forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9006 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
parent
cb9d45386c
commit
6f4bba7edf
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@ -96,8 +96,8 @@ void ComputeCOMMolecule::init()
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void ComputeCOMMolecule::compute_array()
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{
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int i,imol;
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double xbox,ybox,zbox;
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double massone;
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double unwrap[3];
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invoked_array = update->ntimestep;
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@ -113,23 +113,17 @@ void ComputeCOMMolecule::compute_array()
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double *rmass = atom->rmass;
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int nlocal = atom->nlocal;
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double xprd = domain->xprd;
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double yprd = domain->yprd;
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double zprd = domain->zprd;
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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xbox = (image[i] & IMGMASK) - IMGMAX;
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ybox = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
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zbox = (image[i] >> IMG2BITS) - IMGMAX;
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if (rmass) massone = rmass[i];
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else massone = mass[type[i]];
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imol = molecule[i];
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if (molmap) imol = molmap[imol-idlo];
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else imol--;
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com[imol][0] += (x[i][0] + xbox*xprd) * massone;
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com[imol][1] += (x[i][1] + ybox*yprd) * massone;
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com[imol][2] += (x[i][2] + zbox*zprd) * massone;
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domain->unmap(x[i],image[i],unwrap);
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com[imol][0] += unwrap[0] * massone;
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com[imol][1] += unwrap[1] * massone;
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com[imol][2] += unwrap[2] * massone;
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}
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MPI_Allreduce(&com[0][0],&comall[0][0],3*nmolecules,
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@ -83,25 +83,22 @@ void ComputeGyration::compute_vector()
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double *rmass = atom->rmass;
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int nlocal = atom->nlocal;
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int xbox,ybox,zbox;
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double dx,dy,dz,massone;
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double xprd = domain->xprd;
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double yprd = domain->yprd;
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double zprd = domain->zprd;
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double unwrap[3];
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double rg[6];
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rg[0] = rg[1] = rg[2] = rg[3] = rg[4] = rg[5] = 0.0;
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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xbox = (image[i] & IMGMASK) - IMGMAX;
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ybox = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
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zbox = (image[i] >> IMG2BITS) - IMGMAX;
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dx = (x[i][0] + xbox*xprd) - xcm[0];
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dy = (x[i][1] + ybox*yprd) - xcm[1];
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dz = (x[i][2] + zbox*zprd) - xcm[2];
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if (rmass) massone = rmass[i];
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else massone = mass[type[i]];
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domain->unmap(x[i],image[i],unwrap);
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dx = unwrap[0] - xcm[0];
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dy = unwrap[1] - xcm[1];
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dz = unwrap[2] - xcm[2];
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rg[0] += dx*dx * massone;
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rg[1] += dy*dy * massone;
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rg[2] += dz*dz * massone;
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@ -123,8 +123,8 @@ void ComputeGyrationMolecule::init()
