mirror of https://github.com/QMCPACK/qmcpack.git
Merge branch 'develop' into Quality_of_life_fixes
This commit is contained in:
Mark Dewing
GitHub
commit
c270f86a26
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@ -1726,6 +1726,12 @@ def numerics():
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def fileio():
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nunit_all()
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#end def fileio
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def nexus_imports():
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import nexus
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@ -3465,6 +3471,7 @@ NexusTest( generic_extensions )
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NexusTest( developer )
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NexusTest( periodic_table )
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NexusTest( numerics )
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NexusTest( fileio )
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NexusTest( nexus_imports )
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NexusTest( settings_operation , 'settings' )
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NexusTest( machines )
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@ -316,6 +316,7 @@ class XsfFile(StandardFile):
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#end def add_to_image
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# test needed for axsf and bxsf
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def read_text(self,text):
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lines = text.splitlines()
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i=0
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@ -549,6 +550,7 @@ class XsfFile(StandardFile):
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#end def read_text
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# test needed for axsf and bxsf
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def write_text(self):
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c=''
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if self.filetype=='xsf': # only write structure/datagrid if present
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@ -769,6 +771,7 @@ class XsfFile(StandardFile):
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#end def validity_checks
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# test needed
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def incorporate_structure(self,structure):
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s = structure.copy()
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s.change_units('A')
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@ -849,6 +852,7 @@ class XsfFile(StandardFile):
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#end def get_density
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# test needed
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def change_units(self,in_unit,out_unit):
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fac = 1.0/convert(1.0,in_unit,out_unit)**3
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density = self.get_density()
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@ -859,6 +863,7 @@ class XsfFile(StandardFile):
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#end def change_units
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# test needed
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def remove_ghost(self,density=None):
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if density is None:
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density = self.get_density()
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@ -878,6 +883,7 @@ class XsfFile(StandardFile):
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#end def remove_ghost
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# test needed
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def norm(self,density=None,vnorm=True):
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if density is None:
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density = self.get_density()
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@ -895,6 +901,7 @@ class XsfFile(StandardFile):
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#end def norm
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# test needed
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def line_data(self,dim,density=None):
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if density is None:
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density = self.get_density()
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@ -1193,7 +1200,9 @@ class ChgcarFile(StandardFile):
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elif (self.grid<1).sum()>0:
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msgs.append('all grid entries must be greater than zero')
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#end if
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ng = self.grid.prod()
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if self.grid is not None:
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ng = self.grid.prod()
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#end if
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if self.charge_density is None:
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msgs.append('charge_density is missing')
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elif not isinstance(self.charge_density,ndarray):
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@ -1298,7 +1307,7 @@ def read_poscar_chgcar(host,text):
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nlines = len(lines)
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min_lines = 8
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if nlines<min_lines:
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host.error('file {0} must have at least {1} lines\nonly {2} lines found'.format(filepath,min_lines,nlines))
