Review akohlmey

.gitlab-ci.yml

@@ -7,8 +7,12 @@ unit-tests:
   script:
     - echo "Installing dependencies"
     - apt-get update
-    - apt-get install -y cmake make gcc g++ gfortran python3 python3-numpy libblas-dev liblapack-dev
+    - apt-get install -y cmake make gcc g++ gfortran python3 python3-numpy python3-yaml libblas-dev liblapack-dev
     - base_dir=$PWD
+    - echo "Checking code style"
+    - python3 ./tools/coding_standard/homepage.py .
+    - python3 ./tools/coding_standard/whitespace.py .
+    - python3 ./tools/coding_standard/permissions.py .
     - echo "Building lammps in directory $base_dir"
     - mkdir build && cd build
     - cmake ../cmake
@@ -26,13 +30,13 @@ unit-tests:
     - adduser tester
     - chown -R tester $base_dir
     - runuser -u tester ctest
-    - echo "running tests in examples/electrode subdirectory of $base_dir"
+    - echo "running tests in examples/PACKAGES/electrode subdirectory of $base_dir"
     - lmpbin=$base_dir/build/lmp
-    - cd $base_dir/examples/electrode/check_amat/
+    - cd $base_dir/examples/PACKAGES/electrode/check_amat/
     - bash check.sh $lmpbin
-    - cd $base_dir/examples/electrode/check_etypes/
+    - cd $base_dir/examples/PACKAGES/electrode/check_etypes/
     - bash check.sh $lmpbin
-    - cd $base_dir/examples/electrode/check_ffield/
+    - cd $base_dir/examples/PACKAGES/electrode/check_ffield/
     - bash check.sh $lmpbin
-    - cd $base_dir/examples/electrode/check_intel/
+    - cd $base_dir/examples/PACKAGES/electrode/check_intel/
     - bash check.sh $lmpbin

doc/src/Build_extras.rst

@@ -1291,7 +1291,7 @@ be built for the most part with all major versions of the C++ language.
 
 .. _electrode:
 
-ELECTRODE package 
+ELECTRODE package
 -----------------
 
 This package depends on the KSPACE package.

doc/src/Commands_fix.rst

@@ -66,9 +66,6 @@ OPT.
    * :doc:`edpd/source <fix_dpd_source>`
    * :doc:`efield <fix_efield>`
    * :doc:`ehex <fix_ehex>`
-   * :doc:`electrode/conp <fix_electrode_conp>`
-   * :doc:`electrode/conq <fix_electrode_conp>`
-   * :doc:`electrode/thermo <fix_electrode_conp>`
    * :doc:`electrode/conp (i) <fix_electrode_conp>`
    * :doc:`electrode/conq (i) <fix_electrode_conp>`
    * :doc:`electrode/thermo (i) <fix_electrode_conp>`

doc/src/Commands_kspace.rst

@@ -42,6 +42,5 @@ OPT.
    * :doc:`pppm/stagger <kspace_style>`
    * :doc:`pppm/tip4p (o) <kspace_style>`
    * :doc:`pppm/dielectric <kspace_style>`
-   * :doc:`pppm/electrode <kspace_style>`
    * :doc:`pppm/electrode (i) <kspace_style>`
    * :doc:`scafacos <kspace_style>`

doc/src/fix_electrode_conp.rst

@@ -8,20 +8,17 @@
 fix electrode/conp command
 ==========================
 
+Accelerator Variant: *electrode/conp/intel*
+
 fix electrode/conq command
 ==========================
 
+Accelerator Variant: *electrode/conq/intel*
+
 fix electrode/thermo command
 ============================
 
-fix electrode/conp/intel command
-================================
-
-fix electrode/conq/intel command
-================================
-
-fix electrode/thermo/intel command
-==================================
+Accelerator Variant: *electrode/thermo/intel*
 
 Syntax
 """"""
@@ -96,7 +93,7 @@ interactions.  The Kspace styles *ewald/electrode*, *pppm/electrode* and
 
