Update 3.0.0

4 files changed, 493 insertions, 32 deletions

diff --git a/.SRCINFO b/.SRCINFO
index b267fb78caf3..e8c1094e53af 100644
--- a/.SRCINFO
+++ b/.SRCINFO
@@ -1,18 +1,29 @@
 pkgbase = apbs
 	pkgdesc = Electrostatic and solvation properties for complex molecules
-	pkgver = 1.5
-	pkgrel = 4
+	pkgver = 3.0.0
+	pkgrel = 1
 	url = http://www.poissonboltzmann.org/
 	arch = x86_64
-	arch = i686
-	license = MIT
-	makedepends = cmake
+	license = custom
+	makedepends = cmake>=3.12
+	makedepends = make
 	makedepends = git
-	makedepends = gcc
+	makedepends = wget
+	depends = python
+	depends = boost
+	depends = eigen
+	depends = termcap
 	depends = swig
-	depends = python2
-	source = git+https://github.com/Electrostatics/apbs-pdb2pqr.git#commit=aa353941cfadc09ccd113075d261a427864c2979
-	md5sums = SKIP
+	provides = apbs
+	conflicts = apbs-bin
+	options = !makeflags
+	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 4318981be1cb..77b96abd0616 100644
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -1,39 +1,102 @@
 # Maintainer: Viktor Drobot (aka dviktor) linux776 [at] gmail [dot] com
+
 pkgname=apbs
-pkgver=1.5
-pkgrel=4
+pkgver=3.0.0
+pkgrel=1
 pkgdesc="Electrostatic and solvation properties for complex molecules"
-arch=(x86_64 i686)
+arch=(x86_64)
 url="http://www.poissonboltzmann.org/"
-license=('MIT')
-depends=('swig' 'python2')
-makedepends=('cmake' 'git' 'gcc')
-source=("git+https://github.com/Electrostatics/apbs-pdb2pqr.git#commit=aa353941cfadc09ccd113075d261a427864c2979")
-md5sums=('SKIP')
+license=(custom)
+depends=(python boost eigen 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")
+sha256sums=('3cf8b227a205cdcbd13246489427606f256f2356343fc954734fd39975e5cbdb'
+            '6bc1f2dc7a454aa8b0799641f78ee571ba04795821a9bcac356cbe496bdb3df6'
+            '3d8cc3d052a60a36d79ab95b8c89c03d79bdcca9958c2936513d92c23acb097b')
+options=(!makeflags !buildflags)
+
+prepare() {
+    # patch APBS building issues
+    cd "${srcdir}/${pkgname}-${pkgver}/apbs"
+    patch -Np0 -i "${srcdir}/globals_apbs.patch"
+
+    # get external modules
+    cd "${srcdir}/${pkgname}-${pkgver}/apbs/externals"
+
+    # mesh_routines
+    mkdir -p mesh_routines/NanoShaper/Linux64
+    mkdir -p mesh_routines/msms/msms_i86_64Linux2_2.6.1
+    wget https://github.com/lwwilson1/mesh_routines/releases/download/v1.5/NanoShaper_Linux64 -O mesh_routines/NanoShaper/Linux64/NanoShaper
+    wget https://github.com/lwwilson1/mesh_routines/releases/download/v1.5/msms.x86_64Linux2.2.6.1.staticgcc -O mesh_routines/msms/msms_i86_64Linux2_2.6.1/msms.x86_64Linux2.2.6.1.staticgcc
+
+    # PBAM/PBSAM
+    git clone https://github.com/Electrostatics/pb_solvers.git pb_s_am
+    cd pb_s_am
+    git checkout 7ca2a8a491c0cf746074053005fcae026acc4da5
+    cd ..
+
+    # FETK
+    git clone https://github.com/Electrostatics/FETK.git fetk
+    cd fetk
+    git checkout 0c6fdeabe8929acea7481cb1480b5706b343b7e0
+    cd ..
+
+    # Geometric Flow
+    git clone https://github.com/Electrostatics/geoflow_c.git geoflow_c
+    cd geoflow_c
+    git checkout 99446ec841647419411d23bad632d50405913a06
+    cd ..
+
+    # TABI-PB (BEM)
+    git clone https://github.com/Electrostatics/TABIPB.git bem
+    cd bem
+    git checkout de187a41720887d667edcfb6c23bb61fbbe06b5b
+
+    # patch BEM building issues
+    patch -Np0 -i "${srcdir}/globals_bem.patch"
+    cd ..
+}
 
 build() {
-	cd ${srcdir}/apbs-pdb2pqr
+    cd "${srcdir}/${pkgname}-${pkgver}/apbs"
 
-    git submodule init
-    git submodule update
+    mkdir build
+    cd build
 
-    cd apbs
+    cmake \
+        -DCMAKE_INSTALL_PREFIX=/usr \
+        -DCMAKE_BUILD_TYPE=Release \
+        -DENABLE_GEOFLOW=ON \
+        -DENABLE_BEM=ON \
+        -DENABLE_FETK=ON \
+        -DENABLE_OPENMP=ON \
+        -DENABLE_PBAM=ON \
+        -DENABLE_PBSAM=ON \
+        -DENABLE_PYTHON=ON \
+        -DENABLE_TESTS=OFF \
+        -DBUILD_SHARED_LIBS=ON \
+        -DBUILD_DOC=OFF \
+        -Wno-dev \
+        ..
 
