loads of whitespace fixes

doc/src/Howto_triclinic.rst

@@ -92,7 +92,7 @@ restricted triclinic parallelepiped.
    conform to the LAMMPS definition of a restricted triclinic box.
    See the discussion in the next sub-section about general triclinic
    simulation boxes in LAMMPS.
-  
+
 Note that the :doc:`thermo_style custom <thermo_style>` command has
 keywords for outputting the various parameters that define both
 restricted and general triclinic simulation boxes.  Thus you can check

doc/src/create_box.rst

@@ -46,11 +46,11 @@ Examples
    create_box    1 NULL 0 5 0 5 -0.5 0.5
 
 .. code-block:: LAMMPS
- 
+
    # 3d general triclinic box using primitive cell for 3d fcc lattice
    lattice custom 1.0 a2 0.0 0.5 0.5 a1 0.5 0.0 0.5 a3 0.5 0.5 0.0 basis 0.0 0.0 0.0
    create box 1 NULL -5 5 -10 10 0 20
-   
+
 Description
 """""""""""
 

doc/src/dump.rst

@@ -719,9 +719,9 @@ Third, the output for any attribute of the *custom* style which
 represents a per-atom vector quantity will be converted (rotated) to
 be oriented consistent with the general tricinic box and its
 orientation relative to the standard xyz coordinate axes.
- 
+
 This applies to the following *custom* style attributes:
- 
+
 * vx,vy,vz = atom velocities
 * fx,fy,fz = forces on atoms
 * mux,muy,muz = orientation of dipole moment of atom

doc/src/read_data.rst

@@ -148,7 +148,7 @@ keyword must be used.
    triclinic box, the avec, bvec, cvec, and "abc origin" keywords must
    have the same values in subsequent data files.  Also the *shift*
    keyword cannot be used in subsequent read_data commands.
-   
+
 The three choices for the *add* argument affect how the atom IDs and
 molecule IDs of atoms in the data file are treated.  If *append* is
 specified, atoms in the data file are added to the current system,
@@ -494,7 +494,7 @@ periodic sense) back inside the box.  For triclinic boxes, periodicity
 in x,y,z refers to the faces of the parallelepided defined by the
 **A**,**B**,**C** edge vectors of the simuation box.  See the
 :doc:`boundary <boundary>` command doc page for a fuller discussion.
-     
+
 Note that if the *add* option is being used to add atoms to a
 simulation box that already exists, this periodic remapping will be
 performed using simulation box bounds that are the union of the

doc/src/thermo_style.rst

@@ -107,7 +107,7 @@ screen and log files.  The units for each column of output
 corresponding to the list of keywords is determined by the :doc:`units
 <units>` command for the simulation.  E.g. energies will be in energy
 units, temperature in temperature units, pressure in pressure units.
-     
+
 Style *one* prints a single line of thermodynamic info that is the
 equivalent of "thermo_style custom step temp epair emol etotal press".
 The line contains only numeric values.

src/DIELECTRIC/atom_vec_dielectric.cpp

@@ -235,7 +235,7 @@ void AtomVecDielectric::write_data_restore_restricted()
   AtomVec::write_data_restore_restricted();
 
   if (!mu_hold) return;
-  
+
   int nlocal = atom->nlocal;
   for (int i = 0; i < nlocal; i++)
     memcpy(&mu[i],&mu_hold[i],3*sizeof(double));

src/DIPOLE/atom_vec_dipole.cpp

@@ -29,7 +29,7 @@ AtomVecDipole::AtomVecDipole(LAMMPS *lmp) : AtomVec(lmp)
   mass_type = PER_TYPE;
 
   atom->q_flag = atom->mu_flag = 1;
-  
+
   mu_hold = nullptr;
 
   // strings with peratom variables to include in each AtomVec method
@@ -117,7 +117,7 @@ void AtomVecDipole::write_data_restore_restricted()
   AtomVec::write_data_restore_restricted();
 
   if (!mu_hold) return;
-  
+
   int nlocal = atom->nlocal;
   for (int i = 0; i < nlocal; i++)
     memcpy(&mu[i],&mu_hold[i],3*sizeof(double));

src/MACHDYN/atom_vec_smd.cpp

@@ -60,7 +60,7 @@ AtomVecSMD::AtomVecSMD(LAMMPS *lmp) : AtomVec(lmp)
   atom->eff_plastic_strain_rate_flag = 1;
 
   x0_hold = nullptr;
-  
+
   // strings with peratom variables to include in each AtomVec method
   // strings cannot contain fields in corresponding AtomVec default strings
   // order of fields in a string does not matter
@@ -166,7 +166,7 @@ void AtomVecSMD::data_atom_post(int ilocal)
   //   for PBC, shift, etc
   // this means no need for read_data_general_to_restricted() method
   //   to rotate x0 for general triclinic
-  
+
   x0[ilocal][0] = x[ilocal][0];
   x0[ilocal][1] = x[ilocal][1];
   x0[ilocal][2] = x[ilocal][2];

src/SPIN/atom_vec_spin.cpp

@@ -43,7 +43,7 @@ AtomVecSpin::AtomVecSpin(LAMMPS *lmp) : AtomVec(lmp)
   atom->sp_flag = 1;
 
   sp_hold = nullptr;
-  
+
   // strings with peratom variables to include in each AtomVec method
   // strings cannot contain fields in corresponding AtomVec default strings
   // order of fields in a string does not matter
@@ -147,7 +147,7 @@ void AtomVecSpin::write_data_restore_restricted()
   AtomVec::write_data_restore_restricted();
 
   if (!sp_hold) return;
-  
+
   int nlocal = atom->nlocal;
   for (int i = 0; i < nlocal; i++)
     memcpy(&sp[i],&sp_hold[i],3*sizeof(double));

src/atom.cpp

@@ -1052,7 +1052,7 @@ void Atom::data_atoms(int n, char *buf, tagint id_offset, tagint mol_offset,
   auto location = "Atoms section of data file";
 
   // use the first line to detect and validate the number of words/tokens per line
-  
+
   next = strchr(buf,'\n');
   if (!next) error->all(FLERR, "Missing data in {}", location);
   *next = '\0';
@@ -1069,7 +1069,7 @@ void Atom::data_atoms(int n, char *buf, tagint id_offset, tagint mol_offset,
     error->all(FLERR,"Incorrect format in {}: {}", location, utils::trim(buf));
 
   *next = '\n';
-  
+
   // set bounds for my proc
   // if periodic and I am lo/hi proc, adjust bounds by EPSILON
   // ensures all data atoms will be owned even with round-off
@@ -1147,17 +1147,17 @@ void Atom::data_atoms(int n, char *buf, tagint id_offset, tagint mol_offset,
     int nvalues = values.size();
 
     // skip comment lines
-    
+
     if ((nvalues == 0) || (utils::strmatch(values[0],"^#.*"))) {
 
