Ran the four make commands in the src folder: make fix-whitespace; make fix-homepage; make fix-errordocs; make fix-permissions

lib/gpu/lal_atom.h

@@ -285,7 +285,7 @@ class Atom {
   /// Signal that we need to transfer atom data for next timestep
   inline void data_unavail()
     { _x_avail=false; _q_avail=false; _quat_avail=false; _v_avail=false; _extra_avail=false; _resized=false; }
-  
+
   /// Signal that we need to transfer atom extra data for next kernel call
   inline void extra_data_unavail()
     { _extra_avail=false; }

lib/gpu/lal_base_amoeba.cpp

@@ -42,7 +42,7 @@ BaseAmoebaT::~BaseAmoeba() {
   k_polar.clear();
   k_special15.clear();
   k_short_nbor.clear();
-  
+
   #if 0 // !defined(USE_OPENCL) && !defined(USE_HIP)
   if (fft_plan_created) cufftDestroy(plan);
   #endif
@@ -365,7 +365,7 @@ int** BaseAmoebaT::precompute(const int ago, const int inum_full, const int nall
 // ---------------------------------------------------------------------------
 // Compute multipole real-space part
 //   precompute() should be already invoked before mem (re)allocation
-//   this is the first part in a time step done on the GPU for AMOEBA for now 
+//   this is the first part in a time step done on the GPU for AMOEBA for now
 // ---------------------------------------------------------------------------
 template <class numtyp, class acctyp>
 void BaseAmoebaT::compute_multipole_real(const int ago, const int inum_full,
@@ -418,7 +418,7 @@ void BaseAmoebaT::compute_udirect2b(int *host_amtype, int *host_amgroup, double
 
   cast_extra_data(host_amtype, host_amgroup, host_rpole, host_uind, host_uinp, host_pval);
   atom->add_extra_data();
- 
+
   *fieldp_ptr=_fieldp.host.begin();
 
   // specify the correct cutoff and alpha values
@@ -443,7 +443,7 @@ void BaseAmoebaT::compute_umutual2b(int *host_amtype, int *host_amgroup, double
   // only copy the necessary data arrays that are updated over the iterations
   // use nullptr for the other arrays that are already copied from host to device
   cast_extra_data(host_amtype, host_amgroup, nullptr, host_uind, host_uinp, nullptr);
-  atom->add_extra_data();                          
+  atom->add_extra_data();
 
   // set the correct cutoff and alpha
   _off2_polar = off2_polar;
@@ -648,7 +648,7 @@ int BaseAmoebaT::fphi_uind() {
   int ngridxy = _ngridx * _ngridy;
   k_fphi_uind.set_size(GX,BX);
   k_fphi_uind.run(&_thetai1, &_thetai2, &_thetai3, &_igrid, &_cgrid_brick,
-                  &_fdip_phi1, &_fdip_phi2, &_fdip_sum_phi, &_bsorder, &ainum, 
+                  &_fdip_phi1, &_fdip_phi2, &_fdip_sum_phi, &_bsorder, &ainum,
                   &_nzlo_out, &_nylo_out, &_nxlo_out, &ngridxy, &_ngridx);
   time_pair.stop();
 
@@ -738,7 +738,7 @@ void BaseAmoebaT::compute_polar_real(int *host_amtype, int *host_amgroup,
   // cast necessary data arrays from host to device
 
   cast_extra_data(host_amtype, host_amgroup, host_rpole, host_uind, host_uinp, host_pval);
-  atom->add_extra_data();                    
+  atom->add_extra_data();
 
   *tep_ptr=_tep.host.begin();
 
@@ -784,7 +784,7 @@ template <class numtyp, class acctyp>
 void BaseAmoebaT::compute_fft1d(void* in, void* out, const int numel, const int mode)
 {
   // TODO: setting up FFT plan based on the backend (cuFFT or hipFFT)
-  #if 0 // !defined(USE_OPENCL) && !defined(USE_HIP)    
+  #if 0 // !defined(USE_OPENCL) && !defined(USE_HIP)
   if (fft_plan_created == false) {
     int m = numel/2;
     cufftPlan1d(&plan, m, CUFFT_Z2Z, 1);
@@ -793,7 +793,7 @@ void BaseAmoebaT::compute_fft1d(void* in, void* out, const int numel, const int
 
