whitespace fixes

doc/src/compute_mliap.rst

@@ -20,7 +20,7 @@ Syntax
        *model* values = style Nelems Nparams
          style = *linear* or *quadratic*
          Nelems = number of elements
-         Nparams = number of parameters per element 
+         Nparams = number of parameters per element
        *descriptor* values = style filename
          style = *sna*
          filename = name of file containing descriptor definitions
@@ -36,25 +36,25 @@ Description
 """""""""""
 
 Compute style *mliap* provides a general interface to the gradient
-of machine-learning interatomic potentials w.r.t. model parameters. 
+of machine-learning interatomic potentials w.r.t. model parameters.
 It is used primarily for calculating the gradient of energy, force, and
 stress components w.r.t. model parameters, which is useful when training
 :doc:`mliap pair_style <pair_mliap>` models to match target data.
-It provides separate 
+It provides separate
 definitions of the interatomic potential functional form (*model*)
 and the geometric quantities that characterize the atomic positions
-(*descriptor*). By defining *model* and *descriptor* separately, 
+(*descriptor*). By defining *model* and *descriptor* separately,
 it is possible to use many different models with a given descriptor,
-or many different descriptors with a given model. Currently, the 
+or many different descriptors with a given model. Currently, the
 compute supports just two models, *linear* and *quadratic*,
-and one descriptor, *sna*, the SNAP descriptor used by 
+and one descriptor, *sna*, the SNAP descriptor used by
 :doc:`pair_style snap <pair_snap>`, including the linear, quadratic,
 and chem variants. Work is currently underway to extend
 the interface to handle neural network energy models,
 and it is also straightforward to add new descriptor styles.
 
 The compute *mliap* command must be followed by two keywords
-*model* and *descriptor* in either order. 
+*model* and *descriptor* in either order.
 
 The *model* keyword is followed by a model style, currently limited to
 either *linear* or *quadratic*. In both cases,
@@ -62,25 +62,25 @@ this is followed by two arguments. *nelems* is the number of elements.
 It must be equal to the number of LAMMPS atom types. *nparams*
 is the number of parameters per element for this model i.e.
 the number of parameter gradients for each element. Note these definitions
-are identical to those of *nelems* and *nparams* in the 
+are identical to those of *nelems* and *nparams* in the
 :doc:`pair_style mliap <pair_mliap>` model file.
- 
+
 The *descriptor* keyword is followed by a descriptor style, and additional arguments.
-Currently the only descriptor style is *sna*, indicating the bispectrum component 
+Currently the only descriptor style is *sna*, indicating the bispectrum component
-descriptors used by the Spectral Neighbor Analysis Potential (SNAP) potentials of 
+descriptors used by the Spectral Neighbor Analysis Potential (SNAP) potentials of
 :doc:`pair_style snap <pair_snap>`.
-The \'p\' in SNAP is dropped, because keywords that match pair_styles are silently stripped 
+The \'p\' in SNAP is dropped, because keywords that match pair_styles are silently stripped
-out by the LAMMPS command parser. A single additional argument specifies the descriptor filename 
+out by the LAMMPS command parser. A single additional argument specifies the descriptor filename
-containing the parameters and setting used by the SNAP descriptor. 
+containing the parameters and setting used by the SNAP descriptor.
 The descriptor filename usually ends in the *.mliap.descriptor* extension.
-The format of this file is identical to the descriptor file in the 
+The format of this file is identical to the descriptor file in the
 :doc:`pair_style mliap <pair_mliap>`, and is described in detail
-there. 
+there.
 
 .. note::
 
    The number of LAMMPS atom types (and the value of *nelems* in the model)
-   must match the value of *nelems* in the descriptor file. 
+   must match the value of *nelems* in the descriptor file.
 
 Compute *mliap* calculates a global array containing gradient information.
 The number of columns in the array is :math:`nelems \times nparams + 1`.
@@ -89,9 +89,9 @@ each parameter and each element. The last six rows
 of the array contain the corresponding derivatives of the
 virial stress tensor, listed in Voigt notation: *pxx*, *pyy*, *pzz*,
 *pyz*, *pxz*, *pxy*. In between the energy and stress rows are
-the 3\*\ *N* rows containing the derivatives of the force components. 
+the 3\*\ *N* rows containing the derivatives of the force components.
-See section below on output for a detailed description of how 
+See section below on output for a detailed description of how
-rows and columns are ordered. 
+rows and columns are ordered.
 
