while space and source formatting cleanup

doc/src/fix_wall_gran.txt

@@ -17,13 +17,13 @@ wall/gran = style name of this fix command :l
 fstyle = style of force interactions between particles and wall :l
   possible choices: hooke, hooke/history, hertz/history, granular :pre
 fstyle_params = parameters associated with force interaction style :l
-  For {hooke}, {hooke/history}, and {hertz/history}, {fstyle_params} are: 
+  For {hooke}, {hooke/history}, and {hertz/history}, {fstyle_params} are:
-	Kn = elastic constant for normal particle repulsion (force/distance units or pressure units - see discussion below) 
+        Kn = elastic constant for normal particle repulsion (force/distance units or pressure units - see discussion below)
-	Kt = elastic constant for tangential contact (force/distance units or pressure units - see discussion below) 
+        Kt = elastic constant for tangential contact (force/distance units or pressure units - see discussion below)
-	gamma_n = damping coefficient for collisions in normal direction (1/time units or 1/time-distance units - see discussion below) 
+        gamma_n = damping coefficient for collisions in normal direction (1/time units or 1/time-distance units - see discussion below)
-	gamma_t = damping coefficient for collisions in tangential direction (1/time units or 1/time-distance units - see discussion below)  
+        gamma_t = damping coefficient for collisions in tangential direction (1/time units or 1/time-distance units - see discussion below)
-	xmu = static yield criterion (unitless value between 0.0 and 1.0e4) 
+        xmu = static yield criterion (unitless value between 0.0 and 1.0e4)
-	dampflag = 0 or 1 if tangential damping force is excluded or included :pre
+        dampflag = 0 or 1 if tangential damping force is excluded or included :pre
   For {granular}, {fstyle_params} are set using the same syntax as for the {pair_coeff} command of "pair_style granular"_pair_granular.html :pre
 wallstyle = {xplane} or {yplane} or {zplane} or {zcylinder} :l
 args = list of arguments for a particular style :l

doc/src/fix_wall_gran_region.txt

@@ -17,20 +17,20 @@ wall/region = style name of this fix command :l
 fstyle = style of force interactions between particles and wall :l
   possible choices: hooke, hooke/history, hertz/history, granular :pre
 fstyle_params = parameters associated with force interaction style :l
-  For {hooke}, {hooke/history}, and {hertz/history}, {fstyle_params} are: 
+  For {hooke}, {hooke/history}, and {hertz/history}, {fstyle_params} are:
-	Kn = elastic constant for normal particle repulsion (force/distance units or pressure units - see discussion below) 
+        Kn = elastic constant for normal particle repulsion (force/distance units or pressure units - see discussion below)
-	Kt = elastic constant for tangential contact (force/distance units or pressure units - see discussion below) 
+        Kt = elastic constant for tangential contact (force/distance units or pressure units - see discussion below)
-	gamma_n = damping coefficient for collisions in normal direction (1/time units or 1/time-distance units - see discussion below) 
+        gamma_n = damping coefficient for collisions in normal direction (1/time units or 1/time-distance units - see discussion below)
-	gamma_t = damping coefficient for collisions in tangential direction (1/time units or 1/time-distance units - see discussion below)  
+        gamma_t = damping coefficient for collisions in tangential direction (1/time units or 1/time-distance units - see discussion below)
-	xmu = static yield criterion (unitless value between 0.0 and 1.0e4) 
+        xmu = static yield criterion (unitless value between 0.0 and 1.0e4)
-	dampflag = 0 or 1 if tangential damping force is excluded or included :pre
+        dampflag = 0 or 1 if tangential damping force is excluded or included :pre
   For {granular}, {fstyle_params} are set using the same syntax as for the {pair_coeff} command of "pair_style granular"_pair_granular.html :pre
 wallstyle = region (see "fix wall/gran"_fix_wall_gran.html for options for other kinds of walls) :l
 region-ID = region whose boundary will act as wall :l,ule
 
 [Examples:]
 
