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-rw-r--r--.SRCINFO6
-rw-r--r--PKGBUILD15
-rw-r--r--globals_bem.patch318
3 files changed, 6 insertions, 333 deletions
diff --git a/.SRCINFO b/.SRCINFO
index 0c80aa6d1c8b..ab312e74441f 100644
--- a/.SRCINFO
+++ b/.SRCINFO
@@ -1,7 +1,7 @@
pkgbase = apbs
pkgdesc = Software for biomolecular electrostatics and solvation calculations
pkgver = 3.0.0
- pkgrel = 1
+ pkgrel = 2
url = http://www.poissonboltzmann.org/
arch = x86_64
license = custom
@@ -10,8 +10,6 @@ pkgbase = apbs
makedepends = git
makedepends = wget
depends = python
- depends = boost
- depends = eigen
depends = termcap
depends = swig
provides = apbs
@@ -20,10 +18,8 @@ pkgbase = apbs
options = !buildflags
source = https://github.com/Electrostatics/apbs/releases/download/v3.0.0/APBS-3.0.0_Source-Code.tar.gz
source = globals_apbs.patch
- source = globals_bem.patch
sha256sums = 3cf8b227a205cdcbd13246489427606f256f2356343fc954734fd39975e5cbdb
sha256sums = 6bc1f2dc7a454aa8b0799641f78ee571ba04795821a9bcac356cbe496bdb3df6
- sha256sums = 3d8cc3d052a60a36d79ab95b8c89c03d79bdcca9958c2936513d92c23acb097b
pkgname = apbs
diff --git a/PKGBUILD b/PKGBUILD
index 9befa7a6ab26..1c07ff9287ea 100644
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -2,21 +2,19 @@
pkgname=apbs
pkgver=3.0.0
-pkgrel=1
+pkgrel=2
pkgdesc="Software for biomolecular electrostatics and solvation calculations"
arch=(x86_64)
url="http://www.poissonboltzmann.org/"
license=(custom)
-depends=(python boost eigen termcap swig)
+depends=(python termcap swig)
makedepends=('cmake>=3.12' make git wget)
provides=(apbs)
conflicts=(apbs-bin)
source=("https://github.com/Electrostatics/apbs/releases/download/v3.0.0/APBS-3.0.0_Source-Code.tar.gz"
- "globals_apbs.patch"
- "globals_bem.patch")
+ "globals_apbs.patch")
sha256sums=('3cf8b227a205cdcbd13246489427606f256f2356343fc954734fd39975e5cbdb'
- '6bc1f2dc7a454aa8b0799641f78ee571ba04795821a9bcac356cbe496bdb3df6'
- '3d8cc3d052a60a36d79ab95b8c89c03d79bdcca9958c2936513d92c23acb097b')
+ '6bc1f2dc7a454aa8b0799641f78ee571ba04795821a9bcac356cbe496bdb3df6')
options=(!makeflags !buildflags)
prepare() {
@@ -54,10 +52,7 @@ prepare() {
# TABI-PB (BEM)
git clone https://github.com/Electrostatics/TABIPB.git bem
cd bem
- git checkout de187a41720887d667edcfb6c23bb61fbbe06b5b
-
- # patch BEM building issues
- patch -Np0 -i "${srcdir}/globals_bem.patch"
+ git checkout 322a8d66180285250cd2f01e6b60584efcba9b65
cd ..
}
diff --git a/globals_bem.patch b/globals_bem.patch
deleted file mode 100644
index 66e10342d59c..000000000000
--- a/globals_bem.patch
+++ /dev/null
@@ -1,318 +0,0 @@
---- src/gl_variables.c 1970-01-01 03:00:00.000000000 +0300
-+++ src/gl_variables.c 2020-08-25 15:55:39.806472450 +0300
-@@ -0,0 +1,39 @@
-+/*
-+ * C source file for global variables definition of tabipb
-+ *
-+ * C version authored by:
-+ * Jiahui Chen, Southern Methodist University, Dallas, TX
-+ *
-+ * Additional modifications and updates by:
-+ * Leighton Wilson, University of Michigan, Ann Arbor, MI
-+ *
-+ * Based on package originally written in FORTRAN by:
-+ * Weihua Geng, Southern Methodist University, Dallas, TX
-+ * Robery Krasny, University of Michigan, Ann Arbor, MI
-+ *
-+ * Last modified by Viktor Drobot, 08/25/2020
-+ */
-+
-+#include "gl_variables.h"
-+
-+/*constant variables */
-+double pi, one_over_4pi, kcal2j, bulk_coef, units_coef, epsw, epsp, eps;
-+double bulk_strength, kappa2, kappa;
-+
-+
-+/*global scalar variables*/
-+int nface, nspt, natm;
-+
-+
-+/*dynamic allocated variables*/
-+int **extr_v; //[3][nspt]
-+int **extr_f; //[2][nface]
-+int **face;//[3][nface]
-+
-+double **vert, **snrm; //[3][nspt];
-+double *tr_xyz, *tr_q; //[3]*[nface]
-+double *tr_area, *bvct, *xvct; //[nface];
-+double *atmrad, *atmchr, *chrpos; //[natm],[3][nface];