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void ComputeGyrationMolecule::compute_vector()
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{
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int i,imol;
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double xbox,ybox,zbox,dx,dy,dz;
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double massone;
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double dx,dy,dz,massone;
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double unwrap[3];
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invoked_array = update->ntimestep;
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@ -141,21 +141,16 @@ void ComputeGyrationMolecule::compute_vector()
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double *rmass = atom->rmass;
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int nlocal = atom->nlocal;
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double xprd = domain->xprd;
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double yprd = domain->yprd;
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double zprd = domain->zprd;
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for (i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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xbox = (image[i] & IMGMASK) - IMGMAX;
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ybox = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
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zbox = (image[i] >> IMG2BITS) - IMGMAX;
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imol = molecule[i];
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if (molmap) imol = molmap[imol-idlo];
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else imol--;
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dx = (x[i][0] + xbox*xprd) - comall[imol][0];
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dy = (x[i][1] + ybox*yprd) - comall[imol][1];
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dz = (x[i][2] + zbox*zprd) - comall[imol][2];
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domain->unmap(x[i],image[i],unwrap);
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dx = unwrap[0] - comall[imol][0];
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dy = unwrap[1] - comall[imol][1];
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dz = unwrap[2] - comall[imol][2];
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if (rmass) massone = rmass[i];
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else massone = mass[type[i]];
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rg[imol] += (dx*dx + dy*dy + dz*dz) * massone;
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@ -171,8 +166,8 @@ void ComputeGyrationMolecule::compute_vector()
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void ComputeGyrationMolecule::compute_array()
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{
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int i,j,imol;
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double xbox,ybox,zbox,dx,dy,dz;
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double massone;
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double dx,dy,dz,massone;
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double unwrap[3];
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invoked_array = update->ntimestep;
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@ -191,21 +186,15 @@ void ComputeGyrationMolecule::compute_array()
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double *rmass = atom->rmass;
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int nlocal = atom->nlocal;
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double xprd = domain->xprd;
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double yprd = domain->yprd;
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double zprd = domain->zprd;
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for (i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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xbox = (image[i] & IMGMASK) - IMGMAX;
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ybox = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
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zbox = (image[i] >> IMG2BITS) - IMGMAX;
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imol = molecule[i];
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if (molmap) imol = molmap[imol-idlo];
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else imol--;
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dx = (x[i][0] + xbox*xprd) - comall[imol][0];
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dy = (x[i][1] + ybox*yprd) - comall[imol][1];
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dz = (x[i][2] + zbox*zprd) - comall[imol][2];
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domain->unmap(x[i],image[i],unwrap);
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dx = unwrap[0] - comall[imol][0];
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dy = unwrap[1] - comall[imol][1];
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dz = unwrap[2] - comall[imol][2];
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if (rmass) massone = rmass[i];
