def write_script(self):
print 'Writing the lammps script'
_mainpage_ = get_entriesvalue(self.s_entry_c)
_flag_ = True # data ok flag
_entries_ = [
'float', 'int', 'int', 'float:', 'float', 'int', 'float:', 'float',
'float:', 'float'
]
_flag_ *= self.check_datafile(bool)
_flag_ *= min(check_vars(_mainpage_[1:], _entries_))
if _flag_:
self._container_['mainpage'] = _mainpage_
_script_setup_ = [
_mainpage_, self._container_['advanced'][0],
self._container_['restrain']
]
self.master._script_ = self._container_
_flag_ = write_lammps_input(_script_setup_, self._convertdata_)
if _flag_:
print_dec_g('Lammps script done!')
self.master.swapbody(3)
def getdata_and_convert(self):
_autoload_ = self.objt_c[0]
if not _autoload_:
pop_wrg_1('Proceeding without autoload.\nThis means that any ' +
'internal address to files that are not specified ' +
'as GUI input are going to be ignored.')
if self.get_entriesvalues():
data_cont = self.master._convert_['setup']
root_folder = '/'.join(data_cont[1].split('/')[:-1] + [''])
print('Root folder: {}'.format(root_folder))
sim_data, _flags_ = extract_gromacs_data(data_cont[1:-1],
_autoload_)
flag_done_, _sidemol_ = _flags_
config = [data_cont[-1], _sidemol_, _autoload_, root_folder]
if flag_done_:
try:
flag_done_, data_fnam = write_lammps_data(
sim_data, 'data.gro2lam', config)
except KeyError as Err:
err_str = ''
for er in Err.args:
err_str += er + ' '
pop_err_1(
'There are missing or incomplete coefficients in' +
' your input files related to: ' + err_str)
flag_done_ = False
except Exception as Exc:
pop_err_1(
'There are inconsistencies in your input files\n' +
Exc.args[0])
flag_done_ = False
if flag_done_:
print_dec_g('Data file generated as "data.gro2lam"')
self._convertdata_ = sim_data
self._convertdata_['filename'] = data_fnam
self._convertdata_['config'] = config
# Returning the values
self.master._convertdata_ = self._convertdata_
# to ensure freshness of our dependant values
self.master._script_['advanced'] = []
self.master._script_['restrain'] = []
self.master.swapbody(2)
else:
pop_wrg_1('The setup needs some further improvements' +
'to be runed. Please check your inputs')
def getdata_and_convert(self):
_solvatedinfo_ = self.master._convert_['solvation']
if ( self.objt_c[-1].get() and _solvatedinfo_ == []):
pop_wrg_1( 'First perform the solvation configuration.'
+ ' You can do it pressing in solvation settings gears',
_i_=0
)
self.solv_b.invoke()
elif self.get_entriesvalues():
data_cont = self.master._convert_['setup']
config = data_cont[-2:]+[0]
sim_data, flag_done_ = extract_gromacs_data(data_cont[:-2],
_solvatedinfo_,
config[1:])
if flag_done_:
flag_done_ = write_lammps_data( sim_data, 'data.gro2lam',
config
)
if flag_done_:
print_dec_g( 'Data file generated as "data.gro2lam"' )
self._convertdata_ = sim_data
self._convertdata_['config'] = config
# Returning the values
self.master._convertdata_ = self._convertdata_
self.master.swapbody(2)
else:
pop_wrg_1('The setup needs some further improvements'
+'to be runed. Please check your inputs')
def write_lammps_data(_topodata_, data_name, _config_):
''' Write a lammps data file'''
print_dec_g('Writing Lammps data file...')
####--------------- Unpacking data ----------------####
atomstyle, _, _ = _config_
atsty = ['atomic', 'angle', 'full', 'charge', 'bond', 'molecular']
style_str = '####------- ATOM STYLE < {} > --------####'
_flag_ = False
if atomstyle in atsty:
nam = ''.join([chr(ord(l) - 32) for l in atomstyle])
print_dec_g(style_str.format(nam))
_content_ = write_lammps_data_all(_topodata_, data_name, _config_)
_flag_ = True
else: #if atomstyle == 'Angle':
_content_ = ''
exit(('Error 037!! - Atom style {} ' +
'not implemented yet').format(atomstyle))
write_file(data_name, _content_)
print_dec_g('Successful writing!!')
