a few new lib interface methods
This commit is contained in:
Steven J. Plimpton
@ -80,12 +80,59 @@ lmp.commands_list(cmds)
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# initial thermo should be same as step 20
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natoms = lmp.get_natoms()
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type = natoms*[1]
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atype = natoms*[1]
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lmp.command("delete_atoms group all");
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lmp.create_atoms(natoms,None,type,x,v);
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lmp.create_atoms(natoms,None,atype,x,v);
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lmp.command("run 10");
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############
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# test of new gather/scatter and box extract/reset methods
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# can try this in parallel and with/without atom_modify sort enabled
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lmp.command("write_dump all custom tmp.simple id type x y z fx fy fz");
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x = lmp.gather_atoms("x",1,3)
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f = lmp.gather_atoms("f",1,3)
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if me == 0: print("Gather XF:",x[3],x[9],f[3],f[9])
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ids = lmp.gather_atoms_concat("id",0,1)
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x = lmp.gather_atoms_concat("x",1,3)
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f = lmp.gather_atoms_concat("f",1,3)
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if me == 0: print("Gather concat XF:",ids[0],ids[1],x[0],x[3],f[0],f[3])
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ids = (2*ctypes.c_int)()
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ids[0] = 2
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ids[1] = 4
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x = lmp.gather_atoms_subset("x",1,3,2,ids)
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f = lmp.gather_atoms_subset("f",1,3,2,ids)
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if me == 0: print("Gather subset XF:",x[0],x[3],f[0],f[3])
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x[0] = -1.0
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x[1] = 0.0
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x[2] = 0.0
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x[3] = -2.0
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x[4] = 0.0
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x[5] = 0.0
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ids[0] = 100
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ids[1] = 200
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lmp.scatter_atoms_subset("x",1,3,2,ids,x)
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x = lmp.gather_atoms("x",1,3)
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if me == 0: print("Gather post scatter subset:",
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x[3],x[9],x[297],x[298],x[299],x[597],x[598],x[599])
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boxlo,boxhi,xy,yz,xz,periodicity,box_change = lmp.extract_box()
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if me == 0: print("Box info",boxlo,boxhi,xy,yz,xz,periodicity,box_change)
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lmp.reset_box([0,0,0],[10,10,8],0,0,0)
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boxlo,boxhi,xy,yz,xz,periodicity,box_change = lmp.extract_box()
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if me == 0: print("Box info",boxlo,boxhi,xy,yz,xz,periodicity,box_change)
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# uncomment if running in parallel via Pypar
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#print("Proc %d out of %d procs has" % (me,nprocs), lmp)
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156
python/lammps.py
156
python/lammps.py
@ -94,6 +94,39 @@ class lammps(object):
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if not name: self.lib = CDLL("liblammps.so",RTLD_GLOBAL)
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else: self.lib = CDLL("liblammps_%s.so" % name,RTLD_GLOBAL)
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# define ctypes API for each library method
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# NOTE: should add one of these for each lib function
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self.lib.lammps_extract_box.argtypes = \
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[c_void_p,POINTER(c_double),POINTER(c_double),
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POINTER(c_double),POINTER(c_double),POINTER(c_double),
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POINTER(c_int),POINTER(c_int)]
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self.lib.lammps_extract_box.restype = None
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self.lib.lammps_reset_box.argtypes = \
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[c_void_p,POINTER(c_double),POINTER(c_double),c_double,c_double,c_double]
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self.lib.lammps_reset_box.restype = None
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self.lib.lammps_gather_atoms.argtypes = \
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[c_void_p,c_char_p,c_int,c_int,c_void_p]
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self.lib.lammps_gather_atoms.restype = None
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self.lib.lammps_gather_atoms_concat.argtypes = \
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[c_void_p,c_char_p,c_int,c_int,c_void_p]
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self.lib.lammps_gather_atoms_concat.restype = None
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self.lib.lammps_gather_atoms_subset.argtypes = \
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[c_void_p,c_char_p,c_int,c_int,c_int,POINTER(c_int),c_void_p]
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self.lib.lammps_gather_atoms_subset.restype = None
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self.lib.lammps_scatter_atoms.argtypes = \
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[c_void_p,c_char_p,c_int,c_int,c_void_p]
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self.lib.lammps_scatter_atoms.restype = None
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self.lib.lammps_scatter_atoms_subset.argtypes = \
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[c_void_p,c_char_p,c_int,c_int,c_int,POINTER(c_int),c_void_p]
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self.lib.lammps_scatter_atoms_subset.restype = None
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# if no ptr provided, create an instance of LAMMPS
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# don't know how to pass an MPI communicator from PyPar
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# but we can pass an MPI communicator from mpi4py v2.0.0 and later
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@ -177,6 +210,8 @@ class lammps(object):
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self.c_tagint = get_ctypes_int(self.extract_setting("tagint"))
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self.c_imageint = get_ctypes_int(self.extract_setting("imageint"))
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# shut-down LAMMPS instance
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def __del__(self):
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if self.lmp and self.opened:
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self.lib.lammps_close(self.lmp)
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@ -219,10 +254,16 @@ class lammps(object):
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# send a string of commands
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def commands_string(self,multicmd):
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if type(multicmd) is str:
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multicmd = multicmd.encode()
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if type(multicmd) is str: multicmd = multicmd.encode()
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self.lib.lammps_commands_string(self.lmp,c_char_p(multicmd))
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# extract lammps type byte sizes
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def extract_setting(self, name):
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if name: name = name.encode()
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self.lib.lammps_extract_atom.restype = c_int
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return int(self.lib.lammps_extract_setting(self.lmp,name))
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# extract global info
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def extract_global(self,name,type):
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@ -235,8 +276,35 @@ class lammps(object):
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ptr = self.lib.lammps_extract_global(self.lmp,name)
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return ptr[0]
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# extract global info
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def extract_box(self):
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boxlo = (3*c_double)()
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boxhi = (3*c_double)()
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xy = c_double()
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yz = c_double()
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xz = c_double()
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periodicity = (3*c_int)()
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box_change = c_int()
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self.lib.lammps_extract_box(self.lmp,boxlo,boxhi,
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byref(xy),byref(yz),byref(xz),
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periodicity,byref(box_change))
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boxlo = boxlo[:3]
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boxhi = boxhi[:3]
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xy = xy.value
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yz = yz.value
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xz = xz.value
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periodicity = periodicity[:3]
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box_change = box_change.value
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return boxlo,boxhi,xy,yz,xz,periodicity,box_change
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# extract per-atom info
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# NOTE: need to insure are converting to/from correct Python type
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# e.g. for Python list or NumPy or ctypes
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def extract_atom(self,name,type):
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if name: name = name.encode()
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if type == 0:
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@ -250,14 +318,7 @@ class lammps(object):
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else: return None
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ptr = self.lib.lammps_extract_atom(self.lmp,name)
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return ptr
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# extract lammps type byte sizes
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def extract_setting(self, name):
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if name: name = name.encode()
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self.lib.lammps_extract_atom.restype = c_int
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return int(self.lib.lammps_extract_setting(self.lmp,name))
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@property
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def numpy(self):
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if not self._numpy:
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@ -378,15 +439,6 @@ class lammps(object):
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return result
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return None
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# set variable value
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# value is converted to string
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# returns 0 for success, -1 if failed
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def set_variable(self,name,value):
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if name: name = name.encode()
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if value: value = str(value).encode()
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return self.lib.lammps_set_variable(self.lmp,name,value)
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# return current value of thermo keyword
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def get_thermo(self,name):
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@ -399,14 +451,30 @@ class lammps(object):
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def get_natoms(self):
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return self.lib.lammps_get_natoms(self.lmp)
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# return vector of atom properties gathered across procs, ordered by atom ID
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# set variable value
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# value is converted to string
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# returns 0 for success, -1 if failed
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def set_variable(self,name,value):
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if name: name = name.encode()
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if value: value = str(value).encode()
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return self.lib.lammps_set_variable(self.lmp,name,value)
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# reset simulation box size
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def reset_box(self,boxlo,boxhi,xy,yz,xz):
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cboxlo = (3*c_double)(*boxlo)
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cboxhi = (3*c_double)(*boxhi)
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self.lib.lammps_reset_box(self.lmp,cboxlo,cboxhi,xy,yz,xz)
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# return vector of atom properties gathered across procs
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# 3 variants to match src/library.cpp
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# name = atom property recognized by LAMMPS in atom->extract()
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# type = 0 for integer values, 1 for double values
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# count = number of per-atom valus, 1 for type or charge, 3 for x or f
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# returned data is a 1d vector - doc how it is ordered?
