def check_datafile(self, _bflag_=None):
''' function to get the max atom number
also is used in case of no gromacs direct data conversion
to somehow make a check if that file is ok
'''
max_index = 0
_flag_ = True
if self._convertdata_ <> None:
max_index = len(self._convertdata_['atomsdata'][0])
else:
_filename_ = self.s_entry_c[0].get()
try:
with open(_filename_, 'r') as indata:
for k_line in indata:
if not k_line.startswith('#'):
line_c = k_line.split()
if 'atoms' in line_c:
max_index = line_c[0]
break
except IOError:
pop_wrg_1('Data file not found!')
print('Try performing a conversion first!')
_flag_ = False
if _bflag_ <> None:
return _flag_
return max_index
def autoloadstuff(self):
nonerr_flag = True
#_autoload_ = self.objt_c[0].get()
main_top_file = self.objt_c[2].get()
if self.autoload_buffer <> main_top_file:
# self.autoload_buffer = _autoload_
self.autoload_buffer = main_top_file
aux_cont, nonerr_flag = get_ffldfiles(main_top_file)
if nonerr_flag:
for i in [2, 3, 4]:
nonerr_flag *= check_file(aux_cont[i - 2])
self.file_e[i]._entry.delete(0, 'end')
self.file_e[i]._entry.insert(0, aux_cont[i - 2])
self.file_e[i]._entry.xview_moveto(1)
self.file_e[i].setter(0)
self.objt_c[0] = (1)
else:
self.objt_c[0] = (0)
elif self.objt_c[0] and self.autoload_buffer == main_top_file:
pop_wrg_1('Autoload already performed for selected top file.',
_i_=0)
if not self.objt_c[0]:
pop_err_1('Autoload failed!')
self.autoload_buffer = ''
self.autol_b.configure(state='disabled')
for i in [2, 3, 4]:
self.file_e[i].setter(1)
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 solvastuff(self):
'''If this point is reached, some button changed '''
_solvation_ = self.objt_c[-1].get()
if self.sol_buffer <> _solvation_:
self.sol_buffer = _solvation_
if _solvation_:
self.solv_b.configure( state = 'normal')
else:
pop_wrg_1('You are choosing to not consider solvation.'
,' If some solvent molecules are in the'
+' .gro file they will be ignored!', _i_=0)
self.solv_b.configure( state = 'disabled')
def check_file(_in_file_, content=True, string=''):
'''Check the correctness of the given input file address'''
flag = False
try:
_auxf = open(_in_file_, "r")
su = 0
strcheck = False
if content:
if string == '':
for line in _auxf:
su += len(line.rstrip('\n'))
else:
for line in _auxf:
line = line.rstrip('\n')
if string in line:
strcheck = True
_auxf.close()
if content and su == 0 and string == '':
pop_wrg_1(' File {} is empty -- '.format(_in_file_))
elif string <> '' and content and not strcheck:
pop_wrg_1(' Section {} not found in file {} -- '.format(
string, _in_file_))
else:
flag = True
except IOError:
pop_wrg_1(' File {} not found -- '.format(_in_file_))
return flag
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 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 get_ffldfiles( _topfile_):
'''
self explanatory... sub routine to get the force field files
if they are stated in the top file.
starts from the top file
'''
ff_file = ''
nonerr_flag = True
with open( _topfile_, 'r') as indata:
for j_line in indata:
if j_line.startswith('#include'):
ff_file = j_line.split('"')[1]
break
elif j_line.startswith('[ moleculetype ]'):
break
root_folder = '/'.join(_topfile_.split('/')[:-1]+[''])
ff_file = ff_file.lstrip('.').lstrip('/')
if ff_file <> '':
# if there is at least one itp, lets parse it
# first seek for further includes itp
aux_file_cont = [_topfile_, '']
print '----- Loading :'
i = 1
aux_file_cont[i] = root_folder + ff_file
print aux_file_cont[i]
root_folder = '/'.join( aux_file_cont[i].split('/')[:-1]+[''])
try:
with open( aux_file_cont[i], 'r') as indata2:
for k_line in indata2:
if k_line.startswith('#include'):
i+=1
aux_file_cont.append( root_folder+k_line.split('"')[1])
print aux_file_cont[i]
if i==3:
break
except IOError:
exit('xx/0 Read error 030, file not found!!.\n')
# the first one is [ defaults ]
# second nonbonded atomtypes
# third bonded
_directives_ = ['defaults', 'atomtypes', 'bondtypes']
file_cont = []
for _di_ in _directives_:
file_cont.append( seek_for_directive( aux_file_cont, _di_))
if file_cont[-1] == '':
pop_wrg_1('Directive ' + _di_ + ' not found!')
if _di_ == _directives_[-1]:
file_cont[-1] = file_cont[0]
else:
print ('Using :' +file_cont[-1]+' for ' + _di_)
else:
pop_err_1('Force field files #include not found!')
nonerr_flag *= False
# final check of non error flag
if nonerr_flag and len(file_cont) < 3 :
pop_wrg_1('Your structure seems unfamiliar, just ' +
'{} itp found.'.format( len(file_cont)) +
'\nthe conversion could fail!')
# Meaning that the directive seeker could not find the correspondin one
while len(file_cont) < 3:
file_cont.append( file_cont[-1])
# a file integrity check should be done outside
return file_cont, nonerr_flag
