Merge pull request #737 from akohlmey/collected-bugfixes

Collected bugfixes and small updates for next patch

doc/src/create_atoms.txt

@@ -36,9 +36,9 @@ keyword = {mol} or {basis} or {remap} or {var} or {set} or {units} :l
   {set} values = dim name
     dim = {x} or {y} or {z}
     name = name of variable to set with x, y, or z atom position
-  {rotate} values = Rx Ry Rz theta
-    Rx,Ry,Rz = rotation vector for single molecule
+  {rotate} values = theta Rx Ry Rz
     theta = rotation angle for single molecule (degrees)
+    Rx,Ry,Rz = rotation vector for single molecule
   {units} value = {lattice} or {box}
     {lattice} = the geometry is defined in lattice units
     {box} = the geometry is defined in simulation box units :pre
@@ -242,15 +242,15 @@ write_dump      all atom sinusoid.lammpstrj :pre
 
 :c,image(JPG/sinusoid_small.jpg,JPG/sinusoid.jpg)
 
-The {rotate} keyword can be used with the {single} style, when adding
-a single molecule to specify the orientation at which the molecule is
-inserted.  The axis of rotation is determined by the rotation vector
-(Rx,Ry,Rz) that goes through the insertion point.  The specified
-{theta} determines the angle of rotation around that axis.  Note that
-the direction of rotation for the atoms around the rotation axis is
-consistent with the right-hand rule: if your right-hand's thumb points
-along {R}, then your fingers wrap around the axis in the direction of
-rotation.
+The {rotate} keyword can only be used with the {single} style and
+when adding a single molecule. It allows to specify the orientation
+at which the molecule is inserted.  The axis of rotation is
+determined by the rotation vector (Rx,Ry,Rz) that goes through the
+insertion point.  The specified {theta} determines the angle of
+rotation around that axis.  Note that the direction of rotation for
+the atoms around the rotation axis is consistent with the right-hand
+rule: if your right-hand's thumb points along {R}, then your fingers
+wrap around the axis in the direction of rotation.
 
 The {units} keyword determines the meaning of the distance units used
 to specify the coordinates of the one particle created by the {single}

doc/src/create_bonds.txt

@@ -18,7 +18,7 @@ style = {many} or {single/bond} or {single/angle} or {single/dihedral} :ule,l
     group2-ID = ID of second group, bonds will be between atoms in the 2 groups
     btype = bond type of created bonds
     rmin = minimum distance between pair of atoms to bond together
-    rmax = minimum distance between pair of atoms to bond together
+    rmax = maximum distance between pair of atoms to bond together
   {single/bond} args = btype batom1 batom2
     btype = bond type of new bond
     batom1,batom2 = atom IDs for two atoms in bond

lib/atc/Matrix.h

@@ -356,7 +356,7 @@ DenseMatrix<T> Matrix<T>::pow(double n) const
   int sz=this->size(); for(INDEX i=0; i<sz; i++)
   {
     double val = R[i];
-    R[i] = pow(val,n);
+    R[i] = std::pow(val,n);
   }
   return R;
 }

src/Makefile

@@ -17,12 +17,12 @@ SHLINK = liblammps.so
 OBJDIR =   Obj_$@
 OBJSHDIR = Obj_shared_$@
 
-SRC =	$(wildcard *.cpp)
-INC =	$(wildcard *.h)
+SRC =	$(filter-out library.cpp,$(wildcard *.cpp))
+INC =	$(filter-out library.h,$(wildcard *.h))
 OBJ = 	$(SRC:.cpp=.o)
 
-SRCLIB = $(filter-out main.cpp,$(SRC))
-OBJLIB = $(filter-out main.o,$(OBJ))
+SRCLIB = $(filter-out main.cpp,$(SRC)) library.cpp
+OBJLIB = $(filter-out main.o,$(OBJ)) library.o
 
 # Command-line options for mode: exe (default), shexe, lib, shlib
 
@@ -176,7 +176,7 @@ help:
 	  then cp Makefile.package.settings.empty Makefile.package.settings; fi
 	@cp Makefile.package Makefile.package.settings $(objdir)
 	@cd $(objdir); rm -f .depend; \
-	$(MAKE) $(MFLAGS) "SRC = $(SRC)" "INC = $(INC)" depend || :
+	$(MAKE) $(MFLAGS) "SRC = $(SRC) library.cpp" "INC = $(INC) library.h" depend || :
 ifeq ($(mode),exe)
 	@cd $(objdir); \
 	$(MAKE) $(MFLAGS) "OBJ = $(OBJ)" "INC = $(INC)" "SHFLAGS =" \

src/USER-OMP/fix_neigh_history_omp.cpp

@@ -356,7 +356,7 @@ void FixNeighHistoryOMP::pre_exchange_newton()
 #endif
     {
       maxpartner = MAX(m,maxpartner);
-      comm->maxexchange_fix = MAX(comm->maxexchange_fix,4*maxpartner+1);
+      comm->maxexchange_fix = MAX(comm->maxexchange_fix,(dnum+1)*maxpartner+1);
     }
   }
 