-+
-+/* GMRes variables */
-+double *work, *h;
---- src/gl_variables.h 2020-08-25 16:31:43.073197652 +0300
-+++ src/gl_variables.h 2020-08-25 16:31:45.386509224 +0300
-@@ -9,38 +9,38 @@
- *
- * Based on package originally written in FORTRAN by:
- * Weihua Geng, Southern Methodist University, Dallas, TX
- * Robery Krasny, University of Michigan, Ann Arbor, MI
- *
-- * Last modified by Leighton Wilson, 06/20/2016
-+ * Last modified by Viktor Drobot, 08/25/2020
- */
-
- #ifndef H_GLVARS_H
- #define H_GLVARS_H
-
- #include "TABIPBstruct.h"
-
-
- /*constant variables */
--double pi, one_over_4pi, kcal2j, bulk_coef, units_coef, epsw, epsp, eps;
--double bulk_strength, kappa2, kappa;
-+extern double pi, one_over_4pi, kcal2j, bulk_coef, units_coef, epsw, epsp, eps;
-+extern double bulk_strength, kappa2, kappa;
-
-
- /*global scalar variables*/
--int nface, nspt, natm;
-+extern int nface, nspt, natm;
-
-
- /*dynamic allocated variables*/
--int **extr_v; //[3][nspt]
--int **extr_f; //[2][nface]
--int **face;//[3][nface]
--
--double **vert, **snrm; //[3][nspt];
--double *tr_xyz, *tr_q; //[3]*[nface]
--double *tr_area, *bvct, *xvct; //[nface];
--double *atmrad, *atmchr, *chrpos; //[natm],[3][nface];
-+extern int **extr_v; //[3][nspt]
-+extern int **extr_f; //[2][nface]
-+extern int **face;//[3][nface]
-+
-+extern double **vert, **snrm; //[3][nspt];
-+extern double *tr_xyz, *tr_q; //[3]*[nface]
-+extern double *tr_area, *bvct, *xvct; //[nface];
-+extern double *atmrad, *atmchr, *chrpos; //[natm],[3][nface];
-
- /* GMRes variables */
--double *work, *h;
-+extern double *work, *h;
-
-
- #endif /* H_GLVARS_H */
---- src/treecode.c 2020-08-25 16:40:07.671844382 +0300
-+++ src/treecode.c 2020-08-25 16:41:23.934469576 +0300
-@@ -9,11 +9,11 @@
- *
- * Based on package originally written in FORTRAN by:
- * Weihua Geng, Southern Methodist University, Dallas, TX
- * Robery Krasny, University of Michigan, Ann Arbor, MI
- *
-- * Last modified by Leighton Wilson, 06/20/2016
-+ * Last modified by Viktor Drobot, 08/25/2020
- */
-
- #include <time.h>
- #include <stdio.h>
- #include <math.h>
-@@ -21,10 +21,75 @@
-
- #include "gl_variables.h"
- #include "treecode.h"
-
-
-+/* runtime parameters */
-+int numpars, order, maxparnode, iflag, forcedim;
-+double theta;
-+double center[3], r0[3], v0[3];
-+
-+
-+/* arrays for coordinates, charge, potential & force */
-+double *x, *y, *z, *q;
-+double *x_copy, *y_copy, *z_copy, *q_copy;
-+double **tforce, **dforce;
-+int *orderind, *n_clst;
-+
-+
-+/* timing variables */
-+double timebeg, timeend;
-+
-+
-+/* local variables */
-+double xyzminmax[6];
-+double t1, abserr, relerr, adsinf_err, relinf_err;
-+double f_inferr[3], f_relinferr[3], t[3];
-+
-+double ***tchg, ***schg;
-+double ****der_cof;
-+int kk[16][3];
-+
-+
-+/* global variables for taylor expansions */
-+int torder, torder2, torderlim;
-+double *cf, *cf1, *cf2, *cf3;
-+double ***a, ***b;
-+
-+
-+/* global variables to track tree levels */
-+int minlevel, maxlevel;
-+
-+
-+/* global variables used when computing potential/force */
-+int orderoffset;
-+double tarpos[3], tarq[3];
-+double tarchr;
-+
-+
-+/* global variables for position and charge storage */
-+/* arrays are not copied in this version!! orderarr is till valid*/
-+int *orderarr;
-+double *xcopy,*ycopy,*zcopy,*qcopy;
-+
-+
-+/* node pointer and node struct declarations */
-+typedef struct tnode{
-+ int node_idx;
-+ int numpar, ibeg, iend;
-+ double x_min, y_min, z_min;
-+ double x_max, y_max, z_max;
-+ double x_mid, y_mid, z_mid;
-+ double radius, aspect;
-+ int level, num_children, exist_ms;
-+ double ****ms;
-+ struct tnode** child;
-+}tnode;
-+
-+tnode* troot;
-+
-+
- int treecode_initialization(int main_order,int main_maxparnode,double main_theta) {
