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Merge branch 'master' into lammps-icms

Browse Source 
Resolved Conflicts:
	src/REPLICA/verlet_split.cpp
	src/USER-OMP/fix_omp.cpp
This commit is contained in:
Axel Kohlmeyer
2012-10-26 09:50:01 -04:00
parent 3930d66dfb 8663c92293
commit 5a75a6c827
25 changed files with 1511 additions and 1821 deletions
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2
python/README
View File

@ -9,7 +9,7 @@ doc/Section_python.html and in doc/Section_start.html#start_5.
Basically you need to follow these steps in the src directory:
% make makeshlib # creates Makefile.shlib
% make -f Makefile.shlib g++ # or whatever machine target you wish
% make -f Makefile.shlib g++ # build for whatever machine target you wish
% make install-python # may need to do this via sudo
You can replace the last step with running the python/install.py

19
python/examples/demo.py
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@ -22,11 +22,6 @@ me = 0
#nprocs = pypar.size()
from lammps import lammps
from lammps import LMPINT as INT
from lammps import LMPDOUBLE as DOUBLE
from lammps import LMPIPTR as IPTR
from lammps import LMPDPTR as DPTR
from lammps import LMPDPTRPTR as DPTRPTR
lmp = lammps()
@ -36,9 +31,9 @@ lmp.file("in.demo")
if me == 0: print "\nPython output:"
natoms = lmp.extract_global("natoms",DOUBLE)
mass = lmp.extract_atom("mass",DPTR)
x = lmp.extract_atom("x",DPTRPTR)
natoms = lmp.extract_global("natoms",0)
mass = lmp.extract_atom("mass",2)
x = lmp.extract_atom("x",3)
print "Natoms, mass, x[0][0] coord =",natoms,mass[1],x[0][0]
temp = lmp.extract_compute("thermo_temp",0,0)
@ -53,13 +48,13 @@ print "Velocity component from atom-style variable =",vy[1]
natoms = lmp.get_natoms()
print "Natoms from get_natoms =",natoms
xc = lmp.get_coords()
print "Global coords from get_coords =",xc[0],xc[1],xc[31]
xc = lmp.gather_atoms("x",1,3)
print "Global coords from gather_atoms =",xc[0],xc[1],xc[31]
xc[0] = xc[0] + 1.0
lmp.put_coords(xc)
lmp.scatter_atoms("x",1,3,xc)
print "Changed x[0][0] via put_coords =",x[0][0]
print "Changed x[0][0] via scatter_atoms =",x[0][0]
# uncomment if running in parallel via Pypar
#print "Proc %d out of %d procs has" % (me,nprocs), lmp

12
python/lammps.py
View File

@ -24,8 +24,8 @@ class lammps:
# if name = "g++", load liblammps_g++.so
try:
if not name: self.lib = CDLL("liblammps.so")
else: self.lib = CDLL("liblammps_%s.so" % name)
if not name: self.lib = CDLL("liblammps.so",RTLD_GLOBAL)
else: self.lib = CDLL("liblammps_%s.so" % name,RTLD_GLOBAL)
except:
type,value,tb = sys.exc_info()
traceback.print_exception(type,value,tb)
@ -89,11 +89,11 @@ class lammps:
self.lib.lammps_extract_compute.restype = POINTER(c_double)
ptr = self.lib.lammps_extract_compute(self.lmp,id,style,type)
return ptr[0]
elif type == 1:
if type == 1:
self.lib.lammps_extract_compute.restype = POINTER(c_double)
ptr = self.lib.lammps_extract_compute(self.lmp,id,style,type)
return ptr
elif type == 2:
if type == 2:
self.lib.lammps_extract_compute.restype = POINTER(POINTER(c_double))
ptr = self.lib.lammps_extract_compute(self.lmp,id,style,type)
return ptr
@ -110,11 +110,11 @@ class lammps:
result = ptr[0]
self.lib.lammps_free(ptr)
return result
elif type == 1:
if type == 1:
self.lib.lammps_extract_fix.restype = POINTER(c_double)
ptr = self.lib.lammps_extract_fix(self.lmp,id,style,type,i,j)
return ptr
elif type == 2:
if type == 2:
self.lib.lammps_extract_fix.restype = POINTER(POINTER(c_double))
ptr = self.lib.lammps_extract_fix(self.lmp,id,style,type,i,j)
return ptr