Fix more typos in src files

src/COLLOID/pair_lubricateU.cpp

@@ -153,7 +153,7 @@ void PairLubricateU::compute(int eflag, int vflag)
   }
 
   // Stage one of Midpoint method
-  // Solve for velocities based on intial positions
+  // Solve for velocities based on initial positions
 
   stage_one();
 
@@ -651,7 +651,7 @@ void PairLubricateU::compute_Fh(double **x)
     jnum = numneigh[i];
 
     // Find the contribution to stress from isotropic RS0
-    // Set psuedo force to obtain the required contribution
+    // Set pseudo force to obtain the required contribution
     // need to set delx and fy only
 
     fx = 0.0; delx = radi;

src/COLLOID/pair_lubricateU_poly.cpp

@@ -122,7 +122,7 @@ void PairLubricateUPoly::compute(int eflag, int vflag)
   }
 
   // Stage one of Midpoint method
-  // Solve for velocities based on intial positions
+  // Solve for velocities based on initial positions
 
   iterate(atom->x,1);
 
@@ -421,7 +421,7 @@ void PairLubricateUPoly::compute_Fh(double **x)
     pre[0] *= 6.0;
 
     // Find the contribution to stress from isotropic RS0
-    // Set psuedo force to obtain the required contribution
+    // Set pseudo force to obtain the required contribution
     // need to set delx  and fy only
 
     fx = 0.0; delx = radi;

src/DEPEND/fastdep.c

@@ -178,7 +178,7 @@ typedef struct {
  * linked list functions
  ************************************************************************/
 
-/* allocate and intitialize linked list */
+/* allocate and initialize linked list */
 static llist_t *llist_init()
 {
     llist_t *ll;

src/KIM/pair_kim.h

@@ -126,7 +126,7 @@ namespace LAMMPS_NS {
       int lmps_maxalloc;              // max allocated memory value
       int* kim_particleSpecies;       // array of KIM particle species
       double** lmps_force_tmp;        // temp storage for f, when running in
-                                      // hybrid mode needed to avoid reseting
+                                      // hybrid mode needed to avoid resetting
                                       // f to zero in each object
       int* lmps_stripped_neigh_list;  // neighbors of one atom, used when LAMMPS
                                       // is in molecular mode

src/KOKKOS/pair_reax_c_kokkos.cpp

@@ -633,7 +633,7 @@ void PairReaxCKokkos<DeviceType>::LR_vdW_Coulomb( int i, int j, double r_ij, LR_
   }
 
   if(system->reax_param.gp.vdw_type==2 || system->reax_param.gp.vdw_type==3)
-    { // innner wall
+    { // inner wall
       e_core = twbp->ecore * exp(twbp->acore * (1.0-(r_ij/twbp->rcore)));
       lr->e_vdW += Tap * e_core;
 

src/PYTHON/python.cpp

@@ -146,7 +146,7 @@ void Python::command(int narg, char **arg)
 
   int ifunc = create_entry(arg[0]);
 
-  // one-time intitialization of Python interpreter
+  // one-time initialization of Python interpreter
   // Py_SetArgv() enables finding of *.py module files in current dir
   //   only needed for module load, not for direct file read into __main__
   // pymain stores pointer to main module

src/RIGID/fix_rigid_small.cpp

@@ -2488,7 +2488,7 @@ void FixRigidSmall::write_restart_file(char *file)
 {
   FILE *fp;
 
-  // do not write file if bodies have not yet been intialized
+  // do not write file if bodies have not yet been initialized
 
   if (!setupflag) return;
 

src/RIGID/fix_shake.h

@@ -184,7 +184,7 @@ Self-explanatory.
 
 W: Molecule template for fix shake has multiple molecules
 
-The fix shake command will only recoginze molecules of a single
+The fix shake command will only recognize molecules of a single
 type, i.e. the first molecule in the template.
 
 E: Fix shake molecule template must have shake info

src/USER-DPD/fix_eos_table_rx.h

@@ -157,6 +157,6 @@ Self-explanatory.
 
