git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@278 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/MOLECULE/Install.csh

@@ -15,6 +15,7 @@ if ($1 == 1) then
   cp angle_hybrid.cpp ..
   cp atom_vec_angle.cpp ..
   cp atom_vec_bond.cpp ..
+  cp atom_vec_full.cpp ..
   cp atom_vec_molecular.cpp ..
   cp bond.cpp ..
   cp bond_fene.cpp ..
@@ -47,6 +48,7 @@ if ($1 == 1) then
   cp angle_hybrid.h ..
   cp atom_vec_angle.h ..
   cp atom_vec_bond.h ..
+  cp atom_vec_full.h ..
   cp atom_vec_molecular.h ..
 #  cp bond.h ..
   cp bond_fene.h ..
@@ -84,6 +86,7 @@ else if ($1 == 0) then
   rm ../angle_hybrid.cpp
   rm ../atom_vec_angle.cpp
   rm ../atom_vec_bond.cpp
+  rm ../atom_vec_full.cpp
   rm ../atom_vec_molecular.cpp
   rm ../bond.cpp
   rm ../bond_fene.cpp
@@ -116,6 +119,7 @@ else if ($1 == 0) then
   rm ../angle_hybrid.h
   rm ../atom_vec_angle.h
   rm ../atom_vec_bond.h
+  rm ../atom_vec_full.h
   rm ../atom_vec_molecular.h
 #  rm ../bond.h
   rm ../bond_fene.h

src/MOLECULE/atom_vec_molecular.cpp

@@ -40,10 +40,10 @@ AtomVecMolecular::AtomVecMolecular(LAMMPS *lmp, int narg, char **arg) :
   mass_type = 1;
   size_comm = 3;
   size_reverse = 3;
-  size_border = 8;
-  size_data_atom = 7;
+  size_border = 7;
+  size_data_atom = 6;
   size_data_vel = 4;
-  xcol_data = 5;
+  xcol_data = 4;
 }
 
 /* ----------------------------------------------------------------------
@@ -70,8 +70,6 @@ void AtomVecMolecular::grow(int n)
   v = atom->v = memory->grow_2d_double_array(atom->v,nmax,3,"atom:v");
   f = atom->f = memory->grow_2d_double_array(atom->f,nmax,3,"atom:f");
 
-  q = atom->q = (double *) 
-    memory->srealloc(atom->q,nmax*sizeof(double),"atom:q");
   molecule = atom->molecule = (int *) 
     memory->srealloc(atom->molecule,nmax*sizeof(int),"atom:molecule");
 
@@ -158,7 +156,6 @@ void AtomVecMolecular::reset_ptrs()
   v = atom->v;
   f = atom->f;
 
-  q = atom->q;
   molecule = atom->molecule;
   nspecial = atom->nspecial;
   special = atom->special;
@@ -195,7 +192,6 @@ void AtomVecMolecular::reset_ptrs()
 
 void AtomVecMolecular::zero_owned(int i)
 {
-  q[i] = 0.0;
   molecule[i] = 0;
   num_bond[i] = 0;
   num_angle[i] = 0;
@@ -217,7 +213,6 @@ void AtomVecMolecular::zero_ghost(int n, int first)
   int last = first + n;
   for (int i = first; i < last; i++) {
     if (i == nmax) atom->avec->grow(0);
-    q[i] = 0.0;
     molecule[i] = 0;
   }
 }
@@ -239,7 +234,6 @@ void AtomVecMolecular::copy(int i, int j)
   v[j][1] = v[i][1];
   v[j][2] = v[i][2];
 