     // check that line has correct # of words
-        
+
     } else if ((nvalues < nwords) ||
                ((nvalues > nwords) && (!utils::strmatch(values[nwords],"^#")))) {
       error->all(FLERR, "Incorrect format in {}: {}", location, utils::trim(buf));
 
     // extract the atom coords and image flags (if they exist)
-      
+
     } else {
       int imx = 0, imy = 0, imz = 0;
       if (imageflag) {
@@ -1186,14 +1186,14 @@ void Atom::data_atoms(int n, char *buf, tagint id_offset, tagint mol_offset,
           error->all(FLERR,"Read_data atom z coord is non-zero for 2d simulation");
         xdata[2] = 0.0;
       }
-      
+
       // convert atom coords from general to restricted triclinic
       // so can decide which proc owns the atom
-      
+
       if (triclinic_general) domain->general_to_restricted_coords(xdata);
 
       // apply shift if requested by read_data command
-      
+
       if (shiftflag) {
         xdata[0] += shift[0];
         xdata[1] += shift[1];
@@ -1201,11 +1201,11 @@ void Atom::data_atoms(int n, char *buf, tagint id_offset, tagint mol_offset,
       }
 
       // map atom into simulation box for periodic dimensions
-      
+
       domain->remap(xdata,imagedata);
 
       // determine if this proc owns the atom
-      
+
       if (triclinic) {
         domain->x2lamda(xdata,lamda);
         coord = lamda;
@@ -1216,7 +1216,7 @@ void Atom::data_atoms(int n, char *buf, tagint id_offset, tagint mol_offset,
           coord[2] >= sublo[2] && coord[2] < subhi[2]) {
 
         // atom-style specific method parses single line
-        
+
         avec->data_atom(xdata,imagedata,values,typestr);
         typestr = utils::utf8_subst(typestr);
         if (id_offset) tag[nlocal-1] += id_offset;

src/atom_vec.cpp

@@ -70,7 +70,7 @@ AtomVec::AtomVec(LAMMPS *lmp) : Pointers(lmp)
 
   x_hold = nullptr;
   v_hold = omega_hold = angmom_hold = nullptr;
-  
+
   threads = nullptr;
 }
 
@@ -2243,7 +2243,7 @@ void AtomVec::read_data_general_to_restricted(int nlocal_previous, int nlocal)
 
     // operate on v, omega, angmom
     // no other read_data Velocities fields are Nx3 double arrays
-    
+
     if (datatype == Atom::DOUBLE) {
       if (cols == 3) {
         double **array = *((double ***) pdata);
@@ -2283,7 +2283,7 @@ void AtomVec::write_data_restricted_to_general()
 
     // operate on v, omega, angmom
     // no other write_data Velocities fields are Nx3 double arrays
-    
+
     if (datatype == Atom::DOUBLE) {
       if (cols == 3) {
         double **array = *((double ***) pdata);
@@ -2325,10 +2325,10 @@ void AtomVec::write_data_restore_restricted()
     memory->destroy(x_hold);
     x_hold = nullptr;
   }
-  
+
   // operate on v, omega, angmom
   // no other write_data Velocities fields are Nx3 double arrays
-  
+
   if (v_hold) {
     memcpy(&v[0][0],&v_hold[0][0],3*nlocal*sizeof(double));
     memory->destroy(v_hold);
@@ -2340,7 +2340,7 @@ void AtomVec::write_data_restore_restricted()
     memory->destroy(omega_hold);
     omega_hold = nullptr;
   }
-  
+
   if (angmom_hold) {
     memcpy(&atom->angmom[0][0],&angmom_hold[0][0],3*nlocal*sizeof(double));
     memory->destroy(angmom_hold);

src/atom_vec.h

@@ -174,8 +174,8 @@ class AtomVec : protected Pointers {
   double **x, **v, **f;
 
   // copies of original unrotated fields for write_data for general triclinic
-  
+
-  double **x_hold;     
+  double **x_hold;
   double **v_hold, **omega_hold, **angmom_hold;
 
   // standard list of peratom fields always operated on by different methods

src/atom_vec_body.cpp

@@ -648,15 +648,15 @@ void AtomVecBody::write_data_bonus(FILE *fp, int n, double *buf, int /*flag*/)
 void AtomVecBody::read_data_general_to_restricted(int nlocal_previous, int nlocal)
 {
   int j;
-  
+
   AtomVec::read_data_general_to_restricted(nlocal_previous, nlocal);
 
   // quat_g2r = quat that rotates from general to restricted triclinic
   // quat_new = body quat converted to restricted triclinic
-  
+
   double quat_g2r[4],quat_new[4];
   MathExtra::mat_to_quat(domain->rotate_g2r,quat_g2r);
-  
+
   for (int i = nlocal_previous; i < nlocal; i++) {
     if (body[i] < 0) continue;
     j = body[i];
@@ -685,7 +685,7 @@ void AtomVecBody::write_data_restricted_to_general()
 
   // quat_r2g = quat that rotates from restricted to general triclinic
   // quat_new = ellipsoid quat converted to general triclinic
-  
+
   double quat_r2g[4],quat_new[4];
   MathExtra::mat_to_quat(domain->rotate_r2g,quat_r2g);
 

src/atom_vec_body.h

@@ -69,7 +69,7 @@ class AtomVecBody : public AtomVec {
   void read_data_general_to_restricted(int, int);
   void write_data_restricted_to_general();
   void write_data_restore_restricted();
-  
+
   // methods used by other classes to query/set body info
 
   double radius_body(int, int, int *, double *);

src/atom_vec_ellipsoid.cpp

@@ -545,15 +545,15 @@ void AtomVecEllipsoid::write_data_bonus(FILE *fp, int n, double *buf, int /*flag
 void AtomVecEllipsoid::read_data_general_to_restricted(int nlocal_previous, int nlocal)
 {
   int j;
-  
+
   AtomVec::read_data_general_to_restricted(nlocal_previous, nlocal);
 
   // quat_g2r = quat that rotates from general to restricted triclinic
   // quat_new = ellipsoid quat converted to restricted triclinic
-  
+
   double quat_g2r[4],quat_new[4];
   MathExtra::mat_to_quat(domain->rotate_g2r,quat_g2r);
-  
+
   for (int i = nlocal_previous; i < nlocal; i++) {
     if (ellipsoid[i] < 0) continue;
     j = ellipsoid[i];
@@ -582,7 +582,7 @@ void AtomVecEllipsoid::write_data_restricted_to_general()
 