- /* set up variables used in treecode */
- /* local variables*/
- int level, ierr, err, i, j, k, mm, nn, idx, ijk[3];
-
---- src/treecode.h 2020-08-25 16:40:07.675177684 +0300
-+++ src/treecode.h 2020-08-25 16:40:43.728176389 +0300
-@@ -9,79 +9,16 @@
- *
- * Based on package originally written in FORTRAN by:
- * Weihua Geng, Southern Methodist University, Dallas, TX
- * Robery Krasny, University of Michigan, Ann Arbor, MI
- *
-- * Last modified by Leighton Wilson, 06/20/2016
-+ * Last modified by Viktor Drobot, 08/25/2020
- */
-
- #ifndef H_TREECODE_H
- #define H_TREECODE_H
-
-
--/* runtime parameters */
--int numpars, order, maxparnode, iflag, forcedim;
--double theta;
--double center[3], r0[3], v0[3];
--
--
--/* arrays for coordinates, charge, potential & force */
--double *x, *y, *z, *q;
--double *x_copy, *y_copy, *z_copy, *q_copy;
--double **tforce, **dforce;
--int *orderind, *n_clst;
--
--
--/* timing variables */
--double timebeg, timeend;
--
--
--/* local variables */
--double xyzminmax[6];
--double t1, abserr, relerr, adsinf_err, relinf_err;
--double f_inferr[3], f_relinferr[3], t[3];
--
--double ***tchg, ***schg;
--double ****der_cof;
--int kk[16][3];
--
--
--/* global variables for taylor expansions */
--int torder, torder2, torderlim;
--double *cf, *cf1, *cf2, *cf3;
--double ***a, ***b;
--
--
--/* global variables to track tree levels */
--int minlevel, maxlevel;
--
--
--/* global variables used when computing potential/force */
--int orderoffset;
--double tarpos[3], tarq[3];
--double tarchr;
--double ***tchg, ***schg;
--
--
--/* global variables for position and charge storage */
--/* arrays are not copied in this version!! orderarr is till valid*/
--int *orderarr;
--double *xcopy,*ycopy,*zcopy,*qcopy;
--
--
--/* node pointer and node struct declarations */
--typedef struct tnode{
-- int node_idx;
-- int numpar, ibeg, iend;
-- double x_min, y_min, z_min;
-- double x_max, y_max, z_max;
-- double x_mid, y_mid, z_mid;
-- double radius, aspect;
-- int level, num_children, exist_ms;
-- double ****ms;
-- struct tnode** child;
--}tnode;
--
--tnode* troot;
-+extern int *orderarr;
-
-
- #endif /* H_TREECODE_H */
---- CMakeLists.txt 2020-08-25 16:40:07.671844382 +0300
-+++ CMakeLists.txt 2020-08-25 17:01:51.382985737 +0300
-@@ -51,10 +51,11 @@
- src/drot.c
- src/drotg.c
- src/dscal.c
- src/dtrsv.c
- src/f2c.h
-+ src/gl_variables.c
- src/gl_variables.h
- src/gmres.c
- src/readin.c
- src/tabipb.c
- src/TABIPBstruct.h
-@@ -92,17 +93,17 @@
- # C code for standalone; don't include pp_timer.c in Windows version
- if(WIN32)
- add_executable(tabipb
- src/main.c src/tabipb.c src/gmres.c src/daxpy.c src/dcopy.c src/ddot.c
- src/dgemv.c src/dnrm2.c src/drot.c src/drotg.c src/dscal.c src/d_sign.c
-- src/dtrsv.c src/readin.c src/treecode.c
-+ src/dtrsv.c src/readin.c src/treecode.c src/gl_variables.c
- src/xmalloc.c)
- else()
- add_executable(tabipb
- src/main.c src/tabipb.c src/gmres.c src/daxpy.c src/dcopy.c src/ddot.c
- src/dgemv.c src/dnrm2.c src/drot.c src/drotg.c src/dscal.c src/d_sign.c
-- src/dtrsv.c src/readin.c src/pp_timer.c src/treecode.c
-+ src/dtrsv.c src/readin.c src/pp_timer.c src/treecode.c src/gl_variables.c
- src/xmalloc.c)
- endif()
-
-
- ################################################
-@@ -145,11 +146,11 @@
- endif ()
-
- set (LIBFILES
- src/TABIPBWrap.c src/tabipb.c src/gmres.c src/daxpy.c src/dcopy.c src/ddot.c
- src/dgemv.c src/dnrm2.c src/drot.c src/drotg.c src/dscal.c src/d_sign.c
-- src/dtrsv.c src/readin.c src/treecode.c src/xmalloc.c)
-+ src/dtrsv.c src/readin.c src/treecode.c src/gl_variables.c src/xmalloc.c)
-
- message(***** ${CMAKE_INSTALL_PREFIX} *****)
-
- if(NOT DEFINED ${CMAKE_INSTALL_PREFIX})
- set(CMAKE_INSTALL_PREFIX ${CMAKE_BINARY_DIR})