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 run_script( _file_, machine='lammps', _cores_='1'):
core_flag = min(check_vars([_cores_],['int'],'Run aborted!'))
if check_file(_file_) and core_flag:
print _file_
command = '{} -echo both -in {}'.format( machine, _file_)
if int(_cores_)>1:
command = 'mpirun -np {} '.format( _cores_) + command
run_command(command)
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)