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host.error('file {0} must have at least {1} lines\nonly {2} lines found'.format(host.filepath,min_lines,nlines))
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#end if
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description = lines[0]
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dim = 3
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@ -1322,7 +1331,7 @@ def read_poscar_chgcar(host,text):
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c = lines[lcur].lower()[0]
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lcur+=1
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else:
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host.error('file {0} is incomplete (missing positions)'.format(filepath))
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host.error('file {0} is incomplete (missing positions)'.format(host.filepath))
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#end if
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selective_dynamics = c=='s'
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if selective_dynamics: # Selective dynamics
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@ -1330,7 +1339,7 @@ def read_poscar_chgcar(host,text):
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c = lines[lcur].lower()[0]
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lcur+=1
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else:
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host.error('file {0} is incomplete (missing positions)'.format(filepath))
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host.error('file {0} is incomplete (missing positions)'.format(host.filepath))
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#end if
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#end if
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cartesian = c=='c' or c=='k'
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@ -1341,7 +1350,7 @@ def read_poscar_chgcar(host,text):
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#end if
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npos = counts.sum()
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if lcur+npos>len(lines):
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host.error('file {0} is incomplete (missing positions)'.format(filepath))
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host.error('file {0} is incomplete (missing positions)'.format(host.filepath))
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#end if
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spos = []
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for i in range(npos):
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@ -1377,7 +1386,7 @@ def read_poscar_chgcar(host,text):
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cline = lines[lcur].lower()
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lcur+=1
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if lcur+npos>len(lines):
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host.error('file {0} is incomplete (missing velocities)'.format(filepath))
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host.error('file {0} is incomplete (missing velocities)'.format(host.filepath))
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#end if
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cartesian = len(cline)>0 and (cline[0]=='c' or cline[0]=='k')
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if cartesian:
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@ -1403,7 +1412,7 @@ def read_poscar_chgcar(host,text):
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grid = array(lines[lcur].split(),dtype=int)
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lcur+=1
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else:
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host.error('file {0} is incomplete (missing grid)'.format(filepath))
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host.error('file {0} is incomplete (missing grid)'.format(host.filepath))
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#end if
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if lcur<len(lines):
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ng = grid.prod()
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@ -1422,12 +1431,15 @@ def read_poscar_chgcar(host,text):
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#end def is_float
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# remove anything but the densities (e.g. augmentation charges)
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n=0
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while is_float(density[n]) and n+ng<len(density):
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while is_float(density[n]):
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n+=ng
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if n+ng>=len(density):
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break
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#end if
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#end while
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density = array(density[:n],dtype=float)
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else:
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host.error('file {0} is incomplete (missing density)'.format(filepath))
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host.error('file {0} is incomplete (missing density)'.format(host.filepath))
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#end if
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if density.size%ng!=0:
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host.error('number of density data entries is not a multiple of the grid\ngrid shape: {0}\ngrid size: {1}\ndensity size: {2}'.format(grid,ng,density.size))
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@ -1446,10 +1458,10 @@ def read_poscar_chgcar(host,text):
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spin_density[:,i] = density[(i+1)*ng:(i+2)*ng]
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#end for
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else:
