From ee74e0f713d116cb46fc958e3e5e65e6ff7fd2af Mon Sep 17 00:00:00 2001 From: sjplimp Date: Wed, 13 Jun 2012 15:43:58 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8271 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- src/compute_gyration.cpp | 70 +++++++++++- src/compute_gyration.h | 3 +- src/compute_gyration_molecule.cpp | 174 ++++++++++++++++++++++++------ src/compute_gyration_molecule.h | 7 +- 4 files changed, 219 insertions(+), 35 deletions(-) diff --git a/src/compute_gyration.cpp b/src/compute_gyration.cpp index 6eb38b059c..8c4c7d0305 100644 --- a/src/compute_gyration.cpp +++ b/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); +} diff --git a/src/compute_gyration.h b/src/compute_gyration.h index fec374ea98..32d79ef263 100644 --- a/src/compute_gyration.h +++ b/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; diff --git a/src/compute_gyration_molecule.cpp b/src/compute_gyration_molecule.cpp index cb1b2c33f5..df107e8303 100644 --- a/src/compute_gyration_molecule.cpp +++ b/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); } /* ---------------------------------------------------------------------- */ @@ -106,6 +128,114 @@ void ComputeGyrationMolecule::compute_vector() invoked_array = update->ntimestep; + molcom(); + + for (i = 0; i < nmolecules; i++) rg[i] = 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; + imol = molecule[i]; + if (molmap) imol = molmap[imol-idlo]; + else imol--; + 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(rg,vector,nmolecules,MPI_DOUBLE,MPI_SUM,world); + + 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 (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; + imol = molecule[i]; + if (molmap) imol = molmap[imol-idlo]; + else imol--; + 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]]; + 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; + } + + 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; @@ -122,7 +252,7 @@ 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; @@ -144,28 +274,6 @@ void ComputeGyrationMolecule::compute_vector() comall[i][1] /= masstotal[i]; comall[i][2] /= masstotal[i]; } - - for (i = 0; i < nmolecules; i++) rg[i] = 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; - imol = molecule[i]; - if (molmap) imol = molmap[imol-idlo]; - else imol--; - 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(rg,rgall,nmolecules,MPI_DOUBLE,MPI_SUM,world); - - for (i = 0; i < nmolecules; i++) rgall[i] = sqrt(rgall[i]/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; } diff --git a/src/compute_gyration_molecule.h b/src/compute_gyration_molecule.h index 8c30321d89..99910782fa 100644 --- a/src/compute_gyration_molecule.h +++ b/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(); }; }