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else massone = mass[type[i]];
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rgt[imol][0] += dx*dx * massone;
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@ -233,8 +222,8 @@ void ComputeGyrationMolecule::compute_array()
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void ComputeGyrationMolecule::molcom()
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{
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int i,imol;
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double xbox,ybox,zbox,dx,dy,dz;
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double massone;
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double dx,dy,dz,massone;
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double unwrap[3];
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for (i = 0; i < nmolecules; i++)
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com[i][0] = com[i][1] = com[i][2] = 0.0;
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@ -248,23 +237,17 @@ void ComputeGyrationMolecule::molcom()
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double *rmass = atom->rmass;
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int nlocal = atom->nlocal;
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double xprd = domain->xprd;
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double yprd = domain->yprd;
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double zprd = domain->zprd;
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for (i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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xbox = (image[i] & IMGMASK) - IMGMAX;
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ybox = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
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zbox = (image[i] >> IMG2BITS) - IMGMAX;
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if (rmass) massone = rmass[i];
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else massone = mass[type[i]];
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imol = molecule[i];
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if (molmap) imol = molmap[imol-idlo];
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else imol--;
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com[imol][0] += (x[i][0] + xbox*xprd) * massone;
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com[imol][1] += (x[i][1] + ybox*yprd) * massone;
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com[imol][2] += (x[i][2] + zbox*zprd) * massone;
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domain->unmap(x[i],image[i],unwrap);
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if (rmass) massone = rmass[i];
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else massone = mass[type[i]];
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com[imol][0] += unwrap[0] * massone;
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com[imol][1] += unwrap[1] * massone;
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com[imol][2] += unwrap[2] * massone;
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}
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MPI_Allreduce(&com[0][0],&comall[0][0],3*nmolecules,
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@ -111,8 +111,8 @@ void ComputeMSDMolecule::init()
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void ComputeMSDMolecule::compute_array()
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{
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int i,imol;
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double xbox,ybox,zbox,dx,dy,dz;
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double massone;
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double dx,dy,dz,massone;
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double unwrap[3];
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invoked_array = update->ntimestep;
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@ -130,23 +130,17 @@ void ComputeMSDMolecule::compute_array()
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double *rmass = atom->rmass;
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int nlocal = atom->nlocal;
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double xprd = domain->xprd;
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double yprd = domain->yprd;
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double zprd = domain->zprd;
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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xbox = (image[i] & IMGMASK) - IMGMAX;
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ybox = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
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zbox = (image[i] >> IMG2BITS) - IMGMAX;
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if (rmass) massone = rmass[i];
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else massone = mass[type[i]];
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imol = molecule[i];
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if (molmap) imol = molmap[imol-idlo];