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host.error('density data must be present for one of the following situations\n 1) charge density only (1 density)\n2) charge and collinear spin densities (2 densities)\n 3) charge and non-collinear spin densities (4 densities)\nnumber of densities found: {0}'.format(ndens))
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host.error('density data must be present for one of the following situations\n 1) charge density only (1 density)\n 2) charge and collinear spin densities (2 densities)\n 3) charge and non-collinear spin densities (4 densities)\nnumber of densities found: {0}'.format(ndens))
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#end if
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else:
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host.error('file {0} is incomplete (missing density)'.format(filepath))
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host.error('file {0} is incomplete (missing density)'.format(host.filepath))
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#end if
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#end if
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@ -123,4 +123,105 @@ def object_eq(*args,**kwargs):
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# find the path to the Nexus directory and other internal paths
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def nexus_path(append=None,location=None):
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import os
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testing_path = os.path.realpath(__file__)
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assert(isinstance(testing_path,str))
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assert(len(testing_path)>0)
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assert('/' in testing_path)
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tokens = testing_path.split('/')
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assert(len(tokens)>=3)
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assert(tokens[-1].startswith('testing.py'))
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assert(tokens[-2]=='lib')
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assert(tokens[-3]=='nexus')
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path = os.path.dirname(testing_path)
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path = os.path.dirname(path)
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assert(path.endswith('/nexus'))
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if location is not None:
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if location=='unit':
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append = 'tests/unit'
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else:
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print('nexus location "{}" is unknown'.format(location))
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raise ValueError
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#end if
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#end if
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if append is not None:
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path = os.path.join(path,append)
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#end if
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assert(os.path.exists(path))
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return path
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#end def nexus_path
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# find the path to a file associated with a unit test
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def unit_test_file_path(test,file=None):
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import os
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unit_path = nexus_path(location='unit')
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files_dir = 'test_{}_files'.format(test)
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path = os.path.join(unit_path,files_dir)
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if file is not None:
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path = os.path.join(path,file)
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#end if
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assert(os.path.exists(path))
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return path
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#end def unit_test_file_path
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# collect paths to all files associated with a unit test
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def collect_unit_test_file_paths(test,storage):
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import os
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if len(storage)==0:
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test_files_dir = unit_test_file_path(test)
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files = os.listdir(test_files_dir)
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for file in files:
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filepath = os.path.join(test_files_dir,file)
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assert(os.path.exists(filepath))
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storage[file] = filepath
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#end for
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#end if
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return storage
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#end def collect_unit_test_file_paths
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# find the output path for a test
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def unit_test_output_path(test,subtest=None):
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import os
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unit_path = nexus_path(location='unit')
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files_dir = 'test_{}_output'.format(test)