 For systems with non-periodic boundaries in one or two directions dipole
 corrections are available with the :doc:`kspace_modify <kspace_modify>`.  For
-ewald/electrode a two-dimensional Ewald summation :ref:`(Hu) <Hu>` can be used 
+ewald/electrode a two-dimensional Ewald summation :ref:`(Hu) <Hu>` can be used
 by setting "slab ew2d":
 
 .. code-block:: LAMMPS
@@ -115,7 +112,7 @@ moderate mesh size but requires more memory.
    kspace_modify amat onestep/twostep
 
 
-The *fix_modify tf* option allows to specify Thomas-Fermi parameters (:ref:`Scalfi <Scalfi>`) for each atom type. 
+The *fix_modify tf* option allows to specify Thomas-Fermi parameters (:ref:`Scalfi <Scalfi>`) for each atom type.
 
 .. code-block:: LAMMPS
 
@@ -134,6 +131,10 @@ and top of the cell this can be achieved with *processors * * 2*.
 
 ----------
 
+.. include:: accel_styles.rst
+
+----------
+
 .. _Siepmann:
 
 **(Siepmann)** Siepmann and Strik, J. Chem. Phys. 102, 511 (1995).

doc/src/kspace_modify.rst

@@ -56,7 +56,7 @@ Syntax
        *splittol* value = tol
          tol = relative size of two eigenvalues (see discussion below)
        *wire* value = volfactor (available with ELECTRODE package)
-         volfactor = ratio of the total extended dimension used in the 1d 
+         volfactor = ratio of the total extended dimension used in the 1d
            approximation compared with the dimension of the simulation domain
 
 Examples

lib/electrode/Install.py

@@ -0,0 +1 @@
+../Install.py

lib/electrode/Makefile.lammps.empty

@@ -0,0 +1,5 @@
+# Settings that the LAMMPS build will import when this package library is used
+
+electrode_SYSINC =
+electrode_SYSLIB =
+electrode_SYSPATH =

lib/electrode/Makefile.lammps.installed

@@ -0,0 +1,5 @@
+# Settings that the LAMMPS build will import when this package library is used
+
+electrode_SYSINC =
+electrode_SYSLIB = -lblas -llapack
+electrode_SYSPATH =

lib/electrode/Makefile.lammps.linalg

@@ -0,0 +1,5 @@
+# Settings that the LAMMPS build will import when this package library is used
+
+electrode_SYSINC =
+electrode_SYSLIB = -llinalg -lgfortran
+electrode_SYSPATH = -L../../lib/linalg$(LIBOBJDIR)

lib/electrode/Makefile.mpi

@@ -0,0 +1,48 @@
+SHELL = /bin/sh
+
+# which file will be copied to Makefile.lammps
+
+EXTRAMAKE = Makefile.lammps.linalg
+
+# ------ DEFINITIONS ------
+
+LIB = libelectrode.a
+OBJ =   $(SRC:.cpp=.o)
+
+# ------ SETTINGS ------
+
+# include any MPI settings needed for the ELECTRODE library to build with
+# the same MPI library that LAMMPS is built with
+
+CC =	    mpicxx
+CCFLAGS = -O3 -fPIC -DMPICH_IGNORE_CXX_SEEK -DOMPI_SKIP_MPICXX=1
+
+ARCHIVE =	ar
+ARCHFLAG =	-rc
+DEPFLAGS =  -M
+#LINK =         
+#LINKFLAGS =	
+USRLIB =
+SYSLIB =
+
+# ------ MAKE PROCEDURE ------
+
+lib: 	$(OBJ)
+	$(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ)
+	@cp $(EXTRAMAKE) Makefile.lammps
+
+# ------ COMPILE RULES ------
+
+%.o:%.cpp
+	$(CC) $(CCFLAGS) -c $< -o $@
+%.d:%.cpp
+	$(CC) $(CCFLAGS) $(DEPFLAGS) $< > $@		
+
+# ------ DEPENDENCIES ------
+
+DEPENDS = $(OBJ:.o=.d)
+
+# ------ CLEAN ------
+
+clean:
+	-rm -f *.d *~ $(OBJ) $(LIB)