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else imol--;
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com[imol][0] += (x[i][0] + xbox*xprd) * massone;
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com[imol][1] += (x[i][1] + ybox*yprd) * massone;
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com[imol][2] += (x[i][2] + zbox*zprd) * massone;
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domain->unmap(x[i],image[i],unwrap);
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if (rmass) massone = rmass[i];
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else massone = mass[type[i]];
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com[imol][0] += unwrap[0] * massone;
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com[imol][1] += unwrap[1] * massone;
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com[imol][2] += unwrap[2] * massone;
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}
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MPI_Allreduce(&com[0][0],&comall[0][0],3*nmolecules,
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@ -217,12 +217,6 @@ void FixAddForce::min_setup(int vflag)
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void FixAddForce::post_force(int vflag)
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{
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int xbox,ybox,zbox;
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double xprd = domain->xprd;
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double yprd = domain->yprd;
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double zprd = domain->zprd;
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double **x = atom->x;
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double **f = atom->f;
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int *mask = atom->mask;
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@ -247,18 +241,15 @@ void FixAddForce::post_force(int vflag)
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// potential energy = - x dot f in unwrapped coords
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if (varflag == CONSTANT) {
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double unwrap[3];
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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if (iregion >= 0 &&
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!domain->regions[iregion]->match(x[i][0],x[i][1],x[i][2]))
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continue;
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xbox = (image[i] & IMGMASK) - IMGMAX;
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ybox = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
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zbox = (image[i] >> IMG2BITS) - IMGMAX;
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foriginal[0] -= xvalue * (x[i][0]+xbox*xprd) +
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yvalue * (x[i][1]+ybox*yprd) + zvalue * (x[i][2]+zbox*zprd);
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domain->unmap(x[i],image[i],unwrap);
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foriginal[0] -= xvalue*unwrap[0] + yvalue*unwrap[1] + zvalue*unwrap[2];
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foriginal[1] += f[i][0];
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foriginal[2] += f[i][1];
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foriginal[3] += f[i][2];
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@ -57,7 +57,8 @@ FixMomentum::FixMomentum(LAMMPS *lmp, int narg, char **arg) :
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if (linear)
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if (xflag < 0 || xflag > 1 || yflag < 0 || yflag > 1 ||
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zflag < 0 || zflag > 1) error->all(FLERR,"Illegal fix momentum command");
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zflag < 0 || zflag > 1)
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error->all(FLERR,"Illegal fix momentum command");
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// cannot have 0 atoms in group
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@ -121,20 +122,15 @@ void FixMomentum::end_of_step()
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tagint *image = atom->image;
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int nlocal = atom->nlocal;
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int xbox,ybox,zbox;
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double dx,dy,dz;
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double xprd = domain->xprd;
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double yprd = domain->yprd;
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double zprd = domain->zprd;
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double unwrap[3];
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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xbox = (image[i] & IMGMASK) - IMGMAX;
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ybox = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
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zbox = (image[i] >> IMG2BITS) - IMGMAX;