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path = os.path.join(unit_path,files_dir)
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if subtest is not None:
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path = os.path.join(path,subtest)
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#end if
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return path
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#end def unit_test_output_path
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# setup the output directory for a test
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def setup_unit_test_output_directory(test,subtest):
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import os
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import shutil
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path = unit_test_output_path(test,subtest)
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assert('nexus' in path)
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assert('unit' in path)
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assert(os.path.basename(path).startswith('test_'))
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assert(path.endswith('/'+subtest))
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if os.path.exists(path):
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shutil.rmtree(path)
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#end if
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os.makedirs(path)
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assert(os.path.exists(path))
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return path
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#end def setup_unit_test_output_directory
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|
|
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@ -0,0 +1,338 @@
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import testing
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from testing import value_eq,object_eq
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associated_files = dict()
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def get_files():
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return testing.collect_unit_test_file_paths('fileio',associated_files)
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#end def get_files
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def test_files():
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filenames = [
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'scf.in',
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'VO2_R_48.xsf',
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'VO2_R_48.POSCAR',
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'VO2_R_48_dens.xsf',
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'VO2_R_48_dens.CHGCAR',
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]
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files = get_files()
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assert(set(files.keys())==set(filenames))
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#end def test_files
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|
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|
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def test_import():
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import fileio
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from fileio import TextFile
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from fileio import XsfFile
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from fileio import PoscarFile
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from fileio import ChgcarFile
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#end def test_import
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|
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|
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def test_textfile():
|
||||
from fileio import TextFile
|
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|
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files = get_files()
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# test empty initialization
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empty = TextFile()
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# test read
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f = TextFile(files['scf.in'])
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assert(len(f.read())==1225)
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assert(len(f.lines())==55)
|
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assert(len(f.tokens())==125)
|
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|
||||
assert(f.readline()=='&CONTROL\n')
|
||||
assert(f.readline()==" calculation = 'scf'\n")
|
||||
|
||||
assert(f.readline('celldm')=='celldm(1) = 1.0\n')
|
||||
|
||||
assert(f.readtokens('ecutwfc')==['ecutwfc', '=', '272'])
|
||||
|
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val = f.readtokensf('CELL_PARAMETERS',float,float,float)
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||||
ref = [28.34589199, 0.0, 0.0]
|
||||
assert(value_eq(val,ref))
|
||||
|
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f.close()
|
||||
#end def test_textfile
|
||||
|
||||
|
||||
|
||||
|
||||
def test_xsffile():
|
||||
import os
|
||||
import numpy as np
|
||||
from fileio import XsfFile
|
||||
|
||||
tpath = testing.setup_unit_test_output_directory('fileio','test_xsffile')
|
||||
|
||||
files = get_files()
|
||||
|
||||
# test empty initialization
|
||||
empty = XsfFile()
|
||||
assert(not empty.is_valid())
|
||||
|
||||
# populate reference object
|
||||
ref = XsfFile()
|
||||
ref.set(
|
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elem = np.array([8,8,8,8,8,8,8,8,8,8,8,8,8,8,8,8,8,8,8,8,
|
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8,8,8,8,8,8,8,8,8,8,8,8,23,23,23,23,23,
|
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23,23,23,23,23,23,23,23,23,23,23],dtype=int),
|
||||
filetype = 'xsf',
|
||||
periodicity = 'crystal',
|
||||
pos = np.array([
|
||||
[ 1.36683546, 1.36683546, 0. ],