 The element in the last column of each row contains
 the potential energy, force, or stress, according to the row.
@@ -109,7 +109,7 @@ command:
 See section below on output for a detailed explanation of the data
 layout in the global array.
 
-Atoms not in the group do not contribute to this compute. 
+Atoms not in the group do not contribute to this compute.
 Neighbor atoms not in the group do not contribute to this compute.
 The neighbor list needed to compute this quantity is constructed each
 time the calculation is performed (i.e. each time a snapshot of atoms
@@ -120,7 +120,7 @@ too frequently.
 
    If the user-specified reference potentials includes bonded and
    non-bonded pairwise interactions, then the settings of
-   :doc:`special_bonds <special_bonds>` command can remove pairwise 
+   :doc:`special_bonds <special_bonds>` command can remove pairwise
    interactions between atoms in the same bond, angle, or dihedral.  This
    is the default setting for the :doc:`special_bonds <special_bonds>`
    command, and means those pairwise interactions do not appear in the
@@ -128,7 +128,7 @@ too frequently.
    those pairs will not be included in the calculation. The :doc:`rerun <rerun>`
    command is not an option here, since the reference potential is required
    for the last column of the global array. A work-around is to prevent
-   pairwise interactions from being removed by explicitly adding a 
+   pairwise interactions from being removed by explicitly adding a
    *tiny* positive value for every pairwise interaction that would otherwise be
    set to zero in the :doc:`special_bonds <special_bonds>` command.
 
@@ -139,7 +139,7 @@ too frequently.
 Compute *mliap* evaluates a global array.
 The columns are arranged into
 *nelems* blocks, listed in order of element *I*\ . Each block
-contains one column for each of the *nparams* model parameters. 
+contains one column for each of the *nparams* model parameters.
 A final column contains the corresponding energy, force component
 on an atom, or virial stress component. The rows of the array appear
 in the following order:

doc/src/compute_sna_atom.rst

@@ -392,7 +392,7 @@ of :math:`K N_{elem}^3` columns.
 These values can be accessed by any command that uses per-atom values
 from a compute as input.  See the :doc:`Howto output <Howto_output>` doc
 page for an overview of LAMMPS output options. To see how this command
-can be used within a Python workflow to train SNAP potentials, 
+can be used within a Python workflow to train SNAP potentials,
 see the examples in `FitSNAP <https://github.com/FitSNAP/FitSNAP>`_.
 
 Restrictions

doc/src/pair_lj_cut_coul.rst

@@ -7,20 +7,20 @@
 .. index:: pair_style lj/cut/coul/debye/kk
 .. index:: pair_style lj/cut/coul/debye/omp
 .. index:: pair_style lj/cut/coul/dsf
-.. index:: pair_style lj/cut/coul/dsf/gpu 
+.. index:: pair_style lj/cut/coul/dsf/gpu
-.. index:: pair_style lj/cut/coul/dsf/kk 
+.. index:: pair_style lj/cut/coul/dsf/kk
-.. index:: pair_style lj/cut/coul/dsf/omp 
+.. index:: pair_style lj/cut/coul/dsf/omp
-.. index:: pair_style lj/cut/coul/long 
+.. index:: pair_style lj/cut/coul/long
-.. index:: pair_style lj/cut/coul/long/gpu 
+.. index:: pair_style lj/cut/coul/long/gpu
-.. index:: pair_style lj/cut/coul/long/kk 
+.. index:: pair_style lj/cut/coul/long/kk
-.. index:: pair_style lj/cut/coul/long/intel 
+.. index:: pair_style lj/cut/coul/long/intel
-.. index:: pair_style lj/cut/coul/long/opt 
+.. index:: pair_style lj/cut/coul/long/opt
-.. index:: pair_style lj/cut/coul/long/omp 
+.. index:: pair_style lj/cut/coul/long/omp
-.. index:: pair_style lj/cut/coul/msm 
+.. index:: pair_style lj/cut/coul/msm
-.. index:: pair_style lj/cut/coul/msm/gpu 
+.. index:: pair_style lj/cut/coul/msm/gpu
-.. index:: pair_style lj/cut/coul/msm/omp 
+.. index:: pair_style lj/cut/coul/msm/omp
-.. index:: pair_style lj/cut/coul/wolf 
+.. index:: pair_style lj/cut/coul/wolf
-.. index:: pair_style lj/cut/coul/wolf/omp 
+.. index:: pair_style lj/cut/coul/wolf/omp
 
