def PPCheck(xc, element, pp_file_str, **kwargs):
if xc == 'lda':
xc = 'pade'
ne = qtk.n2ve(element)
try:
if 'dcacp' in kwargs and kwargs['dcacp']:
pp_path = os.path.join(xc.upper(), "%s_DCACP_%s" %\
(element, xc.upper()))
if element in qtk.setting.dcacp_dict:
pp_path = pp_path + "_%s" % qtk.setting.dcacp_dict[element]
pp_file = os.path.join(qtk.setting.cpmd_dcacp_url, pp_path)
else:
pp_path = os.path.join(xc,
element + '-q' + str(qtk.n2ve(element)))
pp_file = os.path.join(qtk.setting.cpmd_pp_url, pp_path)
saved_pp_path = os.path.join(qtk.setting.cpmd_pp, pp_file_str)
if not os.path.exists(saved_pp_path) \
and qtk.setting.download_pp:
if pp_file:
new_pp = os.path.join(qtk.setting.cpmd_pp, pp_file_str)
pp_content = urllib2.urlopen(pp_file).read()
qtk.report('PPCheck', 'pp file %s not found in %s, ' \
% (pp_file_str, qtk.setting.cpmd_pp) + \
'but found on internet, download now...')
new_pp_file = open(new_pp, 'w')
new_pp_file.write(pp_content)
new_pp_file.close()
pp_file = new_pp
return saved_pp_path
except:
qtk.warning('something wrong with pseudopotential')
def PPName(**kwargs):
element = kwargs['element'].title()
if 'vdw' in kwargs:
PPvdw = '_dcacp_'
else:
PPvdw = ''
if 'd_shell' in kwargs:
nve = qtk.n2ve(element) + 10
else:
nve = qtk.n2ve(element)
PPStr = element + PPvdw + '_q%d_' % nve +\
self.setting['xc'].lower() + '.psp'
return PPStr, element
def alchemyPP(xc, pp_file_str):
pp_path = os.path.join(qtk.setting.cpmd_pp, pp_file_str)
if not os.path.exists(pp_path):
root, _ = os.path.splitext(pp_file_str)
element_str = re.sub('_.*', '', root)
fraction = float(re.sub('.*_', '', root)) / 100
element1 = re.sub('2.*', '', element_str)
element2 = re.sub('.*2', '', element_str)
str1 = element1 + "_q" + str(qtk.n2ve(element1)) +\
"_" + xc + '.psp'
str2 = element2 + "_q" + str(qtk.n2ve(element2)) +\
"_" + xc + '.psp'
pp1 = PP(PPCheck(xc, element1, str1))
pp2 = PP(PPCheck(xc, element2, str2))
pp = mutatePP(pp1, pp2, fraction)
pp.write(pp_path)
def alchemyPP(xc, pp_file_str):
pp_path = os.path.join(qtk.setting.cpmd_pp, pp_file_str)
if not os.path.exists(pp_path):
root, _ = os.path.splitext(pp_file_str)
element_str = re.sub('_.*', '', root)
fraction = float(re.sub('.*_', '', root))/100
element1 = re.sub('2.*', '', element_str)
element2 = re.sub('.*2', '', element_str)
str1 = element1 + "_q" + str(qtk.n2ve(element1)) +\
"_" + xc + '.psp'
str2 = element2 + "_q" + str(qtk.n2ve(element2)) +\
"_" + xc + '.psp'
pp1 = PP(PPCheck(xc, element1, str1))
pp2 = PP(PPCheck(xc, element2, str2))
pp = mutatePP(pp1, pp2, fraction)
pp.write(pp_path)
def PPName(inp, mol, i, n):
if 'vdw' in inp.setting\
and inp.setting['vdw'].lower == 'dcacp':
PPvdw = '_dcacp_'
else:
PPvdw = ''
element = mol.type_list[i].title()
if 'valence_electrons' in inp.setting\
and element in inp.setting['valence_electrons']:
nve = inp.setting['valence_electrons'][element]
elif 'd_shell' in inp.setting\
and element in inp.setting['d_shell']:
nve = qtk.n2ve(element) + 10
else:
nve = qtk.n2ve(element)
PPStr = element + PPvdw + '_q%d_' % nve +\
inp.setting['pp_theory'].lower() + '.psp'
return PPStr
def PPName(inp, mol, i, n):
if 'vdw' in inp.setting\
and inp.setting['vdw'].lower == 'dcacp':
PPvdw = '_dcacp_'
else:
PPvdw = ''
element = mol.type_list[i].title()
if 'valence_electrons' in inp.setting\
and element in inp.setting['valence_electrons']:
nve = inp.setting['valence_electrons'][element]
elif 'd_shell' in inp.setting\
and element in inp.setting['d_shell']:
nve = qtk.n2ve(element) + 10
else:
nve = qtk.n2ve(element)
PPStr = element + PPvdw + '_q%d_' % nve +\
inp.setting['pp_theory'].lower() + '.psp'
return PPStr
def PPCheck(xc, element, pp_file_str, **kwargs):
ne = qtk.n2ve(element)
try:
pp_path = os.path.join(xc, element + '-q' + str(qtk.n2ve(element)))
pp_file = os.path.join(qtk.setting.cpmd_pp_url, pp_path)
saved_pp_path = os.path.join(qtk.setting.cpmd_pp, pp_file_str)
if not os.path.exists(saved_pp_path) and qtk.setting.download_pp:
if pp_file:
new_pp = os.path.join(qtk.setting.cpmd_pp, pp_file_str)
pp_content = urllib2.urlopen(pp_file).read()
qtk.report('', 'pp file %s not found in %s. ' \
% (pp_file_str, qtk.setting.cpmd_pp) + \
'but found in cp2k page, download now...')
new_pp_file = open(new_pp, 'w')
new_pp_file.write(pp_content)
new_pp_file.close()
pp_file = new_pp
return saved_pp_path
except:
qtk.warning('something wrong with pseudopotential')
def PPCheck(xc, element, pp_file_str, **kwargs):
ne = qtk.n2ve(element)
try:
pp_path = os.path.join(xc, element + '-q' + str(qtk.n2ve(element)))
pp_file = os.path.join(qtk.setting.cpmd_pp_url, pp_path)
saved_pp_path = os.path.join(qtk.setting.cpmd_pp, pp_file_str)
if not os.path.exists(saved_pp_path) and qtk.setting.download_pp:
if pp_file:
new_pp = os.path.join(qtk.setting.cpmd_pp, pp_file_str)
pp_content = urllib2.urlopen(pp_file).read()
qtk.report('', 'pp file %s not found in %s. ' \
% (pp_file_str, qtk.setting.cpmd_pp) + \
'but found in cp2k page, download now...')