   // n = number of double complex
   int n = numel/2;
-  
+
   // copy the host array to the device (data)
   UCL_Vector<cufftDoubleComplex,cufftDoubleComplex> data;
   data.alloc(n, *(this->ucl_device), UCL_READ_WRITE, UCL_READ_WRITE);
@@ -807,7 +807,7 @@ void BaseAmoebaT::compute_fft1d(void* in, void* out, const int numel, const int
   data.update_device(false);
 
   // perform the in-place forward FFT
-  
+
   cufftResult result = cufftExecZ2Z(plan, (cufftDoubleComplex*)&data.device,
     (cufftDoubleComplex*)&data.device, CUFFT_FORWARD);
   if (result != CUFFT_SUCCESS) printf("failed cufft %d\n", result);

lib/gpu/lal_base_amoeba.h

@@ -256,7 +256,7 @@ class BaseAmoeba {
   int _ngridx, _ngridy, _ngridz, _num_grid_points;
 
   int _end_command_queue;
-  
+
   // ------------------------ FORCE/ENERGY DATA -----------------------
 
   Answer<numtyp,acctyp> *ans;
@@ -312,7 +312,7 @@ class BaseAmoeba {
   virtual int fphi_uind();
   virtual int fphi_mpole();
   virtual int polar_real(const int eflag, const int vflag) = 0;
-  
+
 
   #if !defined(USE_OPENCL) && !defined(USE_HIP)
   cufftHandle plan;

lib/gpu/lal_hippo.cpp

@@ -597,11 +597,11 @@ int HippoT::polar_real(const int eflag, const int vflag) {
   int nbor_pitch=this->nbor->nbor_pitch();
 
   // Compute the block size and grid size to keep all cores busy
-  
+
   const int BX=this->block_size();
   const int GX=static_cast<int>(ceil(static_cast<double>(ainum)/(BX/this->_threads_per_atom)));
   /*
-  const int cus = this->device->gpu->cus();  
+  const int cus = this->device->gpu->cus();
   while (GX < cus && GX > 1) {
     BX /= 2;
     GX=static_cast<int>(ceil(static_cast<double>(ainum)/(BX/this->_threads_per_atom)));

lib/gpu/lal_hippo.h

@@ -124,7 +124,7 @@ class Hippo : public BaseAmoeba<numtyp, acctyp> {
   UCL_D_Vec<numtyp4> coeff_amtype;
   /// csix = coeff_amclass.x; adisp = coeff_amclass.y;
   UCL_D_Vec<numtyp4> coeff_amclass;
-  /// sizpr = coeff_rep.x; dmppr = coeff_rep.y; elepr = coeff_rep.z; 
+  /// sizpr = coeff_rep.x; dmppr = coeff_rep.y; elepr = coeff_rep.z;
   UCL_D_Vec<numtyp4> coeff_rep;
   /// Special polar values [0-4]:
   ///   sp_polar.x = special_polar_wscale

lib/gpu/lal_hippo_extra.h

@@ -173,7 +173,7 @@ ucl_inline void damprep(const numtyp r, const numtyp r2, const numtyp rr1,
   dmpik[4] = pre * (s*d2s + ds*ds);
   dmpik[6] = pre * (s*d3s + (numtyp)3.0*ds*d2s);
   dmpik[8] = pre * (s*d4s + (numtyp)4.0*ds*d3s + (numtyp)3.0*d2s*d2s);
-  
+
   if (rorder >= 11) dmpik[10] = pre * (s*d5s + (numtyp)5.0*ds*d4s + (numtyp)10.0*d2s*d3s);
 }
 

lib/gpu/lal_neighbor.cpp

@@ -684,7 +684,7 @@ void Neighbor::build_nbor_list(double **x, const int inum, const int host_inum,
     if (_cutoff < _cell_size) vadjust*=1.46;
     mn=std::max(mn,static_cast<int>(ceil(_max_neighbor_factor*vadjust*mn)));
     if (mn<33) mn+=3;
-    
+
     resize_max_neighbors<numtyp,acctyp>(mn,success);
     set_nbor_block_size(mn/2);
     if (!success)
@@ -837,7 +837,7 @@ void Neighbor::build_nbor_list(double **x, const int inum, const int host_inum,
   time_nbor.stop();
 }
 