 pair_style lj/cut/coul/cut command
 ==================================
@@ -234,7 +234,7 @@ LJ and Coulombic cutoffs specified in the pair_style command are used.
 If only one cutoff is specified, it is used as the cutoff for both LJ
 and Coulombic interactions for this type pair.  If both coefficients
 are specified, they are used as the LJ and Coulombic cutoffs for this
-type pair. 
+type pair.
 
 For *lj/cut/coul/long* and *lj/cut/coul/msm* only the LJ cutoff can be
 specified since a Coulombic cutoff cannot be specified for an individual I,J

doc/src/pair_mliap.rst

@@ -34,8 +34,8 @@ Examples
 Description
 """""""""""
 
-Pair style *mliap* provides a general interface to families of 
+Pair style *mliap* provides a general interface to families of
-machine-learning interatomic potentials. It allows separate 
+machine-learning interatomic potentials. It allows separate
 definitions of the interatomic potential functional form (*model*)
 and the geometric quantities that characterize the atomic positions
 (*descriptor*). By defining *model* and *descriptor* separately,
@@ -61,8 +61,8 @@ where N is the number of LAMMPS atom types.
 
 The *model* keyword is followed by a model style, currently limited to
 either *linear* or *quadratic*. In both cases,
-this is followed by a single argument specifying the model filename containing the 
+this is followed by a single argument specifying the model filename containing the
-parameters for a set of elements. 
+parameters for a set of elements.
 The model filename usually ends in the *.mliap.model* extension.
 It may contain parameters for many elements. The only requirement is that it
 contain at least those element names appearing in the

src/BODY/body_nparticle.cpp

@@ -213,7 +213,7 @@ int BodyNparticle::pack_data_body(tagint atomID, int ibonus, double *buf)
   int nsub = ivalue[0];
 
   if (buf) {
-    
+
     // ID ninteger ndouble
 
     m = 0;
@@ -222,7 +222,7 @@ int BodyNparticle::pack_data_body(tagint atomID, int ibonus, double *buf)
     buf[m++] = ubuf(6 + 3*nsub).d;
 
     // single integer Nsub
-    
+
     buf[m++] = ubuf(nsub).d;
 
     // 6 moments of inertia
@@ -239,7 +239,7 @@ int BodyNparticle::pack_data_body(tagint atomID, int ibonus, double *buf)
     buf[m++] = ispace[1][2];
 
     // 3*Nsub particle coords = displacement from COM in box frame
-    
+
     for (int i = 0; i < nsub; i++) {
       MathExtra::matvec(p,&dvalue[3*i],values);
       buf[m++] = values[0];
@@ -248,7 +248,7 @@ int BodyNparticle::pack_data_body(tagint atomID, int ibonus, double *buf)
     }
 
   } else m = 3 + 1 + 6 + 3*nsub;
-  
+
   return m;
 }
 
@@ -272,10 +272,10 @@ int BodyNparticle::write_data_body(FILE *fp, double *buf)
   fmt::print(fp,"{} {} {} {} {} {}\n",
 	     inertia[0],inertia[1],inertia[2],inertia[3],inertia[4],inertia[5]);
   m += 6;
-  
+
   for (int i = 0; i < nsub; i++)
     fmt::print(fp,"{} {} {}\n",buf[m++],buf[m++],buf[m++]);
-  
+
   return m;
 }
 

src/MLIAP/README

@@ -1,16 +1,16 @@
-This package provides a general interface to families of 
+This package provides a general interface to families of
 machine-learning interatomic potentials (MLIAPs). This interface consists
-of a mliap pair style and a mliap compute. 
+of a mliap pair style and a mliap compute.
 