 E: Maxit exceeded in secant solver
 
-The maximum number of interations was exceeded in the secant solver
+The maximum number of interactions was exceeded in the secant solver
 
 */

src/USER-DPD/pair_exp6_rx.cpp

@@ -1098,7 +1098,7 @@ void PairExp6rx::getMixingWeights(int id,double &epsilon1,double &alpha1,double
       fraction2 = atom->dvector[ispecies][id]/nTotal;
     }
 
-    // If Site1 or Site2 matches is a fluid, then compute the paramters
+    // If Site1 or Site2 matches is a fluid, then compute the parameters
     if (isOneFluidApprox(isite1) || isOneFluidApprox(isite2)) {
       if (isite1 == params[iparam].ispecies || isite2 == params[iparam].ispecies) continue;
       rmi = params[iparam].rm;

src/USER-LB/fix_lb_fluid.cpp

@@ -50,7 +50,7 @@ FixLbFluid::FixLbFluid(LAMMPS *lmp, int narg, char **arg) :
   //  where: nevery:            call this fix every nevery timesteps.
   //		                 (keep this set to 1 for now).
   //         typeLB:            there are two different integrators
-  //                             in the code labelled "1" and "2".
+  //                             in the code labeled "1" and "2".
   //         viscosity:         the viscosity of the fluid.
   //         densityinit_real:  the density of the fluid.
   //

src/USER-MANIFOLD/README

@@ -31,7 +31,7 @@ To add a new manifold, do the following in the "USER-MANIFOLD" directory:
    e. The header file has to contain somewhere the macro ManifoldStyle with as
      first argument the name of the manifold and as second argument the name
      of the class implementing this manifold. The macro expands into some code
-     that registers the manifold during static initialisation, before main is
+     that registers the manifold during static initialization, before main is
      entered.
 
 2. In the source file, make sure you implement the following (of course,
@@ -51,7 +51,7 @@ To add a new manifold, do the following in the "USER-MANIFOLD" directory:
 |                                    | manifold in LAMMPS input scripts.       |
 |  const char *id()                  | Should return whatever type() returns.  |
 |  static int expected_argc()        | Returns the number of arguments needed  |
-|                                    | for the construction/initialisation of  |
+|                                    | for the construction/initialization of  |
 |                                    | your manifold. Example: Sphere only     |
 |                                    | needs a radius, so it returns 1. The    |
 |                                    | spine needs 5 parameters, so it         |

src/USER-MANIFOLD/fix_manifoldforce.cpp

@@ -104,7 +104,7 @@ FixManifoldForce::FixManifoldForce(LAMMPS *lmp, int narg, char **arg) :
   }
 
 
-  // Perform any further initialisation for the manifold that depends on params:
+  // Perform any further initialization for the manifold that depends on params:
   ptr_m->post_param_init();
 }
 

src/USER-MANIFOLD/manifold.h

@@ -65,7 +65,7 @@ namespace user_manifold {
     virtual int nparams() = 0;
     double **get_params(){ return &params; };
 
-    // Overload if any initialisation depends on params:
+    // Overload if any initialization depends on params:
     virtual void post_param_init(){}
     virtual void checkup(){} // Some diagnostics...
    protected:

src/USER-MISC/fix_imd.cpp

@@ -405,7 +405,7 @@ static int imd_recv_fcoords(void *, int32, float *);
 /** Prepare IMD data packet header */
 static void imd_fill_header(IMDheader *header, IMDType type, int32 length);
 /** Write data to socket */
-static int32 imd_writen(void *s, const char *ptr, int32 n);
+static int32 imd_written(void *s, const char *ptr, int32 n);
 
 /* part 2: abstracts platform-dependent routines/APIs for using sockets */
 
@@ -794,7 +794,7 @@ void FixIMD::ioworker()
     } else if (buf_has_data > 0) {
       /* send coordinate data, if client is able to accept */
       if (clientsock && imdsock_selwrite(clientsock,0)) {
-        imd_writen(clientsock, msgdata, msglen);
+        imd_written(clientsock, msgdata, msglen);
       }
       delete[] msgdata;
       buf_has_data=0;
@@ -1097,7 +1097,7 @@ void FixIMD::post_force(int vflag)
 #else
     /* send coordinate data, if client is able to accept */
     if (clientsock && imdsock_selwrite(clientsock,0)) {
-      imd_writen(clientsock, msgdata, msglen);
+      imd_written(clientsock, msgdata, msglen);
     }
     delete[] msgdata;
 #endif
@@ -1401,7 +1401,7 @@ static int32 imd_readn(void *s, char *ptr, int32 n) {
   return n-nleft;
 }
 
