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nexus: update tests for recent changes

This commit is contained in:
Jaron Krogel 2019-06-28 13:43:23 -04:00
parent ba0e62ad98
commit 7c6a745f73
17 changed files with 146 additions and 79 deletions
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12
nexus/bin/nxs-test
View File

@ -2298,11 +2298,11 @@ def machines():
('summit' , 'n2_t2_e' ) : 'jsrun -a 10 -r 2 -b rs -c 20 -d packed -n 4 -g 0 test.x',
('summit' , 'n2_t2_e_g6' ) : 'jsrun -a 3 -r 6 -b rs -c 6 -d packed -n 12 -g 1 test.x',
('summit' , 'n2_t2_g6' ) : 'jsrun -a 3 -r 6 -b rs -c 6 -d packed -n 12 -g 1 test.x',
('supermuc' , 'n1' ) : 'mpiexec -n 40 test.x',
('supermuc' , 'n1' ) : 'mpiexec -n 28 test.x',
('supermuc' , 'n1_p1' ) : 'mpiexec -n 1 test.x',
('supermuc' , 'n2' ) : 'mpiexec -n 80 test.x',
('supermuc' , 'n2_t2' ) : 'mpiexec -n 40 test.x',
('supermuc' , 'n2_t2_e' ) : 'mpiexec -n 40 test.x',
('supermuc' , 'n2' ) : 'mpiexec -n 56 test.x',
('supermuc' , 'n2_t2' ) : 'mpiexec -n 28 test.x',
('supermuc' , 'n2_t2_e' ) : 'mpiexec -n 28 test.x',
('supermuc' , 'n2_t2_p2' ) : 'mpiexec -n 4 test.x',
('supermucng' , 'n1' ) : 'mpiexec -n 48 test.x',
('supermucng' , 'n1_p1' ) : 'mpiexec -n 1 test.x',
@ -2905,6 +2905,10 @@ def pwscf_input():
pseudos = ['V.opt.upf','O.opt.upf'],
kgrid = (6,6,6),
kshift = (0,0,0),
# added for reverse compatibility
celldm = {1:1.0},
cell_option = 'alat',
positions_option = 'alat',
)
generations[infile] = pw