-The mliap pair style is used when running simulations with energies and 
+The mliap pair style is used when running simulations with energies and
-forces calculated by an MLIAP. The interface allows separate 
+forces calculated by an MLIAP. The interface allows separate
 definitions of the interatomic potential functional form (*model*)
 and the geometric quantities that characterize the atomic positions
-(*descriptor*). By defining *model* and *descriptor* separately, 
+(*descriptor*). By defining *model* and *descriptor* separately,
 it is possible to use many different models with a given descriptor,
-or many different descriptors with a given model. Currently, the pair_style 
+or many different descriptors with a given model. Currently, the pair_style
 supports just two models, *linear* and *quadratic*,
-and one descriptor, *sna*, the SNAP descriptor, including the 
+and one descriptor, *sna*, the SNAP descriptor, including the
 linear, quadratic, and chem variants. Work is currently underway to extend
 the interface to handle neural network energy models,
 and it is also straightforward to add new descriptor styles.
@@ -22,8 +22,8 @@ Any *model or *descriptor* that has been implemented for the
 *mliap* pair style can also be accessed by the *mliap* compute.
 In addition to the energy, force, and stress gradients, w.r.t.
 each *model* parameter, the compute also calculates the energy,
-force, and stress contributions from a user-specified 
+force, and stress contributions from a user-specified
-reference potential. 
+reference potential.
 
 To see how this command
 can be used within a Python workflow to train machine-learning interatomic

src/MLIAP/compute_mliap.cpp

@@ -35,7 +35,7 @@ enum{SCALAR,VECTOR,ARRAY};
 
 ComputeMLIAP::ComputeMLIAP(LAMMPS *lmp, int narg, char **arg) :
   Compute(lmp, narg, arg), list(NULL), mliap(NULL),
-  gradforce(NULL), mliapall(NULL), map(NULL), 
+  gradforce(NULL), mliapall(NULL), map(NULL),
   descriptors(NULL), gamma_row_index(NULL), gamma_col_index(NULL),
   gamma(NULL), egradient(NULL), model(NULL), descriptor(NULL)
 {
@@ -263,15 +263,15 @@ void ComputeMLIAP::compute_array()
   // i.e. gamma = d2E/dsigma_l.dB_k
   // sigma_l is a parameter and B_k is a descriptor of atom i
   // for SNAP, this is a sparse natoms*nparams*ndescriptors matrix,
-  // but in general it could be fully dense. 
+  // but in general it could be fully dense.
- 
+
-  model->param_gradient(map, list, descriptors, gamma_row_index, 
+  model->param_gradient(map, list, descriptors, gamma_row_index,
                         gamma_col_index, gamma, egradient);
 
 
   // calculate descriptor gradient contributions to parameter gradients
 
-  descriptor->compute_gradients(map, list, gamma_nnz, gamma_row_index, 
+  descriptor->compute_gradients(map, list, gamma_nnz, gamma_row_index,
                              gamma_col_index, gamma, gradforce,
                              yoffset, zoffset);
 

src/MLIAP/compute_mliap.h

@@ -44,13 +44,13 @@ class ComputeMLIAP : public Compute {
   int nelements;
 
   double** descriptors;        // descriptors for all atoms in list
-  int ndescriptors;            // number of descriptors 
+  int ndescriptors;            // number of descriptors
   int gamma_max;               // number of atoms allocated for beta, descriptors
   int nparams;                 // number of model paramters per element
   int gamma_nnz;               // number of non-zero entries in gamma
   double** gamma;              // gamma element
-  int** gamma_row_index;       // row (parameter) index 
+  int** gamma_row_index;       // row (parameter) index
-  int** gamma_col_index;       // column (descriptor) index 
+  int** gamma_col_index;       // column (descriptor) index
   double* egradient;           // energy gradient w.r.t. parameters
 
   class MLIAPModel* model;

src/MLIAP/mliap_descriptor.h

@@ -24,9 +24,9 @@ public:
   ~MLIAPDescriptor();
   virtual void compute_descriptors(int*, class NeighList*, double**)=0;
   virtual void compute_forces(class PairMLIAP*, class NeighList*, double**, int)=0;
-  virtual void compute_gradients(int*, class NeighList*, int, int**, int**, double**, 
+  virtual void compute_gradients(int*, class NeighList*, int, int**, int**, double**,
                               double**, int, int)=0;
-  virtual void compute_descriptor_gradients(int*, class NeighList*, int, int**, int**, double**, 
+  virtual void compute_descriptor_gradients(int*, class NeighList*, int, int**, int**, double**,
                               double**, int, int)=0;
   virtual void init()=0;
   virtual double memory_usage()=0;
@@ -34,7 +34,7 @@ public:
   int ndescriptors;              // number of descriptors
   int nelements;                 // # of unique elements
   char **elements;               // names of unique elements
-  double **cutsq;                // nelem x nelem rcutsq values 
+  double **cutsq;                // nelem x nelem rcutsq values
   double cutmax;                 // maximum cutoff needed
 protected:
 

src/MLIAP/mliap_descriptor_snap.cpp

@@ -259,8 +259,8 @@ void MLIAPDescriptorSNAP::compute_forces(PairMLIAP* pairmliap, NeighList* list,
    compute force gradient for each atom
    ---------------------------------------------------------------------- */
 