new_pp_file = open(new_pp, 'w')
new_pp_file.write(pp_content)
new_pp_file.close()
pp_file = new_pp
return saved_pp_path
except:
qtk.warning('something wrong with pseudopotential')
def PPCheck(xc, pp_theory, pp_path, element):
theory_dict = {
'lda': 'pade',
'pbe0': 'pbe',
'pbesol': 'pbe',
'hse06': 'pbe',
}
name = '%s_%s_%s' % (element, xc, pp_theory)
pp_file = os.path.join(pp_path, name)
if not os.path.exists(pp_file) and qtk.setting.download_pp:
if pp_theory != 'nlcc':
if pp_theory in theory_dict.keys():
pp_theory = theory_dict[pp_theory]
url_root = qtk.setting.bigdft_pp_url
element_str = element + '-q%d' % qtk.n2ve(element)
url = url_root + '%s/%s' % (pp_theory, element_str)
page = False
try:
page = urllib2.urlopen(url).readlines()
pattern = re.compile(r'^.*</*pre>.*$')
pp_se = filter(pattern.match, page)
pp_start = page.index(pp_se[0])
pp_end = page.index(pp_se[1])
page = page[pp_start:pp_end]
page[0] = page[0].split('>')[-1]
except:
qtk.warning('something wrong with url:%s' % url)
pp = ''.join(page)
else:
url = qtk.setting.bigdft_pp_nlcc_url
page = urllib2.urlopen(url).readlines()
string = filter(lambda x: '"psppar.%s' % element in x, page)[-1]
index = page.index(string) + 2
pp = []
itr = 0
while '</pre>' not in page[index + itr] \
and index + itr < len(page)\
and itr < 20:
pp.append(page[index + itr])
itr = itr + 1
pp = ''.join(pp)
if pp:
qtk.report('', 'pp file %s not found in %s.' %\
(name, pp_path) +\
' But found in cp2k page, download now...')
new_pp_file = open(pp_file, 'w')
new_pp_file.write(pp)
new_pp_file.close()
return pp_file
def PPCheck(xc, pp_theory, pp_path, element):
theory_dict = {
'lda': 'pade',
}
name = '%s_%s_%s' % (element, xc, pp_theory)
pp_file = os.path.join(pp_path, name)
if not os.path.exists(pp_file) and qtk.setting.download_pp:
if pp_theory != 'nlcc':
if pp_theory in theory_dict.keys():
pp_theory = theory_dict[pp_theory]
url_root = qtk.setting.bigdft_pp_url
element_str = element + '-q%d' % qtk.n2ve(element)
url = url_root + '%s/%s' % (pp_theory, element_str)
page = False
try:
page = urllib2.urlopen(url).readlines()
pattern = re.compile(r'^.*</*pre>.*$')
pp_se = filter(pattern.match, page)
pp_start = page.index(pp_se[0])
pp_end = page.index(pp_se[1])
page = page[pp_start:pp_end]
page[0] = page[0].split('>')[-1]
except:
qtk.warning('something wrong with url:%s' % url)
pp = ''.join(page)
else:
url = qtk.setting.bigdft_pp_nlcc_url
page = urllib2.urlopen(url).readlines()
string = filter(lambda x: '"psppar.%s' % element in x, page)[-1]
index = page.index(string) + 2
pp = []
itr = 0
while '</pre>' not in page[index + itr] \
and index + itr < len(page)\
and itr < 20:
pp.append(page[index + itr])
itr = itr + 1
pp = ''.join(pp)
if pp:
qtk.report('', 'pp file %s not found in %s.' %\
(name, pp_path) +\
' But found in cp2k page, download now...')
new_pp_file = open(pp_file, 'w')
new_pp_file.write(pp)
new_pp_file.close()
return pp_file
def PPCheck(xc, element, pp_file_str, **kwargs):
ne = qtk.n2ve(element)
saved_pp_path = os.path.join(qtk.setting.espresso_pp, pp_file_str)
if not os.path.exists(saved_pp_path) and qtk.setting.download_pp:
qtk.status("PPCheck", pp_file_str)
url = os.path.join(qtk.setting.espresso_pp_url, pp_file_str)
try:
pp_content = urllib2.urlopen(url).read()
qtk.report('', 'pp file %s not found in %s. ' \
% (pp_file_str, qtk.setting.espresso_pp) + \
'but found in espresso page, download now...')
new_pp_file = open(saved_pp_path, 'w')
new_pp_file.write(pp_content)
new_pp_file.close()
except:
qtk.warning('something wrong with pseudopotential')
def PPCheck(xc, element, pp_file_str, **kwargs):
ne = qtk.n2ve(element)
saved_pp_path = os.path.join(qtk.setting.espresso_pp, pp_file_str)
if not os.path.exists(saved_pp_path) and qtk.setting.download_pp:
qtk.status("PPCheck", pp_file_str)
url = os.path.join(qtk.setting.espresso_pp_url, pp_file_str)
try:
pp_content = urllib2.urlopen(url).read()
qtk.report('', 'pp file %s not found in %s. ' \
% (pp_file_str, qtk.setting.espresso_pp) + \
'but found in espresso page, download now...')
new_pp_file = open(saved_pp_path, 'w')
new_pp_file.write(pp_content)
new_pp_file.close()
except:
qtk.warning('something wrong with pseudopotential')
def PPString(inp, mol, i, n, outFile):
"""
append PP file names to inp.pp_files
"""
alchemy = re.compile('^\w*2\w*_\d\d\d$')
ppstr = re.sub('\*', '', mol.string[i])
dcacp_flag = False
if ppstr:
PPStr = '*' + ppstr
pp_root, pp_ext = os.path.split(ppstr)
if pp_ext != 'psp':
PPStr = PPStr + '.psp'
elif 'vdw' in inp.setting\
and inp.setting['vdw'].lower() == 'dcacp':
# PPStr: Element_qve_dcacp_theory.psp
PPStr = '*'+mol.type_list[i] + '_dcacp_' +\
inp.setting['pp_theory'].lower() + '.psp'
dcacp_flag = True
else:
# PPStr: Element_qve_theory.psp
element = mol.type_list[i]
if 'valence_electrons' in inp.setting\
and element in inp.setting['valence_electrons']:
nve = inp.setting['valence_electrons'][element]
else:
nve = qtk.n2ve(element)
PPStr = '*'+mol.type_list[i] + '_q%d_' % nve +\
inp.setting['pp_theory'].lower() + '.psp'
outFile.write(PPStr + '\n')
pp_file_str = re.sub('\*', '', PPStr)
xc = inp.setting['pp_theory'].lower()
if not mol.string[i]:
PPCheck(xc, mol.type_list[i].title(), pp_file_str,
dcacp=dcacp_flag, pp_type = inp.setting['pp_type'])
elif alchemy.match(mol.string[i]):
alchemyPP(xc, pp_file_str)
pp_file = os.path.join(qtk.setting.cpmd_pp, pp_file_str)
if inp.setting['pp_type'].title() == 'Goedecker':
lmax = 'F'
outFile.write(' LMAX=%s\n %3d\n' % (lmax, n))
inp.pp_files.append(re.sub('\*', '', PPStr))
def PPString(inp, mol, i, n, outFile):
"""
append PP file names to inp.pp_files
"""
alchemy = re.compile('^\w*2\w*_\d\d\d$')
ppstr = re.sub('\*', '', mol.string[i])
dcacp_flag = False
if ppstr:
PPStr = '*' + ppstr
pp_root, pp_ext = os.path.split(ppstr)
if pp_ext != 'psp':
PPStr = PPStr + '.psp'
elif 'vdw' in inp.setting\
and inp.setting['vdw'].lower() == 'dcacp':
# PPStr: Element_qve_dcacp_theory.psp
PPStr = '*'+mol.type_list[i] + '_dcacp_' +\
inp.setting['pp_theory'].lower() + '.psp'
dcacp_flag = True
else:
# PPStr: Element_qve_theory.psp
element = mol.type_list[i]
if 'valence_electrons' in inp.setting\
and element in inp.setting['valence_electrons']:
nve = inp.setting['valence_electrons'][element]
else:
nve = qtk.n2ve(element)
PPStr = '*'+mol.type_list[i] + '_q%d_' % nve +\
inp.setting['pp_theory'].lower() + '.psp'
outFile.write(PPStr + '\n')
pp_file_str = re.sub('\*', '', PPStr)
xc = inp.setting['pp_theory'].lower()
if not mol.string[i]:
PPCheck(xc, mol.type_list[i].title(), pp_file_str,
dcacp=dcacp_flag, pp_type = inp.setting['pp_type'])
elif alchemy.match(mol.string[i]):
alchemyPP(xc, pp_file_str)
pp_file = os.path.join(qtk.setting.cpmd_pp, pp_file_str)
if inp.setting['pp_type'].title() == 'Goedecker':
lmax = 'F'
outFile.write(' LMAX=%s\n %3d\n' % (lmax, n))
inp.pp_files.append(re.sub('\*', '', PPStr))
def ESP(self, coord=None, **kwargs):
"""
method for electron density
Note: CUBE file is assumed to be orthorohmbic
"""
data = self.data
grid = self.grid
if 'molecule' not in kwargs:
mol = self.molecule
else:
try:
mol = copy.deepcopy(qtk.toMolecule(kwargs['molecule']))
except:
qtk.exit("error when loading molecule:%s" % \
str(kwargs['molecule']))
N = mol.N
Q = self.integrate()
Z_sum = sum(mol.Z)
ne_diff = abs(Q - Z_sum)
ve_diff = abs(Q - mol.getValenceElectrons())
if min(ne_diff, ve_diff) > 1E-2:
qtk.warning("charge not conserved... ESP is wrong!")