   // quat_r2g = quat that rotates from restricted to general triclinic
   // quat_new = ellipsoid quat converted to general triclinic
-  
+
   double quat_r2g[4],quat_new[4];
   MathExtra::mat_to_quat(domain->rotate_r2g,quat_r2g);
 

src/atom_vec_ellipsoid.h

@@ -74,7 +74,7 @@ class AtomVecEllipsoid : public AtomVec {
   double *rmass;
   double **angmom;
   double **quat_hold;
-  
+
   int nghost_bonus, nmax_bonus;
   int ellipsoid_flag;
   double rmass_one;

src/atom_vec_line.cpp

@@ -526,7 +526,7 @@ int AtomVecLine::pack_data_bonus(double *buf, int /*flag*/)
       j = line[i];
       length = bonus[j].length;
       theta = bonus[j].theta;
-      
+
       xc = x_bonus[i][0];
       yc = x_bonus[i][1];
       x1 = xc - 0.5 * cos(theta) * length;
@@ -541,7 +541,7 @@ int AtomVecLine::pack_data_bonus(double *buf, int /*flag*/)
       // if triclinic_general:
       // rotate 4 buf values from restricted to general triclinic
       // output by write_data_bonus() as x1/y1 and x2/y2
-      
+
       if (triclinic_general) {
         coords[0] = buf[m-4]; coords[1] = buf[m-3]; coords[2] = 0.0;
         domain->restricted_to_general_coords(coords);

src/atom_vec_tri.cpp

@@ -510,7 +510,7 @@ void AtomVecTri::data_atom_bonus(int m, const std::vector<std::string> &values)
 
   // convert c1,c2,c3 from general to restricted triclniic
   // x is already restricted triclinic
-  
+
   if (domain->triclinic_general) {
     domain->general_to_restricted_coords(c1);
     domain->general_to_restricted_coords(c2);
@@ -523,11 +523,11 @@ void AtomVecTri::data_atom_bonus(int m, const std::vector<std::string> &values)
   domain->remap_near(c1,x[m]);
   domain->remap_near(c2,x[m]);
   domain->remap_near(c3,x[m]);
-  
+
   // centroid = 1/3 of sum of vertices
   // error if centroid is not within EPSILON of atom x
   // reset atom x to centroid
-  
+
   double centroid[3];
   centroid[0] = (c1[0] + c2[0] + c3[0]) / 3.0;
   centroid[1] = (c1[1] + c2[1] + c3[1]) / 3.0;
@@ -729,7 +729,7 @@ int AtomVecTri::pack_data_bonus(double *buf, int /*flag*/)
   double **x_bonus;
   if (triclinic_general) x_bonus = x_hold;
   else x_bonus = x;
-    
+
   tagint *tag = atom->tag;
   int nlocal = atom->nlocal;
 
@@ -760,7 +760,7 @@ int AtomVecTri::pack_data_bonus(double *buf, int /*flag*/)
       // if triclinic_general:
       // rotate 9 buf values from restricted to general triclinic
       // output by write_data_bonus() as c1,c2,c3
-      
+
       if (triclinic_general) {
         domain->restricted_to_general_coords(&buf[m-9]);
         domain->restricted_to_general_coords(&buf[m-6]);

src/create_atoms.cpp

@@ -358,11 +358,11 @@ void CreateAtoms::command(int narg, char **arg)
   }
 
   // require non-none lattice be defined for BOX or REGION styles
-  
+
   if ((style == BOX) || (style == REGION)) {
     if (nbasis == 0) error->all(FLERR, "Cannot create atoms with undefined lattice");
   }
-  
+
   // apply scaling factor for styles that use distance-dependent factors
 
   if (scaleflag) {
@@ -465,7 +465,7 @@ void CreateAtoms::command(int narg, char **arg)
   atom->avec->clear_bonus();
 
   // add atoms/molecules with appropriate add() method
-  
+
   bigint natoms_previous = atom->natoms;
   int nlocal_previous = atom->nlocal;
 
@@ -1178,7 +1178,7 @@ void CreateAtoms::add_lattice()
 {
   // add atoms on general triclinic lattice if Domain has setting for it
   // verify lattice was defined with triclinic/general option
-  
+
   if (!domain->triclinic_general && domain->lattice->is_general_triclinic())
     error->all(FLERR,"Create_atoms for non general triclinic box cannot use triclinic/general lattice");
   if (domain->triclinic_general && !domain->lattice->is_general_triclinic())
@@ -1228,7 +1228,7 @@ void CreateAtoms::add_lattice()
   // convert 8 corner points of bounding box to lattice coordinates
   // compute new bounding box (xyz min/max) in lattice coords
   // for orthogonal or restricted triclinic, use 8 corner points of bbox lo/hi
-  
+
   if (!domain->triclinic_general) {
     domain->lattice->bbox(1, bboxlo[0], bboxlo[1], bboxlo[2], xmin, ymin, zmin, xmax, ymax, zmax);
     domain->lattice->bbox(1, bboxhi[0], bboxlo[1], bboxlo[2], xmin, ymin, zmin, xmax, ymax, zmax);
@@ -1274,7 +1274,7 @@ void CreateAtoms::add_lattice()
     domain->restricted_to_general_coords(point);
     domain->lattice->bbox(1, point[0], point[1], point[2], xmin, ymin, zmin, xmax, ymax, zmax);
   }
-  
+
   // ilo:ihi,jlo:jhi,klo:khi = loop bounds for lattice overlap of my subbox
   // overlap = any part of a unit cell (face,edge,pt) in common with my subbox
   // in lattice space, subbox is a tilted box
@@ -1284,7 +1284,7 @@ void CreateAtoms::add_lattice()
   //   which can lead to missing atoms in rare cases
   // extra decrement of lo if min < 0, since static_cast(-1.5) = -1
   // for 2d simulation, klo = khi = 0 so just one plane of atoms
-  
+
   ilo = static_cast<int>(xmin) - 1;
   jlo = static_cast<int>(ymin) - 1;
   klo = static_cast<int>(zmin) - 1;
@@ -1297,7 +1297,7 @@ void CreateAtoms::add_lattice()
   if (zmin < 0.0) klo--;
 
   if (domain->dimension == 2) klo = khi = 0;
-  
+
   // count lattice sites on each proc
 
   nlatt_overflow = 0;
@@ -1395,7 +1395,7 @@ void CreateAtoms::loop_lattice(int action)
                 error->all(FLERR,"Create_atoms atom z coord is non-zero for 2d simulation");
               x[2] = 0.0;
             }
-          }          
+          }
 
           // if a region was specified, test if atom is in it
 

src/create_box.cpp

@@ -48,7 +48,7 @@ void CreateBox::command(int narg, char **arg)
 