-fix wall all wall/gran/region hooke/history 1000.0 200.0 200.0 100.0 0.5 1 region myCone 
+fix wall all wall/gran/region hooke/history 1000.0 200.0 200.0 100.0 0.5 1 region myCone
 fix 3 all wall/gran/region granular hooke 1000.0 50.0 tangential linear_nohistory 1.0 0.4 damping velocity region myBox
 fix 4 all wall/gran/region granular jkr 1e5 1500.0 0.3 10.0 tangential mindlin NULL 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall region myCone
 fix 5 all wall/gran/region granular dmt 1e5 0.2 0.3 10.0 tangential mindlin NULL 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall damping tsuji region myCone :pre

doc/src/pair_granular.txt

@@ -66,8 +66,8 @@ mixed coefficients for type 1 - type 2 interactions can be determined from
 mixing rules discussed below.  For additional flexibility,
 coefficients as well as model forms can vary between particle types,
 as shown in the fourth example: type 1 - type 1 interactions are based
-on a Johnson-Kendall-Roberts normal contact model and 2-2 interactions 
+on a Johnson-Kendall-Roberts normal contact model and 2-2 interactions
-are based on a DMT cohesive model (see below).  In that example, 1-1 
+are based on a DMT cohesive model (see below).  In that example, 1-1
 and 2-2 interactions have different model forms, in which case mixing of
 coefficients cannot be determined, so 1-2 interactions must be
 explicitly defined via the {pair_coeff 1 *} command, otherwise an
@@ -215,9 +215,9 @@ For {damping mass_velocity}, the normal damping is given by:
 \end\{equation\}
 
 Here, \(\eta_\{n0\}\) is the damping coefficient specified for the normal
-contact model, in units of {mass}/{time} and 
+contact model, in units of {mass}/{time} and
 \(m_\{eff\} = m_i m_j/(m_i + m_j)\) is the effective mass.
-Use {damping mass_velocity} to reproduce the damping behavior of 
+Use {damping mass_velocity} to reproduce the damping behavior of
 {pair gran/hooke/*}.
 
 The {damping viscoelastic} model is based on the viscoelastic
@@ -228,9 +228,9 @@ damping is given by:
 \eta_n = \eta_\{n0\}\ a m_\{eff\}
 \end\{equation\}
 
-Here, {a} is the contact radius, given by \(a =\sqrt\{R\delta\}\) 
+Here, {a} is the contact radius, given by \(a =\sqrt\{R\delta\}\)
-for all models except {jkr}, for which it is given implicitly according 
+for all models except {jkr}, for which it is given implicitly according
-to \(\delta = a^2/R - 2\sqrt\{\pi \gamma a/E\}\).  For {damping viscoelastic}, 
+to \(\delta = a^2/R - 2\sqrt\{\pi \gamma a/E\}\).  For {damping viscoelastic},
 \(\eta_\{n0\}\) is in units of 1/({time}*{distance}).
 
 The {tsuji} model is based on the work of "(Tsuji et
@@ -583,11 +583,11 @@ The {granular} pair style can reproduce the behavior of the
 minor differences can be expected due to corrections in
 displacement history frame-of-reference, and the application
 of the torque at the center of the contact rather than
-at each particle). The first example above 
+at each particle). The first example above
 is equivalent to {pair gran/hooke 1000.0 NULL 50.0 50.0 0.4 1}.
-The second example is equivalent to 
+The second example is equivalent to
 {pair gran/hooke/history 1000.0 500.0 50.0 50.0 0.4 1}.
-The third example is equivalent to 
+The third example is equivalent to
 {pair gran/hertz/history 1000.0 500.0 50.0 50.0 0.4 1}.
 
 :line
@@ -734,7 +734,7 @@ For the {pair_coeff} settings: {damping viscoelastic}, {rolling none},
 J. M., & Poschel, T. (1996).  Model for collisions in granular
 gases. Physical review E, 53(5), 5382.
 
-:link(Tsuji1992) 
+:link(Tsuji1992)
 [(Tsuji et al, 1992)] Tsuji, Y., Tanaka, T., & Ishida,
 T. (1992). Lagrangian numerical simulation of plug flow of
 cohesionless particles in a horizontal pipe. Powder technology, 71(3),

src/GRANULAR/fix_wall_gran.cpp

@@ -1161,7 +1161,7 @@ void FixWallGran::granular(double rsq, double dx, double dy, double dz,
   if (damping_model == VELOCITY) {
     damp_normal = 1;
   }
-  else if (damping_model == MASS_VELOCITY){
+  else if (damping_model == MASS_VELOCITY) {
     damp_normal = meff;
   }
   else if (damping_model == VISCOELASTIC) {

src/GRANULAR/fix_wall_gran_region.cpp

@@ -121,7 +121,7 @@ void FixWallGranRegion::init()
     region->reset_vel();
   }
 
-  if (motion_resetflag){
+  if (motion_resetflag) {
     char str[256];
     snprintf(str,256,"Region properties for region %s are inconsistent "
              "with restart file, resetting its motion",idregion);
@@ -190,7 +190,7 @@ void FixWallGranRegion::post_force(int /*vflag*/)
     if (mask[i] & groupbit) {
       if (!region->match(x[i][0],x[i][1],x[i][2])) continue;
 
