def minimize(self,gradient=0.1,max_iter=100,
kw=None,summary=1):
if feedback['actions']:
print(' '+str(self.__class__)+': starting minimization run...')
io.xyz.toFile(self.model,self.prefix+"_inp.xyz")
self.counter = self.counter + max_iter
kw_list = [ "parameters "+self.params+"\n" ]
for a in self.keywords.keys():
kw_list.append("%s %s\n" % ( a,str(self.keywords[a])))
kw_list.extend(keyword.get_partial_charge(self.model))
if kw:
kw_list.extend(kw)
kw_list.append("overwrite\n")
kw_list.append("maxiter %d\n" % max_iter)
self.__write_keys(kw_list)
tinker.do('minimize',
self.prefix+"_inp",
self.prefix+"_run",
self.prefix+"_out",
[ tinker.prefix,
str(gradient),],
capture = 1 + self.echo )
io.xyz.updateFromFile(self.model,self.prefix+"_out.xyz")
self.restart = None
if summary:
# get energy information from output file
f = open(self.prefix+"_out.out")
step = 1
flag = 0
self.summary = []
while 1:
lin = f.readline()
if not lin: break
if not flag:
if (lin[0:9]==' CG Iter ' or
lin[0:9]==' QN Iter '):
f.readline() # skip blank
flag = 1
else:
try:
if int(lin[0:6])==step:
step = step + 1
self.summary.append([
int(lin[0:6]),
float(lin[6:19]),
float(lin[19:30]),
float(lin[30:41]),
float(lin[41:51]),
float(lin[51:60]),
int(lin[60:67]),
string.strip(lin[67:])])
except ValueError:
pass
f.close()
else:
self.summary = None
if len(self.summary):
self.energy = self.summary[-1][1]
else:
self.energy = None
def minimize(self, gradient=0.1, max_iter=100, kw=None, summary=1):
if feedback['actions']:
print ' ' + str(self.__class__) + ': starting minimization run...'
io.xyz.toFile(self.model, self.prefix + "_inp.xyz")
self.counter = self.counter + max_iter
kw_list = ["parameters " + self.params + "\n"]
for a in self.keywords.keys():
kw_list.append("%s %s\n" % (a, str(self.keywords[a])))
kw_list.extend(keyword.get_partial_charge(self.model))
if kw:
kw_list.extend(kw)
kw_list.append("overwrite\n")
kw_list.append("maxiter %d\n" % max_iter)
self.__write_keys(kw_list)
tinker.do('minimize',
self.prefix + "_inp",
self.prefix + "_run",
self.prefix + "_out", [
tinker.prefix,
str(gradient),
],
capture=1 + self.echo)
io.xyz.updateFromFile(self.model, self.prefix + "_out.xyz")
self.restart = None
if summary:
# get energy information from output file
f = open(self.prefix + "_out.out")
step = 1
flag = 0
self.summary = []
while 1:
lin = f.readline()
if not lin: break
if not flag:
if (lin[0:9] == ' CG Iter ' or lin[0:9] == ' QN Iter '):
f.readline() # skip blank
flag = 1
else:
try:
if int(lin[0:6]) == step:
step = step + 1
self.summary.append([
int(lin[0:6]),
float(lin[6:19]),
float(lin[19:30]),
float(lin[30:41]),
float(lin[41:51]),
float(lin[51:60]),
int(lin[60:67]),
string.strip(lin[67:])
])
except ValueError:
pass
f.close()
else:
self.summary = None
if len(self.summary):
self.energy = self.summary[-1][1]
else:
self.energy = None
def analyze(self, kw=None, summary=1):
if feedback['actions']:
print ' ' + str(self.__class__) + ': starting energy run...'
io.xyz.toFile(self.model,
self.prefix + "_inp.xyz",
mapping=self.mapping)
kw_list = ["parameters " + self.params + "\n"]
for a in self.keywords.keys():
kw_list.append("%s %s\n" % (a, str(self.keywords[a])))
kw_list.extend(keyword.get_partial_charge(self.model))
if kw:
kw_list.extend(kw)
self.__write_keys(kw_list)
tinker.do('analyze',
self.prefix + "_inp",
self.prefix + "_run",
self.prefix + "_out", [
tinker.prefix,
'E',
],
capture=1 + self.echo)
if summary:
# get energy information from output file
f = open(self.prefix + "_out.out")
self.summary = []
flag = 0
while 1:
lin = f.readline()
if not lin: break
if not flag:
if lin[0:25] == ' Total Potential Energy :':
self.summary.append(
[string.strip(lin[0:23]),
float(lin[25:49])])
flag = 1
else:
tok = string.split(string.strip(lin))
if len(tok):
if (tok[0] != 'Energy'):
self.summary.append([
string.strip(lin[0:23]),
float(lin[25:49]),
int(lin[49:64])
])
f.close()
else:
self.summary = None
if len(self.summary):
self.energy = self.summary[0][1]
else:
self.energy = None
def analyze(self,kw=None,summary=1):
if feedback['actions']:
print(' '+str(self.__class__)+': starting energy run...')
