(masslist)-1):
mass.append('{0} {1}'.format(i+2,masslist[i+1]))
if 'charges' in parameters:
cs = parameters['charges']
parameters['mass'][len(parameters['mass'])-1] +=cs[1]
parameters['newton']+='\natom_style charge'
else:
parameters={'potential_file':None}
print 'WARNING: No LAMMPS potential recognized. Assuming Lennard Jones Potential'
return parameters
def _lammps_input_setup(self, lammps_input_file="INPUT", lammps_data_file="DATA", lammps_trajectory_file="TRAJECTORY"):
"""Function to write a lammps input file
Input:
lammps_input_file = file to write lammps input to
lammps_data_file = file to load lammps data from
lammps_trajectory_file = file to write lammps trajectory to
"""
if isinstance(lammps_input_file, str):
f = open(lammps_input_file, 'w')
else:
f = lammps_input_file
# Write file variable names
f.write('clear\n' +
('variable dump_file string "%s"\n' % lammps_trajectory_file) +
('variable data_file string "%s"\n' % lammps_data_file))
f.write('units metal \n')
#Write to specified log file
#logname = os.path.join(os.path.dirname(lammps_data_file),"LOG")
#f.write('log %s append\n' % logname)
#Get keyword parameters
parameters = dict()
parameters = self._lammps_input_get_non_mast_keywords()
#Copy potential file to current working directory
if 'potential_file' in parameters:
if parameters['potential_file']:
newlocation = os.path.join(os.path.dirname(lammps_data_file),os.path.basename(parameters['potential_file']))
shutil.copyfile(parameters['potential_file'],newlocation)
self.potential_file = newlocation
atoms = AseAtomsAdaptor.get_atoms(self.keywords['structure'])
pbc = atoms.get_pbc()
if ('boundary' in parameters):
f.write('boundary %s \n' % parameters['boundary'])
else:
f.write('boundary %c %c %c \n' % tuple('sp'[x] for x in pbc))
f.write('atom_modify sort 0 0.0 \n')
if ('neighbor' in parameters):
f.write('neighbor %s \n' % parameters['neighbor'])
if ('newton' in parameters):
f.write('newton %s \n' % parameters['newton'])
f.write('\n')
f.write('read_data %s\n' % lammps_data_file)
# Write pair potential information
f.write('\n### interactions \n')
if ( ('pair_style' in parameters) and ('pair_coeff' in parameters) ):
pair_style = parameters['pair_style']
f.write('pair_style %s \n' % pair_style)
if not isinstance(parameters['pair_coeff'],list):
try:
parameters['pair_coeff'] = eval(parameters['pair_coeff'])
except:
parameters['pair_coeff'] = [ parameters['pair_coeff'] ]
for pair_coeff in parameters['pair_coeff']:
f.write('pair_coeff %s \n' % pair_coeff)
if 'mass' in parameters:
if not isinstance(parameter['mass'],list):
try:
parameters['mass'] = eval(parameters['mass'])
except:
parameters['mass'] = [ parameters['mass'] ]
for mass in parameters['mass']:
f.write('mass %s \n' % mass)
else:# Use simple leonnard jones calculation
f.write('pair_style lj/cut 2.5 \n' +
'pair_coeff * * 1 1 \n' +
'mass * 1.0 \n')
#Set up min_style if appropriate
if 'min_style' in parameters:
f.write('min_style %s \n' % parameters['min_style'])
#Write line for thermo arguments and stemps
thermo_args = ['step', 'temp', 'press', 'cpu',
'pxx', 'pyy', 'pzz', 'pxy', 'pxz', 'pyz',
'ke', 'pe', 'etotal',
'vol', 'lx', 'ly', 'lz', 'atoms']
thermo_mark = ' '.join([x.capitalize() for x in thermo_args[0:3]])
if 'thermosteps' not in parameters:
parameters['thermosteps'] = '1'
f.write('\n### run\n' +
'fix fix_nve all nve\n'+
('dump dump_all all custom {0} {1}'.format(parameters['thermosteps'], lammps_trajectory_file))+
' id type x y z vx vy vz fx fy fz'+
'\n')
f.write(('thermo_style custom %s\n' +
'thermo_modify flush yes\n' +
'thermo '+repr(parameters['thermosteps'])+
'\n') % (' '.join(thermo_args)))
if 'minimize' in parameters:
f.write('minimize %s\n' % parameters['minimize'])
if 'run' in parameters:
f.write('run %s\n' % parameters['run'])
if not (('minimize' in parameters) or ('run' in parameters)):
f.write('run 0\n')
f.write('print "CALCULATION HAS FINISHED"\n')
f.write('log /dev/stdout\n') # Force LAMMPS to flush log
f.write('undump dump_all\n') # Force LAMMPS to flush trj
f.close()
return lammps_input_file