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dx = (x[i][0] + xbox*xprd) - xcm[0];
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dy = (x[i][1] + ybox*yprd) - xcm[1];
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dz = (x[i][2] + zbox*zprd) - xcm[2];
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domain->unmap(x[i],image[i],unwrap);
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dx = unwrap[0] - xcm[0];
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dy = unwrap[1] - xcm[1];
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dz = unwrap[2] - xcm[2];
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v[i][0] -= omega[1]*dz - omega[2]*dy;
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v[i][1] -= omega[2]*dx - omega[0]*dz;
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v[i][2] -= omega[0]*dy - omega[1]*dx;
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@ -110,20 +110,15 @@ void FixSpringRG::post_force(int vflag)
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int nlocal = atom->nlocal;
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double massfrac;
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double xprd = domain->xprd;
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double yprd = domain->yprd;
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double zprd = domain->zprd;
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double unwrap[3];
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int xbox,ybox,zbox;
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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domain->unmap(x[i],image[i],unwrap);
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dx = unwrap[0] - xcm[0];
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dy = unwrap[1] - xcm[1];
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dz = unwrap[2] - xcm[2];
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term1 = 2.0 * k * (1.0 - rg0/rg);
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xbox = (image[i] & IMGMASK) - IMGMAX;
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ybox = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
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zbox = (image[i] >> IMG2BITS) - IMGMAX;
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dx = (x[i][0] + xbox*xprd) - xcm[0];
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dy = (x[i][1] + ybox*yprd) - xcm[1];
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dz = (x[i][2] + zbox*zprd) - xcm[2];
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massfrac = mass[type[i]]/masstotal;
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f[i][0] -= term1*dx*massfrac;
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f[i][1] -= term1*dy*massfrac;
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@ -45,9 +45,10 @@ FixSpringSelf::FixSpringSelf(LAMMPS *lmp, int narg, char **arg) :
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if (k <= 0.0) error->all(FLERR,"Illegal fix spring/self command");
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xflag = yflag = zflag = 1;
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if (narg == 5) {
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if (strcmp(arg[4],"xyz") == 0) {
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; /* default */
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xflag = yflag = zflag = 1;
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} else if (strcmp(arg[4],"xy") == 0) {
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zflag = 0;
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} else if (strcmp(arg[4],"xz") == 0) {
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@ -78,20 +79,9 @@ FixSpringSelf::FixSpringSelf(LAMMPS *lmp, int narg, char **arg) :
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tagint *image = atom->image;
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int nlocal = atom->nlocal;
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double xprd = domain->xprd;
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double yprd = domain->yprd;
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double zprd = domain->zprd;
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int xbox,ybox,zbox;
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for (int i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit) {
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xbox = (image[i] & IMGMASK) - IMGMAX;
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ybox = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
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zbox = (image[i] >> IMG2BITS) - IMGMAX;
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xoriginal[i][0] = x[i][0] + xbox*xprd;
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xoriginal[i][1] = x[i][1] + ybox*yprd;
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xoriginal[i][2] = x[i][2] + zbox*zprd;
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} else xoriginal[i][0] = xoriginal[i][1] = xoriginal[i][2] = 0.0;
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if (mask[i] & groupbit) domain->unmap(x[i],image[i],xoriginal[i]);