-  q[j] = q[i];
   molecule[j] = molecule[i];
 
   num_bond[j] = num_bond[i];
@@ -375,7 +369,6 @@ int AtomVecMolecular::pack_border(int n, int *list, double *buf,
       buf[m++] = tag[j];
       buf[m++] = type[j];
       buf[m++] = mask[j];
-      buf[m++] = q[j];
       buf[m++] = molecule[j];
     }
   } else {
@@ -390,7 +383,6 @@ int AtomVecMolecular::pack_border(int n, int *list, double *buf,
       buf[m++] = tag[j];
       buf[m++] = type[j];
       buf[m++] = mask[j];
-      buf[m++] = q[j];
       buf[m++] = molecule[j];
     }
   }
@@ -401,7 +393,6 @@ int AtomVecMolecular::pack_border(int n, int *list, double *buf,
 
 int AtomVecMolecular::pack_border_one(int i, double *buf)
 {
-  buf[0] = q[i];
   buf[1] = molecule[i];
   return 2;
 }
@@ -422,7 +413,6 @@ void AtomVecMolecular::unpack_border(int n, int first, double *buf)
     tag[i] = static_cast<int> (buf[m++]);
     type[i] = static_cast<int> (buf[m++]);
     mask[i] = static_cast<int> (buf[m++]);
-    q[i] = buf[m++];
     molecule[i] = static_cast<int> (buf[m++]);
   }
 }
@@ -431,7 +421,6 @@ void AtomVecMolecular::unpack_border(int n, int first, double *buf)
 
 int AtomVecMolecular::unpack_border_one(int i, double *buf)
 {
-  q[i] = buf[0];
   molecule[i] = static_cast<int> (buf[1]);
   return 2;
 }
@@ -457,7 +446,6 @@ int AtomVecMolecular::pack_exchange(int i, double *buf)
   buf[m++] = mask[i];
   buf[m++] = image[i];
 
-  buf[m++] = q[i];
   buf[m++] = molecule[i];
 
   buf[m++] = num_bond[i];
@@ -526,7 +514,6 @@ int AtomVecMolecular::unpack_exchange(double *buf)
   mask[nlocal] = static_cast<int> (buf[m++]);
   image[nlocal] = static_cast<int> (buf[m++]);
 
-  q[nlocal] = buf[m++];
   molecule[nlocal] = static_cast<int> (buf[m++]);
 
   num_bond[nlocal] = static_cast<int> (buf[m++]);
@@ -633,7 +620,6 @@ int AtomVecMolecular::pack_restart(int i, double *buf)
   buf[m++] = v[i][1];
   buf[m++] = v[i][2];
 
-  buf[m++] = q[i];
   buf[m++] = molecule[i];
  
   buf[m++] = num_bond[i];
@@ -705,7 +691,6 @@ int AtomVecMolecular::unpack_restart(double *buf)
   v[nlocal][1] = buf[m++];
   v[nlocal][2] = buf[m++];
 
-  q[nlocal] = buf[m++];
   molecule[nlocal] = static_cast<int> (buf[m++]);
     
   num_bond[nlocal] = static_cast<int> (buf[m++]);
@@ -772,7 +757,6 @@ void AtomVecMolecular::create_atom(int itype, double x0, double y0, double z0,
   v[nlocal][1] = 0.0;
   v[nlocal][2] = 0.0;
 
-  q[nlocal] = 0.0;
   molecule[nlocal] = 0;
   num_bond[nlocal] = 0;
   num_angle[nlocal] = 0;
@@ -803,8 +787,6 @@ void AtomVecMolecular::data_atom(double xtmp, double ytmp, double ztmp,
   if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes)
     error->one("Invalid atom type in Atoms section of data file");
 
-  q[nlocal] = atof(values[3]);
-
   x[nlocal][0] = xtmp;
   x[nlocal][1] = ytmp;
   x[nlocal][2] = ztmp;

src/MOLECULE/atom_vec_molecular.h

@@ -47,7 +47,6 @@ class AtomVecMolecular : public AtomVec {
  private:
   int *tag,*type,*mask,*image;
   double **x,**v,**f;
-  double *q;
   int *molecule;
   int **nspecial,**special;
   int *num_bond;

src/MOLECULE/style_molecule.h

@@ -30,12 +30,14 @@ AngleStyle(hybrid,AngleHybrid)
 #ifdef AtomInclude
 #include "atom_vec_angle.h"
 #include "atom_vec_bond.h"
+#include "atom_vec_full.h"
 #include "atom_vec_molecular.h"
 #endif
 