qtk.warning("charge integrate to %.2f, " % Q + \
"while nuclear charge adds to %.2f" % Z_sum)
if ve_diff < ne_diff:
Z = [qtk.n2ve(qtk.Z2n(z)) for z in mol.Z]
Z = np.array(Z).reshape(N, 1)
else:
Z = mol.Z.reshape(N, 1)
structure = np.hstack([Z, mol.R * 1.889725989])
if coord is not None:
x, y, z = np.array(coord) * 1.889725989
V = ESP_c.esp_point(grid, structure, data, x, y, z)
return V
else:
qtk.warning("known issue: unidentifed memory leak")
out = copy.deepcopy(self)
out.molecule = mol
out.data = np.nan_to_num(
ESP_cube_c.esp_cube(grid, structure, data)
)
return out
def ESP(self, coord=None, **kwargs):
"""
method for electron density
Note: CUBE file is assumed to be orthorohmbic
"""
data = self.data
grid = self.grid
if 'molecule' not in kwargs:
mol = self.molecule
else:
try:
mol = copy.deepcopy(qtk.toMolecule(kwargs['molecule']))
except:
qtk.exit("error when loading molecule:%s" % \
str(kwargs['molecule']))
N = mol.N
Q = self.integrate()
Z_sum = sum(mol.Z)
ne_diff = abs(Q - Z_sum)
ve_diff = abs(Q - mol.getValenceElectrons())
if min(ne_diff, ve_diff) > 1E-2:
qtk.warning("charge not conserved... ESP is wrong!")
qtk.warning("charge integrate to %.2f, " % Q + \
"while nuclear charge adds to %.2f" % Z_sum)
if ve_diff < ne_diff:
Z = [qtk.n2ve(qtk.Z2n(z)) for z in mol.Z]
Z = np.array(Z).reshape(N, 1)
else:
Z = mol.Z.reshape(N, 1)
structure = np.hstack([Z, mol.R * 1.889725989])
if coord is not None:
x, y, z = np.array(coord) * 1.889725989
V = ESP_c.esp_point(grid, structure, data, x, y, z)
return V
else:
qtk.warning("known issue: unidentifed memory leak")
out = copy.deepcopy(self)
out.molecule = mol
out.data = np.nan_to_num(ESP_cube_c.esp_cube(
grid, structure, data))
return out
def PPCheck(xc, element, pp_file_str, **kwargs):
pp_file = None
pp_content = None
if xc == 'lda':
xc = 'pade'
elif xc == 'pbe0':
xc = 'pbe'
ne = qtk.n2ve(element)
try:
if 'dcacp' in kwargs and kwargs['dcacp']\
and element in qtk.setting.dcscp_list:
pp_path = os.path.join(xc.upper(), "%s_DCACP_%s" %\
(element, xc.upper()))
if element in qtk.setting.dcacp_dict:
pp_path = pp_path + "_%s" % qtk.setting.dcacp_dict[element]
#pp_file = os.path.join(qtk.setting.cpmd_dcacp_url, pp_path)
else:
pp_path = os.path.join(xc,
element + '-q' + str(qtk.n2ve(element)))
pp_file = os.path.join(qtk.setting.cpmd_pp_url, pp_path)
saved_pp_path = os.path.join(qtk.setting.cpmd_pp, pp_file_str)
if not os.path.exists(saved_pp_path) and qtk.setting.download_pp:
new_pp = os.path.join(qtk.setting.cpmd_pp, pp_file_str)
if 'dcacp' in kwargs and kwargs['dcacp']\
and element in qtk.setting.dcscp_list:
root_list = filter(None, qtk.setting.cpmd_dcacp_url.split('/'))
root = '//'.join(root_list[:2])
url = qtk.setting.cpmd_dcacp_url
html = ''.join(urllib2.urlopen(url).readlines())
pp_links = BeautifulSoup(html).body.findAll(
'a', attrs={'class': 'table'}
)
if kwargs['pp_type'].title() == 'Goedecker':
pp_flag = r'/SG/'
elif kwargs['pp_type'].upper() == 'MT':
pp_flag = r'/MT/'
pp_path = filter(lambda x: xc.upper() in x and pp_flag in x,
[l['href'] for l in pp_links if l.text == element.title()])
pp_content = urllib2.urlopen(root + pp_path[0]).readlines()
elif pp_file:
pp_content = urllib2.urlopen(pp_file).readlines()
pattern = re.compile(r'^.*</*pre>.*$')
pp_se = filter(pattern.match, pp_content)
pp_start = pp_content.index(pp_se[0])
pp_end = pp_content.index(pp_se[1])
pp_content = pp_content[pp_start:pp_end]
pp_content[0] = pp_content[0].split('>')[-1]
if pp_content:
for i in range(len(pp_content)):
pp_str = pp_content[i]
pp_content[i] = pp_str.replace('&', '&')
qtk.report('PPCheck', 'pp file %s not found in %s, ' \
% (pp_file_str, qtk.setting.cpmd_pp) + \
'download now...')