   Region *region = nullptr;
   int triclinic_general = 0;
-  
+
   if (strcmp(arg[1],"NULL") == 0) triclinic_general = 1;
   else {
     region = domain->get_region_by_id(arg[1]);
@@ -61,13 +61,13 @@ void CreateBox::command(int narg, char **arg)
   // 3 options: orthogonal, restricted triclinic, general triclinic
 
   int iarg = 2;
-  
+
   if (region) {
-    
+
     // region is not prism
     // setup orthogonal box
     // set simulation domain from region extent
-    
+
     if (strcmp(region->style, "prism") != 0) {
       domain->triclinic = 0;
       domain->boxlo[0] = region->extent_xlo;
@@ -108,7 +108,7 @@ void CreateBox::command(int narg, char **arg)
   } else if (triclinic_general) {
     if (!domain->lattice->is_general_triclinic())
       error->all(FLERR,"Create_box for general triclinic requires triclnic/general lattice");
-    
+
     if (iarg + 6 > narg) utils::missing_cmd_args(FLERR, "create_box general triclinic", error);
 
     double alo = utils::numeric(FLERR, arg[iarg + 0], false, lmp);
@@ -118,14 +118,14 @@ void CreateBox::command(int narg, char **arg)
     double clo = utils::numeric(FLERR, arg[iarg + 4], false, lmp);
     double chi = utils::numeric(FLERR, arg[iarg + 5], false, lmp);
     iarg += 6;
-    
+
     // use lattice2box() to generate origin and ABC vectors
     // origin = abc lo
     // ABC vectors = hi in one dim - origin
-    
+
     double avec[3],bvec[3],cvec[3],origin[3];
     double px,py,pz;
-    
+
     px = alo; py = blo; pz = clo;
     domain->lattice->lattice2box(px,py,pz);
     origin[0] = px;
@@ -157,7 +157,7 @@ void CreateBox::command(int narg, char **arg)
     }
 
     // define general triclinic box within Domain class
-    
+
     domain->define_general_triclinic(avec,bvec,cvec,origin);
   }
 

src/domain.cpp

@@ -293,12 +293,12 @@ void Domain::set_global_box()
 
   // update general triclinic box if defined
   // reset general tri ABC edge vectors from restricted tri box
-  
+
   if (triclinic_general) {
     double aprime[3],bprime[3],cprime[3];
 
     // A'B'C' = edge vectors of restricted triclinic box
-    
+
     aprime[0] = boxhi[0] - boxlo[0];
     aprime[1] = aprime[2] = 0.0;
     bprime[0] = xy;
@@ -309,7 +309,7 @@ void Domain::set_global_box()
     cprime[2] = boxhi[2] - boxlo[2];
 
     // transform restricted A'B'C' to general triclinic ABC
-    
+
     MathExtra::matvec(rotate_r2g,aprime,avec);
     MathExtra::matvec(rotate_r2g,bprime,bvec);
     MathExtra::matvec(rotate_r2g,cprime,cvec);
@@ -556,7 +556,7 @@ void Domain::define_general_triclinic(double *avec_caller, double *bvec_caller,
 {
   if (triclinic || triclinic_general)
     error->all(FLERR,"General triclinic box edge vectors are already set");
-  
+
   triclinic = triclinic_general = 1;
 
   avec[0] = avec_caller[0];
@@ -596,7 +596,7 @@ void Domain::define_general_triclinic(double *avec_caller, double *bvec_caller,
   xy = bprime[0];
   xz = cprime[0];
   yz = cprime[1];
-  
+
   // debug
 
   /*
@@ -656,7 +656,7 @@ void Domain::general_to_restricted_rotation(double *a, double *b, double *c,
   MathExtra::norm3(rot1);
   double theta1 = acos(a[0]/alen);
   MathExtra::axisangle_to_quat(rot1,theta1,quat1);
-  
+
   // rotmat1 = rotation matrix associated with quat1
 
   double rotmat1[3][3];
@@ -674,7 +674,7 @@ void Domain::general_to_restricted_rotation(double *a, double *b, double *c,
   //   Byz1 dot yunit = B1y = |Byz1| cos(theta2)
   // theta2 via acos() is positive (0 to PI)
   //   positive is valid if B1z < 0.0 else flip sign of theta2
-  
+
   double byzvec1[3],quat2[4];
   MathExtra::copy3(b1,byzvec1);
   byzvec1[0] = 0.0;
@@ -705,7 +705,7 @@ void Domain::general_to_restricted_rotation(double *a, double *b, double *c,
 void Domain::general_to_restricted_coords(double *x)
 {
   double xshift[3],xnew[3];
-  
+
   xshift[0] = x[0] - boxlo[0];
   xshift[1] = x[1] - boxlo[1];
   xshift[2] = x[2] - boxlo[2];
@@ -722,7 +722,7 @@ void Domain::general_to_restricted_coords(double *x)
 void Domain::restricted_to_general_coords(double *x)
 {
   double xshift[3],xnew[3];
-  
+
   xshift[0] = x[0] - boxlo[0];
   xshift[1] = x[1] - boxlo[1];
   xshift[2] = x[2] - boxlo[2];
@@ -735,7 +735,7 @@ void Domain::restricted_to_general_coords(double *x)
 void Domain::restricted_to_general_coords(double *x, double *xnew)
 {
   double xshift[3];
-  
+
   xshift[0] = x[0] - boxlo[0];
   xshift[1] = x[1] - boxlo[1];
   xshift[2] = x[2] - boxlo[2];
@@ -752,7 +752,7 @@ void Domain::restricted_to_general_coords(double *x, double *xnew)
 void Domain::general_to_restricted_vector(double *v)
 {
   double vnew[3];
-  
+
   MathExtra::matvec(rotate_g2r,v,vnew);
   v[0] = vnew[0];
   v[1] = vnew[1];
@@ -766,7 +766,7 @@ void Domain::general_to_restricted_vector(double *v)
 void Domain::restricted_to_general_vector(double *v)
 {
   double vnew[3];
-  
+
   MathExtra::matvec(rotate_r2g,v,vnew);
   v[0] = vnew[0];
   v[1] = vnew[1];

src/domain.h

@@ -41,7 +41,7 @@ class Domain : protected Pointers {
 
   int triclinic;          // 0 = orthog box, 1 = triclinic (restricted or general)
   int triclinic_general;  // 1 if general <-> restricted tri mapping is stored, 0 if not
-  
+
   // orthogonal box
 
   double xprd, yprd, zprd;                   // global box dimensions
@@ -96,7 +96,7 @@ class Domain : protected Pointers {
   double rotate_r2g[3][3];           // rotation matrix from restricted --> general tri
 
   // box flags
-  
+
   int box_change;           // 1 if any of next 3 flags are set, else 0
   int box_change_size;      // 1 if box size changes, 0 if not
   int box_change_shape;     // 1 if box shape changes, 0 if not
@@ -145,13 +145,13 @@ class Domain : protected Pointers {
   void general_to_restricted_rotation(double *, double *, double *,
                                       double [3][3],
                                       double *, double *, double *);
-  void general_to_restricted_coords(double *); 
+  void general_to_restricted_coords(double *);
   void restricted_to_general_coords(double *);
   void restricted_to_general_coords(double *, double *);
-  void general_to_restricted_vector(double *); 
+  void general_to_restricted_vector(double *);
   void restricted_to_general_vector(double *);
-  void restricted_to_general_vector(double *, double *x); 
+  void restricted_to_general_vector(double *, double *x);
- 
+
   void set_lattice(int, char **);
   void add_region(int, char **);
   void delete_region(Region *);

src/dump_atom.cpp

@@ -133,7 +133,7 @@ void DumpAtom::init_style()
       }
     }
   }
-  
+
   if (image_flag == 0) convert_choice = &DumpAtom::convert_noimage;
   else convert_choice = &DumpAtom::convert_image;
 