|
||||
[ 3.18776454, 3.18776454, 0. ],
|
||||
[ 3.64413546, 0.91046454, 1.4264 ],
|
||||
[ 5.46506454, -0.91046454, 1.4264 ],
|
||||
[ 1.36683546, 1.36683546, 2.8528 ],
|
||||
[ 3.18776454, 3.18776454, 2.8528 ],
|
||||
[ 3.64413546, 0.91046454, 4.2792 ],
|
||||
[ 5.46506454, -0.91046454, 4.2792 ],
|
||||
[ 5.92143546, 1.36683546, 0. ],
|
||||
[ 3.18776454, -1.36683546, 0. ],
|
||||
[ 3.64413546, -3.64413546, 1.4264 ],
|
||||
[ 0.91046454, -0.91046454, 1.4264 ],
|
||||
[ 5.92143546, 1.36683546, 2.8528 ],
|
||||
[ 3.18776454, -1.36683546, 2.8528 ],
|
||||
[ 3.64413546, -3.64413546, 4.2792 ],
|
||||
[ 0.91046454, -0.91046454, 4.2792 ],
|
||||
[ 1.36683546, 1.36683546, 5.7056 ],
|
||||
[ 3.18776454, 3.18776454, 5.7056 ],
|
||||
[ 3.64413546, 0.91046454, 7.132 ],
|
||||
[ 5.46506454, -0.91046454, 7.132 ],
|
||||
[ 1.36683546, 1.36683546, 8.5584 ],
|
||||
[ 3.18776454, 3.18776454, 8.5584 ],
|
||||
[ 3.64413546, 0.91046454, 9.9848 ],
|
||||
[ 5.46506454, -0.91046454, 9.9848 ],
|
||||
[ 5.92143546, 1.36683546, 5.7056 ],
|
||||
[ 3.18776454, -1.36683546, 5.7056 ],
|
||||
[ 3.64413546, -3.64413546, 7.132 ],
|
||||
[ 0.91046454, -0.91046454, 7.132 ],
|
||||
[ 5.92143546, 1.36683546, 8.5584 ],
|
||||
[ 3.18776454, -1.36683546, 8.5584 ],
|
||||
[ 3.64413546, -3.64413546, 9.9848 ],
|
||||
[ 0.91046454, -0.91046454, 9.9848 ],
|
||||
[ 0. , 0. , 0. ],
|
||||
[ 2.2773 , 2.2773 , 1.4264 ],
|
||||
[ 0. , 0. , 2.8528 ],
|
||||
[ 2.2773 , 2.2773 , 4.2792 ],
|
||||
[ 4.5546 , 0. , 0. ],
|
||||
[ 2.2773 , -2.2773 , 1.4264 ],
|
||||
[ 4.5546 , 0. , 2.8528 ],
|
||||
[ 2.2773 , -2.2773 , 4.2792 ],
|
||||
[ 0. , 0. , 5.7056 ],
|
||||
[ 2.2773 , 2.2773 , 7.132 ],
|
||||
[ 0. , 0. , 8.5584 ],
|
||||
[ 2.2773 , 2.2773 , 9.9848 ],
|
||||
[ 4.5546 , 0. , 5.7056 ],
|
||||
[ 2.2773 , -2.2773 , 7.132 ],
|
||||
[ 4.5546 , 0. , 8.5584 ],
|
||||
[ 2.2773 , -2.2773 , 9.9848 ]
|
||||
],dtype=float),
|
||||
primvec = np.array([
|
||||
[ 4.5546, -4.5546, 0. ],
|
||||
[ 4.5546, 4.5546, 0. ],
|
||||
[ 0. , 0. , 11.4112]
|
||||
],dtype=float),
|
||||
)
|
||||
assert(ref.is_valid())
|
||||
|
||||
# test read
|
||||
f = XsfFile(files['VO2_R_48.xsf'])
|
||||
assert(f.is_valid())
|
||||
assert(object_eq(f,ref))
|
||||
|
||||
# test write
|
||||
outfile = os.path.join(tpath,'test.xsf')
|
||||
f.write(outfile)
|
||||
f2 = XsfFile(outfile)
|
||||
assert(f2.is_valid())
|
||||
assert(object_eq(f2,ref))
|
||||
|
||||
#end def test_xsffile
|
||||
|
||||
|
||||
|
||||
def test_xsffile_density():
|
||||
import os
|
||||
import numpy as np
|
||||
from fileio import XsfFile
|
||||
|
||||
tpath = testing.setup_unit_test_output_directory('fileio','test_xsffile_density')
|
||||
|
||||
files = get_files()
|
||||
|
||||
ref = XsfFile(files['VO2_R_48.xsf'])
|
||||
|
||||
grid = 3,5,7
|
||||
dens = 0.01*np.arange(np.prod(grid),dtype=float)
|
||||
dens.shape=grid
|
||||
|
||||
ref.add_density(ref.primvec,dens,add_ghost=True)
|
||||
assert(ref.is_valid())
|
||||
|
||||
f = XsfFile(files['VO2_R_48_dens.xsf'])
|
||||
assert(f.is_valid())
|
||||
assert(object_eq(f,ref))
|
||||
|
||||
d = f.get_density().values
|
||||
assert(isinstance(d,np.ndarray))
|
||||
assert(d.shape==(4,6,8))
|
||||
|
||||
outfile = os.path.join(tpath,'test_density.xsf')
|
||||
f.write(outfile)
|
||||
f2 = XsfFile(outfile)
|
||||
assert(f2.is_valid())
|
||||
assert(object_eq(f2,ref))
|
||||
#end def test_xsffile_density
|
||||
|
||||
|
||||
|
||||
def test_poscar_file():
|
||||
import os
|
||||
import numpy as np
|
||||
from fileio import PoscarFile
|
||||
|
||||
tpath = testing.setup_unit_test_output_directory('fileio','test_poscarfile')
|
||||
|
||||
files = get_files()
|
||||
|
||||
# test empty initialization
|
||||
empty = PoscarFile()
|
||||
assert(not empty.is_valid())
|
||||
|
||||
# populate reference object
|
||||
ref = PoscarFile()
|
||||
ref.set(
|
||||
axes = np.array([
|
||||
[ 4.5546, -4.5546, 0. ],
|
||||
[ 4.5546, 4.5546, 0. ],
|
||||
[ 0. , 0. , 11.4112]
|
||||
],dtype=float),
|
||||
coord = 'cartesian',
|
||||
description = 'System cell and coordinates',
|
||||
dynamic = None,
|
||||
elem = np.array(['O', 'V'],dtype=str),
|
||||
elem_count = np.array([32, 16],dtype=int),
|
||||
pos = np.array([
|
||||
[ 1.36683546, 1.36683546, 0. ],
|
||||
[ 3.18776454, 3.18776454, 0. ],
|
||||
[ 3.64413546, 0.91046454, 1.4264 ],
|
||||
[ 5.46506454, -0.91046454, 1.4264 ],
|
||||
[ 1.36683546, 1.36683546, 2.8528 ],
|
||||
[ 3.18776454, 3.18776454, 2.8528 ],
|
||||
[ 3.64413546, 0.91046454, 4.2792 ],
|
||||
[ 5.46506454, -0.91046454, 4.2792 ],
|
||||
[ 5.92143546, 1.36683546, 0. ],
|
||||
[ 3.18776454, -1.36683546, 0. ],
|
||||
[ 3.64413546, -3.64413546, 1.4264 ],
|
||||
[ 0.91046454, -0.91046454, 1.4264 ],
|
||||
[ 5.92143546, 1.36683546, 2.8528 ],
|
||||
[ 3.18776454, -1.36683546, 2.8528 ],
|
||||
[ 3.64413546, -3.64413546, 4.2792 ],
|
||||
[ 0.91046454, -0.91046454, 4.2792 ],
|
||||
[ 1.36683546, 1.36683546, 5.7056 ],
|
||||
[ 3.18776454, 3.18776454, 5.7056 ],
|
||||
[ 3.64413546, 0.91046454, 7.132 ],
|
||||
[ 5.46506454, -0.91046454, 7.132 ],
|
||||
[ 1.36683546, 1.36683546, 8.5584 ],
|
||||
[ 3.18776454, 3.18776454, 8.5584 ],
|
||||
[ 3.64413546, 0.91046454, 9.9848 ],
|
||||
[ 5.46506454, -0.91046454, 9.9848 ],
|
||||
[ 5.92143546, 1.36683546, 5.7056 ],
|
||||
[ 3.18776454, -1.36683546, 5.7056 ],
|
||||
[ 3.64413546, -3.64413546, 7.132 ],
|
||||
[ 0.91046454, -0.91046454, 7.132 ],
|
||||
[ 5.92143546, 1.36683546, 8.5584 ],
|
||||
[ 3.18776454, -1.36683546, 8.5584 ],
|
||||
[ 3.64413546, -3.64413546, 9.9848 ],
|
||||
[ 0.91046454, -0.91046454, 9.9848 ],
|
||||
[ 0. , 0. , 0. ],
|
||||
[ 2.2773 , 2.2773 , 1.4264 ],
|
||||
[ 0. , 0. , 2.8528 ],
|
||||
[ 2.2773 , 2.2773 , 4.2792 ],
|
||||
[ 4.5546 , 0. , 0. ],
|
||||
[ 2.2773 , -2.2773 , 1.4264 ],
|
||||
[ 4.5546 , 0. , 2.8528 ],
|
||||
[ 2.2773 , -2.2773 , 4.2792 ],
|
||||
[ 0. , 0. , 5.7056 ],
|
||||
[ 2.2773 , 2.2773 , 7.132 ],
|
||||
[ 0. , 0. , 8.5584 ],
|
||||
[ 2.2773 , 2.2773 , 9.9848 ],
|
||||
[ 4.5546 , 0. , 5.7056 ],
|
||||
[ 2.2773 , -2.2773 , 7.132 ],
|
||||
[ 4.5546 , 0. , 8.5584 ],
|
||||
[ 2.2773 , -2.2773 , 9.9848 ]
|
||||
],dtype=float),
|
||||
scale = 1.0,
|
||||
vel = None,
|
||||
vel_coord = None,
|