123
nexus/lib/pwscf_input.py
View File

@ -204,6 +204,7 @@ class PwscfInputBase(DevBase):
'esm_efield','fcp_mu','london_c6','london_rvdw','xdm_a1','xdm_a2',
# 6.3 additions
'block_1','block_2','block_height','zgate','ts_vdw_econv_thr',
'starting_charge'
]
strs=[
# pre 5.4
@ -245,7 +246,7 @@ class PwscfInputBase(DevBase):
species_arrays = [
'starting_magnetization', 'hubbard_alpha', 'hubbard_u', 'hubbard_j0',
'hubbard_beta', 'hubbard_j', 'angle1', 'angle2',
'london_c6', 'london_rvdw',
'london_c6', 'london_rvdw','starting_charge',
]
species_array_indices = obj(hubbard_j=1)
@ -510,7 +511,11 @@ class Card(Element):
def change_specifier(self,new_specifier):
self.not_implemented()
#end def change_specifier
#end def change_specifier
def change_option(self,*args,**kwargs):
self.change_specifier(*args,**kwargs)
#end def change_option
#end class Card
@ -1050,7 +1055,7 @@ class atomic_positions(Card):
def change_specifier(self,new_specifier,pwi):
scale,axes = pwi.get_common_vars('scale','axes')
scale = pwi.get_common_vars('scale')
pos = self.positions
@ -1062,6 +1067,7 @@ class atomic_positions(Card):
elif spec=='angstrom':
pos *= convert(1.,'A','B')
elif spec=='crystal':
axes = pwi.get_common_vars('axes')
pos = dot(pos,axes)
else:
self.error('old specifier for atomic_positions is invalid\n old specifier: '+spec+'\n valid options: alat, bohr, angstrom, crystal')
@ -1075,6 +1081,7 @@ class atomic_positions(Card):
elif spec=='angstrom':
pos /= convert(1.,'A','B')
elif spec=='crystal':
axes = pwi.get_common_vars('axes')
pos = dot(pos,inv(axes))
else:
self.error('new specifier for atomic_positions is invalid\n new specifier: '+spec+'\n valid options: alat, bohr, angstrom, crystal')
@ -1219,6 +1226,37 @@ class cell_parameters(Card):
def write_text(self):
return array_to_string(self.vectors)
#end def write_text
def change_specifier(self,new_specifier,pwi):
scale = pwi.get_common_vars('scale')
vec = self.vectors
spec = self.specifier
if spec=='alat' or spec=='':
vec *= scale
elif spec=='bohr':
None
elif spec=='angstrom':
vec *= convert(1.,'A','B')
else:
self.error('old specifier for cell_parameters is invalid\nold specifier: '+spec+'\nvalid options: alat, bohr, angstrom')
#end if
spec = new_specifier
if spec=='alat' or spec=='':
vec /= scale
elif spec=='bohr':
None
elif spec=='angstrom':
vec /= convert(1.,'A','B')
else:
self.error('new specifier for cell_parameters is invalid\nnew specifier: '+spec+'\nvalid options: alat, bohr, angstrom')
#end if
self.vectors = vec
self.specifier = new_specifier
#end def change_specifier
#end class cell_parameters
@ -1465,20 +1503,16 @@ class PwscfInput(SimulationInput):
def get_common_vars(self,*vars):
scale = None
scale = 1.0
axes = None
kaxes = None
if 'celldm(1)' in self.system:
scale = self.system['celldm(1)']
elif 'ibrav' in self.system and self.system.ibrav==0:
scale = 1.0
#end if
if scale!=None:
if 'cell_parameters' in self:
axes = scale*array(self.cell_parameters.vectors)
kaxes = 2*pi*inv(axes).T
#end if
if 'cell_parameters' in self:
axes = scale*array(self.cell_parameters.vectors)
kaxes = 2*pi*inv(axes).T
#end if
vals = []
@ -1579,7 +1613,7 @@ class PwscfInput(SimulationInput):
#end if
#end for
self.atomic_positions.specifier = 'alat'
self.atomic_positions.specifier = 'bohr'
self.atomic_positions.positions = s.pos.copy()
self.atomic_positions.atoms = list(s.elem)
if s.frozen!=None:
@ -1670,7 +1704,7 @@ class PwscfInput(SimulationInput):
#end if
#end for
self.atomic_positions.specifier = 'alat'
self.atomic_positions.specifier = 'bohr'
self.atomic_positions.positions = s.pos.copy()
self.atomic_positions.atoms = list(s.elem)
if s.frozen!=None:
@ -1957,20 +1991,34 @@ def generate_any_pwscf_input(**kwargs):
#end for
#process other keywords
use_folded = kwargs.delete_required('use_folded')
kgrid = kwargs.delete_required('kgrid')
kshift = kwargs.delete_required('kshift')
system = kwargs.delete_optional('system',None)
pseudos = kwargs.delete_optional('pseudos',[])
elem_order = kwargs.delete_optional('elem_order',None)
mass = kwargs.delete_optional('mass',None)
elem = kwargs.delete_optional('elem',None)
pos = kwargs.delete_optional('pos',None)
pos_specifier = kwargs.delete_optional('pos_specifier',None)
totmag_sys = kwargs.delete_optional('totmag_sys',False)
start_mag = kwargs.delete_optional('start_mag',None)
bandfac = kwargs.delete_optional('bandfac',None)
nogamma = kwargs.delete_optional('nogamma',False)
use_folded = kwargs.delete_required('use_folded')
kgrid = kwargs.delete_required('kgrid')
kshift = kwargs.delete_required('kshift')
system = kwargs.delete_optional('system',None)
pseudos = kwargs.delete_optional('pseudos',[])
elem_order = kwargs.delete_optional('elem_order',None)
mass = kwargs.delete_optional('mass',None)
elem = kwargs.delete_optional('elem',None)
pos = kwargs.delete_optional('pos',None)
totmag_sys = kwargs.delete_optional('totmag_sys',False)
start_mag = kwargs.delete_optional('start_mag',None)
bandfac = kwargs.delete_optional('bandfac',None)
nogamma = kwargs.delete_optional('nogamma',False)
positions_option = kwargs.delete_optional('pos_specifier',None)
if positions_option is None:
positions_option = kwargs.delete_optional('positions_option',None)
#end if
if positions_option is None:
positions_option = kwargs.delete_optional('atomic_positions_option',None)
#end if
kpoints_option = kwargs.delete_optional('kpoints_option',None)
if kpoints_option is None:
kpoints_option = kwargs.delete_optional('k_points_option',None)
#end if
cell_option = kwargs.delete_optional('cell_option',None)
if cell_option is None:
cell_option = kwargs.delete_optional('cell_parameters_option',None)
#end if
# pseudopotentials
pseudopotentials = obj()
@ -1997,8 +2045,8 @@ def generate_any_pwscf_input(**kwargs):
if pos is None:
PwscfInput.class_error('"pos" must be provided when "elem" is given','generate_pwscf_input')
#end if
if pos_specifier is None:
PwscfInput.class_error('"pos_specifier" must be provided when "elem" is given','generate_pwscf_input')
if positions_option is None:
PwscfInput.class_error('"atomic_positions_option" must be provided when "elem" is given','generate_pwscf_input')
#end if
# fill in atomic_species
@ -2025,7 +2073,7 @@ def generate_any_pwscf_input(**kwargs):
#end for
# fill in atomic_positions
pw.atomic_positions.specifier = pos_specifier
pw.atomic_positions.specifier = positions_option
pw.atomic_positions.positions = array(pos,dtype=float)
pw.atomic_positions.atoms = list(elem)
#end if
@ -2136,6 +2184,21 @@ def generate_any_pwscf_input(**kwargs):
# )
#end if
# adjust card options, if requested
options = obj(
atomic_positions = positions_option,
k_points = kpoints_option,
cell_parameters = cell_option,
)
for card_name,option in options.items():
if option is not None:
if card_name not in pw:
PwscfInput.class_error('Card option provided for card "{}" but card is not present\noption provided: {}'.format(card_name,option))
#end if
pw[card_name].change_option(option,pw)
#end if
#end for
# check for misformatted kpoints
if len(pw.k_points)==0:
PwscfInput.class_error('k_points section has not been filled in\nplease provide k-point information in either of\n 1) the kgrid input argument\n 2) in the PhysicalSystem object (system input argument)','generate_pwscf_input')