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else xoriginal[i][0] = xoriginal[i][1] = xoriginal[i][2] = 0.0;
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}
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espring = 0.0;
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@ -161,21 +151,17 @@ void FixSpringSelf::post_force(int vflag)
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tagint *image = atom->image;
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int nlocal = atom->nlocal;
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double xprd = domain->xprd;
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double yprd = domain->yprd;
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double zprd = domain->zprd;
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int xbox,ybox,zbox;
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double dx,dy,dz;
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double unwrap[3];
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espring = 0.0;
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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xbox = (image[i] & IMGMASK) - IMGMAX;
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ybox = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
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zbox = (image[i] >> IMG2BITS) - IMGMAX;
|
||||
dx = x[i][0] + xbox*xprd - xoriginal[i][0];
|
||||
dy = x[i][1] + ybox*yprd - xoriginal[i][1];
|
||||
dz = x[i][2] + zbox*zprd - xoriginal[i][2];
|
||||
domain->unmap(x[i],image[i],unwrap);
|
||||
dx = unwrap[0] - xoriginal[i][0];
|
||||
dy = unwrap[1] - xoriginal[i][1];
|
||||
dz = unwrap[2] - xoriginal[i][2];
|
||||
if (!xflag) dx = 0.0;
|
||||
if (!yflag) dy = 0.0;
|
||||
if (!zflag) dz = 0.0;
|
||||
|
|
|
@ -98,26 +98,17 @@ FixTMD::FixTMD(LAMMPS *lmp, int narg, char **arg) :
|
|||
double *mass = atom->mass;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
double xprd = domain->xprd;
|
||||
double yprd = domain->yprd;
|
||||
double zprd = domain->zprd;
|
||||
|
||||
double dx,dy,dz;
|
||||
int xbox,ybox,zbox;
|
||||
|
||||
rho_start = 0.0;
|
||||
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
if (mask[i] & groupbit) {
|
||||
xbox = (image[i] & IMGMASK) - IMGMAX;
|
||||
ybox = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
|
||||
zbox = (image[i] >> IMG2BITS) - IMGMAX;
|
||||
dx = x[i][0] + xbox*xprd - xf[i][0];
|
||||
dy = x[i][1] + ybox*yprd - xf[i][1];
|
||||
dz = x[i][2] + zbox*zprd - xf[i][2];
|
||||
domain->unmap(x[i],image[i],xold[i]);
|
||||
dx = xold[i][0] - xf[i][0];
|
||||
dy = xold[i][1] - xf[i][1];
|
||||
dz = xold[i][2] - xf[i][2];
|
||||
rho_start += mass[type[i]]*(dx*dx + dy*dy + dz*dz);
|
||||
xold[i][0] = x[i][0] + xbox*xprd;
|
||||
xold[i][1] = x[i][1] + ybox*yprd;
|
||||
xold[i][2] = x[i][2] + zbox*zprd;
|
||||
} else xold[i][0] = xold[i][1] = xold[i][2] = 0.0;
|
||||
}
|
||||
|
||||
|
@ -190,10 +181,8 @@ void FixTMD::initial_integrate(int vflag)
|
|||
double dxold,dyold,dzold,xback,yback,zback;
|
||||
double gamma_forward,gamma_back,gamma_max,lambda;
|
||||
double kt,fr,kttotal,frtotal,dtfm;
|
||||
double unwrap[3];
|
||||
|
||||
double xprd = domain->xprd;
|
||||
double yprd = domain->yprd;
|
||||
double zprd = domain->zprd;
|
||||
double **x = atom->x;
|
||||
double **v = atom->v;
|
||||
double **f = atom->f;
|
||||
|
@ -202,7 +191,6 @@ void FixTMD::initial_integrate(int vflag)
|
|||
int *type = atom->type;
|
||||
int *mask = atom->mask;
|
||||
int nlocal = atom->nlocal;
|
||||
int xbox,ybox,zbox;
|
||||
|
||||
double delta = update->ntimestep - update->beginstep;
|
||||
delta /= update->endstep - update->beginstep;
|
||||
|
@ -216,12 +204,10 @@ void FixTMD::initial_integrate(int vflag)
|
|||
dxold = xold[i][0] - xf[i][0];
|
||||
dyold = xold[i][1] - xf[i][1];
|
||||
dzold = xold[i][2] - xf[i][2];
|
||||
xbox = (image[i] & IMGMASK) - IMGMAX;
|
||||
ybox = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
|
||||
zbox = (image[i] >> IMG2BITS) - IMGMAX;
|
||||
dx = x[i][0] + xbox*xprd - xf[i][0];
|
||||
dy = x[i][1] + ybox*yprd - xf[i][1];
|
||||
dz = x[i][2] + zbox*zprd - xf[i][2];
|
||||
domain->unmap(x[i],image[i],unwrap);
|
||||
dx = unwrap[0] - xf[i][0];
|
||||
dy = unwrap[1] - xf[i][1];
|
||||
dz = unwrap[2] - xf[i][2];
|
||||
a += mass[type[i]]*(dxold*dxold + dyold*dyold + dzold*dzold);
|
||||
b += mass[type[i]]*(dx *dxold + dy *dyold + dz *dzold);
|
||||
e += mass[type[i]]*(dx *dx + dy *dy + dz *dz);
|
||||
|
@ -258,12 +244,10 @@ void FixTMD::initial_integrate(int vflag)
|
|||
dxold = xold[i][0] - xf[i][0];
|
||||
dyold = xold[i][1] - xf[i][1];
|
||||
dzold = xold[i][2] - xf[i][2];
|
||||
xbox = (image[i] & IMGMASK) - IMGMAX;
|
||||
ybox = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
|
||||
zbox = (image[i] >> IMG2BITS) - IMGMAX;
|
||||
xback = x[i][0] + xbox*xprd + gamma_back*dxold;
|
||||
yback = x[i][1] + ybox*yprd + gamma_back*dyold;
|
||||
zback = x[i][2] + zbox*zprd + gamma_back*dzold;
|
||||
domain->unmap(x[i],image[i],unwrap);
|
||||
xback = unwrap[0] + gamma_back*dxold;
|
||||
yback = unwrap[1] + gamma_back*dyold;
|
||||
zback = unwrap[2] + gamma_back*dzold;
|
||||
dxkt = xback - xold[i][0];
|
||||
dykt = yback - xold[i][1];
|
||||
dzkt = zback - xold[i][2];
|
||||
|