 #ifdef AtomClass
 AtomStyle(angle,AtomVecAngle)
 AtomStyle(bond,AtomVecBond)
+AtomStyle(full,AtomVecFull)
 AtomStyle(molecular,AtomVecMolecular)
 #endif
 

src/dump_custom.cpp

@@ -561,6 +561,7 @@ void DumpCustom::parse_fields(int narg, char **arg)
     } else if (strcmp(arg[iarg],"type") == 0) {
       pack_choice[i] = &DumpCustom::pack_type;
       vtype[i] = INT;
+
     } else if (strcmp(arg[iarg],"x") == 0) {
       pack_choice[i] = &DumpCustom::pack_x;
       vtype[i] = DOUBLE;
@@ -597,6 +598,7 @@ void DumpCustom::parse_fields(int narg, char **arg)
     } else if (strcmp(arg[iarg],"iz") == 0) {
       pack_choice[i] = &DumpCustom::pack_iz;
       vtype[i] = INT;
+
     } else if (strcmp(arg[iarg],"vx") == 0) {
       pack_choice[i] = &DumpCustom::pack_vx;
       vtype[i] = DOUBLE;
@@ -615,6 +617,7 @@ void DumpCustom::parse_fields(int narg, char **arg)
     } else if (strcmp(arg[iarg],"fz") == 0) {
       pack_choice[i] = &DumpCustom::pack_fz;
       vtype[i] = DOUBLE;
+
     } else if (strcmp(arg[iarg],"q") == 0) {
       if (atom->q == NULL)
 	error->all("Dumping an atom quantity that isn't allocated");
@@ -650,6 +653,7 @@ void DumpCustom::parse_fields(int narg, char **arg)
 	error->all("Dumping an atom quantity that isn't allocated");
       pack_choice[i] = &DumpCustom::pack_tqz;
       vtype[i] = DOUBLE;
+
     } else if (strcmp(arg[iarg],"epair") == 0) {
       pack_choice[i] = &DumpCustom::pack_epair;
       vtype[i] = DOUBLE;
@@ -667,6 +671,7 @@ void DumpCustom::parse_fields(int narg, char **arg)
       pack_choice[i] = &DumpCustom::pack_centro;
       vtype[i] = DOUBLE;
       index_centro = add_compute(style_centro,1);
+
     } else if (strcmp(arg[iarg],"sxx") == 0) {
       pack_choice[i] = &DumpCustom::pack_sxx;
       vtype[i] = DOUBLE;

src/style_molecule.h

@@ -30,12 +30,14 @@ AngleStyle(hybrid,AngleHybrid)
 #ifdef AtomInclude
 #include "atom_vec_angle.h"
 #include "atom_vec_bond.h"
+#include "atom_vec_full.h"
 #include "atom_vec_molecular.h"
 #endif
 
 #ifdef AtomClass
 AtomStyle(angle,AtomVecAngle)
 AtomStyle(bond,AtomVecBond)
+AtomStyle(full,AtomVecFull)
 AtomStyle(molecular,AtomVecMolecular)
 #endif
 

src/thermo.cpp

@@ -41,7 +41,8 @@ using namespace LAMMPS_NS;
 
 // step, atoms, cpu, temp, press, pe, ke, etotal, enthalpy
 // evdwl, ecoul, epair, ebond, eangle, edihed, eimp, emol, elong, etail
-// vol, lx, ly, lz, pxx, pyy, pzz, pxy, pxz, pyz
+// vol, lx, ly, lz, xlo, xhi, ylo, yhi, zlo, zhi
+// pxx, pyy, pzz, pxy, pxz, pyz
 // drot, grot (rotational KE for dipole and granular particles)
 // tave, pave, eave, peave (time-averaged quantities)
 