6
nexus/tests/reference/user_examples/qmcpack/H2O/runs/scf.in
View File

@ -12,7 +12,7 @@
/
&SYSTEM
celldm(1) = 1.0
!celldm(1) = 1.0
degauss = 0.001
ecutrho = 400
ecutwfc = 50
@ -38,7 +38,7 @@ ATOMIC_SPECIES
H 1.00794 H.BFD.upf
O 15.999 O.BFD.upf
ATOMIC_POSITIONS alat
ATOMIC_POSITIONS bohr
O 4.05580089 4.05580089 3.00901473
H 4.05580089 1.35193363 5.10258705
H 4.05580089 6.75966815 5.10258705
@ -46,7 +46,7 @@ ATOMIC_POSITIONS alat
K_POINTS automatic
1 1 1 0 0 0
CELL_PARAMETERS alat
CELL_PARAMETERS bohr
8.11160178 0.00000000 0.00000000
0.00000000 8.11160178 0.00000000
0.00000000 0.00000000 8.11160178

6
nexus/tests/reference/user_examples/qmcpack/LiH/runs/nscf.in
View File

@ -12,7 +12,7 @@
/
&SYSTEM
celldm(1) = 1.0
!celldm(1) = 1.0
degauss = 0.0001
ecutrho = 1800
ecutwfc = 450
@ -38,14 +38,14 @@ ATOMIC_SPECIES
H 1.00794 H.TN-DF.upf
Li 6.941 Li.TN-DF.upf
ATOMIC_POSITIONS alat
ATOMIC_POSITIONS bohr
Li 0.00000000 0.00000000 0.00000000
H 3.55000000 3.55000000 3.55000000
K_POINTS automatic
1 1 1 0 0 0
CELL_PARAMETERS alat
CELL_PARAMETERS bohr
3.55000000 3.55000000 0.00000000
-0.00000000 3.55000000 3.55000000
3.55000000 0.00000000 3.55000000