@@ -157,14 +157,14 @@ int DumpAtom::modify_param(int narg, char **arg)
     for (auto &item : keyword_user) item.clear();
     return 2;
   }
-  
+
   if (strcmp(arg[0],"image") == 0) {
     if (narg < 2) error->all(FLERR,"Illegal dump_modify command");
     image_flag = utils::logical(FLERR,arg[1],false,lmp);
     for (auto &item : keyword_user) item.clear();
     return 2;
   }
-  
+
   if (strcmp(arg[0],"triclinic/general") == 0) {
     triclinic_general = 1;
     if (triclinic_general && !domain->triclinic_general)
@@ -172,7 +172,7 @@ int DumpAtom::modify_param(int narg, char **arg)
                  "if simulation box is not general triclinic");
     return 1;
   }
-  
+
   return 0;
 }
 

src/dump_custom.cpp

@@ -1347,7 +1347,7 @@ int DumpCustom::parse_fields(int narg, char **arg)
       if (triclinic_general) pack_choice[iarg] = &DumpCustom::pack_y_triclinic_general;
       else pack_choice[iarg] = &DumpCustom::pack_y;
       vtype[iarg] = Dump::DOUBLE;
-    } else if (strcmp(arg[iarg],"z") == 0) { 
+    } else if (strcmp(arg[iarg],"z") == 0) {
       if (triclinic_general) pack_choice[iarg] = &DumpCustom::pack_z_triclinic_general;
       else pack_choice[iarg] = &DumpCustom::pack_z;
       vtype[iarg] = Dump::DOUBLE;
@@ -1390,7 +1390,7 @@ int DumpCustom::parse_fields(int narg, char **arg)
       if (domain->triclinic) pack_choice[iarg] = &DumpCustom::pack_zsu_triclinic;
       else pack_choice[iarg] = &DumpCustom::pack_zsu;
       vtype[iarg] = Dump::DOUBLE;
-      
+
     } else if (strcmp(arg[iarg],"ix") == 0) {
       pack_choice[iarg] = &DumpCustom::pack_ix;
       vtype[iarg] = Dump::INT;
@@ -1431,7 +1431,7 @@ int DumpCustom::parse_fields(int narg, char **arg)
         error->all(FLERR,"Dumping an atom property that isn't allocated");
       pack_choice[iarg] = &DumpCustom::pack_q;
       vtype[iarg] = Dump::DOUBLE;
-      
+
     } else if (strcmp(arg[iarg],"mux") == 0) {
       if (!atom->mu_flag)
         error->all(FLERR,"Dumping an atom property that isn't allocated");
@@ -1466,7 +1466,7 @@ int DumpCustom::parse_fields(int narg, char **arg)
         error->all(FLERR,"Dumping an atom property that isn't allocated");
       pack_choice[iarg] = &DumpCustom::pack_diameter;
       vtype[iarg] = Dump::DOUBLE;
-      
+
     } else if (strcmp(arg[iarg],"heatflow") == 0) {
       if (!atom->heatflow_flag)
         error->all(FLERR,"Dumping an atom property that isn't allocated");
@@ -1477,7 +1477,7 @@ int DumpCustom::parse_fields(int narg, char **arg)
         error->all(FLERR,"Dumping an atom property that isn't allocated");
       pack_choice[iarg] = &DumpCustom::pack_temperature;
       vtype[iarg] = Dump::DOUBLE;
-      
+
     } else if (strcmp(arg[iarg],"omegax") == 0) {
       if (!atom->omega_flag)
         error->all(FLERR,"Dumping an atom property that isn't allocated");
@@ -1496,7 +1496,7 @@ int DumpCustom::parse_fields(int narg, char **arg)
       if (triclinic_general) pack_choice[iarg] = &DumpCustom::pack_omegaz_triclinic_general;
       else pack_choice[iarg] = &DumpCustom::pack_omegaz;
       vtype[iarg] = Dump::DOUBLE;
-      
+
     } else if (strcmp(arg[iarg],"angmomx") == 0) {
       if (!atom->angmom_flag)
         error->all(FLERR,"Dumping an atom property that isn't allocated");
@@ -1515,7 +1515,7 @@ int DumpCustom::parse_fields(int narg, char **arg)
       if (triclinic_general) pack_choice[iarg] = &DumpCustom::pack_angmomz_triclinic_general;
       else pack_choice[iarg] = &DumpCustom::pack_angmomz;
       vtype[iarg] = Dump::DOUBLE;
-      
+
     } else if (strcmp(arg[iarg],"tqx") == 0) {
       if (!atom->torque_flag)
         error->all(FLERR,"Dumping an atom property that isn't allocated");
@@ -1793,7 +1793,7 @@ int DumpCustom::modify_param(int narg, char **arg)
                  "if simulation box is not general triclinic");
     return 1;
   }
-  
+
   if (strcmp(arg[0],"triclinic/general") == 0) {
     if (narg < 2) error->all(FLERR,"Illegal dump_modify command");
     triclinic_general = utils::logical(FLERR,arg[1],false,lmp);
@@ -2387,7 +2387,7 @@ void DumpCustom::pack_x_triclinic_general(int n)
 {
   double **x = atom->x;
   double xtri[3];
-  
+
   for (int i = 0; i < nchoose; i++) {
     domain->restricted_to_general_coords(x[clist[i]],xtri);
     buf[n] = xtri[0];
@@ -2973,7 +2973,7 @@ void DumpCustom::pack_fx_triclinic_general(int n)
 {
   double **f = atom->f;
   double ftri[3];
-  
+
   for (int i = 0; i < nchoose; i++) {
     domain->restricted_to_general_vector(f[clist[i]],ftri);
     buf[n] = ftri[0];
@@ -3075,7 +3075,7 @@ void DumpCustom::pack_mux_triclinic_general(int n)
 {
   double **mu = atom->mu;
   double mutri[3];
-  
+
   for (int i = 0; i < nchoose; i++) {
     domain->restricted_to_general_vector(mu[clist[i]],mutri);
     buf[n] = mutri[0];
@@ -3089,7 +3089,7 @@ void DumpCustom::pack_muy_triclinic_general(int n)
 {
   double **mu = atom->mu;
   double mutri[3];
-  
+
   for (int i = 0; i < nchoose; i++) {
     domain->restricted_to_general_vector(mu[clist[i]],mutri);
     buf[n] = mutri[1];
@@ -3103,7 +3103,7 @@ void DumpCustom::pack_muz_triclinic_general(int n)
 {
   double **mu = atom->mu;
   double mutri[3];
-  
+
   for (int i = 0; i < nchoose; i++) {
     domain->restricted_to_general_vector(mu[clist[i]],mutri);
     buf[n] = mutri[2];
@@ -3201,7 +3201,7 @@ void DumpCustom::pack_omegax_triclinic_general(int n)
 {
   double **omega = atom->omega;
   double omegatri[3];
-  
+
   for (int i = 0; i < nchoose; i++) {
     domain->restricted_to_general_vector(omega[clist[i]],omegatri);
     buf[n] = omegatri[0];
@@ -3215,7 +3215,7 @@ void DumpCustom::pack_omegay_triclinic_general(int n)
 {
   double **omega = atom->omega;
   double omegatri[3];
-  
+
   for (int i = 0; i < nchoose; i++) {
     domain->restricted_to_general_vector(omega[clist[i]],omegatri);
     buf[n] = omegatri[1];
@@ -3229,7 +3229,7 @@ void DumpCustom::pack_omegaz_triclinic_general(int n)
 {
   double **omega = atom->omega;
   double omegatri[3];
-  
+
   for (int i = 0; i < nchoose; i++) {
     domain->restricted_to_general_vector(omega[clist[i]],omegatri);
     buf[n] = omegatri[2];
@@ -3279,7 +3279,7 @@ void DumpCustom::pack_angmomx_triclinic_general(int n)
 {
   double **angmom = atom->angmom;
   double angmomtri[3];
-  
+
   for (int i = 0; i < nchoose; i++) {
     domain->restricted_to_general_vector(angmom[clist[i]],angmomtri);
     buf[n] = angmomtri[0];
@@ -3293,7 +3293,7 @@ void DumpCustom::pack_angmomy_triclinic_general(int n)
 {
   double **angmom = atom->angmom;
   double angmomtri[3];
-  
+
   for (int i = 0; i < nchoose; i++) {
     domain->restricted_to_general_vector(angmom[clist[i]],angmomtri);
     buf[n] = angmomtri[1];
@@ -3307,7 +3307,7 @@ void DumpCustom::pack_angmomz_triclinic_general(int n)
 {
   double **angmom = atom->angmom;
   double angmomtri[3];
-  
+
   for (int i = 0; i < nchoose; i++) {
     domain->restricted_to_general_vector(angmom[clist[i]],angmomtri);
     buf[n] = angmomtri[2];
@@ -3357,7 +3357,7 @@ void DumpCustom::pack_tqx_triclinic_general(int n)
 {
   double **torque = atom->torque;
   double tqtri[3];
-  
+
   for (int i = 0; i < nchoose; i++) {
     domain->restricted_to_general_vector(torque[clist[i]],tqtri);
     buf[n] = tqtri[0];
@@ -3371,7 +3371,7 @@ void DumpCustom::pack_tqy_triclinic_general(int n)
 {
   double **torque = atom->torque;
   double tqtri[3];
-  
+
   for (int i = 0; i < nchoose; i++) {
     domain->restricted_to_general_vector(torque[clist[i]],tqtri);
     buf[n] = tqtri[1];
@@ -3385,7 +3385,7 @@ void DumpCustom::pack_tqz_triclinic_general(int n)
 {
   double **torque = atom->torque;
   double tqtri[3];
-  
+
   for (int i = 0; i < nchoose; i++) {
     domain->restricted_to_general_vector(torque[clist[i]],tqtri);
     buf[n] = tqtri[2];

