Merge pull request #737 from akohlmey/collected-bugfixes

  {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

: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}

    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

  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;

}

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

	  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 =" \

#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);

    }

  }