-static int32 imd_writen(void *s, const char *ptr, int32 n) {
+static int32 imd_written(void *s, const char *ptr, int32 n) {
   int32 nleft;
   int32 nwritten;
 
@@ -1423,7 +1423,7 @@ int imd_handshake(void *s) {
   IMDheader header;
   imd_fill_header(&header, IMD_HANDSHAKE, 1);
   header.length = IMDVERSION;   /* Not byteswapped! */
-  return (imd_writen(s, (char *)&header, IMDHEADERSIZE) != IMDHEADERSIZE);
+  return (imd_written(s, (char *)&header, IMDHEADERSIZE) != IMDHEADERSIZE);
 }
 
 /* The IMD receive functions */

src/USER-MISC/pair_edip.cpp

@@ -1034,7 +1034,7 @@ void PairEDIP::setup_params()
     if (rtmp > cutmax) cutmax = rtmp;
   }
 
-  // this should be removed for multi species parametrizations
+  // this should be removed for multi species parameterization
 
   A = params[0].A;
   B = params[0].B;

src/USER-MISC/pair_edip.h

@@ -64,7 +64,7 @@ class PairEDIP : public Pair {
   double *tauFunctionGrid;
   double *tauFunctionDerivedGrid;
 
-  // this should be removed for multi species parametrizations
+  // this should be removed for multi species parameterization
   // since these parameters should be addressed through indexes
   // see also the PairEDIP::setup()
 

src/USER-MOLFILE/molfile_interface.cpp

@@ -464,7 +464,7 @@ int MolfileInterface::load_plugin(const char *filename)
     return E_SYMBOL;
   }
 
-  // intialize plugin. skip plugin if it fails.
+  // initialize plugin. skip plugin if it fails.
   if (((initfunc)(ifunc))()) {
     my_dlclose(dso);
     return E_SYMBOL;

src/USER-REAXC/README

@@ -14,7 +14,7 @@ particularly with respect to the charge equilibration calculation.  It
 should also be easier to build and use since there are no complicating
 issues with Fortran memory allocation or linking to a Fortran library.
 
-For technical details about this implemention of ReaxFF, see
+For technical details about this implementation of ReaxFF, see
 this paper:
 
 Parallel and Scalable Reactive Molecular Dynamics: Numerical Methods

src/USER-REAXC/reaxc_nonbonded.cpp

@@ -139,7 +139,7 @@ void vdW_Coulomb_Energy( reax_system *system, control_params *control,
       }
 
       if(system->reax_param.gp.vdw_type==2 || system->reax_param.gp.vdw_type==3)
-        { // innner wall
+        { // inner wall
           e_core = twbp->ecore * exp(twbp->acore * (1.0-(r_ij/twbp->rcore)));
           data->my_en.e_vdW += Tap * e_core;
 
@@ -398,7 +398,7 @@ void LR_vdW_Coulomb( reax_system *system, storage *workspace,
   }
 
   if(system->reax_param.gp.vdw_type==2 || system->reax_param.gp.vdw_type==3)
-    { // innner wall
+    { // inner wall
       e_core = twbp->ecore * exp(twbp->acore * (1.0-(r_ij/twbp->rcore)));
       lr->e_vdW += Tap * e_core;
 

src/USER-SMTBQ/pair_smtbq.cpp

@@ -548,7 +548,7 @@ void PairSMTBQ::read_file(char *file)
     //  ---------------------------------
     m += 1;
 
-    // Ligne 5 - parametre des potentiels
+    // Ligne 5 - parametre des potentials
     fgets(ptr,MAXLINE,fp);  if (verbose) printf ("%s",ptr);
 
     // Lecture des protagonistes
@@ -615,7 +615,7 @@ void PairSMTBQ::read_file(char *file)
       if (verbose) printf (" %s %f %f %f %f\n",words[0],
                            intparams[m].a,intparams[m].p,intparams[m].ksi,intparams[m].q);
 
-      // Ligne 6 - rayon de coupure potentiel SM
+      // Ligne 6 - rayon de coupure potential SM
 
       fgets( ptr, MAXLINE, fp);
       Tokenize( ptr, &words );
@@ -1724,7 +1724,7 @@ void PairSMTBQ::pot_ES (int i, int j, double rsq, double &eng)
 {
 