lib/electrode/Makefile.serial

@@ -0,0 +1,48 @@
+SHELL = /bin/sh
+
+# which file will be copied to Makefile.lammps
+
+EXTRAMAKE = Makefile.lammps.linalg
+
+# ------ DEFINITIONS ------
+
+LIB = libelectrode.a
+OBJ =   $(SRC:.cpp=.o)
+
+# ------ SETTINGS ------
+
+# include any MPI settings needed for the ATC library to build with
+# the same MPI library that LAMMPS is built with
+
+CC =	    g++
+CCFLAGS = -O3 -fPIC -I../../src/STUBS
+
+ARCHIVE =	ar
+ARCHFLAG =	-rc
+DEPFLAGS =  -M
+#LINK =         
+#LINKFLAGS =	
+USRLIB =
+SYSLIB =
+
+# ------ MAKE PROCEDURE ------
+
+lib: 	$(OBJ)
+	$(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ)
+	@cp $(EXTRAMAKE) Makefile.lammps
+
+# ------ COMPILE RULES ------
+
+%.o:%.cpp
+	$(CC) $(CCFLAGS) -c $< -o $@
+%.d:%.cpp
+	$(CC) $(CCFLAGS) $(DEPFLAGS) $< > $@		
+
+# ------ DEPENDENCIES ------
+
+DEPENDS = $(OBJ:.o=.d)
+
+# ------ CLEAN ------
+
+clean:
+	-rm -f *.d *~ $(OBJ) $(LIB)

src/ELECTRODE/Install.sh

@@ -14,33 +14,54 @@ export LC_ALL
 # arg1 = file, arg2 = file it depends on
 
 action () {
-  if (test $mode = 0) then
-    rm -f ../$1
-  elif (! cmp -s $1 ../$1) then
-    if (test -z "$2" || test -e ../$2) then
-      cp $1 ..
-      if (test $mode = 2) then
-        echo "  updating src/$1"
-      fi
+    if (test $mode = 0) then
+        rm -f ../$1
+    elif (! cmp -s $1 ../$1) then
+        if (test -z "$2" || test -e ../$2) then
+            cp $1 ..
+            if (test $mode = 2) then
+                echo "  updating src/$1"
+            fi
+        fi
+    elif (test -n "$2") then
+        if (test ! -e ../$2) then
+            rm -f ../$1
+        fi
     fi
-  elif (test -n "$2") then
-    if (test ! -e ../$2) then
-      rm -f ../$1
-    fi
-  fi
 }
 
 # all package files with no dependencies
 
 for file in *.cpp *.h; do
-  test -f ${file} && action $file
+    test -f ${file} && action $file
 done
 
 if (test $1 = 1) then
+    if (test ! -e ../pppm.cpp) then
+        echo "Must install KSPACE package with ELECTRODE"
+        exit 1
+    fi
+    if (test -e ../Makefile.package) then
+        sed -i -e 's/[^ \t]*electrode[^ \t]* //g' ../Makefile.package
+        sed -i -e 's|^PKG_PATH =[ \t]*|&-L../../lib/electrode |' ../Makefile.package
+        sed -i -e 's|^PKG_LIB =[ \t]*|&-lelectrode |' ../Makefile.package
+        sed -i -e 's|^PKG_SYSPATH =[ \t]*|&$(electrode_SYSPATH) |' ../Makefile.package
+        sed -i -e 's|^PKG_SYSLIB =[ \t]*|&$(electrode_SYSLIB) |' ../Makefile.package
+    fi
+    if (test -e ../Makefile.package.settings) then
+        sed -i -e '/^include.*electrode.*$/d' ../Makefile.package.settings
+        # multiline form needed for BSD sed on Macs
+        sed -i -e '4 i \
+            include ..\/..\/lib\/electrode\/Makefile.lammps
+                    ' ../Makefile.package.settings
+    fi
 