src/compute_msd_chunk.cpp

@@ -126,7 +126,7 @@ void ComputeMSDChunk::setup()
 
   if (fix->nrow == nchunk && fix->ncol == 3) return;
   fix->reset_global(nchunk,3);
-    
+
   double **cominit = fix->astore;
   for (int i = 0; i < nchunk; i++) {
     cominit[i][0] = comall[i][0];

src/fix_ave_chunk.cpp

@@ -63,6 +63,7 @@ FixAveChunk::FixAveChunk(LAMMPS *lmp, int narg, char **arg) :
   strcpy(idchunk,arg[6]);
 
   global_freq = nfreq;
+  peratom_freq = nfreq;
   no_change_box = 1;
 
   // expand args if any have wildcard character "*"

src/fix_neigh_history.cpp

@@ -35,7 +35,7 @@ enum{DEFAULT,NPARTNER,PERPARTNER}; // also set in fix neigh/history/omp
 
 FixNeighHistory::FixNeighHistory(LAMMPS *lmp, int narg, char **arg) :
   Fix(lmp, narg, arg),
-  npartner(NULL), partner(NULL), valuepartner(NULL), pair(NULL), 
+  npartner(NULL), partner(NULL), valuepartner(NULL), pair(NULL),
   ipage_atom(NULL), dpage_atom(NULL), ipage_neigh(NULL), dpage_neigh(NULL)
 {
   if (narg != 4) error->all(FLERR,"Illegal fix NEIGH_HISTORY command");
@@ -295,7 +295,7 @@ void FixNeighHistory::pre_exchange_onesided()
 
   // set maxpartner = max # of partners of any owned atom
   // bump up comm->maxexchange_fix if necessary
-  
+
   maxpartner = 0;
   for (i = 0; i < nlocal_neigh; i++) maxpartner = MAX(maxpartner,npartner[i]);
   comm->maxexchange_fix = MAX(comm->maxexchange_fix,(dnum+1)*maxpartner+1);
@@ -318,7 +318,7 @@ void FixNeighHistory::pre_exchange_newton()
   int *allflags;
   double *allvalues,*onevalues,*jvalues;
 
-  // NOTE: all operations until very end are with 
+  // NOTE: all operations until very end are with
   //   nlocal_neigh  <= current nlocal and nall_neigh
   // b/c previous neigh list was built with nlocal_neigh & nghost_neigh
   // nlocal can be larger if other fixes added atoms at this pre_exchange()
@@ -424,7 +424,7 @@ void FixNeighHistory::pre_exchange_newton()
 
   maxpartner = 0;
   for (i = 0; i < nlocal_neigh; i++) maxpartner = MAX(maxpartner,npartner[i]);
-  comm->maxexchange_fix = MAX(comm->maxexchange_fix,4*maxpartner+1);
+  comm->maxexchange_fix = MAX(comm->maxexchange_fix,(dnum+1)*maxpartner+1);
 
   // zero npartner values from previous nlocal_neigh to current nlocal
 
@@ -526,7 +526,7 @@ void FixNeighHistory::pre_exchange_no_newton()
 
   // set maxpartner = max # of partners of any owned atom
   // bump up comm->maxexchange_fix if necessary
-  
+
   maxpartner = 0;
   for (i = 0; i < nlocal_neigh; i++) maxpartner = MAX(maxpartner,npartner[i]);
   comm->maxexchange_fix = MAX(comm->maxexchange_fix,(dnum+1)*maxpartner+1);
@@ -571,9 +571,9 @@ void FixNeighHistory::post_neighbor()
     memory->sfree(firstflag);
     memory->sfree(firstvalue);
     maxatom = nall;
-    firstflag = (int **) 
+    firstflag = (int **)
       memory->smalloc(maxatom*sizeof(int *),"neighbor_history:firstflag");
-    firstvalue = (double **) 
+    firstvalue = (double **)
       memory->smalloc(maxatom*sizeof(double *),"neighbor_history:firstvalue");
   }
 
@@ -720,7 +720,7 @@ int FixNeighHistory::pack_reverse_comm_size(int n, int first)
   last = first + n;
 
   for (i = first; i < last; i++)
-    m += 1 + 4*npartner[i];
+    m += 1 + (dnum+1)*npartner[i];
 
   return m;
 }

src/fix_store.cpp

@@ -155,8 +155,7 @@ void FixStore::reset_global(int nrow_caller, int ncol_caller)
   else memory->create(astore,nrow,ncol,"fix/store:astore");
   memory->create(rbuf,nrow*ncol+2,"fix/store:rbuf");
 
-
-  printf("AAA HOW GET HERE\n");
+ // printf("AAA HOW GET HERE\n");
 }
 
 /* ----------------------------------------------------------------------