-void Neighbor::transpose(UCL_D_Vec<tagint> &out, const UCL_D_Vec<tagint> &in, 
+void Neighbor::transpose(UCL_D_Vec<tagint> &out, const UCL_D_Vec<tagint> &in,
     const int columns_in, const int rows_in)
 {
   const int b2x=_block_cell_2d;

lib/gpu/lal_neighbor.h

@@ -260,7 +260,7 @@ class Neighbor {
   }
 
   /// Helper function
-  void transpose(UCL_D_Vec<tagint> &out, const UCL_D_Vec<tagint> &in, 
+  void transpose(UCL_D_Vec<tagint> &out, const UCL_D_Vec<tagint> &in,
     const int columns_in, const int rows_in);
 
  private:

src/AMOEBA/amoeba_kspace.cpp

@@ -73,7 +73,7 @@ void PairAmoeba::moduli()
     _nfft_max = maxfft;
     memory->create(_moduli_bsarray,_nfft_max,"amoeba:_moduli_bsarray");
   }
-  
+
   // compute and load the moduli values
 
   double x = 0.0;

src/AMOEBA/amoeba_multipole.cpp

@@ -419,7 +419,7 @@ void PairAmoeba::multipole_real()
           term2i*rr3i + term2k*rr3k + term2ik*rr3ik +
           term3i*rr5i + term3k*rr5k + term3ik*rr5ik;
 
-        
+
 
         // find damped multipole intermediates for force and torque
 
@@ -465,7 +465,7 @@ void PairAmoeba::multipole_real()
         term4 = 2.0 * (-ck*rr5+dkr*rr7-qkr*rr9);
         term5 = 2.0 * (-ci*rr5-dir*rr7-qir*rr9);
         term6 = 4.0 * rr7;
-        
+
       }
 
       empole += e;

src/AMOEBA/pair_amoeba.cpp

@@ -570,7 +570,7 @@ void PairAmoeba::finish()
   double time_mutual_fft = ic_kspace->time_fft;
   MPI_Allreduce(&time_mutual_fft,&ave,1,MPI_DOUBLE,MPI_SUM,world);
   time_mutual_fft = ave/comm->nprocs;
-  
+
   double time_total = (time_init + time_hal + time_repulse + time_disp +
                        time_mpole + time_induce + time_polar + time_qxfer) / 100.0;
 
@@ -597,7 +597,7 @@ void PairAmoeba::finish()
     utils::logmesg(lmp,"      Mpole  time: {:.6g} {:.3g}%\n", time_mpole_rspace, time_mpole_rspace/time_total);
     utils::logmesg(lmp,"      Direct time: {:.6g} {:.3g}%\n", time_direct_rspace, time_direct_rspace/time_total);
     utils::logmesg(lmp,"      Mutual time: {:.6g} {:.3g}%\n", time_mutual_rspace, time_mutual_rspace/time_total);
-    utils::logmesg(lmp,"      Polar  time: {:.6g} {:.3g}%\n", time_polar_rspace, time_polar_rspace/time_total); 
+    utils::logmesg(lmp,"      Polar  time: {:.6g} {:.3g}%\n", time_polar_rspace, time_polar_rspace/time_total);
     utils::logmesg(lmp,"    K-space timing breakdown   : {:.3g}%\n", kspace_time/time_total);
     utils::logmesg(lmp,"      Mpole  time: {:.6g} {:.3g}%\n", time_mpole_kspace, time_mpole_kspace/time_total);
     utils::logmesg(lmp,"      Direct time: {:.6g} {:.3g}%\n", time_direct_kspace, time_direct_kspace/time_total);
@@ -606,7 +606,7 @@ void PairAmoeba::finish()
     utils::logmesg(lmp,"       - FFT     : {:.6g} {:.3g}%\n", time_mutual_fft, time_mutual_fft/time_total);
     utils::logmesg(lmp,"       - Interp  : {:.6g} {:.3g}%\n", time_fphi_uind, time_fphi_uind/time_total);
     utils::logmesg(lmp,"      Polar  time: {:.6g} {:.3g}%\n", time_polar_kspace, time_polar_kspace/time_total);
-    
+
   }
 }
 