@@ -660,6 +661,7 @@ void Thermo::parse_fields(char *str)
       addfield("Atoms",&Thermo::compute_atoms,INT);
     } else if (strcmp(word,"cpu") == 0) {
       addfield("CPU",&Thermo::compute_cpu,FLOAT);
+
     } else if (strcmp(word,"temp") == 0) {
       addfield("Temp",&Thermo::compute_temp,FLOAT);
       index_temp = add_compute(id_temp,0);
@@ -681,6 +683,7 @@ void Thermo::parse_fields(char *str)
       addfield("Enthalpy",&Thermo::compute_enthalpy,FLOAT);
       index_temp = add_compute(id_temp,0);
       index_press = add_compute(id_press,0);
+
     } else if (strcmp(word,"evdwl") == 0) {
       addfield("E_vdwl",&Thermo::compute_evdwl,FLOAT);
     } else if (strcmp(word,"ecoul") == 0) {
@@ -701,6 +704,7 @@ void Thermo::parse_fields(char *str)
       addfield("E_long",&Thermo::compute_elong,FLOAT);
     } else if (strcmp(word,"etail") == 0) {
       addfield("E_tail",&Thermo::compute_etail,FLOAT);
+
     } else if (strcmp(word,"vol") == 0) {
       addfield("Volume",&Thermo::compute_vol,FLOAT);
     } else if (strcmp(word,"lx") == 0) {
@@ -709,6 +713,20 @@ void Thermo::parse_fields(char *str)
       addfield("Ly",&Thermo::compute_ly,FLOAT);
     } else if (strcmp(word,"lz") == 0) {
       addfield("Lz",&Thermo::compute_lz,FLOAT);
+
+    } else if (strcmp(word,"xlo") == 0) {
+      addfield("Xlo",&Thermo::compute_xlo,FLOAT);
+    } else if (strcmp(word,"xhi") == 0) {
+      addfield("Xhi",&Thermo::compute_xhi,FLOAT);
+    } else if (strcmp(word,"ylo") == 0) {
+      addfield("Ylo",&Thermo::compute_ylo,FLOAT);
+    } else if (strcmp(word,"yhi") == 0) {
+      addfield("Yhi",&Thermo::compute_yhi,FLOAT);
+    } else if (strcmp(word,"zlo") == 0) {
+      addfield("Zlo",&Thermo::compute_zlo,FLOAT);
+    } else if (strcmp(word,"zhi") == 0) {
+      addfield("Zhi",&Thermo::compute_zhi,FLOAT);
+
     } else if (strcmp(word,"pxx") == 0) {
       addfield("Pxx",&Thermo::compute_pxx,FLOAT);
       index_temp = add_compute(id_temp,1);
@@ -733,12 +751,14 @@ void Thermo::parse_fields(char *str)
       addfield("Pyz",&Thermo::compute_pyz,FLOAT);
       index_temp = add_compute(id_temp,1);
       index_press = add_compute(id_press,1);
+
     } else if (strcmp(word,"drot") == 0) {
       addfield("RotKEdip",&Thermo::compute_drot,FLOAT);
       index_drot = add_compute(id_drot,0);
     } else if (strcmp(word,"grot") == 0) {
       addfield("RotKEgrn",&Thermo::compute_grot,FLOAT);
       index_grot = add_compute(id_grot,0);
+
     } else if (strcmp(word,"tave") == 0) {
       addfield("T_ave",&Thermo::compute_tave,FLOAT);
       index_temp = add_compute(id_temp,0);
@@ -934,12 +954,14 @@ int Thermo::evaluate_keyword(char *word, double *answer)
     dvalue = ivalue;
   }
   else if (strcmp(word,"cpu") == 0) compute_cpu();
+
   else if (strcmp(word,"temp") == 0) compute_temp();
   else if (strcmp(word,"press") == 0) compute_press();
   else if (strcmp(word,"pe") == 0) compute_pe();
   else if (strcmp(word,"ke") == 0) compute_ke();
   else if (strcmp(word,"etotal") == 0) compute_etotal();
   else if (strcmp(word,"enthalpy") == 0) compute_enthalpy();
+
   else if (strcmp(word,"evdwl") == 0) compute_evdwl();
   else if (strcmp(word,"ecoul") == 0) compute_ecoul();
   else if (strcmp(word,"epair") == 0) compute_epair();
@@ -950,18 +972,29 @@ int Thermo::evaluate_keyword(char *word, double *answer)
   else if (strcmp(word,"emol") == 0) compute_emol();
   else if (strcmp(word,"elong") == 0) compute_elong();
   else if (strcmp(word,"etail") == 0) compute_etail();
+
   else if (strcmp(word,"vol") == 0) compute_vol();
   else if (strcmp(word,"lx") == 0) compute_lx();
   else if (strcmp(word,"ly") == 0) compute_ly();
   else if (strcmp(word,"lz") == 0) compute_lz();
+
+  else if (strcmp(word,"xlo") == 0) compute_xlo();
+  else if (strcmp(word,"xhi") == 0) compute_xhi();
+  else if (strcmp(word,"ylo") == 0) compute_ylo();
+  else if (strcmp(word,"yhi") == 0) compute_yhi();
+  else if (strcmp(word,"zlo") == 0) compute_zlo();
+  else if (strcmp(word,"zhi") == 0) compute_zhi();
+
   else if (strcmp(word,"pxx") == 0) compute_pxx();
   else if (strcmp(word,"pyy") == 0) compute_pyy();
   else if (strcmp(word,"pzz") == 0) compute_pzz();
   else if (strcmp(word,"pxy") == 0) compute_pxy();
   else if (strcmp(word,"pxz") == 0) compute_pxz();
   else if (strcmp(word,"pyz") == 0) compute_pyz();
+
   else if (strcmp(word,"drot") == 0) compute_drot();
   else if (strcmp(word,"grot") == 0) compute_grot();
+
   else if (strcmp(word,"tave") == 0) compute_tave();
   else if (strcmp(word,"pave") == 0) compute_pave();
   else if (strcmp(word,"eave") == 0) compute_eave();
@@ -1291,6 +1324,48 @@ void Thermo::compute_lz()
 
