git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8271 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/compute_gyration.cpp

@@ -11,9 +11,12 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
+#include "math.h"
 #include "compute_gyration.h"
 #include "update.h"
+#include "atom.h"
 #include "group.h"
+#include "domain.h"
 #include "error.h"
 
 using namespace LAMMPS_NS;
@@ -25,8 +28,19 @@ ComputeGyration::ComputeGyration(LAMMPS *lmp, int narg, char **arg) :
 {
   if (narg != 3) error->all(FLERR,"Illegal compute gyration command");
 
-  scalar_flag = 1;
+  scalar_flag = vector_flag = 1;
+  size_vector = 6;
   extscalar = 0;
+  extvector = 0;
+
+  vector = new double[6];
+}
+
+/* ---------------------------------------------------------------------- */
+
+ComputeGyration::~ComputeGyration()
+{
+  delete [] vector;
 }
 
 /* ---------------------------------------------------------------------- */
@@ -47,3 +61,57 @@ double ComputeGyration::compute_scalar()
   scalar = group->gyration(igroup,masstotal,xcm);
   return scalar;
 }
+
+/* ----------------------------------------------------------------------
+   compute the radius-of-gyration tensor of group of atoms
+   around center-of-mass cm
+   must unwrap atoms to compute Rg tensor correctly
+------------------------------------------------------------------------- */
+
+void ComputeGyration::compute_vector()
+{
+  invoked_vector = update->ntimestep;
+
+  double masstotal;
+  double xcm[3];
+  group->xcm(igroup,masstotal,xcm);
+
+  double **x = atom->x;
+  int *mask = atom->mask;
+  int *type = atom->type;
+  int *image = atom->image;
+  double *mass = atom->mass;
+  double *rmass = atom->rmass;
+  int nlocal = atom->nlocal;
+
+  int xbox,ybox,zbox;
+  double dx,dy,dz,massone;
+  double xprd = domain->xprd;
+  double yprd = domain->yprd;
+  double zprd = domain->zprd;
+  
+  double rg[6];
+  rg[0] = rg[1] = rg[2] = rg[3] = rg[4] = rg[5] = 0.0;
+
+  for (int i = 0; i < nlocal; i++)
+    if (mask[i] & groupbit) {
+      xbox = (image[i] & 1023) - 512;
+      ybox = (image[i] >> 10 & 1023) - 512;
+      zbox = (image[i] >> 20) - 512;
+      dx = (x[i][0] + xbox*xprd) - xcm[0];
+      dy = (x[i][1] + ybox*yprd) - xcm[1];
+      dz = (x[i][2] + zbox*zprd) - xcm[2];
+      if (rmass) massone = rmass[i];
+      else massone = mass[type[i]];
+      rg[0] += dx*dx * massone;
+      rg[1] += dy*dy * massone;
+      rg[2] += dz*dz * massone;
+      rg[3] += dx*dy * massone;
+      rg[4] += dx*dz * massone;
+      rg[5] += dy*dz * massone;
+    }
+  MPI_Allreduce(rg,vector,6,MPI_DOUBLE,MPI_SUM,world);
+
+  if (masstotal == 0.0) return;
+  for (int i = 0; i < 6; i++) vector[i] = sqrt(vector[i]/masstotal);
+}

src/compute_gyration.h

@@ -27,9 +27,10 @@ namespace LAMMPS_NS {
 class ComputeGyration : public Compute {
  public:
   ComputeGyration(class LAMMPS *, int, char **);
-  ~ComputeGyration() {}
+  ~ComputeGyration();
   void init();
   double compute_scalar();
+  void compute_vector();
 
  private:
   double masstotal;

src/compute_gyration_molecule.cpp

@@ -12,6 +12,7 @@
 ------------------------------------------------------------------------- */
 
 #include "math.h"
+#include "string.h"
 #include "compute_gyration_molecule.h"
 #include "atom.h"
 #include "update.h"
@@ -27,26 +28,47 @@ ComputeGyrationMolecule::ComputeGyrationMolecule(LAMMPS *lmp,
                                                  int narg, char **arg) :
   Compute(lmp, narg, arg)
 {
-  if (narg != 3) error->all(FLERR,"Illegal compute gyration/molecule command");
+  if (narg < 3) error->all(FLERR,"Illegal compute gyration/molecule command");
 
   if (atom->molecular == 0)
     error->all(FLERR,"Compute gyration/molecule requires molecular atom style");
 
-  vector_flag = 1;
-  extvector = 0;
+  tensor = 0;
+
+  int iarg = 3;
+  while (iarg < narg) {
+    if (strcmp(arg[iarg],"tensor") == 0) {
+      tensor = 1;
+      iarg++;
+    } else error->all(FLERR,"Illegal compute gyration/molecule command");
+  }
 
