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doc/src/pair_amoeba.rst

@@ -68,7 +68,7 @@ while the HIPPO force field contains these terms:
 
 .. math::
 
-   U_{hippo} = U_{multipole} + U_{polar} + U_{qxfer} + U_{repulsion} + U_{dispersion} 
+   U_{hippo} = U_{multipole} + U_{polar} + U_{qxfer} + U_{repulsion} + U_{dispersion}
 
 Conceptually, these terms compute the following interactions:
 
@@ -85,7 +85,7 @@ this doc page give full details for both force fields.
 
 The formulas for the AMOEBA energy terms are:
 
-.. math:: 
+.. math::
 
    U_{hal} = \epsilon_{ij} \left( \frac{1.07}{\rho_{ij} + 0.07} \right)^7 \left( \frac{1.12}{\rho_{ij}^7 + 0.12} - 2 \right)
    U_{multipole} = \vec{M_i}\bold{T_{ij}}\vec{M_j}
@@ -94,7 +94,7 @@ The formulas for the AMOEBA energy terms are:
 
 The formulas for the HIPPO energy terms are:
 
-.. math:: 
+.. math::
 
    U_{multipole} = Z_i \frac{1}{r_{ij}} Z_j + Z_i T_{ij}^{damp} \vec{M_j} + Z_j T_{ji}^{damp} \vec{M_i} + \vec{M_i} T_{ij}^{damp} \vec{M_j}
       \vec{M} = \left( Q, \vec{\mu_{perm}}, \bold{\Theta} \right)

src/AMOEBA/amoeba_file.cpp

@@ -863,7 +863,7 @@ void PairAmoeba::file_ffield(int nwords, char **words)
              strcmp(words[0],"direct-13-scale") == 0 ||
              strcmp(words[0],"direct-14-scale") == 0) {
     double tmp = utils::numeric(FLERR,words[1],true,lmp);
-    if (tmp != 1.0) 
+    if (tmp != 1.0)
       error->all(FLERR,"AMOEBA FF file direct-scale 1-2, 1-3, 1-4 values should be 1.0");
 
   } else if (strcmp(words[0],"mutual-11-scale") == 0) {
@@ -872,7 +872,7 @@ void PairAmoeba::file_ffield(int nwords, char **words)
              strcmp(words[0],"mutual-13-scale") == 0 ||
              strcmp(words[0],"mutual-14-scale") == 0) {
     double tmp = utils::numeric(FLERR,words[1],true,lmp);
-    if (tmp != 1.0) 
+    if (tmp != 1.0)
       error->all(FLERR,"AMOEBA FF file mutual-scale 1-2, 1-3, 1-4 values should be 1.0");
 
   // error if LAMMPS does not recognize keyword

src/AMOEBA/amoeba_multipole.cpp

@@ -498,7 +498,7 @@ void PairAmoeba::multipole_real()
         vyy = -yr * frcy;
         vyz = -0.5 * (zr*frcy+yr*frcz);
         vzz = -zr * frcz;
-      
+
         virmpole[0] -= vxx;
         virmpole[1] -= vyy;
         virmpole[2] -= vzz;
@@ -534,7 +534,7 @@ void PairAmoeba::multipole_real()
     xiy = x[iy][0] - x[i][0];
     yiy = x[iy][1] - x[i][1];
     ziy = x[iy][2] - x[i][2];
-    
+
     vxx = xix*fix[0] + xiy*fiy[0] + xiz*fiz[0];
     vxy = 0.5 * (yix*fix[0] + yiy*fiy[0] + yiz*fiz[0] +
                  xix*fix[1] + xiy*fiy[1] + xiz*fiz[1]);
@@ -544,7 +544,7 @@ void PairAmoeba::multipole_real()
     vyz = 0.5 * (zix*fix[1] + ziy*fiy[1] + ziz*fiz[1] +
                  yix*fix[2] + yiy*fiy[2] + yiz*fiz[2]);
     vzz = zix*fix[2] + ziy*fiy[2] + ziz*fiz[2];
-    
+
     virmpole[0] -= vxx;
     virmpole[1] -= vyy;
     virmpole[2] -= vzz;

src/AMOEBA/amoeba_polar.cpp

@@ -111,7 +111,7 @@ void PairAmoeba::polar()
     xiy = x[iy][0] - x[i][0];
     yiy = x[iy][1] - x[i][1];
     ziy = x[iy][2] - x[i][2];
-    
+
     vxx = xix*fix[0] + xiy*fiy[0] + xiz*fiz[0];
     vyy = yix*fix[1] + yiy*fiy[1] + yiz*fiz[1];
     vzz = zix*fix[2] + ziy*fiy[2] + ziz*fiz[2];
@@ -122,7 +122,7 @@ void PairAmoeba::polar()
                  xix*fix[2] + xiy*fiy[2] + xiz*fiz[2]);
     vyz = 0.5 * (zix*fix[1] + ziy*fiy[1] + ziz*fiz[1] +
                  yix*fix[2] + yiy*fiy[2] + yiz*fiz[2]);
-    
+
     virpolar[0] -= vxx;
     virpolar[1] -= vyy;
     virpolar[2] -= vzz;

src/AMOEBA/amoeba_utils.cpp

@@ -70,7 +70,7 @@ void PairAmoeba::kmpole()
     flag = 0;
 
     // create a sorted version of bond/angle neighs from special[][]
-    // NOTE: this is to try and do it identically to Tinker 
+    // NOTE: this is to try and do it identically to Tinker
     //   b/c I think in Tinker, atom order matters as to which case is seen fist
 
     for (j = 0; j < nspecial[i][0]; j++)

src/AMOEBA/pair_amoeba.cpp

@@ -232,7 +232,7 @@ PairAmoeba::~PairAmoeba()
 
   memory->destroy(qfac);
   memory->destroy(gridfft1);
- 
+
   delete m_kspace;
   delete p_kspace;
   delete pc_kspace;
@@ -489,7 +489,7 @@ void PairAmoeba::finish()
   double ave;
   MPI_Allreduce(&time_init,&ave,1,MPI_DOUBLE,MPI_SUM,world);
   time_init = ave/comm->nprocs;
-  
+
   MPI_Allreduce(&time_hal,&ave,1,MPI_DOUBLE,MPI_SUM,world);
   time_hal = ave/comm->nprocs;
 
@@ -2292,7 +2292,7 @@ double PairAmoeba::memory_usage()
   if (use_ewald || use_dewald) {
     bytes += (double) 12 * bsordermax * nmax *sizeof(double);   // theta123
     bytes += (double) 3 * nmax *sizeof(int);                    // igrid
-  }    
+  }
 
   bytes += (double) nmax * sizeof(int);        // numneigh_dipole
   bytes += (double) nmax * sizeof(int *);      // firstneigh_dipole

src/AMOEBA/pair_amoeba.h

@@ -332,7 +332,7 @@ class PairAmoeba : public Pair {
   double *gridfft1;                // copy of p_kspace FFT grid
 
   double **cmp,**fmp;              // Cartesian and fractional multipoles
-  double **cphi,**fphi;     
+  double **cphi,**fphi;
 
   // params for current KSpace solve and FFT being worked on