src/dump_custom.h

@@ -37,7 +37,7 @@ class DumpCustom : public Dump {
   int nevery;        // dump frequency for output
   char *idregion;    // region ID, nullptr if no region
   int triclinic_general;  // 1 if output box & per-atom info for general triclinic
-  
+
   int nthresh;                        // # of defined thresholds
   int nthreshlast;                    // # of defined thresholds with value = LAST
                                       //
@@ -159,7 +159,7 @@ class DumpCustom : public Dump {
   void pack_x_triclinic_general(int);
   void pack_y_triclinic_general(int);
   void pack_z_triclinic_general(int);
-  
+
   void pack_xs(int);
   void pack_ys(int);
   void pack_zs(int);
@@ -190,11 +190,11 @@ class DumpCustom : public Dump {
 
   void pack_vx(int);
   void pack_vy(int);
-  void pack_vz(int); 
+  void pack_vz(int);
   void pack_vx_triclinic_general(int);
   void pack_vy_triclinic_general(int);
   void pack_vz_triclinic_general(int);
-   
+
   void pack_fx(int);
   void pack_fy(int);
   void pack_fz(int);
@@ -214,7 +214,7 @@ class DumpCustom : public Dump {
 
   void pack_radius(int);
   void pack_diameter(int);
-  
+
   void pack_heatflow(int);
   void pack_temperature(int);
 
@@ -224,14 +224,14 @@ class DumpCustom : public Dump {
   void pack_omegax_triclinic_general(int);
   void pack_omegay_triclinic_general(int);
   void pack_omegaz_triclinic_general(int);
-  
+
   void pack_angmomx(int);
   void pack_angmomy(int);
   void pack_angmomz(int);
   void pack_angmomx_triclinic_general(int);
   void pack_angmomy_triclinic_general(int);
   void pack_angmomz_triclinic_general(int);
-  
+
   void pack_tqx(int);
   void pack_tqy(int);
   void pack_tqz(int);

src/lattice.cpp

@@ -141,7 +141,7 @@ Lattice::Lattice(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
   // process optional args
 
   int triclinic_general = 0;
-  
+
   int iarg = 2;
   while (iarg < narg) {
     if (strcmp(arg[iarg],"origin") == 0) {
@@ -230,7 +230,7 @@ Lattice::Lattice(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
     } else if (strcmp(arg[iarg],"triclinic/general") == 0) {
       triclinic_general = 1;
       iarg++;
-      
+
     } else error->all(FLERR,"Unknown lattice keyword: {}", arg[iarg]);
   }
 
@@ -267,7 +267,7 @@ Lattice::Lattice(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
 
   // additional requirements for a general triclinic lattice
   // a123 prime are used to compute lattice spacings
-  
+
   if (triclinic_general) {
     if (style != CUSTOM)
       error->all(FLERR,"Lattice triclnic/general must be style = CUSTOM");
@@ -285,11 +285,11 @@ Lattice::Lattice(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
     double rotmat[3][3];
     domain->general_to_restricted_rotation(a1,a2,a3,rotmat,a1_prime,a2_prime,a3_prime);
   }
-  
+
   // reset scale for LJ units (input scale is rho*)
   // scale = (Nbasis/(Vprimitive * rho*)) ^ (1/dim)
   // use fabs() in case a1,a2,a3 are not right-handed for general triclinic
-  
+
   if (strcmp(update->unit_style,"lj") == 0) {
     double vec[3];
     MathExtra::cross3(a2,a3,vec);
@@ -321,7 +321,7 @@ Lattice::Lattice(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
     // reset transform used by bbox() to be based on rotated a123 prime vectors
 
     if (triclinic_general) setup_transform(a1_prime,a2_prime,a3_prime);
-    
+
     bbox(0,0.0,0.0,0.0,xmin,ymin,zmin,xmax,ymax,zmax);
     bbox(0,1.0,0.0,0.0,xmin,ymin,zmin,xmax,ymax,zmax);
     bbox(0,0.0,1.0,0.0,xmin,ymin,zmin,xmax,ymax,zmax);
@@ -334,13 +334,13 @@ Lattice::Lattice(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
     // restore original general triclinic a123 transform
 
     if (triclinic_general) setup_transform(a2,a2,a3);
-    
+
     xlattice = xmax - xmin;
     ylattice = ymax - ymin;
     zlattice = zmax - zmin;
 