return _flag_
def config_solvation( self):
title_txt = ' '*15+'Input Water name'
instructions = 'Enter the atom tag letters of:'
askfor = ['O in the non bonded file',
'H in the non bonded file',
'O in the .gro file',
'H in the .gro file',
'H - O partial charge'
#'Na+ in the .gro file (if are present)',
#'Cl- in the .gro file (if are present)'
]
_solvatedinfo_ = self.master._convert_['solvation']
if _solvatedinfo_ == []:
defaultanswer = ['opls_116','opls_117','OW','HW1, HW2','0.4238'
#,'Na','Cl'
]
else:
defaultanswer = _solvatedinfo_
self.solv_b.config(bg = 'gray40', width = 45) #cyan')
self.master._aux_ = []
pop = PromptPopUp(master = self.master,
title = title_txt,
briefing = instructions,
entries_txt = askfor,
entries_val = defaultanswer
)
pop.wait_window()
if self.master._aux_ <> [] and self.get_entriesvalues():
_app_aux_ = self.master._aux_
#============ Check inputs =================
_flag_ = 1
nb_Ox, nbHy, gro_Oxs, gro_Hys, pch= _app_aux_
_gro_f, _, _, _nbn_f, _, _, _= self.master._convert_['setup']
_flags = check_in_file( _nbn_f, nb_Ox, nbHy)
print ([nb_Ox, nbHy])
list_aux = [Ox.strip(' ') for Ox in gro_Oxs.split(',')]
list_aux += [Ox.strip(' ') for Ox in gro_Hys.split(',')]
_flags += check_in_file( _gro_f, *list_aux)
print (list_aux)
try:
x = float(pch)
if -10<x<10:
_flags += [1]
partial_charges = 'Partial charges for H: {} and for O: {}'
print partial_charges.format( x, x*-2)
else:
_flags += [0]
except:
_flags += [0]
list_aux = [nb_Ox, nbHy] + list_aux
for v in range(len(_flags)):
err_txt = ''
if not _flags[v] and v <> (len(_flags)-1):
filename = _nbn_f
if v>1:
filename = _gro_f
err_txt = 'Atom tag {} not found in {}'
if '/' in filename:
filename = filename.split('/')[-1]
err_txt = err_txt.format( list_aux[v], filename)
_flag_*=0
elif not _flags[v]:
err_txt = 'Non valid partial charge {}'.format( pch)
_flag_*=0
if err_txt<>'':
pop_err_1(err_txt+'\nSetup not saved')
#============ Done! =================
if _flag_:
self.master._convert_['solvation'] = _app_aux_
print_dec_g('Solvation setup saved!')
#self.solv_b.focus()
self.solv_b.config(bg = 'lightgrey', width = 28)
def config_restrain(self):
title_txt = ' ' * 28 + '+ Restrain Goups'
instructions = 'Select the group to restrain'
#============ grouping ================
max_index = self.check_datafile()
if max_index:
_defvals_ = self._container_['restrain']
if _defvals_ == []:
g_names = ['all_group']
d_ids = ['{}:{}'.format(1, max_index)]
kxyz_c = ['1:xyz']
rest_ens = ['1-2'] #restrained_ensembles
ck_init = [0]
second_c = None
if self._convertdata_ <> None:
_mol_niifi_ = self._convertdata_['atomsdata'][1]
for mt in range(len(_mol_niifi_)):
g_names.append(_mol_niifi_[mt][0])
d_ids.append('{}:{}'.format(*_mol_niifi_[mt][1:]))
kxyz_c += ['1:xyz']
rest_ens += ['1-2']
ck_init += [0]
else:
g_names, d_ids, kxyz_c, rest_ens, ck_init = _defvals_[0]
#print g_names,'\n', d_ids,'\n', kxyz_c,'\n', ck_init
if _defvals_[1] <> None:
second_c = _defvals_[1]
else:
second_c = None
self.resb.config(bg='gray70') #, width = 45) #cyan')
self.master._aux_ = []
pop = PromptPopUp_wck(
master=self.master,
title=title_txt,
briefing=instructions,
entries_txt=g_names,
entries_val=kxyz_c,
width=530,
#height = 365,
range_id=d_ids,
res_ens=rest_ens,
chck_init=ck_init,
extra_but=second_c,
)
pop.wait_window()
if self.master._aux_ <> []:
sim_len = 0
for x in self._container_['advanced'][0][-2].split('-'):
if x.strip(' ') <> 'R':
sim_len += 1
_res_flag_ = [[], []]
_restrain_ = self.master._aux_[:]
_, _d_ids, _kxyz_c, _runs_c, _res_flag_[0] = _restrain_[0]
if _restrain_[1] <> None:
_, au2, au3, au4, au5 = _restrain_[1][:]
_restrain_aux = _d_ids + au2 + _kxyz_c + au3 + _runs_c + au4
_res_flag_[1] = au5
else:
_restrain_aux = _d_ids + _kxyz_c + _runs_c
_multi_ = len(_restrain_aux) / 3
_entries_ = ([['<int:int<', 1, max_index]] * _multi_ +
['float:xyz'] * _multi_ +
[['<int-x-int<:0', 1, sim_len]] * _multi_)
_aux_ = check_vars(_restrain_aux, _entries_,
'Restrain groups not saved!')