-void MLIAPDescriptorSNAP::compute_gradients(int *map, NeighList* list, 
+void MLIAPDescriptorSNAP::compute_gradients(int *map, NeighList* list,
-                                         int gamma_nnz, int **gamma_row_index, 
+                                         int gamma_nnz, int **gamma_row_index,
                                          int **gamma_col_index, double **gamma, double **gradforce,
                                          int yoffset, int zoffset)
 {
@@ -345,9 +345,9 @@ void MLIAPDescriptorSNAP::compute_gradients(int *map, NeighList* list,
                                snaptr->rcutij[jj],jj, 0);
 
       snaptr->compute_dbidrj();
-      
+
       // Accumulate gamma_lk*dB_k/dRi, -gamma_lk**dB_k/dRj
-      
+
       for (int inz = 0; inz < gamma_nnz; inz++) {
         const int l = gamma_row_index[ii][inz];
         const int k = gamma_col_index[ii][inz];
@@ -358,7 +358,7 @@ void MLIAPDescriptorSNAP::compute_gradients(int *map, NeighList* list,
         gradforce[j][l+yoffset] -= gamma[ii][inz]*snaptr->dblist[k][1];
         gradforce[j][l+zoffset] -= gamma[ii][inz]*snaptr->dblist[k][2];
       }
-      
+
     }
   }
 
@@ -368,8 +368,8 @@ void MLIAPDescriptorSNAP::compute_gradients(int *map, NeighList* list,
    compute descriptor gradients for each neighbor atom
    ---------------------------------------------------------------------- */
 
-void MLIAPDescriptorSNAP::compute_descriptor_gradients(int *map, NeighList* list, 
+void MLIAPDescriptorSNAP::compute_descriptor_gradients(int *map, NeighList* list,
-                                         int gamma_nnz, int **gamma_row_index, 
+                                         int gamma_nnz, int **gamma_row_index,
                                          int **gamma_col_index, double **gamma, double **graddesc,
                                          int yoffset, int zoffset)
 {
@@ -464,7 +464,7 @@ void MLIAPDescriptorSNAP::compute_descriptor_gradients(int *map, NeighList* list
         graddesc[j][k] = -snaptr->dblist[k][0];
         graddesc[j][k] = -snaptr->dblist[k][1];
         graddesc[j][k] = -snaptr->dblist[k][2];
-      } 
+      }
     }
   }
 

src/MLIAP/mliap_descriptor_snap.h

@@ -24,9 +24,9 @@ public:
   ~MLIAPDescriptorSNAP();
   virtual void compute_descriptors(int*, class NeighList*, double**);
   virtual void compute_forces(class PairMLIAP*, class NeighList*, double**, int);
-  virtual void compute_gradients(int*, class NeighList*, int, int**, int**, double**, 
+  virtual void compute_gradients(int*, class NeighList*, int, int**, int**, double**,
                               double**, int, int);
-  virtual void compute_descriptor_gradients(int*, class NeighList*, int, int**, int**, double**, 
+  virtual void compute_descriptor_gradients(int*, class NeighList*, int, int**, int**, double**,
                               double**, int, int);
   virtual void init();
   virtual double memory_usage();

src/MLIAP/mliap_model_linear.cpp

@@ -36,7 +36,7 @@ MLIAPModelLinear::MLIAPModelLinear(LAMMPS* lmp, char* coefffilename) :
 