-      if (pairstyle == GRANULAR && normal_model == JKR){
+      if (pairstyle == GRANULAR && normal_model == JKR) {
         nc = region->surface(x[i][0],x[i][1],x[i][2],
                              radius[i]+pulloff_distance(radius[i]));
       }
@@ -232,8 +232,8 @@ void FixWallGranRegion::post_force(int /*vflag*/)
 
         rsq = region->contact[ic].r*region->contact[ic].r;
 
-        if (pairstyle == GRANULAR && normal_model == JKR){
+        if (pairstyle == GRANULAR && normal_model == JKR) {
-          if (history_many[i][c2r[ic]][0] == 0.0 && rsq > radius[i]*radius[i]){
+          if (history_many[i][c2r[ic]][0] == 0.0 && rsq > radius[i]*radius[i]) {
             for (m = 0; m < size_history; m++)
               history_many[i][0][m] = 0.0;
             continue;
@@ -253,7 +253,7 @@ void FixWallGranRegion::post_force(int /*vflag*/)
         if (fix_rigid && mass_rigid[i] > 0.0) meff = mass_rigid[i];
 
         // store contact info
-        if (peratom_flag){
+        if (peratom_flag) {
           array_atom[i][0] = (double)atom->tag[i];
           array_atom[i][4] = x[i][0] - dx;
           array_atom[i][5] = x[i][1] - dy;
@@ -382,7 +382,7 @@ void FixWallGranRegion::copy_arrays(int i, int j, int /*delflag*/)
 {
   int m,n,iwall;
 
-  if (use_history){
+  if (use_history) {
     n = ncontact[i];
     for (iwall = 0; iwall < n; iwall++) {
       walls[j][iwall] = walls[i][iwall];
@@ -392,7 +392,7 @@ void FixWallGranRegion::copy_arrays(int i, int j, int /*delflag*/)
     ncontact[j] = ncontact[i];
   }
 
-  if (peratom_flag){
+  if (peratom_flag) {
     for (int m = 0; m < size_peratom_cols; m++)
       array_atom[j][m] = array_atom[i][m];
   }
@@ -406,7 +406,7 @@ void FixWallGranRegion::set_arrays(int i)
 {
   if (use_history)
     ncontact[i] = 0;
-  if (peratom_flag){
+  if (peratom_flag) {
     for (int m = 0; m < size_peratom_cols; m++)
       array_atom[i][m] = 0;
   }
@@ -421,7 +421,7 @@ int FixWallGranRegion::pack_exchange(int i, double *buf)
   int m;
 
   int n = 0;
-  if (use_history){
+  if (use_history) {
     int count = ncontact[i];
     buf[n++] = ubuf(count).d;
     for (int iwall = 0; iwall < count; iwall++) {
@@ -430,7 +430,7 @@ int FixWallGranRegion::pack_exchange(int i, double *buf)
         buf[n++] = history_many[i][iwall][m];
     }
   }
-  if (peratom_flag){
+  if (peratom_flag) {
     for (int m = 0; m < size_peratom_cols; m++)
       buf[n++] = array_atom[i][m];
   }
@@ -448,7 +448,7 @@ int FixWallGranRegion::unpack_exchange(int nlocal, double *buf)
 
 
   int n = 0;
-  if (use_history){
+  if (use_history) {
     int count = ncontact[nlocal] = (int) ubuf(buf[n++]).i;
     for (int iwall = 0; iwall < count; iwall++) {
       walls[nlocal][iwall] = (int) ubuf(buf[n++]).i;
@@ -456,7 +456,7 @@ int FixWallGranRegion::unpack_exchange(int nlocal, double *buf)
         history_many[nlocal][iwall][m] = buf[n++];
     }
   }
-  if (peratom_flag){
+  if (peratom_flag) {
     for (int m = 0; m < size_peratom_cols; m++)
       array_atom[nlocal][m] = buf[n++];
   }

src/GRANULAR/pair_granular.cpp

@@ -418,7 +418,7 @@ void PairGranular::compute(int eflag, int vflag)
           }
           // rotate and update displacements.
           // see e.g. eq. 17 of Luding, Gran. Matter 2008, v10,p235
-          if (historyupdate){
+          if (historyupdate) {
             rsht = history[0]*nx + history[1]*ny + history[2]*nz;
             if (fabs(rsht) < EPSILON) rsht = 0;
             if (rsht > 0) {
@@ -958,7 +958,7 @@ void PairGranular::coeff(int narg, char **arg)
 }
 
 /* ----------------------------------------------------------------------
-	 init specific to this pair style
+  init specific to this pair style
 ------------------------------------------------------------------------- */
 
 void PairGranular::init_style()