#print _aux_
_flag_ = min(_aux_)
if _flag_:
if max(max(_res_flag_)):
self._container_['restrain'] = _restrain_
print_dec_g('Restrain data saved')
else:
print('Creating 0 groups, Restraining 0 atoms')
self.resb.config(bg='gray86') #, width = 45)
def further_config_script(self):
defvals = []
title_txt = ' ' * 3 + '+ Simulation Parameters'
instructions = 'Input further simulation parameters'
askfor = [
'Thermo output every [#ts]',
'Atom mapping',
'Pairwise interactions',
"L-J/Buck rcutoff [" + u'\u00c5' + "]",
"Coulomb rcutoff [" + u'\u00c5' + "]",
"Neighbor skin distance [" + u'\u00c5' + "]",
'Long-range solver',
'Long-range relative error',
'Interaction 1-2:1-3:1-4',
'Neighbor delay [#ts]',
'Neighbor update [#ts]',
'Pressure control',
'Force mixing rule',
'Simulation order',
'Velocity creation Temp [K]',
]
_pair_style_ = [
'lj/cut/coul/long',
'lj/cut/coul/cut',
'lj/cut',
'buck/coul/long',
'buck',
'buck/coul/cut',
#'lj/cut/tip4p/cut', 'lj/cut/tip4p/long',
#'lj/gromacs', 'lj/gromacs/coul/gromacs',
'zero',
'none'
]
if self._convertdata_ <> None:
buckorlj = int(self._convertdata_['defaults'][0])
if buckorlj == 1:
_pair_style_ = _pair_style_[:3] + _pair_style_[-2:]
else:
_pair_style_ = _pair_style_[3:]
self._container_['advanced'][0][2] = _pair_style_[3]
_kspace_ = [
'pppm',
'pppm/cg',
'ewald',
'pppm/disp',
'ewald/disp',
#'pppm/tip4p', 'pppm/disp/tip4p'
]
_comb_rule_ = ['No', 'geometric', 'arithmetic', 'sixthpower']
self._container_['advanced'][1] = [
'', ['array', 'hash'], _pair_style_, '', '', '', _kspace_, '', '',
'', '', ['aniso', 'iso', 'tri'], _comb_rule_, '', ''
]
_defvals_ = []
for _ad_ in range(len(self._container_['advanced'][0])):
if self._container_['advanced'][1][_ad_] <> '':
_def_ = self._container_['advanced'][0][_ad_]
_dfli_ = self._container_['advanced'][1][_ad_]
_defvals_.append([_def_, _dfli_])
else:
_defvals_.append(self._container_['advanced'][0][_ad_])
self.fcb.config(bg='gray70') #, width = 155) #cyan')
self.master._aux_ = []
pop = PromptPopUp(master=self.master,
title=title_txt,
briefing=instructions,
entries_txt=askfor,
entries_val=_defvals_,
width=400,
height=565)
pop.wait_window()
if self.master._aux_ <> []:
_advanced_ = self.master._aux_
_entries_ = [
'int', '', '', 'float', 'float', 'float', '', 'float',
'float::', 'int', 'int', '', '',
[list, '-', 'NVE', 'NVT', 'NPT', 'R'], 'float'
]
_flag_ = min(
check_vars(_advanced_, _entries_,
'Advanced settings not saved!'))