-  if (test -e ../Makefile.package) then
-    sed -i -e 's/[^ \t]*conp[^ \t]* //g' ../Makefile.package
-    sed -i -e 's|^PKG_LIB =[ \t]*|&-llinalg -L../../lib/linalg$(LIBOBJDIR) -lgfortran |' ../Makefile.package
-  fi
+elif (test $1 = 0) then
+    if (test -e ../Makefile.package) then
+        sed -i -e 's/[^ \t]*electrode[^ \t]* //g' ../Makefile.package
+    fi
+    if (test -e ../Makefile.package.settings) then
+        sed -i -e '/^include.*electrode.*$/d' ../Makefile.package.settings
+    fi
 fi
 

src/ELECTRODE/boundary_correction.cpp

@@ -1,6 +1,6 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   https://lammps.sandia.gov/, Sandia National Laboratories
+   https://www.lammps.org/, Sandia National Laboratories
    Steve Plimpton, sjplimp@sandia.gov
 
    Copyright (2003) Sandia Corporation.  Under the terms of Contract
@@ -17,14 +17,11 @@
 
 #include "boundary_correction.h"
 
-#include <iostream>
-
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
 
 using namespace LAMMPS_NS;
-using namespace std;
 
 // use EW3DC slab correction
 //
@@ -52,24 +49,24 @@ void BoundaryCorrection::setup(double x, double y, double z, double g)
   g_ewald = g;
 }
 
-vector<int> BoundaryCorrection::gather_recvcounts(int n)
+std::vector<int> BoundaryCorrection::gather_recvcounts(int n)
 {
   int const nprocs = comm->nprocs;
-  vector<int> recvcounts = vector<int>(nprocs);
+  std::vector<int> recvcounts = std::vector<int>(nprocs);
   MPI_Allgather(&n, 1, MPI_INT, &recvcounts.front(), 1, MPI_INT, world);
   return recvcounts;
 }
 
-vector<int> BoundaryCorrection::gather_displs(vector<int> recvcounts)
+std::vector<int> BoundaryCorrection::gather_displs(const std::vector<int> &recvcounts)
 {
   int const nprocs = comm->nprocs;
-  vector<int> displs = vector<int>(nprocs);
+  std::vector<int> displs = std::vector<int>(nprocs);
   displs[0] = 0;
   for (int i = 1; i < nprocs; i++) displs[i] = displs[i - 1] + recvcounts[i - 1];
   return displs;
 }
 
-vector<bigint> BoundaryCorrection::gather_jmat(bigint *imat)
+std::vector<bigint> BoundaryCorrection::gather_jmat(bigint *imat)
 {
   int nlocal = atom->nlocal;
   bigint ngroup = 0;
@@ -78,16 +75,16 @@ vector<bigint> BoundaryCorrection::gather_jmat(bigint *imat)
     if (imat[i] > -1) ngrouplocal++;
   MPI_Allreduce(&ngrouplocal, &ngroup, 1, MPI_INT, MPI_SUM, world);
 
-  vector<bigint> jmat_local = vector<bigint>(ngrouplocal);
+  std::vector<bigint> jmat_local = std::vector<bigint>(ngrouplocal);
   for (int i = 0, n = 0; i < nlocal; i++) {
     if (imat[i] < 0) continue;
     jmat_local[n++] = imat[i];
   }
 
   // gather global matrix indexing
-  vector<bigint> jmat = vector<bigint>(ngroup);
-  vector<int> recvcounts = gather_recvcounts(ngrouplocal);
-  vector<int> displs = gather_displs(recvcounts);
+  std::vector<bigint> jmat = std::vector<bigint>(ngroup);
+  std::vector<int> recvcounts = gather_recvcounts(ngrouplocal);
+  std::vector<int> displs = gather_displs(recvcounts);
   MPI_Allgatherv(&jmat_local.front(), ngrouplocal, MPI_LMP_BIGINT, &jmat.front(),
                  &recvcounts.front(), &displs.front(), MPI_LMP_BIGINT, world);
   return jmat;

src/ELECTRODE/boundary_correction.h

@@ -1,6 +1,6 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   https://lammps.sandia.gov/, Sandia National Laboratories
+   https://www.lammps.org/, Sandia National Laboratories
    Steve Plimpton, sjplimp@sandia.gov
 