 /* ---------------------------------------------------------------------- */
 
-MLIAPModelLinear::MLIAPModelLinear(LAMMPS* lmp, int nelements_in, int nparams_in) : 
+MLIAPModelLinear::MLIAPModelLinear(LAMMPS* lmp, int nelements_in, int nparams_in) :
   MLIAPModel(lmp, nelements_in, nparams_in)
 {
   ndescriptors = nparams - 1;
@@ -47,7 +47,7 @@ MLIAPModelLinear::MLIAPModelLinear(LAMMPS* lmp, int nelements_in, int nparams_in
 MLIAPModelLinear::~MLIAPModelLinear(){}
 
 /* ----------------------------------------------------------------------
-   Calculate model gradients w.r.t descriptors 
+   Calculate model gradients w.r.t descriptors
    for each atom beta_i = dE(B_i)/dB_i
    ---------------------------------------------------------------------- */
 
@@ -87,22 +87,22 @@ void MLIAPModelLinear::gradient(PairMLIAP* pairmliap, NeighList* list, double **
 
 /* ----------------------------------------------------------------------
    Calculate model double gradients w.r.t descriptors and parameters
-   for each atom energy gamma_lk = d2E(B)/dB_k/dsigma_l, 
+   for each atom energy gamma_lk = d2E(B)/dB_k/dsigma_l,
-   where sigma_l is a parameter, B_k a descriptor, 
+   where sigma_l is a parameter, B_k a descriptor,
    and atom subscript i is omitted
 
    gamma is in CSR format:
       nnz = number of non-zero values
-      gamma_row_index[inz] = l indices, 0 <= l < nparams 
+      gamma_row_index[inz] = l indices, 0 <= l < nparams
       gamma_col_indexiinz] = k indices, 0 <= k < ndescriptors
       gamma[i][inz] = non-zero values, 0 <= inz < nnz
 
    egradient is derivative of energy w.r.t. parameters
    ---------------------------------------------------------------------- */
 
-void MLIAPModelLinear::param_gradient(int *map, NeighList* list, 
+void MLIAPModelLinear::param_gradient(int *map, NeighList* list,
-                                         double **descriptors, 
+                                         double **descriptors,
-                                         int **gamma_row_index, int **gamma_col_index, 
+                                         int **gamma_row_index, int **gamma_col_index,
                                          double **gamma, double *egradient)
 {
   int i;
@@ -112,7 +112,7 @@ void MLIAPModelLinear::param_gradient(int *map, NeighList* list,
 
   for (int l = 0; l < nelements*nparams; l++)
     egradient[l] = 0.0;
-    
+
   for (int ii = 0; ii < list->inum; ii++) {
 
     i = list->ilist[ii];
@@ -128,12 +128,12 @@ void MLIAPModelLinear::param_gradient(int *map, NeighList* list,
     }
 
     // gradient of energy of atom I w.r.t. parameters
-    
+
     l = elemoffset;
     egradient[l++] += 1.0;
     for (int icoeff = 0; icoeff < ndescriptors; icoeff++)
       egradient[l++] += descriptors[ii][icoeff];
-    
+
   }
 
 }

src/MLIAP/mliap_model_quadratic.cpp

@@ -37,7 +37,7 @@ MLIAPModelQuadratic::MLIAPModelQuadratic(LAMMPS* lmp, char* coefffilename) :
 
 /* ---------------------------------------------------------------------- */
 
-MLIAPModelQuadratic::MLIAPModelQuadratic(LAMMPS* lmp, int nelements_in, int nparams_in) : 
+MLIAPModelQuadratic::MLIAPModelQuadratic(LAMMPS* lmp, int nelements_in, int nparams_in) :
   MLIAPModel(lmp, nelements_in, nparams_in)
 {
   nonlinearflag = 1;
@@ -113,22 +113,22 @@ void MLIAPModelQuadratic::gradient(PairMLIAP* pairmliap, NeighList* list, double
 
 /* ----------------------------------------------------------------------
    Calculate model double gradients w.r.t descriptors and parameters
-   for each atom energy gamma_lk = d2E(B)/dB_k/dsigma_l, 
+   for each atom energy gamma_lk = d2E(B)/dB_k/dsigma_l,
-   where sigma_l is a parameter, B_k a descriptor, 
+   where sigma_l is a parameter, B_k a descriptor,
    and atom subscript i is omitted
 
    gamma is in CSR format:
       nnz = number of non-zero values
-      gamma_row_index[inz] = l indices, 0 <= l < nparams 
+      gamma_row_index[inz] = l indices, 0 <= l < nparams
       gamma_col_indexiinz] = k indices, 0 <= k < ndescriptors
       gamma[i][inz] = non-zero values, 0 <= inz < nnz
 
    egradient is derivative of energy w.r.t. parameters
    ---------------------------------------------------------------------- */
 