src/AMOEBA/pair_amoeba.h

@@ -347,8 +347,8 @@ class PairAmoeba : public Pair {
 
   class AmoebaConvolution *m_kspace;   // multipole KSpace
   class AmoebaConvolution *p_kspace;   // polar KSpace
-  class AmoebaConvolution *pc_kspace;  
+  class AmoebaConvolution *pc_kspace;
-  class AmoebaConvolution *d_kspace;   // dispersion KSpace 
+  class AmoebaConvolution *d_kspace;   // dispersion KSpace
   class AmoebaConvolution *i_kspace;   // induce KSpace
   class AmoebaConvolution *ic_kspace;
 

src/GPU/amoeba_convolution_gpu.cpp

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/ Sandia National Laboratories
-   Steve Plimpton, sjplimp@sandia.gov
+   LAMMPS Development team: developers@lammps.org
 
    Copyright (2003) Sandia Corporation.  Under the terms of Contract
    DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains

src/GPU/amoeba_convolution_gpu.h

@@ -1,7 +1,7 @@
 /* -*- c++ -*- ----------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/ Sandia National Laboratories
-   Steve Plimpton, sjplimp@sandia.gov
+   LAMMPS Development team: developers@lammps.org
 
    Copyright (2003) Sandia Corporation.  Under the terms of Contract
    DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains

src/GPU/pair_amoeba_gpu.cpp

@@ -2,7 +2,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
-   Steve Plimpton, sjplimp@sandia.gov
+   LAMMPS Development team: developers@lammps.org
 
    Copyright (2003) Sandia Corporation.  Under the terms of Contract
    DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@@ -283,7 +283,7 @@ void PairAmoebaGPU::multipole_real()
                                     success, aewald, felec, off2, atom->q,
                                     domain->boxlo, domain->prd, &tq_pinned);
 
-  
+
 
   // reference to the tep array from GPU lib
 
@@ -400,7 +400,7 @@ void PairAmoebaGPU::induce()
       }
 
       for (i = 0; i < nlocal; i++) {
-	      itype = amtype[i];
+              itype = amtype[i];
         for (j = 0; j < 3; j++) {
           uopt[i][m][j] = polarity[itype] * field[i][j];
           uoptp[i][m][j] = polarity[itype] * fieldp[i][j];
@@ -666,7 +666,7 @@ void PairAmoebaGPU::induce()
 
     if (iter >= maxiter || eps > epsold)
       if (comm->me == 0)
-	      error->warning(FLERR,"AMOEBA induced dipoles did not converge");
+              error->warning(FLERR,"AMOEBA induced dipoles did not converge");
   }
 
   // update the lists of previous induced dipole values
@@ -958,7 +958,7 @@ void PairAmoebaGPU::ufield0c(double **field, double **fieldp)
   //   field and fieldp may already have some nonzero values from kspace (umutual1 and self)
 
   amoeba_gpu_update_fieldp(&fieldp_pinned);
-  
+
   int inum = atom->nlocal;
   double *field_ptr = (double *)fieldp_pinned;
 
