|
|
|
apbs/contrib/iapbs/src/apbs_driver.c | 6 +++---
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|
|
|
apbs/src/CMakeLists.txt | 1 +
|
|
|
|
apbs/tools/CMakeLists.txt | 2 +-
|
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|
|
apbs/tools/python/CMakeLists.txt | 1 +
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|
|
|
apbs/tools/python/apbslib.c | 4 ++--
|
|
|
|
apbs/tools/python/apbslib.i | 4 ++--
|
|
|
|
apbs/tools/python/setup.py | 16 ++++++++++++++++
|
|
|
|
7 files changed, 26 insertions(+), 8 deletions(-)
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|
|
|
|
|
|
|
diff --git a/contrib/iapbs/src/apbs_driver.c b/contrib/iapbs/src/apbs_driver.c
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|
|
|
index c9e443b..e1ad67f 100644
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|
|
|
--- a/contrib/iapbs/src/apbs_driver.c
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|
|
|
+++ b/contrib/iapbs/src/apbs_driver.c
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|
|
|
@@ -595,7 +595,7 @@ int apbsdrv_(
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|
|
|
printPBEPARM(pbeparm);
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|
|
|
|
|
|
|
/* Refine mesh */
|
|
|
|
- if (!preRefineFE(i, nosh, feparm, fetk)) {
|
|
|
|
+ if (!preRefineFE(i, feparm, fetk)) {
|
|
|
|
Vnm_tprint( 2, "Error pre-refining mesh!\n");
|
|
|
|
VJMPERR1(0);
|
|
|
|
}
|
|
|
|
@@ -609,7 +609,7 @@ int apbsdrv_(
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|
|
Vnm_tprint(1, " Beginning solve-estimate-refine cycle:\n");
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|
|
|
for (isolve=0; isolve<feparm->maxsolve; isolve++) {
|
|
|
|
Vnm_tprint(1, " Solve #%d...\n", isolve);
|
|
|
|
- if (!solveFE(i, nosh, pbeparm, feparm, fetk)) {
|
|
|
|
+ if (!solveFE(i, pbeparm, feparm, fetk)) {
|
|
|
|
Vnm_tprint(2, "ERROR SOLVING EQUATION!\n");
|
|
|
|
VJMPERR1(0);
|
|
|
|
}
|
|
|
|
@@ -622,7 +622,7 @@ int apbsdrv_(
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|
|
/* We're not going to refine if we've hit the max number
|
|
|
|
* of solves */
|
|
|
|
if (isolve < (feparm->maxsolve)-1) {
|
|
|
|
- if (!postRefineFE(i, nosh, feparm, fetk)) break;
|
|
|
|
+ if (!postRefineFE(i, feparm, fetk)) break;
|
|
|
|
}
|
|
|
|
bytesTotal = Vmem_bytesTotal();
|
|
|
|
highWater = Vmem_highWaterTotal();
|
|
|
|
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
|
|
|
|
index 44d20fa..2577343 100644
|
|
|
|
--- a/src/CMakeLists.txt
|
|
|
|
+++ b/src/CMakeLists.txt
|
|
|
|
@@ -68,6 +68,7 @@ configure_file(
|
|
|
|
|
|
|
|
if(ENABLE_iAPBS)
|
|
|
|
ADD_LIBRARY(apbs_routines routines.c routines.h)
|
|
|
|
+ target_link_libraries(apbs_routines apbs_mg apbs_fem)
|
|
|
|
INSTALL(TARGETS apbs_routines DESTINATION ${LIBRARY_INSTALL_PATH})
|
|
|
|
INSTALL(FILES apbscfg.h DESTINATION ${HEADER_INSTALL_PATH})
|
|
|
|
endif()
|
|
|
|
diff --git a/tools/CMakeLists.txt b/tools/CMakeLists.txt
|
|
|
|
index 1982a3c..4acbe68 100644
|
|
|
|
--- a/tools/CMakeLists.txt
|
|
|
|
+++ b/tools/CMakeLists.txt
|
|
|
|
@@ -4,5 +4,5 @@ add_subdirectory(mesh)
|
|
|
|
add_subdirectory(manip)
|
|
|
|
|
|
|
|
if(ENABLE_PYTHON)
|
|
|
|
- add_subdirectory(manip)
|
|
|
|
+ add_subdirectory(python)
|
|
|
|
endif(ENABLE_PYTHON)
|
|
|
|
diff --git a/tools/python/CMakeLists.txt b/tools/python/CMakeLists.txt
|
|
|
|
new file mode 100644
|
|
|
|
index 0000000..8b13789
|
|
|
|
--- /dev/null
|
|
|
|
+++ b/tools/python/CMakeLists.txt
|
|
|
|
@@ -0,0 +1 @@
|
|
|
|
+
|
|
|
|
diff --git a/tools/python/apbslib.c b/tools/python/apbslib.c
|
|
|
|
index fef5cc8..feaaa2c 100644
|
|
|
|
--- a/tools/python/apbslib.c
|
|
|
|
+++ b/tools/python/apbslib.c
|
|
|
|
@@ -2504,8 +2504,8 @@ static swig_module_info swig_module = {swig_types, 24, 0, 0, 0, 0};
|
|
|
|
#include "maloc/maloc.h"
|
|
|
|
#include "apbscfg.h"
|
|
|
|
#include "routines.h"
|
|
|
|
-#include "apbs/valist.h"
|
|
|
|
-#include "apbs/vatom.h"
|
|
|
|
+#include "generic/valist.h"
|
|
|
|
+#include "generic/vatom.h"
|
|
|
|
|
|
|
|
|
|
|
|
#include <limits.h>
|
|
|
|
diff --git a/tools/python/apbslib.i b/tools/python/apbslib.i
|
|
|
|
index 17fe521..44d05ea 100644
|
|
|
|
--- a/tools/python/apbslib.i
|
|
|
|
+++ b/tools/python/apbslib.i
|
|
|
|
@@ -15,8 +15,8 @@ Header files:
|
|
|
|
#include "maloc/maloc.h"
|
|
|
|
#include "apbscfg.h"
|
|
|
|
#include "routines.h"
|
|
|
|
-#include "apbs/valist.h"
|
|
|
|
-#include "apbs/vatom.h"
|
|
|
|
+#include "generic/valist.h"
|
|
|
|
+#include "generic/vatom.h"
|
|
|
|
%}
|
|
|
|
|
|
|
|
/*
|
|
|
|
diff --git a/tools/python/setup.py b/tools/python/setup.py
|
|
|
|
new file mode 100644
|
|
|
|
index 0000000..4a20198
|
|
|
|
--- /dev/null
|
|
|
|
+++ b/tools/python/setup.py
|
|
|
|
@@ -0,0 +1,16 @@
|
|
|
|
+from distutils.core import setup, Extension
|
|
|
|
+setup(name='apbs',
|
|
|
|
+ version='1.4.1',
|
|
|
|
+ package_dir={'apbs': '', 'vgrid': 'vgrid'},
|
|
|
|
+ packages=['apbs', 'vgrid'],
|
|
|
|
+ py_modules=['apbslib', 'main', 'noinput'],
|
|
|
|
+ ext_modules=[
|
|
|
|
+ Extension(
|
|
|
|
+ '_apbslib',
|
|
|
|
+ ['apbslib.i'],
|
|
|
|
+ swig_opts=['-module', 'apbslib', '-I../include'],
|
|
|
|
+ include_dirs=["../../src"],
|
|
|
|
+ libraries=["apbs_generic", "apbs_routines"]
|
|
|
|
+ )
|
|
|
|
+ ],
|
|
|
|
+ )
|