   /* ===================================================================
-     Coulombian potentiel energy calcul between i and j atoms
+     Coulombian potential energy calcul between i and j atoms
      with fafb table make in sm_table().
      fafb[i][j] : i is the table's step (r)
      j is the interaction's # (in intype[itype][jtype])
@@ -2655,7 +2655,7 @@ void PairSMTBQ::Charge()
     forward(q) ; // reverse(q);
 
 
-    //   Calcul des potentiel
+    //   Calcul des potential
     //  ----------------------
     QForce_charge(iloop);
 
@@ -2736,7 +2736,7 @@ void PairSMTBQ::Charge()
 
   //:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
   // ==========================================
-  //   Ecriture des potentiels dans un fichier
+  //   Ecriture des potentials dans un fichier
   // ==========================================
 
   if (strcmp(writepot,"true") == 0 && fmod(static_cast<double>(step), Neverypot) == 0.0) {

src/atom.cpp

@@ -1634,7 +1634,7 @@ int Atom::find_molecule(char *id)
 
 /* ----------------------------------------------------------------------
    add info to current atom ilocal from molecule template onemol and its iatom
-   offset = atom ID preceeding IDs of atoms in this molecule
+   offset = atom ID preceding IDs of atoms in this molecule
    called by fixes and commands that add molecules
 ------------------------------------------------------------------------- */
 

src/atom_vec_hybrid.cpp

@@ -82,7 +82,7 @@ void AtomVecHybrid::process_args(int narg, char **arg)
   delete [] allstyles;
 
   // hybrid settings are MAX or MIN of sub-style settings
-  // hybrid sizes are minimial values plus extra values for each sub-style
+  // hybrid sizes are minimal values plus extra values for each sub-style
 
   molecular = 0;
   comm_x_only = comm_f_only = 1;

src/compute_chunk_atom.cpp

@@ -1298,7 +1298,7 @@ int ComputeChunkAtom::setup_sphere_bins()
   }
 
   // if pbcflag set, sradmax must be < 1/2 box in any periodic dim
-  // treat orthongonal and triclinic the same
+  // treat orthogonal and triclinic the same
   // check every time bins are created
 
   if (pbcflag) {
@@ -1363,7 +1363,7 @@ int ComputeChunkAtom::setup_cylinder_bins()
   }
 
   // if pbcflag set, sradmax must be < 1/2 box in any periodic non-axis dim
-  // treat orthongonal and triclinic the same
+  // treat orthogonal and triclinic the same
   // check every time bins are created
 
   if (pbcflag) {

src/create_atoms.cpp

@@ -806,7 +806,7 @@ void CreateAtoms::add_molecule(double *center, double *quat_user)
   onemol->quat_external = quat;
 
   // create atoms in molecule with atom ID = 0 and mol ID = 0
-  // reset in caller after all moleclues created by all procs
+  // reset in caller after all molecules created by all procs
   // pass add_molecule_atom an offset of 0 since don't know
   //   max tag of atoms in previous molecules at this point
 

src/domain.cpp

@@ -514,7 +514,7 @@ void Domain::pbc()
 
   double *coord;
   int n3 = 3*nlocal;
-  coord = &x[0][0];  // note: x is always initialzed to at least one element.
+  coord = &x[0][0];  // note: x is always initialized to at least one element.
   int flag = 0;
   for (i = 0; i < n3; i++)
     if (!ISFINITE(*coord++)) flag = 1;

src/fix_group.h

@@ -77,7 +77,7 @@ The variable must be an atom-style variable.
 