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# NOTE: how could we insure are converting to correct Python type
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# e.g. for Python list or NumPy, etc
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# ditto for extract_atom() above
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# NOTE: need to insure are converting to/from correct Python type
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# e.g. for Python list or NumPy or ctypes
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def gather_atoms(self,name,type,count):
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if name: name = name.encode()
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@ -419,19 +487,47 @@ class lammps(object):
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self.lib.lammps_gather_atoms(self.lmp,name,type,count,data)
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else: return None
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return data
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def gather_atoms_concat(self,name,type,count):
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if name: name = name.encode()
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natoms = self.lib.lammps_get_natoms(self.lmp)
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if type == 0:
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data = ((count*natoms)*c_int)()
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self.lib.lammps_gather_atoms_concat(self.lmp,name,type,count,data)
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elif type == 1:
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data = ((count*natoms)*c_double)()
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self.lib.lammps_gather_atoms_concat(self.lmp,name,type,count,data)
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else: return None
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return data
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# scatter vector of atom properties across procs, ordered by atom ID
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def gather_atoms_subset(self,name,type,count,ndata,ids):
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if name: name = name.encode()
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if type == 0:
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data = ((count*ndata)*c_int)()
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self.lib.lammps_gather_atoms_subset(self.lmp,name,type,count,ndata,ids,data)
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elif type == 1:
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data = ((count*ndata)*c_double)()
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self.lib.lammps_gather_atoms_subset(self.lmp,name,type,count,ndata,ids,data)
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else: return None
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return data
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# scatter vector of atom properties across procs
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# 2 variants to match src/library.cpp
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# name = atom property recognized by LAMMPS in atom->extract()
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# type = 0 for integer values, 1 for double values
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# count = number of per-atom valus, 1 for type or charge, 3 for x or f
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# assume data is of correct type and length, as created by gather_atoms()
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# NOTE: how could we insure are passing correct type to LAMMPS
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# e.g. for Python list or NumPy, etc
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# NOTE: need to insure are converting to/from correct Python type
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# e.g. for Python list or NumPy or ctypes
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def scatter_atoms(self,name,type,count,data):
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if name: name = name.encode()
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self.lib.lammps_scatter_atoms(self.lmp,name,type,count,data)
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def scatter_atoms_subset(self,name,type,count,ndata,ids,data):
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if name: name = name.encode()
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self.lib.lammps_scatter_atoms_subset(self.lmp,name,type,count,ndata,ids,data)
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# create N atoms on all procs
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# N = global number of atoms
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# id = ID of each atom (optional, can be None)
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@ -457,8 +553,8 @@ class lammps(object):
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type_lmp = (c_int * n)()
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type_lmp[:] = type
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self.lib.lammps_create_atoms(self.lmp,n,id_lmp,type_lmp,x,v,image_lmp,shrinkexceed)
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self.lib.lammps_create_atoms(self.lmp,n,id_lmp,type_lmp,x,v,image_lmp,
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shrinkexceed)
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@property
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def uses_exceptions(self):
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