   // user-defined lattice spacings
-    
+
   } else {
     xlattice *= scale;
     ylattice *= scale;
@@ -542,7 +542,7 @@ void Lattice::setup_transform(double *a, double *b, double *c)
 ------------------------------------------------------------------------- */
 
 void Lattice::lattice2box(double &x, double &y, double &z)
-{ 
+{
   double x1 = primitive[0][0]*x + primitive[0][1]*y + primitive[0][2]*z;
   double y1 = primitive[1][0]*x + primitive[1][1]*y + primitive[1][2]*z;
   double z1 = primitive[2][0]*x + primitive[2][1]*y + primitive[2][2]*z;
@@ -615,7 +615,7 @@ void Lattice::add_basis(double x, double y, double z)
 void Lattice::bbox(int flag, double x, double y, double z,
                    double &xmin, double &ymin, double &zmin,
                    double &xmax, double &ymax, double &zmax)
-{ 
+{
   if (flag == 0) lattice2box(x,y,z);
   else box2lattice(x,y,z);
 

src/lattice.h

@@ -28,7 +28,7 @@ class Lattice : protected Pointers {
   int nbasis;                             // # of basis atoms in unit cell
   double **basis;                         // fractional coords of each basis atom
                                           // within unit cell (0 <= coord < 1)
-  
+
   Lattice(class LAMMPS *, int, char **);
   ~Lattice() override;
   void lattice2box(double &, double &, double &);
@@ -36,7 +36,7 @@ class Lattice : protected Pointers {
   void bbox(int, double, double, double,
             double &, double &, double &, double &, double &, double &);
   int is_general_triclinic();
-  
+
  private:
   int triclinic_general;     // 1 if general triclinic, else 0
   int oriented;              // 1 if non-default orient xyz, else 0
@@ -51,10 +51,10 @@ class Lattice : protected Pointers {
   double rotaterow[3][3];
   double rotatecol[3][3];
 
-  double a1_prime[3];   // a123 rotated to restricted triclinic orientation  
+  double a1_prime[3];   // a123 rotated to restricted triclinic orientation
   double a2_prime[3];
   double a3_prime[3];
-  
+
   int orthogonal();
   int right_handed_orientation();
   int right_handed_primitive();

src/math_extra.cpp

@@ -381,7 +381,7 @@ void mat_to_quat(double mat[3][3], double *q)
   ez[0] = mat[0][2];
   ez[1] = mat[1][2];
   ez[2] = mat[2][2];
-  
+
   MathExtra::exyz_to_q(ex,ey,ez,q);
 }
 

src/read_data.cpp

@@ -474,7 +474,7 @@ void ReadData::command(int narg, char **arg)
   int atomflag, topoflag;
   int bondflag, angleflag, dihedralflag, improperflag;
   int ellipsoidflag, lineflag, triflag, bodyflag;
-  
+
   atomflag = topoflag = 0;
   bondflag = angleflag = dihedralflag = improperflag = 0;
   ellipsoidflag = lineflag = triflag = bodyflag = 0;
@@ -492,14 +492,14 @@ void ReadData::command(int narg, char **arg)
   boxlo[0] = boxlo[1] = boxlo[2] = -0.5;
   boxhi[0] = boxhi[1] = boxhi[2] = 0.5;
   xy = xz = yz = 0.0;
-  
+
   avec[0] = bvec[1] = cvec[2] = 1.0;
   avec[1] = avec[2] = 0.0;
   bvec[0] = bvec[2] = 0.0;
   cvec[0] = cvec[1] = 0.0;
   abc_origin[0] = abc_origin[1] = abc_origin[2] = 0.0;
   if (domain->dimension == 2) abc_origin[2] = -0.5;
-  
+
   keyword[0] = '\0';
 
   nlocal_previous = atom->nlocal;
@@ -542,7 +542,7 @@ void ReadData::command(int narg, char **arg)
                      "2d simulation with general triclinic box");
       }
     }
-    
+
     // problem setup using info from header
     // only done once, if firstpass and first data file
     // apply extra settings before grow(), even if no topology in file
@@ -577,7 +577,7 @@ void ReadData::command(int narg, char **arg)
       if (!triclinic_general) {
 
         // orthogonal or restricted triclinic box
-        
+
         domain->boxlo[0] = boxlo[0];
         domain->boxhi[0] = boxhi[0];
         domain->boxlo[1] = boxlo[1];
@@ -586,7 +586,7 @@ void ReadData::command(int narg, char **arg)
         domain->boxhi[2] = boxhi[2];
 
         // restricted triclinic box
-        
+
         if (triclinic) {
           domain->triclinic = 1;
           domain->xy = xy;
@@ -597,7 +597,7 @@ void ReadData::command(int narg, char **arg)
       // general triclinic box
       // define_general_triclinic() converts
       //   ABC edge vectors + abc_origin to restricted triclinic
-        
+
       } else if (triclinic_general) {
         domain->define_general_triclinic(avec,bvec,cvec,abc_origin);
       }
@@ -612,7 +612,7 @@ void ReadData::command(int narg, char **arg)
       // first data file must also be general triclinic
       // avec,bvec,vec and origin must match first data file
       // shift not allowed
-      
+
       if (triclinic_general) {
         if (!domain->triclinic_general)
           error->all(FLERR,"Read_data subsequent file cannot switch to general triclinic");
@@ -633,14 +633,14 @@ void ReadData::command(int narg, char **arg)
 
       // restricted triclinic
       // tilt factors must match first data file
-        
+
       } else if (triclinic) {
         if (!domain->triclinic || domain->triclinic_general)
           error->all(FLERR,"Read_data subsequent file cannot switch to restricted triclinic");
         if (xy != domain->xy || xz != domain->xz || yz != domain->yz)
           error->all(FLERR,"Read_data subsequent file tilt factors must be same as first file");
       }
-      
+
       double oldboxlo[3] = {domain->boxlo[0], domain->boxlo[1], domain->boxlo[2]};
       double oldboxhi[3] = {domain->boxhi[0], domain->boxhi[1], domain->boxhi[2]};
       domain->boxlo[0] = MIN(domain->boxlo[0], boxlo[0] + shift[0]);
@@ -652,7 +652,7 @@ void ReadData::command(int narg, char **arg)
 