   // setup molecule-based data
 
   nmolecules = molecules_in_group(idlo,idhi);
-  size_vector = nmolecules;
 
   memory->create(massproc,nmolecules,"gyration/molecule:massproc");
   memory->create(masstotal,nmolecules,"gyration/molecule:masstotal");
   memory->create(com,nmolecules,3,"gyration/molecule:com");
   memory->create(comall,nmolecules,3,"gyration/molecule:comall");
-  memory->create(rg,nmolecules,"gyration/molecule:rg");
-  memory->create(rgall,nmolecules,"gyration/molecule:rgall");
-  vector = rgall;
+
+  rg = vector = NULL;
+  rgt = array = NULL;
+
+  if (tensor) {
+    memory->create(rgt,nmolecules,6,"gyration/molecule:rgt");
+    memory->create(array,nmolecules,6,"gyration/molecule:array");
+    array_flag = 1;
+    size_array_rows = nmolecules;
+    size_array_cols = 6;
+    extarray = 0;
+  } else {
+    memory->create(rg,nmolecules,"gyration/molecule:rg");
+    memory->create(vector,nmolecules,"gyration/molecule:vector");
+    vector_flag = 1;
+    size_vector = nmolecules;
+    extvector = 0;
+  }
 
   // compute masstotal for each molecule
 
@@ -84,7 +106,7 @@ ComputeGyrationMolecule::~ComputeGyrationMolecule()
   memory->destroy(com);
   memory->destroy(comall);
   memory->destroy(rg);
-  memory->destroy(rgall);
+  memory->destroy(rgt);
 }
 
 /* ---------------------------------------------------------------------- */
@@ -106,8 +128,9 @@ void ComputeGyrationMolecule::compute_vector()
 
   invoked_array = update->ntimestep;
 
-  for (i = 0; i < nmolecules; i++)
-    com[i][0] = com[i][1] = com[i][2] = 0.0;
+  molcom();
+
+  for (i = 0; i < nmolecules; i++) rg[i] = 0.0;
 
   double **x = atom->x;
   int *mask = atom->mask;
@@ -122,32 +145,57 @@ void ComputeGyrationMolecule::compute_vector()
   double yprd = domain->yprd;
   double zprd = domain->zprd;
 
-  for (int i = 0; i < nlocal; i++)
+  for (i = 0; i < nlocal; i++)
     if (mask[i] & groupbit) {
       xbox = (image[i] & 1023) - 512;
       ybox = (image[i] >> 10 & 1023) - 512;
       zbox = (image[i] >> 20) - 512;
-      if (rmass) massone = rmass[i];
-      else massone = mass[type[i]];
       imol = molecule[i];
       if (molmap) imol = molmap[imol-idlo];
       else imol--;
-      com[imol][0] += (x[i][0] + xbox*xprd) * massone;
-      com[imol][1] += (x[i][1] + ybox*yprd) * massone;
-      com[imol][2] += (x[i][2] + zbox*zprd) * massone;
+      dx = (x[i][0] + xbox*xprd) - comall[imol][0];
+      dy = (x[i][1] + ybox*yprd) - comall[imol][1];
+      dz = (x[i][2] + zbox*zprd) - comall[imol][2];
+      if (rmass) massone = rmass[i];
+      else massone = mass[type[i]];
+      rg[imol] += (dx*dx + dy*dy + dz*dz) * massone;
     }
 
-  MPI_Allreduce(&com[0][0],&comall[0][0],3*nmolecules,
-                MPI_DOUBLE,MPI_SUM,world);
-  for (i = 0; i < nmolecules; i++) {
-    comall[i][0] /= masstotal[i];
-    comall[i][1] /= masstotal[i];
-    comall[i][2] /= masstotal[i];
-  }
+  MPI_Allreduce(rg,vector,nmolecules,MPI_DOUBLE,MPI_SUM,world);
 
-  for (i = 0; i < nmolecules; i++) rg[i] = 0.0;
+  for (i = 0; i < nmolecules; i++) vector[i] = sqrt(vector[i]/masstotal[i]);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputeGyrationMolecule::compute_array()
+{
+  int i,j,imol;
+  double xbox,ybox,zbox,dx,dy,dz;
+  double massone;
+
+  invoked_array = update->ntimestep;
+
+  molcom();
+
+  for (i = 0; i < nmolecules; i++)
+    for (j = 0; j < 6; j++) 
+      rgt[i][j] = 0.0;
+
+  double **x = atom->x;
+  int *mask = atom->mask;
+  int *molecule = atom->molecule;
+  int *type = atom->type;
+  int *image = atom->image;
+  double *mass = atom->mass;
+  double *rmass = atom->rmass;
+  int nlocal = atom->nlocal;
+
+  double xprd = domain->xprd;
+  double yprd = domain->yprd;
+  double zprd = domain->zprd;
 