 /* ---------------------------------------------------------------------- */
 
+void Thermo::compute_xlo()
+{
+  dvalue = domain->boxxlo;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void Thermo::compute_xhi()
+{
+  dvalue = domain->boxxhi;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void Thermo::compute_ylo()
+{
+  dvalue = domain->boxylo;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void Thermo::compute_yhi()
+{
+  dvalue = domain->boxyhi;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void Thermo::compute_zlo()
+{
+  dvalue = domain->boxzlo;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void Thermo::compute_zhi()
+{
+  dvalue = domain->boxzhi;
+}
+
+/* ---------------------------------------------------------------------- */
+
 void Thermo::compute_pxx()
 {
   if (!thermoflag) {

src/thermo.h

@@ -119,12 +119,14 @@ class Thermo : protected Pointers {
   void compute_step();    
   void compute_atoms();
   void compute_cpu();
+
   void compute_temp();
   void compute_press();
   void compute_pe();
   void compute_ke();
   void compute_etotal();
   void compute_enthalpy();
+
   void compute_evdwl();
   void compute_ecoul();
   void compute_epair();
@@ -135,18 +137,29 @@ class Thermo : protected Pointers {
   void compute_emol();
   void compute_elong();
   void compute_etail();
+
   void compute_vol();
   void compute_lx();
   void compute_ly();
   void compute_lz();
+
+  void compute_xlo();
+  void compute_xhi();
+  void compute_ylo();
+  void compute_yhi();
+  void compute_zlo();
+  void compute_zhi();
+
   void compute_pxx();
   void compute_pyy();
   void compute_pzz();
   void compute_pxy();
   void compute_pyz();
   void compute_pxz();
+
   void compute_drot();
   void compute_grot();
+
   void compute_tave();
   void compute_pave();
   void compute_eave();