6
nexus/tests/reference/user_examples/qmcpack/LiH/runs/scf.in
View File

@ -12,7 +12,7 @@
/
&SYSTEM
celldm(1) = 1.0
!celldm(1) = 1.0
degauss = 0.0001
ecutrho = 1800
ecutwfc = 450
@ -38,14 +38,14 @@ ATOMIC_SPECIES
H 1.00794 H.TN-DF.upf
Li 6.941 Li.TN-DF.upf
ATOMIC_POSITIONS alat
ATOMIC_POSITIONS bohr
Li 0.00000000 0.00000000 0.00000000
H 3.55000000 3.55000000 3.55000000
K_POINTS automatic
7 7 7 1 1 1
CELL_PARAMETERS alat
CELL_PARAMETERS bohr
3.55000000 3.55000000 0.00000000
-0.00000000 3.55000000 3.55000000
3.55000000 0.00000000 3.55000000

6
nexus/tests/reference/user_examples/qmcpack/c20/runs/c20/scf/scf.in
View File

@ -12,7 +12,7 @@
/
&SYSTEM
celldm(1) = 1.0
!celldm(1) = 1.0
degauss = 0.0001
ecutrho = 600
ecutwfc = 150
@ -38,7 +38,7 @@
ATOMIC_SPECIES
C 12.011 C.BFD.upf
ATOMIC_POSITIONS alat
ATOMIC_POSITIONS bohr
C 5.67201488 2.07077135 6.12363826
C 6.75261319 10.35385673 6.12363826
C 7.08201324 3.22522394 3.94377340
@ -63,7 +63,7 @@ ATOMIC_POSITIONS alat
K_POINTS automatic
1 1 1 0 0 0
CELL_PARAMETERS alat
CELL_PARAMETERS bohr
12.42462807 0.00000000 0.00000000
0.00000000 12.42462807 0.00000000
0.00000000 0.00000000 12.42462807

6
nexus/tests/reference/user_examples/qmcpack/diamond/runs/diamond/scf/scf.in
View File

@ -7,7 +7,7 @@
/
&SYSTEM
celldm(1) = 1.0
!celldm(1) = 1.0
ecutwfc = 200
ibrav = 0
input_dft = 'lda'
@ -26,7 +26,7 @@
ATOMIC_SPECIES
C 12.011 C.BFD.upf
ATOMIC_POSITIONS alat
ATOMIC_POSITIONS bohr
C 0.00000000 0.00000000 0.00000000
C 1.68658058 1.68658058 1.68658058
@ -41,7 +41,7 @@ K_POINTS crystal
0.00000000 0.50000000 0.50000000 0.12500000
0.50000000 0.50000000 0.50000000 0.12500000
CELL_PARAMETERS alat
CELL_PARAMETERS bohr
3.37316115 3.37316115 0.00000000
0.00000000 3.37316115 3.37316115
3.37316115 0.00000000 3.37316115

6
nexus/tests/reference/user_examples/qmcpack/diamond/runs/diamond_vacancy/relax/relax.in
View File

@ -6,7 +6,7 @@
/
&SYSTEM
celldm(1) = 1.0
!celldm(1) = 1.0
ecutwfc = 35
ibrav = 0
input_dft = 'lda'
@ -28,7 +28,7 @@
ATOMIC_SPECIES
C 12.011 C.BFD.upf
ATOMIC_POSITIONS alat
ATOMIC_POSITIONS bohr
C 0.00000000 0.00000000 0.00000000
C 3.37316115 3.37316115 0.00000000
C 5.05974172 5.05974172 1.68658057
@ -48,7 +48,7 @@ ATOMIC_POSITIONS alat
K_POINTS automatic
2 2 2 0 0 0
CELL_PARAMETERS alat
CELL_PARAMETERS bohr
6.74632229 6.74632229 0.00000000
-0.00000000 6.74632229 6.74632229
6.74632229 0.00000000 6.74632229

6
nexus/tests/reference/user_examples/qmcpack/diamond/runs/diamond_vacancy/scf/scf.in
View File