-  for (int i = 0; i < nlocal; i++)
+  for (i = 0; i < nlocal; i++)
     if (mask[i] & groupbit) {
       xbox = (image[i] & 1023) - 512;
       ybox = (image[i] >> 10 & 1023) - 512;
@@ -160,12 +208,72 @@ void ComputeGyrationMolecule::compute_vector()
       dz = (x[i][2] + zbox*zprd) - comall[imol][2];
       if (rmass) massone = rmass[i];
       else massone = mass[type[i]];
-      rg[imol] += (dx*dx + dy*dy + dz*dz) * massone;
+      rgt[imol][0] += dx*dx * massone;
+      rgt[imol][1] += dy*dy * massone;
+      rgt[imol][2] += dz*dz * massone;
+      rgt[imol][3] += dx*dy * massone;
+      rgt[imol][4] += dx*dz * massone;
+      rgt[imol][5] += dy*dz * massone;
     }
 
-  MPI_Allreduce(rg,rgall,nmolecules,MPI_DOUBLE,MPI_SUM,world);
+  if (nmolecules)
+    MPI_Allreduce(&rgt[0][0],&array[0][0],nmolecules*6,
+                  MPI_DOUBLE,MPI_SUM,world);
+
+  for (i = 0; i < nmolecules; i++) 
+    for (j = 0; j < 6; j++) 
+      array[i][j] = sqrt(array[i][j]/masstotal[i]);
+}
+
+
+/* ----------------------------------------------------------------------
+   calculate per-molecule COM
+------------------------------------------------------------------------- */
+
+void ComputeGyrationMolecule::molcom()
+{
+  int i,imol;
+  double xbox,ybox,zbox,dx,dy,dz;
+  double massone;
+
+  for (i = 0; i < nmolecules; i++)
+    com[i][0] = com[i][1] = com[i][2] = 0.0;
+
+  double **x = atom->x;
+  int *mask = atom->mask;
+  int *molecule = atom->molecule;
+  int *type = atom->type;
+  int *image = atom->image;
+  double *mass = atom->mass;
+  double *rmass = atom->rmass;
+  int nlocal = atom->nlocal;
+
+  double xprd = domain->xprd;
+  double yprd = domain->yprd;
+  double zprd = domain->zprd;
+
+  for (i = 0; i < nlocal; i++)
+    if (mask[i] & groupbit) {
+      xbox = (image[i] & 1023) - 512;
+      ybox = (image[i] >> 10 & 1023) - 512;
+      zbox = (image[i] >> 20) - 512;
+      if (rmass) massone = rmass[i];
+      else massone = mass[type[i]];
+      imol = molecule[i];
+      if (molmap) imol = molmap[imol-idlo];
+      else imol--;
+      com[imol][0] += (x[i][0] + xbox*xprd) * massone;
+      com[imol][1] += (x[i][1] + ybox*yprd) * massone;
+      com[imol][2] += (x[i][2] + zbox*zprd) * massone;
+    }
 
-  for (i = 0; i < nmolecules; i++) rgall[i] = sqrt(rgall[i]/masstotal[i]);
+  MPI_Allreduce(&com[0][0],&comall[0][0],3*nmolecules,
+                MPI_DOUBLE,MPI_SUM,world);
+  for (i = 0; i < nmolecules; i++) {
+    comall[i][0] /= masstotal[i];
+    comall[i][1] /= masstotal[i];
+    comall[i][2] /= masstotal[i];
+  }
 }
 
 /* ----------------------------------------------------------------------
@@ -174,8 +282,10 @@ void ComputeGyrationMolecule::compute_vector()
 
 double ComputeGyrationMolecule::memory_usage()
 {
-  double bytes = 4*nmolecules * sizeof(double);
+  double bytes = 2*nmolecules * sizeof(double);
   if (molmap) bytes += (idhi-idlo+1) * sizeof(int);
   bytes += 2*nmolecules*3 * sizeof(double);
+  if (tensor) bytes += 2*6*nmolecules * sizeof(double);
+  else bytes += 2*nmolecules * sizeof(double);
   return bytes;
 }

src/compute_gyration_molecule.h

@@ -30,15 +30,20 @@ class ComputeGyrationMolecule : public Compute {
   ~ComputeGyrationMolecule();
   void init();
   void compute_vector();
+  void compute_array();
   double memory_usage();
 
  private:
+  int tensor;
   int nmolecules;
   int idlo,idhi;
 
   double *massproc,*masstotal;
   double **com,**comall;
-  double *rg,*rgall;
+  double *rg;
+  double **rgt;
+
+  void molcom();
 };
 
 }