@@ -1015,8 +1015,8 @@ void PairAmoebaGPU::umutual1(double **field, double **fieldp)
     fuind[i][1] = a[1][0]*uind[i][0] + a[1][1]*uind[i][1] + a[1][2]*uind[i][2];
     fuind[i][2] = a[2][0]*uind[i][0] + a[2][1]*uind[i][1] + a[2][2]*uind[i][2];
   }
-    
+
-  for (int i = 0; i < nlocal; i++) {      
+  for (int i = 0; i < nlocal; i++) {
     fuinp[i][0] = a[0][0]*uinp[i][0] + a[0][1]*uinp[i][1] + a[0][2]*uinp[i][2];
     fuinp[i][1] = a[1][0]*uinp[i][0] + a[1][1]*uinp[i][1] + a[1][2]*uinp[i][2];
     fuinp[i][2] = a[2][0]*uinp[i][0] + a[2][1]*uinp[i][1] + a[2][2]*uinp[i][2];
@@ -1037,7 +1037,7 @@ void PairAmoebaGPU::umutual1(double **field, double **fieldp)
 
   time1 = MPI_Wtime();
   time_grid_uind += (time1 - time0);
- 
+
   // pre-convolution operations including forward FFT
   // gridfft = my portion of complex 3d grid in FFT decomposition
 
@@ -1137,7 +1137,7 @@ void PairAmoebaGPU::fphi_uind(double ****grid, double **fdip_phi1,
   void* fdip_sum_phi_pinned = nullptr;
   amoeba_gpu_fphi_uind(grid, &fdip_phi1_pinned, &fdip_phi2_pinned,
                        &fdip_sum_phi_pinned);
-  
+
   int nlocal = atom->nlocal;
   double *_fdip_phi1_ptr = (double *)fdip_phi1_pinned;
   for (int i = 0; i < nlocal; i++) {
@@ -1356,7 +1356,7 @@ void PairAmoebaGPU::polar_kspace()
     bspline_fill();
 
     // allocate memory and make early host-device transfers
-  
+
     // NOTE: this is for p_kspace, and igrid and thetai[1-3] are filled by bpsline_fill
     if (gpu_fphi_mpole_ready) {
        amoeba_gpu_precompute_kspace(atom->nlocal, bsorder,
@@ -1365,7 +1365,7 @@ void PairAmoebaGPU::polar_kspace()
                                     p_kspace->nylo_out, p_kspace->nyhi_out,
                                     p_kspace->nxlo_out, p_kspace->nxhi_out);
     }
-      
+
 
     // convert Cartesian multipoles to fractional coordinates
 
@@ -1435,7 +1435,7 @@ void PairAmoebaGPU::polar_kspace()
     double ***gridpost = (double ***) p_kspace->post_convolution();
 
     // get potential
-    
+
     if (!gpu_fphi_mpole_ready) {
       fphi_mpole(gridpost,fphi);
 
@@ -1447,7 +1447,7 @@ void PairAmoebaGPU::polar_kspace()
     } else {
       void* fphi_pinned = nullptr;
       amoeba_gpu_fphi_mpole(gridpost, &fphi_pinned, felec);
-    
+
       double *_fphi_ptr = (double *)fphi_pinned;
       for (int i = 0; i < nlocal; i++) {
         int idx = i;
@@ -1457,7 +1457,7 @@ void PairAmoebaGPU::polar_kspace()
         }
       }
 
-    }   
+    }
 
     // convert field from fractional to Cartesian
 

src/GPU/pair_amoeba_gpu.h

@@ -1,7 +1,7 @@
 /* -*- c++ -*- ----------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
-   Steve Plimpton, sjplimp@sandia.gov
+   LAMMPS Development team: developers@lammps.org
 
    Copyright (2003) Sandia Corporation.  Under the terms of Contract
    DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@@ -71,16 +71,3 @@ class PairAmoebaGPU : public PairAmoeba {
 }    // namespace LAMMPS_NS
 #endif
 #endif
-
-/* ERROR/WARNING messages:
-
-E: Insufficient memory on accelerator
-
-There is insufficient memory on one of the devices specified for the gpu
-package
-
-E: Pair style amoeba/gpu requires atom attribute q
-
-The atom style defined does not have this attribute.
-
-*/

src/GPU/pair_hippo_gpu.cpp

@@ -2,7 +2,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
-   Steve Plimpton, sjplimp@sandia.gov
+   LAMMPS Development team: developers@lammps.org
 
