doc page updates and changed domain->remap() call

doc/src/Build_extras.txt

@@ -47,6 +47,7 @@ This is the list of packages that may require additional steps.
 "USER-OMP"_#user-omp,
 "USER-QMMM"_#user-qmmm,
 "USER-QUIP"_#user-quip,
+"USER-SCAFACOS"_#user-scafacos,
 "USER-SMD"_#user-smd,
 "USER-VTK"_#user-vtk :tb(c=6,ea=c,a=l)
 
@@ -894,6 +895,45 @@ successfully build on your system.
 
 :line
 
+USER-SCAFACOS package :h4,link(user-scafacos)
+
+To build with this package, you must download and build the "ScaFaCoS
+Coulomb solver library"_scafacos_home
+
+:link(scafacos_home,http://www.scafacos.de)
+
+[CMake build]:
+
+-D DOWNLOAD_SCAFACOS=value    # download ScaFaCoS for build, value = no (default) or yes
+-D SCAFACOS_LIBRARY=path      # ScaFaCos library file (only needed if at custom location) 
+-D SCAFACOS_INCLUDE_DIR=path  # ScaFaCoS include directory (only needed if at custom location) :pre
+
+If DOWNLOAD_SCAFACOS is set, the ScaFaCoS library will be downloaded
+and built inside the CMake build directory.  If the ScaFaCoS library
+is already on your system (in a location CMake cannot find it),
+SCAFACOS_LIBRARY is the filename (plus path) of the ScaFaCoS library
+file, not the directory the library file is in.  SCAFACOS_INCLUDE_DIR
+is the directory the ScaFaCoS include file is in.
+
+[Traditional make]:
+
+You can download and build the ScaFaCoS library manually if you
+prefer; follow the instructions in lib/scafacos/README.  You can also
+do it in one step from the lammps/src dir, using a command like these,
+which simply invoke the lib/scafacos/Install.py script with the
+specified args:
+
+make lib-scafacos                         # print help message
+make lib-scafacos args="-b"               # download and build in lib/scafacos/scafacos-<version>
+make lib-scafacos args="-p $HOME/scafacos  # use existing ScaFaCoS installation in $HOME/scafacos
+
+Note that 2 symbolic (soft) links, "includelink" and "liblink", are
+created in lib/scafacos to point to the ScaFaCoS src dir.  When LAMMPS
+builds in src it will use these links.  You should not need to edit
+the lib/scafacos/Makefile.lammps file.
+
+:line
+
 USER-SMD package :h4,link(user-smd)
 
 To build with this package, you must download the Eigen3 library.

doc/src/Build_package.txt

@@ -58,6 +58,7 @@ packages:
 "USER-OMP"_Build_extras.html#user-omp,
 "USER-QMMM"_Build_extras.html#user-qmmm,
 "USER-QUIP"_Build_extras.html#user-quip,
+"USER-SCAFACOS"_#Build_extras.html#user-scafacos,
 "USER-SMD"_Build_extras.html#user-smd,
 "USER-VTK"_Build_extras.html#user-vtk :tb(c=6,ea=c,a=l)
 

doc/src/Packages_details.txt

@@ -92,6 +92,7 @@ as contained in the file name.
 "USER-QTB"_#PKG-USER-QTB,
 "USER-QUIP"_#PKG-USER-QUIP,
 "USER-REAXC"_#PKG-USER-REAXC,
+"USER-SCAFACOS"_#USER-SCAFACOS,
 "USER-SMD"_#PKG-USER-SMD,
 "USER-SMTBQ"_#PKG-USER-SMTBQ,
 "USER-SPH"_#PKG-USER-SPH,
@@ -1839,6 +1840,41 @@ examples/reax :ul
 