-    cmake -Wno-dev -DCMAKE_EXE_LINKER_FLAGS="" -DCMAKE_MODULE_LINKER_FLAGS="" -DCMAKE_SHARED_LINKER_FLAGS="" -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=/usr -DPYTHON_EXECUTABLE=/usr/bin/python2 -DPYTHON_INCLUDE_DIR=/usr/include/python2.7 -DPYTHON_LIBRARY=/usr/lib/libpython2.7.so -DPYTHON_LIBRARIES=/usr/lib/libpython2.7.so -DENABLE_PYTHON=ON -DBUILD_SHARED_LIBS=ON .
-	make
+    make
 }
 
 package() {
-	cd ${srcdir}/apbs-pdb2pqr/apbs
+    cd "${srcdir}/${pkgname}-${pkgver}/apbs/build"
+
+    # install base components
+    make DESTDIR="$pkgdir" install
 
-	make DESTDIR=$pkgdir install
+    # install license
+    install -Dm644 "${srcdir}/${pkgname}-${pkgver}/apbs/LICENSE.md" "${pkgdir}/usr/share/licenses/${pkgname}/LICENSE"
 
-    # fix python versions in scripts
-    sed -i 's|/bin/python|/usr/bin/python2|g' ${pkgdir}/usr/share/apbs/examples/protein-rna/apbs_unix_dx.py
-    sed -i 's|/usr/bin/env python|/usr/bin/python2|g' ${pkgdir}/usr/share/apbs/examples/protein-rna/fit.py
-    sed -i 's|/usr/bin/env python|/usr/bin/python2|g' ${pkgdir}/usr/share/apbs/tools/manip/psize.py
-    sed -i 's|/usr/bin/python|/usr/bin/python2|g' ${pkgdir}/usr/share/apbs/tools/python/noinput.py
+    # cleanup conflicting symlinks
+    cd "${pkgdir}/usr/lib"
 
-    find "${pkgdir}/usr/share/apbs/tests" -name '*.py' -type f -exec \
-       sed -i 's|/usr/bin/env python|/usr/bin/python2|g' {} \;
+    rm -f libamd.so libblas.so libsuperlu.so libumfpack.so
 }
diff --git a/globals_apbs.patch b/globals_apbs.patch
new file mode 100644
index 000000000000..b5756c7747a2
--- /dev/null
+++ b/globals_apbs.patch
@@ -0,0 +1,69 @@
+--- src/pmgc/mgsubd.c	2020-05-30 04:47:30.000000000 +0300
++++ src/pmgc/mgsubd.c	2020-08-19 13:08:27.503698756 +0300
+@@ -52,10 +52,12 @@
+  * @endverbatim

+  */

+ 

+ #include "mgsubd.h"

+ 

++double bf, oh, cputme;

++

+ VPUBLIC void Vbuildops(

+         int *nx, int *ny, int *nz,

+         int *nlev, int *ipkey, int *iinfo,

+         int *ido, int *iz,

+         int *mgprol, int *mgcoar, int *mgsolv, int *mgdisc, int *ipc,

+--- src/pmgc/mgsubd.h	2020-05-30 04:47:30.000000000 +0300
++++ src/pmgc/mgsubd.h	2020-08-19 13:08:54.266813098 +0300
+@@ -253,11 +253,11 @@
+         int n3  ///< The third grid size

+         );

+ 

+ 

+ /// @todo  Get rid of these globals in refactor

+-double bf, oh, cputme;

++extern double bf, oh, cputme;

+ 

+ /** @brief   This routine prints out some info and such from inside multigrid.

+  *  @author  Tucker Beck [C Translation], Michael Holst [Original]

+  *  @note    Replaces prtstp from mgsubd.f

+  */

+--- src/pmgc/mypdec.c	2020-05-30 04:47:30.000000000 +0300
++++ src/pmgc/mypdec.c	2020-08-19 13:09:34.939813105 +0300
+@@ -52,10 +52,15 @@
+  * @endverbatim

+  */

+ 

+ #include "mypdec.h"

+ 

++double v1, v2, v3, conc1, conc2, conc3, vol, relSize;

++int nion;

++double charge[MAXIONS];

++double sconc[MAXIONS];

++

+ VPUBLIC void Vmypdefinitlpbe(int *tnion, double *tcharge, double *tsconc) {

+ 

+     int i;

+ 

+     nion = *tnion;

+--- src/pmgc/mypdec.h	2020-05-30 04:47:30.000000000 +0300
++++ src/pmgc/mypdec.h	2020-08-19 13:09:56.172972195 +0300
+@@ -65,14 +65,14 @@
+ #define ZLARGE     1.0e20

+ #define SINH_MIN -85.0

+ #define SINH_MAX  85.0

+ 

+ /// @todo  Remove dependencies on global variables

+-double v1, v2, v3, conc1, conc2, conc3, vol, relSize;

+-int nion;

+-double charge[MAXIONS];

+-double sconc[MAXIONS];

++extern double v1, v2, v3, conc1, conc2, conc3, vol, relSize;

++extern int nion;

++extern double charge[MAXIONS];

++extern double sconc[MAXIONS];

+ 

+ #define Na 6.022045000e-04

+ 

+ /** @brief   Set up the ionic species to be used in later calculations.  This

+  *           must be called before any other of the routines in this file.

diff --git a/globals_bem.patch b/globals_bem.patch
new file mode 100644
index 000000000000..66e10342d59c
--- /dev/null
+++ b/globals_bem.patch
@@ -0,0 +1,318 @@
+--- 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})