@ -6,7 +6,7 @@
/
&SYSTEM
celldm(1) = 1.0
!celldm(1) = 1.0
ecutwfc = 75
ibrav = 0
input_dft = 'lda'
@ -24,7 +24,7 @@
ATOMIC_SPECIES
C 12.011 C.BFD.upf
ATOMIC_POSITIONS alat
ATOMIC_POSITIONS bohr
C 0.00000000 0.00000000 0.00000000
C 3.37316115 3.37316115 0.00000000
C 5.05974172 5.05974172 1.68658057
@ -44,7 +44,7 @@ ATOMIC_POSITIONS alat
K_POINTS automatic
2 2 2 0 0 0
CELL_PARAMETERS alat
CELL_PARAMETERS bohr
6.74632229 6.74632229 0.00000000
0.00000000 6.74632229 6.74632229
6.74632229 0.00000000 6.74632229

6
nexus/tests/reference/user_examples/qmcpack/graphene/runs/graphene/nscf/nscf.in
View File

@ -12,7 +12,7 @@
/
&SYSTEM
celldm(1) = 1.0
!celldm(1) = 1.0
degauss = 0.0001
ecutrho = 600
ecutwfc = 150
@ -38,7 +38,7 @@
ATOMIC_SPECIES
C 12.011 C.BFD.upf
ATOMIC_POSITIONS alat
ATOMIC_POSITIONS bohr
C 0.00000000 0.00000000 0.00000000
C 2.32625287 1.34306272 0.00000000
@ -49,7 +49,7 @@ K_POINTS crystal
0.25000000 0.75000000 0.50000000 0.25000000
0.75000000 0.75000000 0.50000000 0.25000000
CELL_PARAMETERS alat
CELL_PARAMETERS bohr
4.65250574 0.00000000 0.00000000
-2.32625287 4.02918816 0.00000000
-0.00000000 0.00000000 18.89726133

6
nexus/tests/reference/user_examples/qmcpack/graphene/runs/graphene/nscf_opt/nscf.in
View File

@ -12,7 +12,7 @@
/
&SYSTEM
celldm(1) = 1.0
!celldm(1) = 1.0
degauss = 0.0001
ecutrho = 600
ecutwfc = 150
@ -38,14 +38,14 @@
ATOMIC_SPECIES
C 12.011 C.BFD.upf
ATOMIC_POSITIONS alat
ATOMIC_POSITIONS bohr
C 0.00000000 0.00000000 0.00000000
C 2.32625287 1.34306272 0.00000000
K_POINTS automatic
1 1 1 0 0 0
CELL_PARAMETERS alat
CELL_PARAMETERS bohr
4.65250574 0.00000000 0.00000000
-2.32625287 4.02918816 0.00000000
0.00000000 -0.00000000 18.89726133

6
nexus/tests/reference/user_examples/qmcpack/graphene/runs/graphene/scf/scf.in
View File

@ -12,7 +12,7 @@
/
&SYSTEM
celldm(1) = 1.0
!celldm(1) = 1.0
degauss = 0.0001
ecutrho = 600
ecutwfc = 150
@ -38,14 +38,14 @@
ATOMIC_SPECIES
C 12.011 C.BFD.upf
ATOMIC_POSITIONS alat
ATOMIC_POSITIONS bohr
C 0.00000000 0.00000000 0.00000000
C 2.32625287 1.34306272 0.00000000
K_POINTS automatic
8 8 8 1 1 1
CELL_PARAMETERS alat
CELL_PARAMETERS bohr
4.65250574 0.00000000 0.00000000
-2.32625287 4.02918816 0.00000000
0.00000000 0.00000000 18.89726133

6
nexus/tests/reference/user_examples/qmcpack/oxygen_dimer/scale_1.0/scf.in
View File

@ -12,7 +12,7 @@
/
&SYSTEM
celldm(1) = 1.0
!!celldm(1) = 1.0
degauss = 0.0001
ecutrho = 800
ecutwfc = 200
@ -40,14 +40,14 @@
ATOMIC_SPECIES
O 15.999 O.BFD.upf
ATOMIC_POSITIONS alat
ATOMIC_POSITIONS bohr
O 13.03211833 14.17294600 14.17294600
O 15.31377366 14.17294600 14.17294600
K_POINTS automatic
1 1 1 0 0 0
CELL_PARAMETERS alat
CELL_PARAMETERS bohr
28.34589199 0.00000000 0.00000000
0.00000000 28.34589199 0.00000000
0.00000000 0.00000000 28.34589199

6
nexus/tests/reference/user_examples/quantum_espresso/relax_Ge_T_vs_kpoints/runs/relax/kgrid_111/relax.in
View File