 W: One or more dynamic groups may not be updated at correct point in timestep
 
-If there are other fixes that act immediately after the intitial stage
+If there are other fixes that act immediately after the initial stage
 of time integration within a timestep (i.e. after atoms move), then
 the command that sets up the dynamic group should appear after those
 fixes.  This will insure that dynamic group assignments are made

src/kspace.h

@@ -62,14 +62,14 @@ class KSpace : protected Pointers {
 
   int order,order_6,order_allocated;
   double accuracy;                  // accuracy of KSpace solver (force units)
-  double accuracy_absolute;         // user-specifed accuracy in force units
+  double accuracy_absolute;         // user-specified accuracy in force units
   double accuracy_relative;         // user-specified dimensionless accuracy
                                     // accurary = acc_rel * two_charge_force
   double accuracy_real_6;           // real space accuracy for
                                     // dispersion solver (force units)
   double accuracy_kspace_6;         // reciprocal space accuracy for
                                     // dispersion solver (force units)
-  int auto_disp_flag;		    // use automatic paramter generation for pppm/disp
+  int auto_disp_flag;		    // use automatic parameter generation for pppm/disp
   double two_charge_force;          // force in user units of two point
                                     // charges separated by 1 Angstrom
 

src/library.cpp

@@ -140,7 +140,7 @@ void lammps_open(int argc, char **argv, MPI_Comm communicator, void **ptr)
 /* ----------------------------------------------------------------------
    create an instance of LAMMPS and return pointer to it
    caller doesn't know MPI communicator, so use MPI_COMM_WORLD
-   intialize MPI if needed
+   initialize MPI if needed
 ------------------------------------------------------------------------- */
 
 void lammps_open_no_mpi(int argc, char **argv, void **ptr)
@@ -646,7 +646,7 @@ void *lammps_extract_variable(void *ptr, char *name, char *group)
 /* ----------------------------------------------------------------------
    reset simulation box parameters
    see domain.h for definition of these arguments
-   assumes domain->set_intiial_box() has been invoked previously
+   assumes domain->set_initial_box() has been invoked previously
 ------------------------------------------------------------------------- */
 
 void lammps_reset_box(void *ptr, double *boxlo, double *boxhi,

src/lmptype.h

@@ -13,7 +13,7 @@
 
 // define integer data types used by LAMMPS and associated size limits
 
-// smallint = variables for on-procesor system (nlocal, nmax, etc)
+// smallint = variables for on-processor system (nlocal, nmax, etc)
 // imageint = variables for atom image flags (image)
 // tagint = variables for atom IDs and molecule IDs (tag,molecule)
 // bigint = variables for total system (natoms, ntimestep, etc)

src/molecule.cpp

@@ -1395,7 +1395,7 @@ void Molecule::check_attributes(int flag)
       if (atom->maxspecial < onemol->maxspecial) mismatch = 1;
 
       if (mismatch)
-        error->all(FLERR,"Molecule toplogy/atom exceeds system topology/atom");
+        error->all(FLERR,"Molecule topology/atom exceeds system topology/atom");
     }
 
     // warn if molecule topology defined but no special settings

src/molecule.h

@@ -406,7 +406,7 @@ The number of bond, angle, etc types in the molecule exceeds the
 system setting.  See the create_box command for how to specify these
 values.
 
-E: Molecule toplogy/atom exceeds system topology/atom
+E: Molecule topology/atom exceeds system topology/atom
 
 The number of bonds, angles, etc per-atom in the molecule exceeds the
 system setting.  See the create_box command for how to specify these

src/rerun.cpp

@@ -124,7 +124,7 @@ void Rerun::command(int narg, char **arg)
   if (nremain) rd->setup_reader(nremain,&arg[narg-nremain]);
   else rd->setup_reader(0,NULL);
 
-  // perform the psuedo run
+  // perform the pseudo run
   // invoke lmp->init() only once
   // read all relevant snapshots
   // use setup_minimal() since atoms are already owned by correct procs

src/thermo.cpp

@@ -1054,7 +1054,7 @@ int Thermo::add_variable(const char *id)
    compute a single thermodynamic value, word is any keyword in custom list
    called when a variable is evaluated by Variable class
    return value as double in answer
-   return 0 if str is recoginzed keyword, 1 if unrecognized
+   return 0 if str is recognized keyword, 1 if unrecognized
    customize a new keyword by adding to if statement
 ------------------------------------------------------------------------- */
 

src/variable.h

@@ -210,7 +210,7 @@ This is to insure they stay in sync.
 E: Variable has circular dependency
 
 A circular dependency is when variable "a" in used by variable "b" and
-variable "b" is also used by varaible "a".  Circular dependencies with
+variable "b" is also used by variable "a".  Circular dependencies with
 longer chains of dependence are also not allowed.
 
 E: Python variable does not match Python function