    Copyright (2003) Sandia Corporation.  Under the terms of Contract
@@ -43,7 +43,7 @@ class BoundaryCorrection : protected Pointers {
 
   std::vector<bigint> gather_jmat(bigint *);
   std::vector<int> gather_recvcounts(int);
-  std::vector<int> gather_displs(std::vector<int>);
+  std::vector<int> gather_displs(const std::vector<int> &);
 };
 }    // namespace LAMMPS_NS
 #endif

src/ELECTRODE/electrode_accel_interface.cpp

@@ -1,20 +0,0 @@
-/* ----------------------------------------------------------------------
-   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   https://lammps.sandia.gov/, Sandia National Laboratories
-   Steve Plimpton, sjplimp@sandia.gov
-
-   Copyright (2003) Sandia Corporation.  Under the terms of Contract
-   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
-   certain rights in this software.  This software is distributed under
-   the GNU General Public License.
-
-   See the README file in the top-level LAMMPS directory.
-------------------------------------------------------------------------- */
-
-/* ----------------------------------------------------------------------
-   Contributing authors: Ludwig Ahrens-Iwers (TUHH), Shern Tee (UQ), Robert Meißner (TUHH)
-------------------------------------------------------------------------- */
-
-#include "electrode_accel_interface.h"
-
-LAMMPS_NS::ElectrodeAccelInterface::~ElectrodeAccelInterface() {}

src/ELECTRODE/electrode_accel_interface.h

@@ -1,6 +1,6 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   https://lammps.sandia.gov/, Sandia National Laboratories
+   https://www.lammps.org/, Sandia National Laboratories
    Steve Plimpton, sjplimp@sandia.gov
 
    Copyright (2003) Sandia Corporation.  Under the terms of Contract
@@ -25,7 +25,7 @@ namespace LAMMPS_NS {
 class ElectrodeAccelInterface : protected Pointers {
  public:
   ElectrodeAccelInterface(class LAMMPS *lmp) : Pointers(lmp) {}
-  virtual ~ElectrodeAccelInterface();
+  virtual ~ElectrodeAccelInterface() {}
   virtual void intel_find_fix() {}
   virtual void intel_pack_buffers() {}
 };

src/ELECTRODE/electrode_kspace.h

@@ -1,6 +1,6 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   https://lammps.sandia.gov/, Sandia National Laboratories
+   https://www.lammps.org/, Sandia National Laboratories
    Steve Plimpton, sjplimp@sandia.gov
 
    Copyright (2003) Sandia Corporation.  Under the terms of Contract

src/ELECTRODE/electrode_matrix.cpp

@@ -1,6 +1,6 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   https://lammps.sandia.gov/, Sandia National Laboratories
+   https://www.lammps.org/, Sandia National Laboratories
    Steve Plimpton, sjplimp@sandia.gov
 
    Copyright (2003) Sandia Corporation.  Under the terms of Contract
@@ -19,6 +19,7 @@
 
 #include "atom.h"
 #include "comm.h"
+#include "electrode_kspace.h"
 #include "error.h"
 #include "force.h"
 #include "group.h"
@@ -51,7 +52,7 @@ ElectrodeMatrix::ElectrodeMatrix(LAMMPS *lmp, int electrode_group, double eta) :
 
 /* ---------------------------------------------------------------------- */
 
-void ElectrodeMatrix::setup(std::map<tagint, int> tag_ids, class Pair *fix_pair,
+void ElectrodeMatrix::setup(const std::map<tagint, int> &tag_ids, class Pair *fix_pair,
                             class NeighList *fix_neighlist)
 {
   pair = fix_pair;
@@ -64,9 +65,10 @@ void ElectrodeMatrix::setup(std::map<tagint, int> tag_ids, class Pair *fix_pair,
 
   tag_to_iele = tag_ids;
 }
+
 /* ---------------------------------------------------------------------- */
 
-void ElectrodeMatrix::setup_tf(std::map<int, double> tf_types)
+void ElectrodeMatrix::setup_tf(const std::map<int, double> &tf_types)
 {
   tfflag = true;
   this->tf_types = tf_types;