||||
)
|
||||
|
||||
# test read
|
||||
f = PoscarFile(files['VO2_R_48.POSCAR'])
|
||||
assert(f.is_valid())
|
||||
assert(object_eq(f,ref))
|
||||
|
||||
# test write
|
||||
outfile = os.path.join(tpath,'test.POSCAR')
|
||||
f.write(outfile)
|
||||
f2 = PoscarFile(outfile)
|
||||
assert(f2.is_valid())
|
||||
assert(object_eq(f2,ref))
|
||||
|
||||
# test incorporate xsf
|
||||
from fileio import XsfFile
|
||||
x = XsfFile(files['VO2_R_48.xsf'])
|
||||
f = PoscarFile()
|
||||
f.incorporate_xsf(x)
|
||||
assert(f.is_valid())
|
||||
assert(object_eq(f,ref))
|
||||
#end def test_poscar_file
|
||||
|
||||
|
||||
|
||||
def test_chgcar_file():
|
||||
import os
|
||||
from fileio import XsfFile
|
||||
from fileio import PoscarFile
|
||||
from fileio import ChgcarFile
|
||||
|
||||
tpath = testing.setup_unit_test_output_directory('fileio','test_chgcarfile')
|
||||
|
||||
files = get_files()
|
||||
|
||||
empty = ChgcarFile()
|
||||
assert(not empty.is_valid())
|
||||
|
||||
# get reference poscar and xsf files
|
||||
p = PoscarFile(files['VO2_R_48.POSCAR'])
|
||||
x = XsfFile(files['VO2_R_48_dens.xsf'])
|
||||
|
||||
# create and test reference chgcar file
|
||||
ref = ChgcarFile()
|
||||
ref.incorporate_xsf(x)
|
||||
assert(ref.is_valid())
|
||||
assert(object_eq(ref.poscar,p))
|
||||
|
||||
# test read
|
||||
f = ChgcarFile(files['VO2_R_48_dens.CHGCAR'])
|
||||
assert(f.is_valid())
|
||||
assert(object_eq(f,ref))
|
||||
|
||||
# test write
|
||||
outfile = os.path.join(tpath,'test.CHGCAR')
|
||||
f.write(outfile)
|
||||
f2 = ChgcarFile(outfile)
|
||||
assert(f2.is_valid())
|
||||
assert(object_eq(f2,ref))
|
||||
#end def test_chgcar_file
|
||||
|
|
@ -0,0 +1,56 @@
|
|||
System cell and coordinates
|
||||
1.0
|
||||
4.55460000000000 -4.55460000000000 0.00000000000000
|
||||
4.55460000000000 4.55460000000000 0.00000000000000
|
||||
0.00000000000000 0.00000000000000 11.41120000000000
|
||||
O V
|
||||
32 16
|
||||
cartesian
|
||||
1.36683546000000 1.36683546000000 0.00000000000000
|
||||
3.18776454000000 3.18776454000000 0.00000000000000
|
||||
3.64413546000000 0.91046454000000 1.42640000000000
|
||||
5.46506454000000 -0.91046454000000 1.42640000000000
|
||||
1.36683546000000 1.36683546000000 2.85280000000000
|
||||
3.18776454000000 3.18776454000000 2.85280000000000
|
||||
3.64413546000000 0.91046454000000 4.27920000000000
|
||||
5.46506454000000 -0.91046454000000 4.27920000000000
|
||||
5.92143546000000 1.36683546000000 0.00000000000000
|
||||
3.18776454000000 -1.36683546000000 0.00000000000000
|
||||
3.64413546000000 -3.64413546000000 1.42640000000000
|
||||
0.91046454000000 -0.91046454000000 1.42640000000000
|
||||
5.92143546000000 1.36683546000000 2.85280000000000
|
||||
3.18776454000000 -1.36683546000000 2.85280000000000
|
||||
3.64413546000000 -3.64413546000000 4.27920000000000
|
||||
0.91046454000000 -0.91046454000000 4.27920000000000
|
||||
1.36683546000000 1.36683546000000 5.70560000000000
|
||||
3.18776454000000 3.18776454000000 5.70560000000000
|
||||
3.64413546000000 0.91046454000000 7.13200000000000
|
||||
5.46506454000000 -0.91046454000000 7.13200000000000
|
||||
1.36683546000000 1.36683546000000 8.55840000000000
|
||||
3.18776454000000 3.18776454000000 8.55840000000000
|
||||
3.64413546000000 0.91046454000000 9.98480000000000
|
||||
5.46506454000000 -0.91046454000000 9.98480000000000
|
||||
5.92143546000000 1.36683546000000 5.70560000000000
|
||||
3.18776454000000 -1.36683546000000 5.70560000000000
|
||||
3.64413546000000 -3.64413546000000 7.13200000000000
|
||||
0.91046454000000 -0.91046454000000 7.13200000000000
|
||||
5.92143546000000 1.36683546000000 8.55840000000000
|
||||
3.18776454000000 -1.36683546000000 8.55840000000000
|
||||
3.64413546000000 -3.64413546000000 9.98480000000000
|
||||
0.91046454000000 -0.91046454000000 9.98480000000000
|
||||
0.00000000000000 0.00000000000000 0.00000000000000
|
||||
2.27730000000000 2.27730000000000 1.42640000000000
|
||||
0.00000000000000 0.00000000000000 2.85280000000000
|
||||
2.27730000000000 2.27730000000000 4.27920000000000
|
||||
4.55460000000000 0.00000000000000 0.00000000000000
|
||||
2.27730000000000 -2.27730000000000 1.42640000000000
|
||||
4.55460000000000 0.00000000000000 2.85280000000000
|
||||
2.27730000000000 -2.27730000000000 4.27920000000000
|
||||
0.00000000000000 0.00000000000000 5.70560000000000
|
||||
2.27730000000000 2.27730000000000 7.13200000000000
|
||||
0.00000000000000 0.00000000000000 8.55840000000000
|
||||
2.27730000000000 2.27730000000000 9.98480000000000
|
||||
4.55460000000000 0.00000000000000 5.70560000000000
|
||||
2.27730000000000 -2.27730000000000 7.13200000000000
|
||||
4.55460000000000 0.00000000000000 8.55840000000000
|
||||
2.27730000000000 -2.27730000000000 9.98480000000000
|
||||
|
|
@ -0,0 +1,55 @@
|
|||
CRYSTAL
|
||||
PRIMVEC
|
||||
4.55460000 -4.55460000 0.00000000
|
||||
4.55460000 4.55460000 0.00000000
|
||||
0.00000000 0.00000000 11.41120000
|
||||
PRIMCOORD
|
||||
48 1
|
||||
8 1.36683546 1.36683546 0.00000000
|
||||
8 3.18776454 3.18776454 0.00000000
|
||||
8 3.64413546 0.91046454 1.42640000
|
||||
8 5.46506454 -0.91046454 1.42640000
|
||||
8 1.36683546 1.36683546 2.85280000
|
||||
8 3.18776454 3.18776454 2.85280000
|
||||
8 3.64413546 0.91046454 4.27920000
|
||||
8 5.46506454 -0.91046454 4.27920000
|
||||
8 5.92143546 1.36683546 0.00000000
|
||||
8 3.18776454 -1.36683546 0.00000000
|
||||
8 3.64413546 -3.64413546 1.42640000
|
||||
8 0.91046454 -0.91046454 1.42640000
|
||||
8 5.92143546 1.36683546 2.85280000
|
||||
8 3.18776454 -1.36683546 2.85280000
|
||||
8 3.64413546 -3.64413546 4.27920000
|
||||
8 0.91046454 -0.91046454 4.27920000
|
||||
8 1.36683546 1.36683546 5.70560000
|
||||
8 3.18776454 3.18776454 5.70560000
|
||||
8 3.64413546 0.91046454 7.13200000
|
||||
8 5.46506454 -0.91046454 7.13200000
|
||||
8 1.36683546 1.36683546 8.55840000
|
||||
8 3.18776454 3.18776454 8.55840000
|
||||
8 3.64413546 0.91046454 9.98480000
|
||||
8 5.46506454 -0.91046454 9.98480000
|
||||
8 5.92143546 1.36683546 5.70560000
|
||||
8 3.18776454 -1.36683546 5.70560000
|
||||
8 3.64413546 -3.64413546 7.13200000
|
||||
8 0.91046454 -0.91046454 7.13200000
|
||||
8 5.92143546 1.36683546 8.55840000
|
