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This commit is contained in:
Axel Kohlmeyer
2021-05-09 20:25:20 -04:00
parent 92fe1373a5
commit 54b7baea7b
1 changed files with 36 additions and 35 deletions
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71
python/lammps/core.py
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@ -777,6 +777,7 @@ class lammps(object):
target_type = float target_type = float
elif dtype == LAMMPS_STRING: elif dtype == LAMMPS_STRING:
self.lib.lammps_extract_global.restype = c_char_p self.lib.lammps_extract_global.restype = c_char_p
target_type = str
ptr = self.lib.lammps_extract_global(self.lmp, name) ptr = self.lib.lammps_extract_global(self.lmp, name)
if ptr: if ptr:
@ -1112,20 +1113,20 @@ class lammps(object):
# return vector of atom properties gathered across procs # return vector of atom properties gathered across procs
# 3 variants to match src/library.cpp # 3 variants to match src/library.cpp
# name = atom property recognized by LAMMPS in atom->extract() # name = atom property recognized by LAMMPS in atom->extract()
# type = 0 for integer values, 1 for double values # dtype = 0 for integer values, 1 for double values
# count = number of per-atom valus, 1 for type or charge, 3 for x or f # count = number of per-atom valus, 1 for type or charge, 3 for x or f
# returned data is a 1d vector - doc how it is ordered? # returned data is a 1d vector - doc how it is ordered?
# NOTE: need to insure are converting to/from correct Python type # NOTE: need to insure are converting to/from correct Python type
# e.g. for Python list or NumPy or ctypes # e.g. for Python list or NumPy or ctypes
def gather_atoms(self,name,type,count): def gather_atoms(self,name,dtype,count):
if name: name = name.encode() if name: name = name.encode()
natoms = self.get_natoms() natoms = self.get_natoms()
with ExceptionCheck(self): with ExceptionCheck(self):
if type == 0: if dtype == 0:
data = ((count*natoms)*c_int)() data = ((count*natoms)*c_int)()
self.lib.lammps_gather_atoms(self.lmp,name,type,count,data) self.lib.lammps_gather_atoms(self.lmp,name,type,count,data)
elif type == 1: elif dtype == 1:
data = ((count*natoms)*c_double)() data = ((count*natoms)*c_double)()
self.lib.lammps_gather_atoms(self.lmp,name,type,count,data) self.lib.lammps_gather_atoms(self.lmp,name,type,count,data)
else: else:
@ -1134,29 +1135,29 @@ class lammps(object):
# ------------------------------------------------------------------------- # -------------------------------------------------------------------------
def gather_atoms_concat(self,name,type,count): def gather_atoms_concat(self,name,dtype,count):
if name: name = name.encode() if name: name = name.encode()
natoms = self.get_natoms() natoms = self.get_natoms()
with ExceptionCheck(self): with ExceptionCheck(self):
if type == 0: if dtype == 0:
data = ((count*natoms)*c_int)() data = ((count*natoms)*c_int)()
self.lib.lammps_gather_atoms_concat(self.lmp,name,type,count,data) self.lib.lammps_gather_atoms_concat(self.lmp,name,type,count,data)
elif type == 1: elif dtype == 1:
data = ((count*natoms)*c_double)() data = ((count*natoms)*c_double)()
self.lib.lammps_gather_atoms_concat(self.lmp,name,type,count,data) self.lib.lammps_gather_atoms_concat(self.lmp,name,type,count,data)
else: else:
return None return None
return data return data
def gather_atoms_subset(self,name,type,count,ndata,ids): def gather_atoms_subset(self,name,dtype,count,ndata,ids):
if name: name = name.encode() if name: name = name.encode()
with ExceptionCheck(self): with ExceptionCheck(self):
if type == 0: if dtype == 0:
data = ((count*ndata)*c_int)() data = ((count*ndata)*c_int)()
self.lib.lammps_gather_atoms_subset(self.lmp,name,type,count,ndata,ids,data) self.lib.lammps_gather_atoms_subset(self.lmp,name,dtype,count,ndata,ids,data)
elif type == 1: elif dtype == 1:
data = ((count*ndata)*c_double)() data = ((count*ndata)*c_double)()
self.lib.lammps_gather_atoms_subset(self.lmp,name,type,count,ndata,ids,data) self.lib.lammps_gather_atoms_subset(self.lmp,name,dtype,count,ndata,ids,data)
else: else:
return None return None
return data return data
@ -1172,17 +1173,17 @@ class lammps(object):
# NOTE: need to insure are converting to/from correct Python type # NOTE: need to insure are converting to/from correct Python type
# e.g. for Python list or NumPy or ctypes # e.g. for Python list or NumPy or ctypes
def scatter_atoms(self,name,type,count,data): def scatter_atoms(self,name,dtype,count,data):
if name: name = name.encode() if name: name = name.encode()
with ExceptionCheck(self): with ExceptionCheck(self):
self.lib.lammps_scatter_atoms(self.lmp,name,type,count,data) self.lib.lammps_scatter_atoms(self.lmp,name,dtype,count,data)
# ------------------------------------------------------------------------- # -------------------------------------------------------------------------
def scatter_atoms_subset(self,name,type,count,ndata,ids,data): def scatter_atoms_subset(self,name,dtype,count,ndata,ids,data):
if name: name = name.encode() if name: name = name.encode()
with ExceptionCheck(self): with ExceptionCheck(self):
self.lib.lammps_scatter_atoms_subset(self.lmp,name,type,count,ndata,ids,data) self.lib.lammps_scatter_atoms_subset(self.lmp,name,dtype,count,ndata,ids,data)
# return vector of atom/compute/fix properties gathered across procs # return vector of atom/compute/fix properties gathered across procs
# 3 variants to match src/library.cpp # 3 variants to match src/library.cpp
@ -1192,43 +1193,43 @@ class lammps(object):