new_pp_file = open(new_pp, 'w')
new_pp_file.write(''.join(pp_content))
new_pp_file.close()
pp_file = new_pp
return saved_pp_path
except Exception as e:
qtk.warning('something wrong with pseudopotential with error: '+\
str(e))
def PPCheck(xc, element, pp_file_str, **kwargs):
pp_file = None
pp_content = None
if xc == 'lda':
xc = 'pade'
elif xc == 'pbe0':
xc = 'pbe'
ne = qtk.n2ve(element)
try:
if 'dcacp' in kwargs and kwargs['dcacp']\
and element in qtk.setting.dcscp_list:
pp_path = os.path.join(xc.upper(), "%s_DCACP_%s" %\
(element, xc.upper()))
if element in qtk.setting.dcacp_dict:
pp_path = pp_path + "_%s" % qtk.setting.dcacp_dict[element]
#pp_file = os.path.join(qtk.setting.cpmd_dcacp_url, pp_path)
else:
pp_path = os.path.join(xc,
element + '-q' + str(qtk.n2ve(element)))
pp_file = os.path.join(qtk.setting.cpmd_pp_url, pp_path)
saved_pp_path = os.path.join(qtk.setting.cpmd_pp, pp_file_str)
if not os.path.exists(saved_pp_path) and qtk.setting.download_pp:
new_pp = os.path.join(qtk.setting.cpmd_pp, pp_file_str)
if 'dcacp' in kwargs and kwargs['dcacp']\
and element in qtk.setting.dcscp_list:
root_list = filter(None, qtk.setting.cpmd_dcacp_url.split('/'))
root = '//'.join(root_list[:2])
url = qtk.setting.cpmd_dcacp_url
html = ''.join(urllib2.urlopen(url).readlines())
pp_links = BeautifulSoup(html).body.findAll(
'a', attrs={'class': 'table'}
)
if kwargs['pp_type'].title() == 'Goedecker':
pp_flag = r'/SG/'
elif kwargs['pp_type'].upper() == 'MT':
pp_flag = r'/MT/'
pp_path = filter(lambda x: xc.upper() in x and pp_flag in x,
[l['href'] for l in pp_links if l.text == element.title()])
pp_content = urllib2.urlopen(root + pp_path[0]).readlines()
elif pp_file:
pp_content = urllib2.urlopen(pp_file).readlines()
pattern = re.compile(r'^.*</*pre>.*$')
pp_se = filter(pattern.match, pp_content)
pp_start = pp_content.index(pp_se[0])
pp_end = pp_content.index(pp_se[1])
pp_content = pp_content[pp_start:pp_end]
pp_content[0] = pp_content[0].split('>')[-1]
if pp_content:
for i in range(len(pp_content)):
pp_str = pp_content[i]
pp_content[i] = pp_str.replace('&', '&')
qtk.report('PPCheck', 'pp file %s not found in %s, ' \
% (pp_file_str, qtk.setting.cpmd_pp) + \
'download now...')
new_pp_file = open(new_pp, 'w')
new_pp_file.write(''.join(pp_content))
new_pp_file.close()
pp_file = new_pp
return saved_pp_path
except Exception as e:
qtk.warning('something wrong with pseudopotential with error: '+\
str(e))
def writeInp(name=None, **setting):
self.setting.update(setting)
self.setting['no_molecule'] = False
inp, molecule = \
super(PlanewaveInput, self).write(name, **self.setting)
molecule.sort()
type_index = molecule.index
type_list = molecule.type_list
self.pp_path = qtk.setting.bigdft_pp
if 'pp_path' in self.setting:
self.pp_path = self.setting['pp_path']
if 'pp_theory' not in self.setting:
self.setting['pp_theory'] = self.setting['theory']
pp_files = []
typat = []
for a in range(len(type_index) - 1):
start = type_index[a]
end = type_index[a + 1]
for i in range(end - start):
typat.append(a + 1)
for i in range(molecule.N):
pp_file = 'psppar.' + molecule.type_list[i]
pp_list = set([pp[1] for pp in pp_files])
if pp_file not in pp_list:
pp_src = PPCheck(self.setting['theory'],
self.setting['pp_theory'], self.pp_path,
molecule.type_list[i])
pp_files.append([pp_src, pp_file])
##################
# scf section #
##################
self.content['scf'] = odict()
# restart check #
if 'restart' in self.setting and self.setting['restart']\
and 'band_scan' not in self.setting\
and 'dos_mesh' not in self.setting:
self.content['scf']['irdwfk'] = 1
self.content['scf']['getwfk'] = -1
if 'restart_density' in self.setting \
and self.setting['restart_density']\
and 'band_scan' not in self.setting\
and 'dos_mesh' not in self.setting:
self.content['scf']['irdden'] = 1
self.content['scf']['getden'] = -1
if 'kmesh' not in self.setting:
self.setting['kmesh'] = [1, 1, 1]
if 'kshift' not in self.setting:
self.setting['kshift'] = [0.0, 0.0, 0.0]
# kpoints check #
if 'kpoints' in self.setting:
self.content['scf']['kptopt'] = 0
self.content['scf']['nkpt'] = len(self.setting['kpoints'])
self.content['scf']['kpt'] = self.setting['kpoints']
else:
if self.setting['full_kmesh']:
self.content['scf']['kptopt'] = 3
self.content['scf']['ngkpt'] = self.setting['kmesh']
if len(np.array(self.setting['kshift']).shape) > 1:
self.content['scf']['nshiftk'] = len(
self.setting['kshift'])
self.content['scf']['shiftk'] = self.setting['kshift']
nbnd = None
if 'ks_states' in self.setting and self.setting['ks_states']:
vs = int(round(molecule.getValenceElectrons() / 2.0))
nbnd = self.setting['ks_states'] + vs
if 'd_shell' in self.setting:
for a in molecule.type_list:
if a in self.setting['d_shell'] and qtk.n2ve(a) < 10:
nbnd += 5
if 'band_scan' not in self.setting \
and 'dos_mesh' not in self.setting:
self.content['scf']['nband'] = nbnd
# system setup #
if molecule.charge != 0:
self.content['scf']['charge='] = molecule.charge
if molecule.multiplicity != 1:
self.content['scf']['nsppol'] = 2
self.content['scf']['occopt'] = 7
if 'save_restart' not in self.setting \
or not self.setting['save_restart']:
if 'restart' in self.setting and self.setting['restart']\
and ('band_scan' not in self.setting\
and 'dos_mesh' not in self.setting):
self.content['scf']['prtwf'] = 0
#if 'wf_convergence' in self.setting:
if 'band_scan' in self.setting\
or 'dos_mesh' in self.setting:
if 'restart' not in self.setting\
or not self.setting['restart']:
self.content['scf']['tolwfr'] = \
self.setting['wf_convergence']
else:
self.content['scf']['tolwfr'] = \
self.setting['wf_convergence']
# clean up for the case of restart
if 'restart' in self.setting and self.setting['restart']\
and ('band_scan' in self.setting or 'dos_mesh' in self.setting):
keep_lst = [
'nband',
'tolwfr',
'nstep',
'ecut',
'irdwfk',
'irdden',
'getwfk',
'getden',
]
for key in self.content['scf'].iterkeys():
if key not in keep_lst and 'prt' not in key:
self.content['scf'].pop(key)
######################
# additional setting #
######################
if 'abinit_setting' in self.setting:
self.content['additional'] = odict([])
for item in self.setting['abinit_setting']:
self.content['additional'][item] = ' '
def is_strnum(q):
if isinstance(q, Number) or type(q) is str:
return True
else:
return False
#################
# bandstructure #
#################
if 'band_scan' in self.setting and self.setting['band_scan']:
if molecule.symmetry and molecule.symmetry.lower() == 'fcc':
if 'kshift' not in self.setting:
self.setting['kshift'] = [
[0.5, 0.5, 0.5],
[0.5, 0.0, 0.0],
[0.0, 0.5, 0.0],
[0.0, 0.0, 0.5],