||||
8 3.18776454 -1.36683546 8.55840000
|
||||
8 3.64413546 -3.64413546 9.98480000
|
||||
8 0.91046454 -0.91046454 9.98480000
|
||||
23 0.00000000 0.00000000 0.00000000
|
||||
23 2.27730000 2.27730000 1.42640000
|
||||
23 0.00000000 0.00000000 2.85280000
|
||||
23 2.27730000 2.27730000 4.27920000
|
||||
23 4.55460000 0.00000000 0.00000000
|
||||
23 2.27730000 -2.27730000 1.42640000
|
||||
23 4.55460000 0.00000000 2.85280000
|
||||
23 2.27730000 -2.27730000 4.27920000
|
||||
23 0.00000000 0.00000000 5.70560000
|
||||
23 2.27730000 2.27730000 7.13200000
|
||||
23 0.00000000 0.00000000 8.55840000
|
||||
23 2.27730000 2.27730000 9.98480000
|
||||
23 4.55460000 0.00000000 5.70560000
|
||||
23 2.27730000 -2.27730000 7.13200000
|
||||
23 4.55460000 0.00000000 8.55840000
|
||||
23 2.27730000 -2.27730000 9.98480000
|
||||
|
|
@ -0,0 +1,79 @@
|
|||
System cell and coordinates
|
||||
1.0
|
||||
4.55460000000000 -4.55460000000000 0.00000000000000
|
||||
4.55460000000000 4.55460000000000 0.00000000000000
|
||||
0.00000000000000 0.00000000000000 11.41120000000000
|
||||
O V
|
||||
32 16
|
||||
cartesian
|
||||
1.36683546000000 1.36683546000000 0.00000000000000
|
||||
3.18776454000000 3.18776454000000 0.00000000000000
|
||||
3.64413546000000 0.91046454000000 1.42640000000000
|
||||
5.46506454000000 -0.91046454000000 1.42640000000000
|
||||
1.36683546000000 1.36683546000000 2.85280000000000
|
||||
3.18776454000000 3.18776454000000 2.85280000000000
|
||||
3.64413546000000 0.91046454000000 4.27920000000000
|
||||
5.46506454000000 -0.91046454000000 4.27920000000000
|
||||
5.92143546000000 1.36683546000000 0.00000000000000
|
||||
3.18776454000000 -1.36683546000000 0.00000000000000
|
||||
3.64413546000000 -3.64413546000000 1.42640000000000
|
||||
0.91046454000000 -0.91046454000000 1.42640000000000
|
||||
5.92143546000000 1.36683546000000 2.85280000000000
|
||||
3.18776454000000 -1.36683546000000 2.85280000000000
|
||||
3.64413546000000 -3.64413546000000 4.27920000000000
|
||||
0.91046454000000 -0.91046454000000 4.27920000000000
|
||||
1.36683546000000 1.36683546000000 5.70560000000000
|
||||
3.18776454000000 3.18776454000000 5.70560000000000
|
||||
3.64413546000000 0.91046454000000 7.13200000000000
|
||||
5.46506454000000 -0.91046454000000 7.13200000000000
|
||||
1.36683546000000 1.36683546000000 8.55840000000000
|
||||
3.18776454000000 3.18776454000000 8.55840000000000
|
||||
3.64413546000000 0.91046454000000 9.98480000000000
|
||||
5.46506454000000 -0.91046454000000 9.98480000000000
|
||||
5.92143546000000 1.36683546000000 5.70560000000000
|
||||
3.18776454000000 -1.36683546000000 5.70560000000000
|
||||
3.64413546000000 -3.64413546000000 7.13200000000000
|
||||
0.91046454000000 -0.91046454000000 7.13200000000000
|
||||
5.92143546000000 1.36683546000000 8.55840000000000
|
||||
3.18776454000000 -1.36683546000000 8.55840000000000
|
||||
3.64413546000000 -3.64413546000000 9.98480000000000
|
||||
0.91046454000000 -0.91046454000000 9.98480000000000
|
||||
0.00000000000000 0.00000000000000 0.00000000000000
|
||||
2.27730000000000 2.27730000000000 1.42640000000000
|
||||
0.00000000000000 0.00000000000000 2.85280000000000
|
||||
2.27730000000000 2.27730000000000 4.27920000000000
|
||||
4.55460000000000 0.00000000000000 0.00000000000000
|
||||
2.27730000000000 -2.27730000000000 1.42640000000000
|
||||
4.55460000000000 0.00000000000000 2.85280000000000
|
||||
2.27730000000000 -2.27730000000000 4.27920000000000
|
||||
0.00000000000000 0.00000000000000 5.70560000000000
|
||||
2.27730000000000 2.27730000000000 7.13200000000000
|
||||
0.00000000000000 0.00000000000000 8.55840000000000
|
||||
2.27730000000000 2.27730000000000 9.98480000000000
|
||||
4.55460000000000 0.00000000000000 5.70560000000000
|
||||
2.27730000000000 -2.27730000000000 7.13200000000000
|
||||
4.55460000000000 0.00000000000000 8.55840000000000
|
||||
2.27730000000000 -2.27730000000000 9.98480000000000
|
||||
|
||||
3 5 7
|
||||
0.000000000000E+00 3.500000000000E-01 7.000000000000E-01 7.000000000000E-02 4.200000000000E-01
|
||||
7.700000000000E-01 1.400000000000E-01 4.900000000000E-01 8.400000000000E-01 2.100000000000E-01
|
||||
5.600000000000E-01 9.100000000000E-01 2.800000000000E-01 6.300000000000E-01 9.800000000000E-01
|
||||
1.000000000000E-02 3.600000000000E-01 7.100000000000E-01 8.000000000000E-02 4.300000000000E-01
|
||||
7.800000000000E-01 1.500000000000E-01 5.000000000000E-01 8.500000000000E-01 2.200000000000E-01
|
||||
5.700000000000E-01 9.200000000000E-01 2.900000000000E-01 6.400000000000E-01 9.900000000000E-01
|
||||
2.000000000000E-02 3.700000000000E-01 7.200000000000E-01 9.000000000000E-02 4.400000000000E-01
|
||||
7.900000000000E-01 1.600000000000E-01 5.100000000000E-01 8.600000000000E-01 2.300000000000E-01
|
||||
5.800000000000E-01 9.300000000000E-01 3.000000000000E-01 6.500000000000E-01 1.000000000000E+00
|
||||
3.000000000000E-02 3.800000000000E-01 7.300000000000E-01 1.000000000000E-01 4.500000000000E-01
|
||||
8.000000000000E-01 1.700000000000E-01 5.200000000000E-01 8.700000000000E-01 2.400000000000E-01
|
||||
5.900000000000E-01 9.400000000000E-01 3.100000000000E-01 6.600000000000E-01 1.010000000000E+00
|
||||
4.000000000000E-02 3.900000000000E-01 7.400000000000E-01 1.100000000000E-01 4.600000000000E-01
|
||||
8.100000000000E-01 1.800000000000E-01 5.300000000000E-01 8.800000000000E-01 2.500000000000E-01
|
||||
6.000000000000E-01 9.500000000000E-01 3.200000000000E-01 6.700000000000E-01 1.020000000000E+00
|
||||
5.000000000000E-02 4.000000000000E-01 7.500000000000E-01 1.200000000000E-01 4.700000000000E-01
|
||||
8.200000000000E-01 1.900000000000E-01 5.400000000000E-01 8.900000000000E-01 2.600000000000E-01
|
||||
6.100000000000E-01 9.600000000000E-01 3.300000000000E-01 6.800000000000E-01 1.030000000000E+00
|
||||
6.000000000000E-02 4.100000000000E-01 7.600000000000E-01 1.300000000000E-01 4.800000000000E-01
|
||||
8.300000000000E-01 2.000000000000E-01 5.500000000000E-01 9.000000000000E-01 2.700000000000E-01
|
||||
6.200000000000E-01 9.700000000000E-01 3.400000000000E-01 6.900000000000E-01 1.040000000000E+00
|
||||
|
|
@ -0,0 +1,113 @@
|
|||
CRYSTAL
|
||||
PRIMVEC
|
||||
4.55460000 -4.55460000 0.00000000
|
||||
4.55460000 4.55460000 0.00000000