 :line
 
+USER-SCAFACOS package :link(USER-SCAFACOS),h4
+
+[Contents:]
+
+A KSpace style which wraps the "ScaFaCoS Coulomb solver
+library"_http://www.scafacos.de to compute long-range Coulombic
+interactions.
+
+To use this package you must have the ScaFaCoS library available on
+your system.
+
+[Author:] Rene Halver (JSC) wrote the scafacos LAMMPS command.
+
+ScaFaCoS itself was developed by a consortium of German research
+facilities with a BMBF (German Ministry of Science and Education)
+funded project in 2009-2012. Participants of the consortium were the
+Universities of Bonn, Chemnitz, Stuttgart, and Wuppertal as well as
+the Forschungszentrum Juelich.
+
+[Install:]
+
+This package has "specific installation
+instructions"_Build_extras.html#user-scafacos on the "Build
+extras"_Build_extras.html doc page.
+
+[Supporting info:]
+
+src/USER-SCAFACOS: filenames -> commands
+src/USER-SCAFACOS/README
+"kspace_style scafacos"_kspace_style.html
+"kspace_modify"_kspace_modify.html
+examples/USER/scafacos :ul
+
+:line
+
 USER-SMD package :link(PKG-USER-SMD),h4
 
 [Contents:]

doc/src/Packages_user.txt

@@ -66,6 +66,7 @@ Package, Description, Doc page, Example, Library
 "USER-QTB"_Packages_details.html#PKG-USER-QTB, quantum nuclear effects,"fix qtb"_fix_qtb.html "fix qbmsst"_fix_qbmsst.html, qtb, no
 "USER-QUIP"_Packages_details.html#PKG-USER-QUIP, QUIP/libatoms interface,"pair_style quip"_pair_quip.html, USER/quip, ext
 "USER-REAXC"_Packages_details.html#PKG-USER-REAXC, ReaxFF potential (C/C++) ,"pair_style reaxc"_pair_reaxc.html, reax, no
+"USER-SCAFACOS"_Packages_details.html#PKG-USER-SCAFACOS, wrapper on ScaFaCoS solver,"kspace_style scafacos"_kspace_style.html, USER/scafacos, ext
 "USER-SMD"_Packages_details.html#PKG-USER-SMD, smoothed Mach dynamics,"SMD User Guide"_PDF/SMD_LAMMPS_userguide.pdf, USER/smd, ext
 "USER-SMTBQ"_Packages_details.html#PKG-USER-SMTBQ, second moment tight binding QEq potential,"pair_style smtbq"_pair_smtbq.html, USER/smtbq, no
 "USER-SPH"_Packages_details.html#PKG-USER-SPH, smoothed particle hydrodynamics,"SPH User Guide"_PDF/SPH_LAMMPS_userguide.pdf, USER/sph, no

doc/src/kspace_style.txt

@@ -252,7 +252,7 @@ These are the ScaFaCoS methods currently available from LAMMPS:
 {p2nfft} = FFT-based Coulomb solver
 {ewald} = Ewald summation
 {direct} = direct O(N^2) summation
-{p3m} = PPPM
+{p3m} = PPPM :ul
 
 We plan to support additional ScaFaCoS solvers from LAMMPS in the
 future.  For an overview of the included solvers, refer to
@@ -268,7 +268,7 @@ energy or the total Columic energy.  To select from these options, see
 the "kspace_modify scafacos accuracy"_kspace_modify.html doc page.
 
 The "kspace_modify scafacos"_kspace_modify.html command also explains
-all the ScaFaCoS options currently exposed to LAMMPS.
+other ScaFaCoS options currently exposed to LAMMPS.
 
 :line
 

src/USER-SCAFACOS/scafacos.cpp

@@ -199,7 +199,6 @@ void Scafacos::compute(int eflag, int vflag)
     eflag_atom = 0;
     vflag_global = 0;
   }
-
   
   // grow xpbc, epot, efield if necessary
 
@@ -223,6 +222,8 @@ void Scafacos::compute(int eflag, int vflag)
   // pack coords into xpbc and apply PBC
   memcpy(xpbc,&x[0][0],3*nlocal*sizeof(double));
 
+  // RENE: remove this section (see RENE below)
+
   //int j = 0;
   for (int i = 0; i < nlocal; i++) {
     if (domain->xperiodic) domain->remap(&xpbc[3*i]);
@@ -231,6 +232,15 @@ void Scafacos::compute(int eflag, int vflag)
     //j += 3;
   }
 
+  // RENE: I think the call to domain->remap needs to be this way
+  // b/c the remap() method checks for PBC and does all 3 dims at once
+
+  int j = 0;
+  for (int i = 0; i < nlocal; i++) {
+    domain->remap(&xpbc[j]);
+    j += 3;
+  }
+
   // if simulation box has changed, call fcs_tune()
 
   if (box_has_changed()) {