From 93be2d264ef8b9f7746a29ad46f67ed9e3127f57 Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Sat, 15 Jul 2017 14:52:08 -0500
Subject: [PATCH] Detect correct integer type in lammps python interface
---
examples/python/py_integrate.py | 15 ++++++++++----
python/lammps.py | 36 ++++++++++++++++++++++++---------
2 files changed, 37 insertions(+), 14 deletions(-)
diff --git a/examples/python/py_integrate.py b/examples/python/py_integrate.py
index ca45c0bcd0..5884ae19e8 100644
--- a/examples/python/py_integrate.py
+++ b/examples/python/py_integrate.py
@@ -4,9 +4,14 @@ import ctypes
import traceback
import numpy as np
-class LAMMPSIntegrator(object):
- def __init__(self, ptr):
+class LAMMPSFix(object):
+ def __init__(self, ptr, group_name="all"):
self.lmp = lammps.lammps(ptr=ptr)
+ self.group_name = group_name
+
+class LAMMPSIntegrator(LAMMPSFix):
+ def __init__(self, ptr, group_name="all"):
+ super(LAMMPSIntegrator, self).__init__(ptr, group_name)
def init(self):
pass
@@ -29,8 +34,9 @@ class LAMMPSIntegrator(object):
class NVE(LAMMPSIntegrator):
""" Python implementation of fix/nve """
- def __init__(self, ptr):
+ def __init__(self, ptr, group_name="all"):
super(NVE, self).__init__(ptr)
+ assert(self.group_name == "all")
def init(self):
dt = self.lmp.extract_global("dt", 1)
@@ -66,8 +72,9 @@ class NVE(LAMMPSIntegrator):
class NVE_Opt(LAMMPSIntegrator):
""" Tuned Python implementation of fix/nve """
- def __init__(self, ptr):
+ def __init__(self, ptr, group_name="all"):
super(NVE_Opt, self).__init__(ptr)
+ assert(self.group_name == "all")
def init(self):
dt = self.lmp.extract_global("dt", 1)
diff --git a/python/lammps.py b/python/lammps.py
index 944eaeabf5..a53bc431be 100644
--- a/python/lammps.py
+++ b/python/lammps.py
@@ -37,7 +37,7 @@ def get_ctypes_int(size):
return c_int32
elif size == 8:
return c_int64
- return c_int
+ return c_int
class MPIAbortException(Exception):
def __init__(self, message):
@@ -266,25 +266,41 @@ class lammps(object):
def __init__(self, lmp):
self.lmp = lmp
+ def _ctype_to_numpy_int(self, ctype_int):
+ if ctype_int == c_int32:
+ return np.int32
+ elif ctype_int == c_int64:
+ return np.int64
+ return np.intc
+
def extract_atom_iarray(self, name, nelem, dim=1):
+ if name in ['id', 'molecule']:
+ c_int_type = self.lmp.c_tagint
+ elif name in ['image']:
+ c_int_type = self.lmp.c_imageint
+ else:
+ c_int_type = c_int
+
+ np_int_type = self._ctype_to_numpy_int(c_int_type)
+
if dim == 1:
- tmp = self.lmp.extract_atom(name, 0)
- ptr = cast(tmp, POINTER(c_int * nelem))
+ tmp = self.lmp.extract_atom(name, 0)
+ ptr = cast(tmp, POINTER(c_int_type * nelem))
else:
- tmp = self.lmp.extract_atom(name, 1)
- ptr = cast(tmp[0], POINTER(c_int * nelem * dim))
+ tmp = self.lmp.extract_atom(name, 1)
+ ptr = cast(tmp[0], POINTER(c_int_type * nelem * dim))
- a = np.frombuffer(ptr.contents, dtype=np.intc)
+ a = np.frombuffer(ptr.contents, dtype=np_int_type)
a.shape = (nelem, dim)
return a
def extract_atom_darray(self, name, nelem, dim=1):
if dim == 1:
- tmp = self.lmp.extract_atom(name, 2)
- ptr = cast(tmp, POINTER(c_double * nelem))
+ tmp = self.lmp.extract_atom(name, 2)
+ ptr = cast(tmp, POINTER(c_double * nelem))
else:
- tmp = self.lmp.extract_atom(name, 3)
- ptr = cast(tmp[0], POINTER(c_double * nelem * dim))
+ tmp = self.lmp.extract_atom(name, 3)
+ ptr = cast(tmp[0], POINTER(c_double * nelem * dim))
a = np.frombuffer(ptr.contents)
a.shape = (nelem, dim)
--
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