|
||||
0.00000000 0.00000000 11.41120000
|
||||
PRIMCOORD
|
||||
48 1
|
||||
8 1.36683546 1.36683546 0.00000000
|
||||
8 3.18776454 3.18776454 0.00000000
|
||||
8 3.64413546 0.91046454 1.42640000
|
||||
8 5.46506454 -0.91046454 1.42640000
|
||||
8 1.36683546 1.36683546 2.85280000
|
||||
8 3.18776454 3.18776454 2.85280000
|
||||
8 3.64413546 0.91046454 4.27920000
|
||||
8 5.46506454 -0.91046454 4.27920000
|
||||
8 5.92143546 1.36683546 0.00000000
|
||||
8 3.18776454 -1.36683546 0.00000000
|
||||
8 3.64413546 -3.64413546 1.42640000
|
||||
8 0.91046454 -0.91046454 1.42640000
|
||||
8 5.92143546 1.36683546 2.85280000
|
||||
8 3.18776454 -1.36683546 2.85280000
|
||||
8 3.64413546 -3.64413546 4.27920000
|
||||
8 0.91046454 -0.91046454 4.27920000
|
||||
8 1.36683546 1.36683546 5.70560000
|
||||
8 3.18776454 3.18776454 5.70560000
|
||||
8 3.64413546 0.91046454 7.13200000
|
||||
8 5.46506454 -0.91046454 7.13200000
|
||||
8 1.36683546 1.36683546 8.55840000
|
||||
8 3.18776454 3.18776454 8.55840000
|
||||
8 3.64413546 0.91046454 9.98480000
|
||||
8 5.46506454 -0.91046454 9.98480000
|
||||
8 5.92143546 1.36683546 5.70560000
|
||||
8 3.18776454 -1.36683546 5.70560000
|
||||
8 3.64413546 -3.64413546 7.13200000
|
||||
8 0.91046454 -0.91046454 7.13200000
|
||||
8 5.92143546 1.36683546 8.55840000
|
||||
8 3.18776454 -1.36683546 8.55840000
|
||||
8 3.64413546 -3.64413546 9.98480000
|
||||
8 0.91046454 -0.91046454 9.98480000
|
||||
23 0.00000000 0.00000000 0.00000000
|
||||
23 2.27730000 2.27730000 1.42640000
|
||||
23 0.00000000 0.00000000 2.85280000
|
||||
23 2.27730000 2.27730000 4.27920000
|
||||
23 4.55460000 0.00000000 0.00000000
|
||||
23 2.27730000 -2.27730000 1.42640000
|
||||
23 4.55460000 0.00000000 2.85280000
|
||||
23 2.27730000 -2.27730000 4.27920000
|
||||
23 0.00000000 0.00000000 5.70560000
|
||||
23 2.27730000 2.27730000 7.13200000
|
||||
23 0.00000000 0.00000000 8.55840000
|
||||
23 2.27730000 2.27730000 9.98480000
|
||||
23 4.55460000 0.00000000 5.70560000
|
||||
23 2.27730000 -2.27730000 7.13200000
|
||||
23 4.55460000 0.00000000 8.55840000
|
||||
23 2.27730000 -2.27730000 9.98480000
|
||||
BEGIN_BLOCK_DATAGRID_3D
|
||||
density
|
||||
BEGIN_DATAGRID_3D_density
|
||||
4 6 8
|
||||
0.00000000 0.00000000 0.00000000
|
||||
4.55460000 -4.55460000 0.00000000
|
||||
4.55460000 4.55460000 0.00000000
|
||||
0.00000000 0.00000000 11.41120000
|
||||
0.00000000 0.35000000 0.70000000 0.00000000
|
||||
0.07000000 0.42000000 0.77000000 0.07000000
|
||||
0.14000000 0.49000000 0.84000000 0.14000000
|
||||
0.21000000 0.56000000 0.91000000 0.21000000
|
||||
0.28000000 0.63000000 0.98000000 0.28000000
|
||||
0.00000000 0.35000000 0.70000000 0.00000000
|
||||
0.01000000 0.36000000 0.71000000 0.01000000
|
||||
0.08000000 0.43000000 0.78000000 0.08000000
|
||||
0.15000000 0.50000000 0.85000000 0.15000000
|
||||
0.22000000 0.57000000 0.92000000 0.22000000
|
||||
0.29000000 0.64000000 0.99000000 0.29000000
|
||||
0.01000000 0.36000000 0.71000000 0.01000000
|
||||
0.02000000 0.37000000 0.72000000 0.02000000
|
||||
0.09000000 0.44000000 0.79000000 0.09000000
|
||||
0.16000000 0.51000000 0.86000000 0.16000000
|
||||
0.23000000 0.58000000 0.93000000 0.23000000
|
||||
0.30000000 0.65000000 1.00000000 0.30000000
|
||||
0.02000000 0.37000000 0.72000000 0.02000000
|
||||
0.03000000 0.38000000 0.73000000 0.03000000
|
||||
0.10000000 0.45000000 0.80000000 0.10000000
|
||||
0.17000000 0.52000000 0.87000000 0.17000000
|
||||
0.24000000 0.59000000 0.94000000 0.24000000
|
||||
0.31000000 0.66000000 1.01000000 0.31000000
|
||||
0.03000000 0.38000000 0.73000000 0.03000000
|
||||
0.04000000 0.39000000 0.74000000 0.04000000
|
||||
0.11000000 0.46000000 0.81000000 0.11000000
|
||||
0.18000000 0.53000000 0.88000000 0.18000000
|
||||
0.25000000 0.60000000 0.95000000 0.25000000
|
||||
0.32000000 0.67000000 1.02000000 0.32000000
|
||||
0.04000000 0.39000000 0.74000000 0.04000000
|
||||
0.05000000 0.40000000 0.75000000 0.05000000
|
||||
0.12000000 0.47000000 0.82000000 0.12000000
|
||||
0.19000000 0.54000000 0.89000000 0.19000000
|
||||
0.26000000 0.61000000 0.96000000 0.26000000
|
||||
0.33000000 0.68000000 1.03000000 0.33000000
|
||||
0.05000000 0.40000000 0.75000000 0.05000000
|
||||
0.06000000 0.41000000 0.76000000 0.06000000
|
||||
0.13000000 0.48000000 0.83000000 0.13000000
|
||||
0.20000000 0.55000000 0.90000000 0.20000000
|
||||
0.27000000 0.62000000 0.97000000 0.27000000
|
||||
0.34000000 0.69000000 1.04000000 0.34000000
|
||||
0.06000000 0.41000000 0.76000000 0.06000000
|
||||
0.00000000 0.35000000 0.70000000 0.00000000
|
||||
0.07000000 0.42000000 0.77000000 0.07000000
|
||||
0.14000000 0.49000000 0.84000000 0.14000000
|
||||
0.21000000 0.56000000 0.91000000 0.21000000
|
||||
0.28000000 0.63000000 0.98000000 0.28000000
|
||||
0.00000000 0.35000000 0.70000000 0.00000000
|
||||
END_DATAGRID_3D_density
|
||||
END_BLOCK_DATAGRID_3D
|
||||
|
|
@ -0,0 +1,55 @@
|
|||
&CONTROL
|
||||
calculation = 'scf'
|
||||
disk_io = 'low'
|
||||
outdir = 'pwscf_output'
|
||||
prefix = 'pwscf'
|
||||
pseudo_dir = './'
|
||||
restart_mode = 'from_scratch'
|
||||
tprnfor = .false.
|
||||
tstress = .false.
|
||||
verbosity = 'high'
|
||||
wf_collect = .true.
|
||||
/
|
||||
|
||||
&SYSTEM
|
||||
celldm(1) = 1.0
|
||||
degauss = 0.0001
|
||||
ecutrho = 1088
|
||||
ecutwfc = 272
|
||||
exxdiv_treatment = 'gygi-baldereschi'
|
||||
ibrav = 0
|
||||
input_dft = 'hse'
|
||||
nat = 1
|
||||
nosym = .true.
|
||||
nspin = 2
|
||||
ntyp = 1
|
||||
occupations = 'smearing'
|
||||
smearing = 'fermi-dirac'
|
||||
tot_charge = 0
|
||||
tot_magnetization = 4
|
||||
/
|
||||
|
||||
&ELECTRONS
|
||||
conv_thr = 1e-06
|
||||
diagonalization = 'david'
|
||||
electron_maxstep = 1000
|
||||
mixing_beta = 0.2
|
||||
mixing_mode = 'plain'
|
||||
/
|
||||
|
||||
|
||||
ATOMIC_SPECIES
|
||||
Fe 55.845 Fe.opt.upf
|
||||
|
||||
ATOMIC_POSITIONS alat
|
||||
Fe 14.17294600 14.17294741 14.17294883
|
||||
|
||||
K_POINTS automatic
|
||||
1 1 1 0 0 0
|
||||
|
||||
CELL_PARAMETERS cubic
|
||||
28.34589199 0.00000000 0.00000000
|
||||
0.00000000 28.34589483 0.00000000
|
||||
-0.00000000 0.00000000 28.34589766
|
||||
|
||||
|
||||
Loading…
Reference in New Issue