io.xyz.toFile(self.model,self.prefix+"_inp.xyz",
mapping = self.mapping)
kw_list = [ "parameters "+self.params+"\n" ]
for a in self.keywords.keys():
kw_list.append("%s %s\n" % ( a,str(self.keywords[a])))
kw_list.extend(keyword.get_partial_charge(self.model))
if kw:
kw_list.extend(kw)
self.__write_keys(kw_list)
tinker.do('analyze',
self.prefix+"_inp",
self.prefix+"_run",
self.prefix+"_out",
[ tinker.prefix,
'E',],
capture = 1 + self.echo )
if summary:
# get energy information from output file
f = open(self.prefix+"_out.out")
self.summary = []
flag = 0
while 1:
lin = f.readline()
if not lin: break
if not flag:
if lin[0:25]==' Total Potential Energy :':
self.summary.append([
string.strip(lin[0:23]),
float(lin[25:49])])
flag = 1
else:
tok = string.split(string.strip(lin))
if len(tok):
if(tok[0]!='Energy'):
self.summary.append([
string.strip(lin[0:23]),
float(lin[25:49]),
int(lin[49:64])])
f.close()
else:
self.summary = None
if len(self.summary):
self.energy = self.summary[0][1]
else:
self.energy = None
def dynamics(self,steps=100,
timestep=None,
interval=None,
temperature=None,
kw=None,summary=1):
if feedback['actions']:
print(' '+str(self.__class__)+': starting dynamics run...')
io.xyz.toFile(self.model,self.prefix+"_inp.xyz")
self.counter = self.counter + steps * timestep
# if restart is available, then use it.
if self.restart:
f = open(self.prefix+"_inp.dyn","w")
f.writelines(self.restart)
f.close()
if feedback['actions']:
print(' '+str(self.__class__)+': using restart information...')
#
kw_list = [ "parameters "+self.params+"\n" ]
for a in self.keywords.keys():
kw_list.append("%s %s\n" % ( a,str(self.keywords[a])))
kw_list.extend(keyword.get_partial_charge(self.model))
if kw:
kw_list.extend(kw)
kw_list.append("archive\n")
self.__write_keys(kw_list)
if not timestep:
timestep = self.default['timestep']
if not temperature:
temperature = self.default['temperature']
if not interval:
interval = (timestep*steps)/1000.0
else:
interval = interval/1000.0
tinker.do('dynamic',
self.prefix+"_inp",
self.prefix+"_run",
self.prefix+"_out",
[ tinker.prefix,
str(steps),
str(timestep),
str(interval),
str(temperature)],
capture = 1 + self.echo )
self.frames = io.arc.fromFile(self.prefix+"_out.arc")
if len(self.frames):
c = 0
atm = self.model.atom
for a in self.frames[-1]:
atm[c].coord = copy.deepcopy(a)
c = c + 1
# get restart information
f = open(self.prefix+"_out.dyn")
self.restart = f.readlines()
f.close()
# get energy information from output file
if summary:
f = open(self.prefix+"_out.out")
step = 1
flag = 0
self.summary = []
while 1:
lin = f.readline()
if not lin: break
if not flag:
if lin[0:12]==' MD Step ':
f.readline() # skip blank
flag = 1
else:
try:
if int(lin[0:10])==step:
step = step + 1
self.summary.append([
int(lin[0:10]),
float(lin[10:24]),
float(lin[24:38]),
float(lin[38:50]),
float(lin[50:61])])
except ValueError:
pass
f.close()
else:
self.summary = None
if len(self.summary):
self.energy = self.summary[-1][1]
else:
self.energy = None
def dynamics(self,
steps=100,
timestep=None,
interval=None,
temperature=None,
kw=None,
summary=1):
if feedback['actions']:
print ' ' + str(self.__class__) + ': starting dynamics run...'
io.xyz.toFile(self.model, self.prefix + "_inp.xyz")
self.counter = self.counter + steps * timestep
# if restart is available, then use it.
if self.restart:
f = open(self.prefix + "_inp.dyn", "w")
f.writelines(self.restart)
f.close()
if feedback['actions']:
print ' ' + str(
self.__class__) + ': using restart information...'
#
kw_list = ["parameters " + self.params + "\n"]
for a in self.keywords.keys():
kw_list.append("%s %s\n" % (a, str(self.keywords[a])))
kw_list.extend(keyword.get_partial_charge(self.model))
if kw:
kw_list.extend(kw)
kw_list.append("archive\n")
self.__write_keys(kw_list)
if not timestep:
timestep = self.default['timestep']
if not temperature:
temperature = self.default['temperature']
if not interval:
interval = (timestep * steps) / 1000.0
else:
interval = interval / 1000.0
tinker.do('dynamic',
self.prefix + "_inp",
self.prefix + "_run",
self.prefix + "_out", [
tinker.prefix,
str(steps),
str(timestep),
str(interval),
str(temperature)
],
capture=1 + self.echo)
self.frames = io.arc.fromFile(self.prefix + "_out.arc")
if len(self.frames):
c = 0
atm = self.model.atom
for a in self.frames[-1]:
atm[c].coord = copy.deepcopy(a)
c = c + 1
# get restart information
f = open(self.prefix + "_out.dyn")
self.restart = f.readlines()
f.close()
# get energy information from output file
if summary:
f = open(self.prefix + "_out.out")
step = 1
flag = 0
self.summary = []
while 1:
lin = f.readline()
if not lin: break
if not flag:
if lin[0:12] == ' MD Step ':
f.readline() # skip blank
flag = 1
else:
try:
if int(lin[0:10]) == step:
step = step + 1
self.summary.append([
int(lin[0:10]),
float(lin[10:24]),
float(lin[24:38]),
float(lin[38:50]),
float(lin[50:61])
])
except ValueError:
pass
f.close()
else:
self.summary = None
if len(self.summary):
self.energy = self.summary[-1][1]
else:
self.energy = None