]
bnds = self.setting['band_scan']
if len(bnds) != 2 \
or is_strnum(bnds[0]) \
or len(bnds[0]) != len(bnds[1]) - 1:
qtk.exit('band_scan format: [lst_div, lst_coord]')
bnd_content = odict([
('iscf', -2),
('getden', -1),
('kptopt', -len(bnds[0])),
('tolwfr', self.setting['wf_convergence']),
('ndivk', bnds[0]),
('kptbounds', bnds[1]),
])
if nbnd:
bnd_content['nband'] = nbnd
if 'save_restart' not in self.setting \
or not self.setting['save_restart']:
bnd_content['prtwf'] = 0
else:
bnd_content['prtwf'] = 1
if 'save_density' not in self.setting \
or not self.setting['save_density']:
bnd_content['prtden'] = 0
else:
bnd_content['prtden'] = 1
if 'dos_mesh' in self.setting:
bnd_content['prtden'] = 1
if 'restart' in self.setting and self.setting['restart']:
bnd_content['irdden'] = 1
bnd_content['irdwfk'] = 1
bnd_content['getwfk'] = -1
self.content['band_scan'] = bnd_content
#####################
# density of states #
#####################
if 'dos_mesh' in self.setting and self.setting['dos_mesh']:
dos_content = odict([
('iscf', -3),
('ngkpt', self.setting['dos_mesh']),
('shiftk', [0.0, 0.0, 0.0]),
('tolwfr', self.setting['wf_convergence']),
('prtwf', 0),
])
if 'band_scan' in self.setting:
dos_content['getden'] = -2
else:
dos_content['getden'] = -1
if 'smearing' in self.setting:
smr = self.setting['smearing']
smr_dict = {
'fermi': 3,
'marzari': 4,
'marzari_monotonic': 5,
'paxton': 6,
'gaussian': 7,
}
if smr in smr_dict:
dos_content['occopt'] = smr_dict[smr]
dos_content['prtdos'] = 1
else:
qtk.warning("%s for occupation scheme not found" % smr)
if nbnd:
dos_content['nband'] = nbnd
if 'save_restart' not in self.setting \
or not self.setting['save_restart']:
dos_content['prtwf'] = 0
else:
dos_content['prtwf'] = 1
if 'save_density' not in self.setting \
or not self.setting['save_density']:
dos_content['prtden'] = 0
else:
dos_content['prtden'] = 1
if 'restart' in self.setting and self.setting['restart']:
dos_content['irdden'] = 1
dos_content['irdwfk'] = 1
dos_content['getwfk'] = -1
self.content['dos'] = dos_content
################
# cell section #
################
self.content['cell'] = odict([
('ecut', float(self.setting['cutoff'] / 2.)),
('nstep', self.setting['scf_step']),
])
self.content['cell']['acell'] = '3*1.889726124993'
self.celldm2lattice()
if not molecule.symmetry:
self.content['cell']['chkprim'] = 0
self.content['cell']['rprim'] = self.setting['lattice']
#################
# atoms section #
#################
znucl = []
for a in range(len(type_index) - 1):
symb = type_list[type_index[a]]
znucl.append(int(qtk.n2Z(symb)))
self.content['atoms'] = odict([
('natom', molecule.N),
('ntypat', (len(type_index) - 1)),
('typat', typat),
('znucl', znucl),
])
if hasattr(molecule, 'scale') and molecule.scale:
if hasattr(molecule, 'R_scale'):
R_scale = molecule.R_scale.copy()
for i in range(3):
s = molecule.scale[i]
if s > 0: R_scale[:, i] = R_scale[:, i] / s
self.content['atoms']['xred'] = R_scale
else:
qtk.warning('R_scale not found but scale is set')
self.content['atoms']['xangst'] = molecule.R
else:
self.content['atoms']['xangst'] = molecule.R
#########################
# write content to file #
#########################
datasets = 1
for key in ['band_scan', 'dos']:
if key in self.content:
datasets += 1
if self.setting['restart'] and datasets > 1:
datasets -= 1
self.content['datasets']['ndtset'] = datasets
inp.write('# abinit input generated by qctoolkit\n')
ds_itr = 0
ds_str = ''
if self.content['datasets']['ndtset'] == 1:
self.content['datasets'].pop('ndtset')
for section_key in self.content.iterkeys():
if len(self.content[section_key]) > 0:
inp.write('\n# %s section\n' % section_key)
if section_key in ['scf', 'band_scan', 'dos'] and datasets > 1:
ds_itr += 1
ds_str = str(ds_itr)
for key, value in self.content[section_key].iteritems():
if ds_str and section_key in ['scf', 'band_scan', 'dos']:
key = key + ds_str
if is_strnum(value):
inp.write('%s %s\n' % (key, str(value)))
else:
inp.write('%s' % key)
head = ''.join([' ' for _ in key])
if 'xangst' in key\
or 'xcart' in key\
or 'xred' in key:
inp.write('\n\n')
for vec in value:
inp.write('%s' % head)
for v in vec:
inp.write(' %s' % str(v))
inp.write('\n')
elif is_strnum(value[0]):
for v in value:
inp.write(' %s' % str(v))
inp.write('\n')
else:
for v in value[0]:
inp.write(' %s' % str(v))
inp.write('\n')
for vec in value[1:]:
inp.write('%s' % head)
for v in vec:
inp.write(' %s' % str(v))
inp.write('\n')
if 'restart_wavefunction_path' in self.setting:
rstwf_path = self.setting['restart_wavefunction_path']
if os.path.exists(rstwf_path):
wf_lst = sorted(
glob.glob(os.path.join(rstwf_path, '*o_*WFK')))
assert len(wf_lst) > 0
wf_src = os.path.abspath(wf_lst[-1])
pp_files.append([wf_src, name + 'i_WFK'])
else:
qtk.warning('%s not found' % rstwf_path)
if 'restart_wavefunction_file' in self.setting:
rst_file = self.setting['restart_wavefunction_file']
if os.path.exists(rst_file):
pp_files.append([rst_file, name + 'i_WFK'])
else:
qtk.warning('%s not found' % rst_file)
if 'restart_density_path' in self.setting:
rstdn_path = self.setting['restart_density_path']
if os.path.exists(rstdn_path):
dn_lst = sorted(
glob.glob(os.path.join(rstdn_path, '*o_*DEN')))
assert len(dn_lst) > 0
dn_src = os.path.abspath(dn_lst[-1])
pp_files.append([dn_src, name + 'i_DEN'])
else:
qtk.warning('%s not found' % rstdn_path)
if 'restart_density_file' in self.setting:
rst_file = self.setting['restart_density_file']
if os.path.exists(rst_file):
pp_files.append([rst_file, name + 'i_DEN'])
else:
qtk.warning('%s not found' % rst_file)
inp.close(dependent_files=pp_files)
if hasattr(inp, 'final_name'):
self.setting['no_molecule'] = True
self.setting['root_dir'] = name
files = \
super(PlanewaveInput, self).write(name, **self.setting)
files.extension = 'files'
files.write(inp.final_name + '\n')
root = os.path.splitext(inp.final_name)[0]
files.write(root + '.out\n')
files.write(root + 'i\n')
files.write(root + 'o\n')
files.write(root + 'x\n')
for pp in pp_files:
files.write(pp[1] + '\n')
files.close(no_cleanup=True)
return inp
def writeInp(name=None, **setting):
inp, molecule = \
PlanewaveInput.write(self, name, **setting)
molecule.sort()
type_index = molecule.index
type_list = molecule.type_list
pp_files = []
self.content['system']['nat'] = molecule.N
self.content['system']['ntyp'] = len(type_index) - 1
if setting['full_kmesh']:
self.content['system']['nosym'] = True
self.content['system']['noinv'] = True
if 'restart' in setting and setting['restart']:
self.content['control']['restart_mode'] = 'restart'
if 'save_density' in setting and setting['save_density']:
self.content['control']['wf_collect'] = True
if 'save_wf' in setting and setting['save_wf']:
self.content['control']['wf_collect'] = True
if 'print_force' not in setting or not setting['print_force']:
self.content['control']['tprnfor'] = True
if not setting['periodic']:
self.content['system']['assume_isolated'] = 'mt'
if 'exx' in setting and setting['exx'] == 'anisotropic':
self.content['system']['exxdiv_treatment'] = 'vcut_ws'
self.content['system']['ecutvcut'] = 0.7
self.content['system']['x_gamma_extrapolation'] = False
if molecule.charge != 0:
self.content['system']['tot_charge'] = molecule.charge
if molecule.multiplicity != 1:
self.content['system']['nspin'] = 2
diff = molecule.multiplicity - 1
self.content['system']['tot_magnetization'] = diff
if 'theory' in setting:
if self.setting['theory'] in dft_dict:
self.content['system']['input_dft'] = \
dft_dict[self.setting['theory']]
else:
self.content['system']['input_dft'] = self.setting['theory']
if 'scf_step' in setting:
self.content['electrons']['electron_maxstep'] =\
setting['scf_step']
if 'ks_states' in setting and setting['ks_states']:
vs = int(round(self.molecule.getValenceElectrons() / 2.0))
self.content['system']['nbnd'] = setting['ks_states'] + vs
if 'd_shell' in setting:
for a in molecule.type_list:
if a in setting['d_shell'] and qtk.n2ve(a) < 10:
self.content['system']['nbnd'] += 5
if 'symmetry' in setting:
if setting['symmetry'] == 'fcc':
self.content['system']['ibrav'] = 2
setting['fractional_coordinate'] = True
dm = ['A', 'B', 'C', 'cosBC', 'cosAC', 'cosAB']
for i in range(6):
self.content['system'][dm[i]] = float(self
.molecule.celldm[i])
for section_key in self.content.iterkeys():
section = '&' + section_key + '\n'
inp.write(section)
for key, value in self.content[section_key].iteritems():
if type(value) is str:
entry = " %s = '%s',\n" % (key, value)
elif type(value) is int:
entry = ' %s = %d,\n' % (key, value)
elif type(value) is float:
entry = ' %s = %14.8E,\n' % (key, value)
elif type(value) is bool:
if value:
entry = ' %s = .true.,\n' % key
else:
entry = ' %s = .false.,\n' % key
inp.write(entry)
inp.write('/\n')
inp.write("ATOMIC_SPECIES\n")
for a in range(len(type_index)-1):
type_n = type_index[a+1] - type_index[a]
PPStr = PPString(self, molecule,
type_index[a], type_n, inp)
stem, ext = os.path.splitext(PPStr)
if ext != '.UPF':
PPStr = PPStr + '.UPF'
mass = qtk.n2m(type_list[type_index[a]])
inp.write(' %-3s % 6.3f %s\n' % \
(type_list[type_index[a]], mass, PPStr))
pp_files.append(PPStr)
inp.write("\n")
inp.write("ATOMIC_POSITIONS ")
if self.content['system']['ibrav'] == 0:
if not setting['fractional_coordinate']:
inp.write("angstrom\n")
R = molecule.R
else:
inp.write("crystal\n")
R = molecule.R_scale
else:
inp.write("\n")
R = molecule.R_scale
for a in range(len(type_list)):
inp.write(' %-3s' % type_list[a])
for i in range(3):
inp.write(' % 12.8f' % R[a, i])
inp.write("\n")
inp.write("\n")
if 'kmesh' in setting and setting['kmesh']:
inp.write("K_POINTS automatic\n")
for k in setting['kmesh']:
inp.write(" %d" % k)
for s in range(3):
inp.write(" 0")
inp.write('\n\n')
if 'save_restart' in setting and setting['save_restart']:
inp.write("ALCHEMY reference\n\n")
if 'restart' in setting and setting['restart']:
if 'scf_step' in setting and setting['scf_step'] == 1:
inp.write("ALCHEMY prediction\n\n")
if self.content['system']['ibrav'] == 0:
inp.write("CELL_PARAMETERS angstrom\n")
if 'lattice' not in self.setting:
self.celldm2lattice()
lattice_vec = self.setting['lattice']
for vec in lattice_vec:
for component in vec:
inp.write(' % 11.6f' % component)
inp.write('\n')
for pp in pp_files:
pp_file = os.path.join(qtk.setting.espresso_pp, pp)
if pp not in inp.dependent_files:
inp.dependent_files.append(pp_file)
if 'no_cleanup' in setting and setting['no_cleanup']:
inp.close(no_cleanup=True)
else:
inp.close()
return inp
def write(self, name=None, **kwargs):
self.setting.update(kwargs)
self.setting['no_molecule'] = False
inp, molecule = \
super(PlanewaveInput, self).write(name, **self.setting)
molecule.sort()
type_index = molecule.index
type_list = molecule.type_list
self.pp_path = qtk.setting.bigdft_pp
if 'pp_path' in self.setting:
self.pp_path = self.setting['pp_path']
if 'pp_theory' not in self.setting:
self.setting['pp_theory'] = self.setting['theory']
pp_files = []
inp.write('# abinit input generated by qctoolkit\n')
# restart section
if 'restart' in self.setting and self.setting['restart']:
inp.write('\n# restart, reading wavefunction from file\n')
inp.write('irdwfk 1\n')
inp.write('getwfk -1\n')
# cell definition
inp.write('\n# cell definition\n')
# cell specified by Bohr
if not molecule.symmetry:
inp.write('# NOTE: cell defined by lattice vector, ')
inp.write('NOT supported by abinit spacegroup detector!\n')
inp.write('acell 3*1.889726124993\n')
if 'lattice' not in self.setting:
self.celldm2lattice()
lattice_vec = self.setting['lattice']
inp.write('chkprim 0\n')
elif molecule.symmetry.lower() == 'fcc':
inp.write("# fcc primitive cell\n")
a0 = molecule.celldm[0] * 1.889726124993
inp.write('acell 1 1 1\n')
lattice_vec = 0.5 * a0 * np.array([
[0, 1, 1],
[1, 0, 1],
[1, 1, 0],
])
elif molecule.symmetry.lower() == 'bcc':
inp.write("# bcc primitive cell\n")
inp.write('acell 1 1 1\n')
a0 = molecule.celldm[0] * 1.889726124993
lattice_vec = 0.5 * a0 * np.array([
[-1, 1, 1],
[ 1,-1, 1],
[ 1, 1,-1],
])
strList = ['rprim', '', '']
for i in range(3):
vec = lattice_vec[i]
inp.write('%5s % 11.6f % 11.6f % 11.6f\n' % (
strList[i], vec[0], vec[1], vec[2],
))
# atom definition
inp.write("\n# atom definition\n")
inp.write('ntypat %d\n' % (len(type_index) - 1))
inp.write('znucl')
for a in range(len(type_index)-1):
symb = type_list[type_index[a]]
Z = qtk.n2Z(symb)
inp.write(' %d' % Z)
inp.write('\n')
# atom position
inp.write("\n# atom position\n")
inp.write("natom %d\n" % molecule.N)
inp.write('typat')
for a in range(len(type_index)-1):
start = type_index[a]
end = type_index[a+1]
for i in range(end - start):
inp.write(' %d' % (a+1))
inp.write('\nxangst\n\n')
for i in range(molecule.N):
inp.write(' ')
for j in range(3):
inp.write(' % 11.6f' % molecule.R[i][j])
inp.write('\n')
# construct pp files depandency
pp_file = 'psppar.' + molecule.type_list[i]
pp_list = set([pp[1] for pp in pp_files])
if pp_file not in pp_list:
pp_src = PPCheck(self.setting['theory'],
self.setting['pp_theory'],
self.pp_path,
molecule.type_list[i])
pp_files.append([pp_src, pp_file])
inp.write('\n')
# system setting
inp.write("\n# system settings\n")
# cutoff in Hartree
inp.write('ecut %.2f\n' % float(self.setting['cutoff']/2.))