# returned data is a 1d vector - doc how it is ordered? # returned data is a 1d vector - doc how it is ordered?
# NOTE: need to insure are converting to/from correct Python type # NOTE: need to insure are converting to/from correct Python type
# e.g. for Python list or NumPy or ctypes # e.g. for Python list or NumPy or ctypes
def gather(self,name,type,count): def gather(self,name,dtype,count):
if name: name = name.encode() if name: name = name.encode()
natoms = self.get_natoms() natoms = self.get_natoms()
with ExceptionCheck(self): with ExceptionCheck(self):
if type == 0: if dtype == 0:
data = ((count*natoms)*c_int)() data = ((count*natoms)*c_int)()
self.lib.lammps_gather(self.lmp,name,type,count,data) self.lib.lammps_gather(self.lmp,name,dtype,count,data)
elif type == 1: elif dtype == 1:
data = ((count*natoms)*c_double)() data = ((count*natoms)*c_double)()
self.lib.lammps_gather(self.lmp,name,type,count,data) self.lib.lammps_gather(self.lmp,name,dtype,count,data)
else: else:
return None return None
return data return data
def gather_concat(self,name,type,count): def gather_concat(self,name,dtype,count):
if name: name = name.encode() if name: name = name.encode()
natoms = self.get_natoms() natoms = self.get_natoms()
with ExceptionCheck(self): with ExceptionCheck(self):
if type == 0: if dtype == 0:
data = ((count*natoms)*c_int)() data = ((count*natoms)*c_int)()
self.lib.lammps_gather_concat(self.lmp,name,type,count,data) self.lib.lammps_gather_concat(self.lmp,name,dtype,count,data)
elif type == 1: elif dtype == 1:
data = ((count*natoms)*c_double)() data = ((count*natoms)*c_double)()
self.lib.lammps_gather_concat(self.lmp,name,type,count,data) self.lib.lammps_gather_concat(self.lmp,name,dtype,count,data)
else: else:
return None return None
return data return data
def gather_subset(self,name,type,count,ndata,ids): def gather_subset(self,name,dtype,count,ndata,ids):
if name: name = name.encode() if name: name = name.encode()
with ExceptionCheck(self): with ExceptionCheck(self):
if type == 0: if dtype == 0:
data = ((count*ndata)*c_int)() data = ((count*ndata)*c_int)()
self.lib.lammps_gather_subset(self.lmp,name,type,count,ndata,ids,data) self.lib.lammps_gather_subset(self.lmp,name,dtype,count,ndata,ids,data)
elif type == 1: elif dtype == 1:
data = ((count*ndata)*c_double)() data = ((count*ndata)*c_double)()
self.lib.lammps_gather_subset(self.lmp,name,type,count,ndata,ids,data) self.lib.lammps_gather_subset(self.lmp,name,dtype,count,ndata,ids,data)
else: else:
return None return None
return data return data
@ -1242,15 +1243,15 @@ class lammps(object):
# NOTE: need to insure are converting to/from correct Python type # NOTE: need to insure are converting to/from correct Python type
# e.g. for Python list or NumPy or ctypes # e.g. for Python list or NumPy or ctypes
def scatter(self,name,type,count,data): def scatter(self,name,dtype,count,data):
if name: name = name.encode() if name: name = name.encode()
with ExceptionCheck(self): with ExceptionCheck(self):
self.lib.lammps_scatter(self.lmp,name,type,count,data) self.lib.lammps_scatter(self.lmp,name,dtype,count,data)
def scatter_subset(self,name,type,count,ndata,ids,data): def scatter_subset(self,name,dtype,count,ndata,ids,data):
if name: name = name.encode() if name: name = name.encode()
with ExceptionCheck(self): with ExceptionCheck(self):
self.lib.lammps_scatter_subset(self.lmp,name,type,count,ndata,ids,data) self.lib.lammps_scatter_subset(self.lmp,name,dtype,count,ndata,ids,data)
# ------------------------------------------------------------------------- # -------------------------------------------------------------------------