@ -10,7 +10,7 @@
/
&SYSTEM
celldm(1) = 1.0
!celldm(1) = 1.0
degauss = 0.0001
ecutrho = 200
ecutwfc = 50
@ -43,7 +43,7 @@
ATOMIC_SPECIES
Ge 72.61 Ge.pbe-kjpaw.UPF
ATOMIC_POSITIONS alat
ATOMIC_POSITIONS bohr
Ge 5.34792496 5.34792496 5.34792496
Ge 0.00000000 0.00000000 0.00000000
Ge 2.67396248 2.67396248 2.67396248
@ -65,7 +65,7 @@ ATOMIC_POSITIONS alat
K_POINTS automatic
1 1 1 1 1 1
CELL_PARAMETERS alat
CELL_PARAMETERS bohr
10.69584991 10.69584991 0.00000000
0.00000000 10.69584991 10.69584991
10.69584991 0.00000000 10.69584991

6
nexus/tests/reference/user_examples/quantum_espresso/relax_Ge_T_vs_kpoints/runs/relax/kgrid_222/relax.in
View File

@ -10,7 +10,7 @@
/
&SYSTEM
celldm(1) = 1.0
!celldm(1) = 1.0
degauss = 0.0001
ecutrho = 200
ecutwfc = 50
@ -43,7 +43,7 @@
ATOMIC_SPECIES
Ge 72.61 Ge.pbe-kjpaw.UPF
ATOMIC_POSITIONS alat
ATOMIC_POSITIONS bohr
Ge 5.34792496 5.34792496 5.34792496
Ge 0.00000000 0.00000000 0.00000000
Ge 2.67396248 2.67396248 2.67396248
@ -65,7 +65,7 @@ ATOMIC_POSITIONS alat
K_POINTS automatic
2 2 2 1 1 1
CELL_PARAMETERS alat
CELL_PARAMETERS bohr
10.69584991 10.69584991 0.00000000
0.00000000 10.69584991 10.69584991
10.69584991 0.00000000 10.69584991

6
nexus/tests/reference/user_examples/quantum_espresso/relax_Ge_T_vs_kpoints/runs/relax/kgrid_444/relax.in
View File

@ -10,7 +10,7 @@
/
&SYSTEM
celldm(1) = 1.0
!celldm(1) = 1.0
degauss = 0.0001
ecutrho = 200
ecutwfc = 50
@ -43,7 +43,7 @@
ATOMIC_SPECIES
Ge 72.61 Ge.pbe-kjpaw.UPF
ATOMIC_POSITIONS alat
ATOMIC_POSITIONS bohr
Ge 5.34792496 5.34792496 5.34792496
Ge 0.00000000 0.00000000 0.00000000
Ge 2.67396248 2.67396248 2.67396248
@ -65,7 +65,7 @@ ATOMIC_POSITIONS alat
K_POINTS automatic
4 4 4 1 1 1
CELL_PARAMETERS alat
CELL_PARAMETERS bohr
10.69584991 10.69584991 0.00000000
0.00000000 10.69584991 10.69584991
10.69584991 0.00000000 10.69584991

6
nexus/tests/reference/user_examples/quantum_espresso/relax_Ge_T_vs_kpoints/runs/relax/kgrid_666/relax.in
View File

@ -10,7 +10,7 @@
/
&SYSTEM
celldm(1) = 1.0
!celldm(1) = 1.0
degauss = 0.0001
ecutrho = 200
ecutwfc = 50
@ -43,7 +43,7 @@
ATOMIC_SPECIES
Ge 72.61 Ge.pbe-kjpaw.UPF
ATOMIC_POSITIONS alat
ATOMIC_POSITIONS bohr
Ge 5.34792496 5.34792496 5.34792496
Ge 0.00000000 0.00000000 0.00000000
Ge 2.67396248 2.67396248 2.67396248
@ -65,7 +65,7 @@ ATOMIC_POSITIONS alat
K_POINTS automatic
6 6 6 1 1 1
CELL_PARAMETERS alat
CELL_PARAMETERS bohr
10.69584991 10.69584991 0.00000000
0.00000000 10.69584991 10.69584991
10.69584991 0.00000000 10.69584991