if _flag_:
self._container_['advanced'][0] = _advanced_
print_dec_g('Advanced settings saved')
self.fcb.config(bg='gray86') #, width = 145)
def further_config_script( self ):
''' Section for advaced settings
'''
pop_wrg_1('Advanced settings!\nChanging these parameters could result'
+' in a different simulation than the base one')
defvals = []
title_txt = ' '*3+'+ Simulation Parameters'
instructions = 'Input further simulation parameters'
askfor = ['Thermo output every [#ts]',
'Atom mapping',
'Pairwise interactions',
"L-J/Buck rcutoff ["+u'\u00c5'+"]",
"Coulomb rcutoff ["+u'\u00c5'+"]",
"Neighbor skin distance ["+u'\u00c5'+"]",
'Long-range solver',
'Long-range relative error',
'L-J interaction 1-2:1-3:1-4',
'Coul interaction 1-2:1-3:1-4',
'Neighbor delay [#ts]',
'Neighbor update [#ts]',
'Pressure control',
'Force mixing rule',
'Velocity creation Temp [K]',
'Energy minimization tolerance',
'Simulation order',
'---',
'Shake tolerance',
'Shake bonds [b#]',
'Shake angles [a#]',
]
_pair_style_ = ['lj/cut/coul/long','lj/cut/coul/cut', 'lj/cut',
'lj/charmm/coul/long',
'buck/coul/long', 'buck', 'buck/coul/cut',
#'lj/cut/tip4p/cut', 'lj/cut/tip4p/long',
#'lj/gromacs', 'lj/gromacs/coul/gromacs',
#, 'none',
'zero']
if self._convertdata_ <> None:
buckorlj = int( self._convertdata_['defaults'][0])
if buckorlj == 1:
_pair_style_ = _pair_style_[ :3] + [_pair_style_[ -1]]
else:
_pair_style_ = _pair_style_[ 3:]
_kspace_ = ['pppm', 'pppm/cg', 'ewald', 'pppm/disp', 'ewald/disp',
#'pppm/tip4p', 'pppm/disp/tip4p'
]
_comb_rule_ = ['No','geometric', 'arithmetic', 'sixthpower']
# ['advanced'][1] in case of drop down lists, to show the other cases
self._container_['advanced'][1] = [ '', ['array', 'hash'],
_pair_style_,
'','','', _kspace_,
'', '', '', '', '',
['aniso', 'iso', 'tri'],
_comb_rule_, '','','',
'', '', ''
]
_defvals_ = []
for _ad_ in range(len(self._container_['advanced'][0])):
if self._container_['advanced'][1][_ad_] <> '':
_def_ = self._container_['advanced'][0][_ad_]
_dfli_ = self._container_['advanced'][1][_ad_]
_defvals_.append([ _def_, _dfli_])
else:
_defvals_.append(self._container_['advanced'][0][_ad_])
self.fcb.config(bg = 'gray70')#, width = 155) #cyan')
self.master._aux_ = []
pop = PromptPopUp(master = self.master,
title = title_txt,
briefing = instructions,
entries_txt = askfor,
entries_val = _defvals_ ,
width = 400,
height = 665
)
pop.wait_window()
_, bnty_len, anty_len = self.check_datafile()
print bnty_len, anty_len
if self.master._aux_ <> []:
_advanced_ = self.master._aux_
_entries_ = [ 'int', '', '', 'float', 'float', 'float', '',
'float',
['<float::<', 0.0, 1.0],['<float::<', 0.0, 1.0],
'int', 'int', '', '',
'float', 'float',[list, '-','NVE','NVT','NPT','R','M']
,'float',
['<int-x-int<:0', 1, bnty_len],
['<int-x-int<:0', 1, anty_len]
]
_flag_ = min( check_vars( _advanced_, _entries_,
'Advanced settings not saved!'))