-void MLIAPModelQuadratic::param_gradient(int *map, NeighList* list, 
+void MLIAPModelQuadratic::param_gradient(int *map, NeighList* list,
-                                         double **descriptors, 
+                                         double **descriptors,
-                                         int **gamma_row_index, int **gamma_col_index, 
+                                         int **gamma_row_index, int **gamma_col_index,
                                          double **gamma, double *egradient)
 {
   int i;
@@ -138,7 +138,7 @@ void MLIAPModelQuadratic::param_gradient(int *map, NeighList* list,
 
   for (int l = 0; l < nelements*nparams; l++)
     egradient[l] = 0.0;
-    
+
   for (int ii = 0; ii < list->inum; ii++) {
 
     i = list->ilist[ii];
@@ -179,14 +179,14 @@ void MLIAPModelQuadratic::param_gradient(int *map, NeighList* list,
     }
 
     // gradient of energy of atom I w.r.t. parameters
-    
+
     l = elemoffset;
     egradient[l++] += 1.0;
     for (int icoeff = 0; icoeff < ndescriptors; icoeff++)
       egradient[l++] += descriptors[ii][icoeff];
-    
+
     // quadratic contributions
-    
+
     for (int icoeff = 0; icoeff < ndescriptors; icoeff++) {
       double bveci = descriptors[ii][icoeff];
       egradient[l++] += 0.5*bveci*bveci;

src/USER-MESONT/pair_mesocnt.h

@@ -34,7 +34,7 @@ class PairMesoCNT : public Pair {
   double r_ang,rsq_ang,d_ang,rc_ang,rcsq_ang,cutoff_ang,cutoffsq_ang;
   double sig,sig_ang,comega,ctheta;
   double hstart_uinf,hstart_gamma,
-	 hstart_phi,psistart_phi,hstart_usemi,xistart_usemi;
+         hstart_phi,psistart_phi,hstart_usemi,xistart_usemi;
   double delh_uinf,delh_gamma,delh_phi,delpsi_phi,delh_usemi,delxi_usemi;
 
   double p1[3],p2[3],p[3],m[3];
@@ -55,7 +55,7 @@ class PairMesoCNT : public Pair {
   void read_file();
   void read_data(FILE *, double *, double &, double &, int);
   void read_data(FILE *, double **, double &, double &,
-		             double &, double &, int);
+                             double &, double &, int);
 
   void spline_coeff(double *, double **, double, int);
   void spline_coeff(double **, double ****, double, double, int);
@@ -63,17 +63,17 @@ class PairMesoCNT : public Pair {
   double spline(double, double, double, double **, int);
   double dspline(double, double, double, double **, int);
   double spline(double, double, double, double, double, double,
-		            double ****, int);
+                            double ****, int);
   double dxspline(double, double, double, double, double, double,
-		              double ****, int);
+                              double ****, int);
   double dyspline(double, double, double, double, double, double,
-		              double ****, int);
+                              double ****, int);
 
   void geometry(const double *, const double *, const double *,
-		            const double *, const double *,
+                            const double *, const double *,
                 double *, double *, double *, double **);
   void weight(const double *, const double *, const double *,
-		          const double *, double &, double *, double *,
+                          const double *, double &, double *, double *,
               double *, double *);
 
   void finf(const double *, double &, double **);
@@ -97,7 +97,7 @@ class PairMesoCNT : public Pair {
   inline double s5(double x) {
     double x2 = x * x;
     return heaviside(-x)
-	    + heaviside(x)*heaviside(1-x)*(1 - x2*x*(6*x2 - 15*x + 10));
+            + heaviside(x)*heaviside(1-x)*(1 - x2*x*(6*x2 - 15*x + 10));
   }
 
   inline double ds5(double x) {

src/atom_vec_body.cpp

@@ -587,7 +587,7 @@ void AtomVecBody::pack_data_pre(int ilocal)
 int AtomVecBody::pack_data_bonus(double *buf, int /*flag*/)
 {
   int i,j;
-  
+
   tagint *tag = atom->tag;
   int nlocal = atom->nlocal;
 