if 'kmesh' not in self.setting:
self.setting['kmesh'] = [1,1,1]
if self.setting['full_kmesh']:
inp.write('kptopt 3\n')
inp.write('ngkpt')
for k in self.setting['kmesh']:
inp.write(' %d' % k)
if 'kshift' not in self.setting:
inp.write('\nshiftk 0.0 0.0 0.0')
if 'ks_states' in self.setting and self.setting['ks_states']:
vs = int(round(molecule.getValenceElectrons() / 2.0))
nbnd = self.setting['ks_states'] + vs
if 'd_shell' in self.setting:
for a in molecule.type_list:
if a in self.setting['d_shell'] and qtk.n2ve(a) < 10:
nbnd += 5
inp.write('\nnband %d' % nbnd)
inp.write('\nnstep %d\n' % self.setting['scf_step'])
if 'wf_convergence' in self.setting:
inp.write('toldfe %.2E\n' % self.setting['wf_convergence'])
if molecule.charge != 0:
inp.write('charge=%d\n' % molecule.charge)
if molecule.multiplicity != 1:
inp.write('nsppol 2 # for spin polarized\n')
inp.write('occopt 7 # for relaxed occupation\n')
if 'save_restart' in self.setting and self.setting['save_restart']:
pass
else:
inp.write('prtwf 0\n')
for item in self.content:
inp.write(item)
inp.close(dependent_files=pp_files)
if hasattr(inp, 'final_name'):
self.setting['no_molecule'] = True
self.setting['root_dir'] = name
files = \
super(PlanewaveInput, self).write(name, **self.setting)
files.extension = 'files'
files.write(inp.final_name + '\n')
root = os.path.splitext(inp.final_name)[0]
files.write(root + '.out\n')
files.write(root + 'i\n')
files.write(root + 'o\n')
files.write(root + 'x\n')
for pp in pp_files:
files.write(pp[1] + '\n')
files.close(no_cleanup = True)
return inp
def PPString(inp, mol, i, n, outFile):
"""
append PP file names to inp.pp_files
"""
alchemy = re.compile('^\w*2\w*_\d\d\d$')
ppstr = re.sub('\*', '', mol.string[i])
if ppstr:
PPStr = ppstr
pp_root, pp_ext = os.path.split(ppstr)
else:
if inp.setting['pp_type'] == 'geodecker':
element = mol.type_list[i].title()
if 'd_shell' in inp.setting:
if type(inp.setting['d_shell']) is not list:
inp.setting['d_shell'] = [inp.setting['d_shell']]
if qtk.n2ve(mol.type_list[i].title()) > 10:
shell = '-d'
elif 'd_shell' in inp.setting \
and element in inp.setting['d_shell']:
shell = '-d'
else:
element = qtk.element[mol.type_list[i].title()]
if element.group < 3 and mol.Z[i] > 1:
if mol.Z[i] != 3:
shell = '-sp'
else:
shell = '-s'
else:
shell = ''
pp_xc_dict = {
'lda': 'pz',
'pbe0': 'pbe',
'b3lyp': 'blyp',
}
pp_xc = inp.setting['pp_theory'].lower()
if pp_xc in pp_xc_dict:
pp_xc = pp_xc_dict[pp_xc]
PPStr = ''.join([c for c in mol.type_list[i] if not c.isdigit()])\
+ '.' + pp_xc + shell + '-hgh.UPF'
elif inp.setting['pp_type'] == 'cpmd':
PPStr = PPName(inp, mol, i, n)
xc = inp.setting['pp_theory'].lower()
if not mol.string[i]:
if inp.setting['pp_type'] == 'geodecker':
PPCheck(pp_xc, mol.type_list[i].title(), PPStr)
elif inp.setting['pp_type'] == 'cpmd':
saved_pp = PPCheck_cpmd(pp_xc, mol.type_list[i].title(), PPStr)
new_pp1 = saved_pp + '.UPF'
conv_pp = sp.Popen("%s %s" % \
(qtk.setting.espresso_cpmd2upf_exe, saved_pp),
shell=True)
conv_pp.wait()
new_pp1_file = os.path.split(new_pp1)[1]
new_pp1_trg = os.path.join(qtk.setting.espresso_pp, new_pp1_file)
if not os.path.exists(new_pp1_trg):
shutil.copy(new_pp1, qtk.setting.espresso_pp)
PPStr = PPStr + '.UPF'
elif alchemy.match(mol.string[i]):
cpmd_pp = alchemyPP(xc, PPStr)
new_pp1 = cpmd_pp + '.UPF'
if not os.path.exists(new_pp1):
qtk.report('espresso', "rewrite Goedecker's PP to UPF")
conv_pp = sp.Popen("%s %s" % \
(qtk.setting.espresso_cpmd2upf_exe, cpmd_pp),
shell=True)
conv_pp.wait()
if conv_pp.returncode != 0:
# dirty fix for espresso alchemy conversion routine
qtk.warning('conversion failed..., trying path end points')
root, _ = os.path.splitext(PPStr)
element_str = re.sub('_.*', '', root)
element1 = re.sub('2.*', '', element_str)
element2 = re.sub('.*2', '', element_str)
fraction = float(re.sub('.*_', '', root))/100
if fraction == 0.0:
strpp = element1 + "_q" + str(qtk.n2ve(element1)) +\
"_" + xc + '.psp'
elif fraction == 1.0:
strpp = element2 + "_q" + str(qtk.n2ve(element2)) +\
"_" + xc + '.psp'
else:
qtk.exit("PP conversion failed for intermediate lambda")
strpp = os.path.join(qtk.setting.cpmd_pp, strpp)
conv_pp = sp.Popen("%s %s" % \
(qtk.setting.espresso_cpmd2upf_exe, strpp),
shell=True)
conv_pp.wait()
os.rename(strpp + '.UPF', new_pp1)
new_pp1_file = os.path.split(new_pp1)[1]
new_pp1_trg = os.path.join(qtk.setting.espresso_pp, new_pp1_file)
if not os.path.exists(new_pp1_trg):
shutil.copy(new_pp1, qtk.setting.espresso_pp)
PPStr = PPStr + '.UPF'
return PPStr
def writeInp(name=None, **setting):
inp, molecule = \
PlanewaveInput.write(self, name, **setting)
molecule.sort()
type_index = molecule.index
type_list = molecule.type_list
pp_files = []
self.content['system']['nat'] = molecule.N
self.content['system']['ntyp'] = len(type_index) - 1
if setting['full_kmesh']:
self.content['system']['nosym'] = True
self.content['system']['noinv'] = True
if 'restart' in setting and setting['restart']:
self.content['control']['restart_mode'] = 'restart'
if 'save_density' in setting and setting['save_density']:
self.content['control']['wf_collect'] = True
if 'save_wf' in setting and setting['save_wf']:
self.content['control']['wf_collect'] = True
if 'print_force' not in setting or not setting['print_force']:
self.content['control']['tprnfor'] = True
if not setting['periodic']:
self.content['system']['assume_isolated'] = 'mt'
if 'exx' in setting and setting['exx'] == 'anisotropic':
self.content['system']['exxdiv_treatment'] = 'vcut_ws'
self.content['system']['ecutvcut'] = 0.7
self.content['system']['x_gamma_extrapolation'] = False
if molecule.charge != 0:
self.content['system']['tot_charge'] = molecule.charge
if molecule.multiplicity != 1:
self.content['system']['nspin'] = 2
diff = molecule.multiplicity - 1
self.content['system']['tot_magnetization'] = diff
if 'theory' in setting:
if self.setting['theory'] in dft_dict:
self.content['system']['input_dft'] = \
dft_dict[self.setting['theory']]
else:
self.content['system']['input_dft'] = self.setting[
'theory']
if 'scf_step' in setting:
self.content['electrons']['electron_maxstep'] =\
setting['scf_step']
if 'ks_states' in setting and setting['ks_states']:
vs = int(round(self.molecule.getValenceElectrons() / 2.0))
self.content['system']['nbnd'] = setting['ks_states'] + vs
if 'd_shell' in setting:
for a in molecule.type_list:
if a in setting['d_shell'] and qtk.n2ve(a) < 10:
self.content['system']['nbnd'] += 5
if 'symmetry' in setting:
if setting['symmetry'] == 'fcc':
self.content['system']['ibrav'] = 2
setting['fractional_coordinate'] = True
dm = ['A', 'B', 'C', 'cosBC', 'cosAC', 'cosAB']
for i in range(6):
self.content['system'][dm[i]] = float(
self.molecule.celldm[i])
for section_key in self.content.iterkeys():
section = '&' + section_key + '\n'
inp.write(section)
for key, value in self.content[section_key].iteritems():
if type(value) is str:
entry = " %s = '%s',\n" % (key, value)
elif type(value) is int:
entry = ' %s = %d,\n' % (key, value)
elif type(value) is float:
entry = ' %s = %14.8E,\n' % (key, value)
elif type(value) is bool:
if value:
entry = ' %s = .true.,\n' % key
else:
entry = ' %s = .false.,\n' % key
inp.write(entry)
inp.write('/\n')
inp.write("ATOMIC_SPECIES\n")
for a in range(len(type_index) - 1):
type_n = type_index[a + 1] - type_index[a]
PPStr = PPString(self, molecule, type_index[a], type_n, inp)
stem, ext = os.path.splitext(PPStr)
if ext != '.UPF':
PPStr = PPStr + '.UPF'
mass = qtk.n2m(type_list[type_index[a]])
inp.write(' %-3s % 6.3f %s\n' % \
(type_list[type_index[a]], mass, PPStr))
pp_files.append(PPStr)
inp.write("\n")
inp.write("ATOMIC_POSITIONS ")
if self.content['system']['ibrav'] == 0:
if not setting['fractional_coordinate']:
inp.write("angstrom\n")
R = molecule.R
else:
inp.write("crystal\n")
R = molecule.R_scale
else:
inp.write("\n")
R = molecule.R_scale
for a in range(len(type_list)):
inp.write(' %-3s' % type_list[a])
for i in range(3):
inp.write(' % 12.8f' % R[a, i])
inp.write("\n")
inp.write("\n")
if 'kmesh' in setting and setting['kmesh']:
inp.write("K_POINTS automatic\n")
for k in setting['kmesh']:
inp.write(" %d" % k)
for s in range(3):
inp.write(" 0")
inp.write('\n\n')
if 'save_restart' in setting and setting['save_restart']:
inp.write("ALCHEMY reference\n\n")
if 'restart' in setting and setting['restart']:
if 'scf_step' in setting:
if setting['scf_step'] != 1:
qtk.warning('alchemy with optimization...')
inp.write("ALCHEMY prediction\n\n")
if self.content['system']['ibrav'] == 0:
inp.write("CELL_PARAMETERS angstrom\n")
if 'lattice' not in self.setting:
self.celldm2lattice()
lattice_vec = self.setting['lattice']
for vec in lattice_vec:
for component in vec:
inp.write(' % 11.6f' % component)
inp.write('\n')
for pp in pp_files:
pp_file = os.path.join(qtk.setting.espresso_pp, pp)
if pp not in inp.dependent_files:
inp.dependent_files.append(pp_file)
if 'no_cleanup' in setting and setting['no_cleanup']:
inp.close(no_cleanup=True)
else:
inp.close()
return inp
def PPString(inp, mol, i, n, outFile):
"""
append PP file names to inp.pp_files
"""
alchemy = re.compile('^\w*2\w*_\d\d\d$')
ppstr = re.sub('\*', '', mol.string[i])
if ppstr:
PPStr = ppstr
pp_root, pp_ext = os.path.split(ppstr)
else:
if inp.setting['pp_type'] == 'geodecker':
element = mol.type_list[i].title()
if 'd_shell' in inp.setting:
if type(inp.setting['d_shell']) is not list:
inp.setting['d_shell'] = [inp.setting['d_shell']]
if qtk.n2ve(mol.type_list[i].title()) > 10:
shell = '-d'
elif 'd_shell' in inp.setting \
and element in inp.setting['d_shell']:
shell = '-d'
else:
element = qtk.element[mol.type_list[i].title()]
if element.group < 3 and mol.Z[i] > 1:
if mol.Z[i] != 3:
shell = '-sp'
else:
shell = '-s'
else:
shell = ''
pp_xc_dict = {
'lda': 'pz',
'pbe0': 'pbe',
'b3lyp': 'blyp',
}
pp_xc = inp.setting['pp_theory'].lower()
if pp_xc in pp_xc_dict:
pp_xc = pp_xc_dict[pp_xc]
PPStr = ''.join([c for c in mol.type_list[i] if not c.isdigit()])\
+ '.' + pp_xc + shell + '-hgh.UPF'
elif inp.setting['pp_type'] == 'cpmd':
PPStr = PPName(inp, mol, i, n)
xc = inp.setting['pp_theory'].lower()
if not mol.string[i]:
if inp.setting['pp_type'] == 'geodecker':
PPCheck(pp_xc, mol.type_list[i].title(), PPStr)
elif inp.setting['pp_type'] == 'cpmd':
saved_pp = PPCheck_cpmd(pp_xc, mol.type_list[i].title(), PPStr)
new_pp1 = saved_pp + '.UPF'
conv_pp = sp.Popen("%s %s" % \
(qtk.setting.espresso_cpmd2upf_exe, saved_pp),
shell=True)
conv_pp.wait()
new_pp1_file = os.path.split(new_pp1)[1]
new_pp1_trg = os.path.join(qtk.setting.espresso_pp, new_pp1_file)
if not os.path.exists(new_pp1_trg):
shutil.copy(new_pp1, qtk.setting.espresso_pp)
PPStr = PPStr + '.UPF'
elif alchemy.match(mol.string[i]):
cpmd_pp = alchemyPP(xc, PPStr)
new_pp1 = cpmd_pp + '.UPF'
if not os.path.exists(new_pp1):
qtk.report('espresso', "rewrite Goedecker's PP to UPF")
conv_pp = sp.Popen("%s %s" % \
(qtk.setting.espresso_cpmd2upf_exe, cpmd_pp),
shell=True)
conv_pp.wait()
if conv_pp.returncode != 0:
# dirty fix for espresso alchemy conversion routine
qtk.warning('conversion failed..., trying path end points')
root, _ = os.path.splitext(PPStr)
element_str = re.sub('_.*', '', root)
element1 = re.sub('2.*', '', element_str)
element2 = re.sub('.*2', '', element_str)
fraction = float(re.sub('.*_', '', root)) / 100
if fraction == 0.0:
strpp = element1 + "_q" + str(qtk.n2ve(element1)) +\
"_" + xc + '.psp'
elif fraction == 1.0:
strpp = element2 + "_q" + str(qtk.n2ve(element2)) +\
"_" + xc + '.psp'
else:
qtk.exit("PP conversion failed for intermediate lambda")
strpp = os.path.join(qtk.setting.cpmd_pp, strpp)
conv_pp = sp.Popen("%s %s" % \
(qtk.setting.espresso_cpmd2upf_exe, strpp),
shell=True)
conv_pp.wait()
os.rename(strpp + '.UPF', new_pp1)
new_pp1_file = os.path.split(new_pp1)[1]
new_pp1_trg = os.path.join(qtk.setting.espresso_pp, new_pp1_file)
if not os.path.exists(new_pp1_trg):
shutil.copy(new_pp1, qtk.setting.espresso_pp)
PPStr = PPStr + '.UPF'
return PPStr