if _flag_:
self._container_['advanced'][0] = _advanced_
print_dec_g('Advanced settings saved')
self.fcb.config(bg = 'gray86')#, width = 145)
def write_lammps_input(_simconfig_, _topodata_=None, in_name='in.gro2lam'):
''' _simconfig_ contains the data gathered from the gui
_topodata_ comes from the converted gromacs file
in_name is intended as name for the input'''
#===================================================
'''==== Gathering and ordering the data ====='''
#===================================================
#===================================================
####----------- SIM RAW CONFIG --------####
_simconfig_ = _simconfig_[:]
(data_file, timestep, nve_steps, nvt_steps, nvt_tss, nvt_tdamp, npt_steps,
npt_pss, npt_pdamp, npt_tss, npt_tdamp) = _simconfig_[0]
nvt_tstart, nvt_tend = nvt_tss.split(':')
npt_pstart, npt_pend = npt_pss.split(':')
npt_tstart, npt_tend = npt_tss.split(':')
#print (data_file, timestep, nve_steps, nvt_steps, nvt_tstart, nvt_tend,
#nvt_tdamp, npt_steps, npt_pstart, npt_pend, npt_tdamp, npt_tdamp,
#npt_ystart, npt_yend)
i = 5
thermo, atommap, pairwiseint, lj_rcutoff, c_rcutoff = _simconfig_[1][:i]
neighbordistance, lrsolver, lrerror, in12_13_14 = _simconfig_[1][i:i + 4]
neighbordelay, neighborupdate, npt_kind = _simconfig_[1][i + 4:i + 7]
f_comb_rule, _order_, T_init_vel = _simconfig_[1][i + 7:]
#===================================================
####------------ RESTRAIN DATA --------####
rest_line = ''
group_lines = ''
torestrain = []
ens_af = []
if _simconfig_[2] <> []:
g_names, g_aids, k_xyz_c, runs_c, ch_init = _simconfig_[2][0][:]
if _simconfig_[2][1] <> None:
####### ------------------------------------ Super interesante!!
## este es uno de esos casos donde no es posible
## utilizar += a pesar de desligar con [:] ...
aux1, aux2, aux3, aux4, aux5 = _simconfig_[2][1][:]
g_names = g_names + aux1
g_aids = g_aids + aux2
k_xyz_c = k_xyz_c + aux3
runs_c = runs_c + aux4
ch_init = ch_init + aux5
print '\n'
for re in range(len(g_names)):
if ch_init[re] == 1:
print 'Restraining group ' + g_names[re] + ' in ' + runs_c[re]
groupinfo = [g_names[re], g_aids[re]]
group_lines += 'group {} id {}\n'.format(*groupinfo)
if runs_c[re] not in ['', 'No', 'no', '0']:
ens = [int(x) - 1 for x in runs_c[re].split('-')]
torestrain.append([g_names[re], k_xyz_c[re], ens])
for e in ens:
if e not in ens_af:
ens_af.append(e)
if group_lines <> '':
group_lines += '\n'
mix_value = {
'1': 'geometric',
'2': 'arithmetic',
'3': 'geometric',
'4': 'sixthpower'
}
#for mt in range(len( _mtype_)):
#group_lines += 'group {} id {}:{}\n'.format(*_mtype_[mt])
_asty_d_ = {
'atomic': 1,
'charge': 2,
'bond': 3,
'angle': 4,
'full': 5,
'molecular': 5
}
#===================================================
####------------ TOPO DATA --------####
print '\n' + data_file + '\n'
if _topodata_ <> None:
atomstyle, _solvated_, _parametric_ = _topodata_['config']
buckorlj, comb_rule, _, f_LJ, _ = _topodata_['defaults']
else:
print 'non _topodata_'
atomstyle = 'full'
comb_rule = ''
buckorlj = 0
if f_comb_rule in mix_value.values():
mix_value_s = ' mix ' + f_comb_rule
elif f_comb_rule == 'from_gromacs' and _topodata_ <> None:
mix_value_s = ' mix ' + mix_value[comb_rule]
else:
print 'Using default mixing rule'
mix_value_s = ''
#===================================================
'''======= Writing Lammps data file ======='''
#===================================================
_dtxt_ = '\n' + '#INIT\n' + 'units real\n' + 'boundary p p p\n' + 'atom_style '
# as I understand lammps default is 3
#_dtxt_+= '%s %d\n'.format('dimension',dimension)
_dtxt_ += atomstyle + '\n'
if atomstyle not in ['full', 'charge]']: # no charges
if 'coul' in pairwiseint:
pairwiseint = pairwiseint.split('/coul')[0]
if 'none' in pairwiseint:
lj_rcutoff = ''
c_rcutoff = ''
elif 'coul' not in pairwiseint:
c_rcutoff = ''
_dtxt_ += '\natom_modify map {}\n'.format(atommap)
#===================================================
####------------ SYSTEM CONFIGURATION --------####
_dsc_txt = ['pair_style {} {}'.format(pairwiseint, lj_rcutoff)]
_dsc_txt.append(' {}\n'.format(c_rcutoff))
_dsc_txt.append('bond_style harmonic\n')
_dsc_txt.append('angle_style harmonic\n')
_dsc_txt.append('dihedral_style charmm\n')
_dtxt_ += ''.join(_dsc_txt[:_asty_d_[atomstyle]]) + '\n'
if 'data' in data_file:
_dtxt_ += 'read_data {}\n'.format(data_file)
else:
_dtxt_ += 'read_restart {}\n'.format(data_file)
#===================================================
####-------------- NEIGHBOR LIST -----------####
_dtxt_ += '\nneighbor {} bin\n'.format(neighbordistance)
if lrsolver <> '' and atomstyle in ['full', 'charge']:
if '/coul/long' in pairwiseint:
_dtxt_ += 'kspace_style {} {}\n'.format(lrsolver, lrerror)
_dtxt_ += 'pair_modify shift no tail yes' + mix_value_s + '\n'
_dtxt_ += 'special_bonds lj/coul {} {} {}\n'.format(*in12_13_14.split(':'))
_aux_s_ = 'neigh_modify every {} delay {} check yes\n\n'
_dtxt_ += _aux_s_.format(neighborupdate, neighbordelay)
#===================================================
####--------------- TIMESTEP ----------------####
_dtxt_ += 'timestep {}\n\n\n'.format(timestep)
_dtxt_ += 'thermo {}\n'.format(thermo)
_dtxt_ += ('thermo_style custom step temp press vol ' +
'epair emol etotal enthalpy' + '\n\n')
#===================================================
####-------------- Init VELOCITIES ----------####
aux_vel_str = 'velocity all create {} 1234567 rot yes dist gaussian\n\n'
_dtxt_ += aux_vel_str.format(T_init_vel)
#===================================================
####---------------- GROUPS ----------------####
_dtxt_ += group_lines
#===================================================
####--------------- SIMULATION ------------####
ensembles = _order_.split('-')
curr_time = 0
timestep = float(timestep)
tounfix = [[], []]
_dtxt_ += '\n'
for en in range(len(ensembles)):
if ens_af <> [] and en in ens_af: # RESTRAIN
for re in range(len(torestrain)):
if en in torestrain[re][2]:
if en - 1 not in torestrain[re][2]:
spring_f = 'fix rest_{0}_{1} {0} spring/self {2} {3}\n'
k, xyz = torestrain[re][1].split(':')
_dtxt_ += spring_f.format(torestrain[re][0], en + 1, k,
xyz)
unr = 0 + en
while unr + 1 in torestrain[re][2]:
unr += 1
name_2uf = 'rest_{0}_{1}'.format(
torestrain[re][0], en + 1)
tounfix = [tounfix[0] + [unr], tounfix[1] + [name_2uf]]
_dtxt_ += '\n'
if ensembles[en] == 'NVE' and nve_steps <> '' and nve_steps.isdigit():
steps = int(nve_steps)
nve_frm = 'fix nve_name1 all nve\nrun {}\nunfix nve_name1\n\n'
_dtxt_ += nve_frm.format(steps)
curr_time += steps * timestep
elif ensembles[en] == 'NPT' and npt_steps <> '' and npt_steps.isdigit(
):
steps = int(npt_steps)
npt_frm = 'fix npt_name1 all npt temp {} {} {} {} {} {} {}\n'
_dtxt_ += npt_frm.format(npt_tstart, npt_tend, npt_tdamp, npt_kind,
npt_pstart, npt_pend, npt_pdamp)
_dtxt_ += 'run {}\nunfix npt_name1\n\n'.format(steps)
curr_time += steps * timestep
elif ensembles[en] == 'NVT' and nvt_steps <> '' and nvt_steps.isdigit(
):
steps = int(nvt_steps)
nvt_frm = 'fix nvt_name1 all nvt temp {} {} {}\n'
_dtxt_ += nvt_frm.format(nvt_tstart, nvt_tend, nvt_tdamp)
_dtxt_ += 'run {}\nunfix nvt_name1\n\n'.format(steps)
curr_time += steps * timestep
elif ensembles[en] == 'R':
restart_txt = '\nwrite_restart restart.g2l_{}fs\n'
_dtxt_ += restart_txt.format(int(curr_time))
if tounfix <> [[], []] and en in tounfix[0]: # UNFIX RESTRAIN
for unf in range(len(tounfix[0])):
if tounfix[0][unf] == en:
_dtxt_ += 'unfix ' + tounfix[1][unf] + '\n'
print('Writing Lammps input script...')
write_file(in_name, _dtxt_)
print_dec_g('Successful writing!!')
#-------------------- here would be optimum some further check
return True