@@ -596,7 +596,7 @@ int AtomVecBody::pack_data_bonus(double *buf, int /*flag*/)
     if (body[i] < 0) continue;
     m += bptr->pack_data_body(tag[i],body[i],buf);
   }
-  
+
   return m;
 }
 

src/atom_vec_ellipsoid.cpp

@@ -490,7 +490,7 @@ void AtomVecEllipsoid::pack_data_post(int ilocal)
 int AtomVecEllipsoid::pack_data_bonus(double *buf, int /*flag*/)
 {
   int i,j;
-  
+
   tagint *tag = atom->tag;
   int nlocal = atom->nlocal;
 

src/atom_vec_ellipsoid.h

@@ -58,7 +58,7 @@ class AtomVecEllipsoid : public AtomVec {
 
   int pack_data_bonus(double *, int);
   void write_data_bonus(FILE *, int, double *, int);
-  
+
   // unique to AtomVecEllipsoid
 
   void set_shape(int, double, double, double);

src/atom_vec_hybrid.cpp

@@ -469,7 +469,7 @@ int AtomVecHybrid::pack_data_bonus(double *buf, int flag)
     if (flag == LINE && strcmp(keywords[k],"line") != 0) continue;
     if (flag == TRIANGLE && strcmp(keywords[k],"tri") != 0) continue;
     if (flag == BODY && strcmp(keywords[k],"body") != 0) continue;
-    
+
     return styles[k]->pack_data_bonus(buf,flag);
   }
   return 0;

src/atom_vec_line.cpp

@@ -465,7 +465,7 @@ int AtomVecLine::pack_data_bonus(double *buf, int /*flag*/)
   int i,j;
   double length,theta;
   double xc,yc,x1,x2,y1,y2;
-  
+
   double **x = atom->x;
   tagint *tag = atom->tag;
   int nlocal = atom->nlocal;

src/body.h

@@ -45,7 +45,7 @@ class Body : protected Pointers {
   virtual void data_body(int, int, int, int*, double *) = 0;
   virtual int pack_data_body(tagint, int, double *) = 0;
   virtual int write_data_body(FILE *, double *) = 0;
- 
+
   virtual int noutrow(int) = 0;
   virtual int noutcol() = 0;
   virtual void output(int, int, double *) = 0;

src/write_data.cpp

@@ -198,14 +198,14 @@ void WriteData::write(const std::string &file)
 
   // molecular topology info if defined
   // do not write molecular topology for atom_style template
-  
+
   if (atom->molecular == 1) {
     if (atom->nbonds && nbonds) bonds();
     if (atom->nangles && nangles) angles();
     if (atom->ndihedrals) dihedrals();
     if (atom->nimpropers) impropers();
   }
-  
+
   // bonus info if defined
 
   if (natoms && atom->ellipsoid_flag) bonus(ELLIPSOID);
@@ -214,7 +214,7 @@ void WriteData::write(const std::string &file)
   if (natoms && atom->body_flag) bonus(BODY);
 
   // extra sections managed by fixes
-  
+
   if (fixflag)
     for (int i = 0; i < modify->nfix; i++)
       if (modify->fix[i]->wd_section)
@@ -261,7 +261,7 @@ void WriteData::header()
   if (atom->body_flag) fmt::print(fp,"{} bodies\n",atom->nbodies);
 
   // fix info
-  
+
   if (fixflag)
     for (int i = 0; i < modify->nfix; i++)
       if (modify->fix[i]->wd_header)
@@ -671,7 +671,7 @@ void WriteData::bonus(int flag)
   // pack my bonus data into buf
 
   atom->avec->pack_data_bonus(buf,flag);
-    
+
   // write one chunk of info per proc to file
   // proc 0 pings each proc, receives its chunk, writes to file
   // all other procs wait for ping, send their chunk to proc 0
@@ -686,7 +686,7 @@ void WriteData::bonus(int flag)
     if (flag == LINE) fprintf(fp,"\nLines\n\n");
     if (flag == TRIANGLE) fprintf(fp,"\nTriangles\n\n");
     if (flag == BODY) fprintf(fp,"\nBodies\n\n");
-    
+
     for (int iproc = 0; iproc < nprocs; iproc++) {
       if (iproc) {
         MPI_Irecv(buf,maxvalues,MPI_DOUBLE,iproc,0,world,&request);