    Copyright (2003) Sandia Corporation.  Under the terms of Contract
    DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@@ -517,7 +517,7 @@ void PairHippoGPU::induce()
       }
 
       for (i = 0; i < nlocal; i++) {
-	      itype = amtype[i];
+              itype = amtype[i];
         for (j = 0; j < 3; j++) {
           uopt[i][m][j] = polarity[itype] * field[i][j];
           uoptp[i][m][j] = polarity[itype] * fieldp[i][j];
@@ -785,7 +785,7 @@ void PairHippoGPU::induce()
 
     if (iter >= maxiter || eps > epsold)
       if (comm->me == 0)
-	      error->warning(FLERR,"HIPPO induced dipoles did not converge");
+              error->warning(FLERR,"HIPPO induced dipoles did not converge");
   }
 
   // update the lists of previous induced dipole values
@@ -1045,7 +1045,7 @@ void PairHippoGPU::ufield0c(double **field, double **fieldp)
 
   memset(&field[0][0], 0, 3*nall *sizeof(double));
   memset(&fieldp[0][0], 0, 3*nall *sizeof(double));
- 
+
   // get the real space portion of the mutual field first
 
   MPI_Barrier(world);
@@ -1078,7 +1078,7 @@ void PairHippoGPU::ufield0c(double **field, double **fieldp)
   //   field and fieldp may already have some nonzero values from kspace (umutual1 and self)
 
   hippo_gpu_update_fieldp(&fieldp_pinned);
-  
+
   int inum = atom->nlocal;
   double *field_ptr = (double *)fieldp_pinned;
 
@@ -1136,8 +1136,8 @@ void PairHippoGPU::umutual1(double **field, double **fieldp)
     fuind[i][1] = a[1][0]*uind[i][0] + a[1][1]*uind[i][1] + a[1][2]*uind[i][2];
     fuind[i][2] = a[2][0]*uind[i][0] + a[2][1]*uind[i][1] + a[2][2]*uind[i][2];
   }
-    
+
-  for (int i = 0; i < nlocal; i++) {      
+  for (int i = 0; i < nlocal; i++) {
     fuinp[i][0] = a[0][0]*uinp[i][0] + a[0][1]*uinp[i][1] + a[0][2]*uinp[i][2];
     fuinp[i][1] = a[1][0]*uinp[i][0] + a[1][1]*uinp[i][1] + a[1][2]*uinp[i][2];
     fuinp[i][2] = a[2][0]*uinp[i][0] + a[2][1]*uinp[i][1] + a[2][2]*uinp[i][2];
@@ -1266,7 +1266,7 @@ void PairHippoGPU::fphi_uind(double ****grid, double **fdip_phi1,
   void* fdip_sum_phi_pinned = nullptr;
   hippo_gpu_fphi_uind(grid, &fdip_phi1_pinned, &fdip_phi2_pinned,
                       &fdip_sum_phi_pinned);
-  
+
   int nlocal = atom->nlocal;
   double *_fdip_phi1_ptr = (double *)fdip_phi1_pinned;
   for (int i = 0; i < nlocal; i++) {

src/GPU/pair_hippo_gpu.h

@@ -1,7 +1,7 @@
 /* -*- c++ -*- ----------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
-   Steve Plimpton, sjplimp@sandia.gov
+   LAMMPS Development team: developers@lammps.org
 
    Copyright (2003) Sandia Corporation.  Under the terms of Contract
    DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@@ -71,16 +71,3 @@ class PairHippoGPU : public PairAmoeba {
 }    // namespace LAMMPS_NS
 #endif
 #endif
-
-/* ERROR/WARNING messages:
-
-E: Insufficient memory on accelerator
-
-There is insufficient memory on one of the devices specified for the gpu
-package
-
-E: Pair style hippo/gpu requires atom attribute q
-
-The atom style defined does not have this attribute.
-
-*/