       // check if box has changed
       // if yes, warn about non-zero image flags
-      
+
       if ((oldboxlo[0] != domain->boxlo[0]) || (oldboxlo[1] != domain->boxlo[1]) ||
           (oldboxlo[2] != domain->boxlo[2]) || (oldboxhi[0] != domain->boxhi[0]) ||
           (oldboxhi[1] != domain->boxhi[1]) || (oldboxhi[2] != domain->boxhi[2])) {
@@ -673,7 +673,7 @@ void ReadData::command(int narg, char **arg)
     }
 
     // setup simulation box and paritioning in Domain and Comm classes
-    
+
     domain->print_box("  ");
     domain->set_initial_box();
     domain->set_global_box();
@@ -1228,7 +1228,7 @@ void ReadData::header(int firstpass)
   // initialize type counts by the "extra" numbers so they get counted
   // in case the corresponding "types" line is missing and thus the extra
   // value will not be processed
-  
+
   if (addflag == NONE) {
     atom->ntypes = extra_atom_types;
     atom->nbondtypes = extra_bond_types;
@@ -1244,7 +1244,7 @@ void ReadData::header(int firstpass)
     if (eof == nullptr) error->one(FLERR, "Unexpected end of data file");
 
     // check for units keyword in first line and print warning on mismatch
-    
+
     auto units = Tokenizer(utils::strfind(line, "units = \\w+")).as_vector();
     if (units.size() > 2) {
       if (units[2] != update->unit_style)
@@ -1433,7 +1433,7 @@ void ReadData::header(int firstpass)
       xy = utils::numeric(FLERR, words[0], false, lmp);
       xz = utils::numeric(FLERR, words[1], false, lmp);
       yz = utils::numeric(FLERR, words[2], false, lmp);
-      
+
     } else if (utils::strmatch(line, "^\\s*\\f+\\s+\\f+\\s+\\f+\\s+\\avec\\s")) {
       avec_flag = 1;
       avec[0] = utils::numeric(FLERR, words[0], false, lmp);
@@ -1522,7 +1522,7 @@ void ReadData::atoms()
     if (eof) error->all(FLERR, "Unexpected end of data file");
     if (tlabelflag && !lmap->is_complete(Atom::ATOM))
       error->all(FLERR, "Label map is incomplete: all types must be assigned a unique type label");
-    atom->data_atoms(nchunk, buffer, id_offset, mol_offset, toffset, 
+    atom->data_atoms(nchunk, buffer, id_offset, mol_offset, toffset,
                      shiftflag, shift, tlabelflag, lmap->lmap2lmap.atom, triclinic_general);
     nread += nchunk;
   }

src/read_data.h

@@ -64,12 +64,12 @@ class ReadData : public Command {
   int triclinic, triclinic_general;
   int xloxhi_flag, yloyhi_flag, zlozhi_flag, tilt_flag;
   int avec_flag, bvec_flag, cvec_flag, abc_origin_flag;
-  
+
   double boxlo[3], boxhi[3];
   double xy, xz, yz;
   double avec[3], bvec[3], cvec[3];
   double abc_origin[3];
-  
+
   // optional args
 
   int addflag, offsetflag, shiftflag, coeffflag, settypeflag;

src/thermo.cpp

@@ -980,7 +980,7 @@ void Thermo::parse_fields(const std::string &str)
         addfield("Pxy", &Thermo::compute_pxy_triclinic_general, FLOAT);
       else addfield("Pxy", &Thermo::compute_pxy, FLOAT);
       index_press_vector = add_compute(id_press, VECTOR);
-    } else if (word == "pxz") { 
+    } else if (word == "pxz") {
       if (triclinic_general)
         addfield("Pxz", &Thermo::compute_pxz_triclinic_general, FLOAT);
       else addfield("Pxz", &Thermo::compute_pxz, FLOAT);
@@ -1223,7 +1223,7 @@ void Thermo::check_press_vector(const std::string &keyword)
     pressure->invoked_flag |= Compute::INVOKED_VECTOR;
 
     // store 3x3 matrix form of symmetric pressure tensor for use in triclinic_general()
-    
+
     if (triclinic_general) {
       press_tensor[0][0] = pressure->vector[0];
       press_tensor[1][1] = pressure->vector[1];

src/thermo.h

@@ -83,7 +83,7 @@ class Thermo : protected Pointers {
   std::string image_fname;
 
   // data used by routines that compute single values
-  
+
   int ivalue;          // integer value to print
   double dvalue;       // double value to print
   bigint bivalue;      // big integer value to print
@@ -96,7 +96,7 @@ class Thermo : protected Pointers {
   // index = where they are in computes list
   // id = ID of Compute objects
   // Compute * = ptrs to the Compute objects
-  
+
   int index_temp, index_press_scalar, index_press_vector, index_pe;
   class Compute *temperature, *pressure, *pe;
   double press_tensor[3][3];

src/write_data.cpp

@@ -74,7 +74,7 @@ void WriteData::command(int narg, char **arg)
   fixflag = 1;
   triclinic_general = 0;
   lmapflag = 1;
-  
+
   // store current (default) setting since we may change it
 
   int domain_triclinic_general = domain->triclinic_general;
@@ -227,9 +227,9 @@ void WriteData::write(const std::string &file)
   // reset internal per-atom data that needs rotation
 
   if (domain->triclinic_general) atom->avec->write_data_restricted_to_general();
-  
+
   // per atom info in Atoms and Velocities sections
-  
+
   if (natoms) atoms();
   if (natoms) velocities();
 
@@ -261,7 +261,7 @@ void WriteData::write(const std::string &file)
   // restore internal per-atom data that was rotated
 
   if (domain->triclinic_general) atom->avec->write_data_restore_restricted();
-  
+
   // close data file
 
   if (me == 0) fclose(fp);
@@ -326,7 +326,7 @@ void WriteData::header()
                domain->boxlo[2],domain->boxhi[2]);
     if (domain->triclinic)
       fmt::print(fp,"{} {} {} xy xz yz\n",domain->xy,domain->xz,domain->yz);
-    
+
   } else if (domain->triclinic_general) {
     fmt::print(fp,"\n{} {} {} avec\n{} {} {} bvec\n{} {} {} cvec\n",
                domain->avec[0],domain->avec[1],domain->avec[2],

src/write_restart.cpp

@@ -451,7 +451,7 @@ void WriteRestart::header()
   write_int(TRICLINIC_GENERAL,domain->triclinic_general);
   if (domain->triclinic_general)
     write_double_vec(ROTATE_G2R,9,&domain->rotate_g2r[0][0]);
-  
+
   write_double_vec(SPECIAL_LJ,3,&force->special_lj[1]);
   write_double_vec(SPECIAL_COUL,3,&force->special_coul[1]);