@ -314,12 +298,7 @@ void FixTMD::initial_integrate(int vflag)
|
|||
x[i][2] += gamma_forward*dzold;
|
||||
v[i][2] += gamma_forward*dzold/dtv;
|
||||
f[i][2] += gamma_forward*dzold/dtv/dtfm;
|
||||
xbox = (image[i] & IMGMASK) - IMGMAX;
|
||||
ybox = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
|
||||
zbox = (image[i] >> IMG2BITS) - IMGMAX;
|
||||
xold[i][0] = x[i][0] + xbox*xprd;
|
||||
xold[i][1] = x[i][1] + ybox*yprd;
|
||||
xold[i][2] = x[i][2] + zbox*zprd;
|
||||
domain->unmap(x[i],image[i],xold[i]);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
|
176
src/group.cpp
176
src/group.cpp
|
@ -766,34 +766,27 @@ void Group::xcm(int igroup, double masstotal, double *cm)
|
|||
|
||||
double cmone[3];
|
||||
cmone[0] = cmone[1] = cmone[2] = 0.0;
|
||||
double xprd = domain->xprd;
|
||||
double yprd = domain->yprd;
|
||||
double zprd = domain->zprd;
|
||||
|
||||
int xbox,ybox,zbox;
|
||||
double massone;
|
||||
double unwrap[3];
|
||||
|
||||
if (rmass) {
|
||||
for (int i = 0; i < nlocal; i++)
|
||||
if (mask[i] & groupbit) {
|
||||
xbox = (image[i] & IMGMASK) - IMGMAX;
|
||||
ybox = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
|
||||
zbox = (image[i] >> IMG2BITS) - IMGMAX;
|
||||
massone = rmass[i];
|
||||
cmone[0] += (x[i][0] + xbox*xprd) * massone;
|
||||
cmone[1] += (x[i][1] + ybox*yprd) * massone;
|
||||
cmone[2] += (x[i][2] + zbox*zprd) * massone;
|
||||
domain->unmap(x[i],image[i],unwrap);
|
||||
cmone[0] += unwrap[0] * massone;
|
||||
cmone[1] += unwrap[1] * massone;
|
||||
cmone[2] += unwrap[2] * massone;
|
||||
}
|
||||
} else {
|
||||
for (int i = 0; i < nlocal; i++)
|
||||
if (mask[i] & groupbit) {
|
||||
xbox = (image[i] & IMGMASK) - IMGMAX;
|
||||
ybox = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
|
||||
zbox = (image[i] >> IMG2BITS) - IMGMAX;
|
||||
massone = mass[type[i]];
|
||||
cmone[0] += (x[i][0] + xbox*xprd) * massone;
|
||||
cmone[1] += (x[i][1] + ybox*yprd) * massone;
|
||||
cmone[2] += (x[i][2] + zbox*zprd) * massone;
|
||||
domain->unmap(x[i],image[i],unwrap);
|
||||
cmone[0] += unwrap[0] * massone;
|
||||
cmone[1] += unwrap[1] * massone;
|
||||
cmone[2] += unwrap[2] * massone;
|
||||
}
|
||||
}
|
||||
|
||||
|
@ -827,34 +820,27 @@ void Group::xcm(int igroup, double masstotal, double *cm, int iregion)
|
|||
|
||||
double cmone[3];
|
||||
cmone[0] = cmone[1] = cmone[2] = 0.0;
|
||||
double xprd = domain->xprd;
|
||||
double yprd = domain->yprd;
|
||||
double zprd = domain->zprd;
|
||||
|
||||
int xbox,ybox,zbox;
|
||||
double massone;
|
||||
double unwrap[3];
|
||||
|
||||
if (rmass) {
|
||||
for (int i = 0; i < nlocal; i++)
|
||||
if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) {
|
||||
xbox = (image[i] & IMGMASK) - IMGMAX;
|
||||
ybox = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
|
||||
zbox = (image[i] >> IMG2BITS) - IMGMAX;
|
||||
massone = rmass[i];
|
||||
cmone[0] += (x[i][0] + xbox*xprd) * massone;
|
||||
cmone[1] += (x[i][1] + ybox*yprd) * massone;
|
||||
cmone[2] += (x[i][2] + zbox*zprd) * massone;
|
||||
domain->unmap(x[i],image[i],unwrap);
|
||||
cmone[0] += unwrap[0] * massone;
|
||||
cmone[1] += unwrap[1] * massone;
|
||||
cmone[2] += unwrap[2] * massone;
|
||||
}
|
||||
} else {
|
||||
for (int i = 0; i < nlocal; i++)
|
||||
if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) {
|
||||
xbox = (image[i] & IMGMASK) - IMGMAX;
|
||||
ybox = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
|
||||
zbox = (image[i] >> IMG2BITS) - IMGMAX;
|
||||
massone = mass[type[i]];
|
||||
cmone[0] += (x[i][0] + xbox*xprd) * massone;
|
||||
cmone[1] += (x[i][1] + ybox*yprd) * massone;
|
||||
cmone[2] += (x[i][2] + zbox*zprd) * massone;
|
||||
domain->unmap(x[i],image[i],unwrap);
|
||||
cmone[0] += unwrap[0] * massone;
|
||||
cmone[1] += unwrap[1] * massone;
|
||||
cmone[2] += unwrap[2] * massone;
|
||||
}
|
||||
}
|
||||
|
||||
|
@ -1102,21 +1088,16 @@ double Group::gyration(int igroup, double masstotal, double *cm)
|
|||
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 unwrap[3];
|
||||
double rg = 0.0;
|
||||
|
||||
for (int i = 0; i < nlocal; i++)
|
||||
if (mask[i] & groupbit) {
|
||||
xbox = (image[i] & IMGMASK) - IMGMAX;
|
||||
ybox = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
|
||||
zbox = (image[i] >> IMG2BITS) - IMGMAX;
|
||||
dx = (x[i][0] + xbox*xprd) - cm[0];
|
||||
dy = (x[i][1] + ybox*yprd) - cm[1];
|
||||
dz = (x[i][2] + zbox*zprd) - cm[2];
|
||||
domain->unmap(x[i],image[i],unwrap);
|
||||
dx = unwrap[0] - cm[0];
|
||||
dy = unwrap[1] - cm[1];
|
||||
dz = unwrap[2] - cm[2];
|
||||
if (rmass) massone = rmass[i];
|
||||
else massone = mass[type[i]];
|
||||
rg += (dx*dx + dy*dy + dz*dz) * massone;
|
||||
|
@ -1147,21 +1128,16 @@ double Group::gyration(int igroup, double masstotal, double *cm, int iregion)
|
|||
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 unwrap[3];
|
||||
double rg = 0.0;
|
||||
|
||||
for (int i = 0; i < nlocal; i++)
|
||||
if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) {
|
||||
xbox = (image[i] & IMGMASK) - IMGMAX;
|
||||
ybox = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
|
||||
zbox = (image[i] >> IMG2BITS) - IMGMAX;
|
||||
dx = (x[i][0] + xbox*xprd) - cm[0];
|
||||
dy = (x[i][1] + ybox*yprd) - cm[1];
|
||||
dz = (x[i][2] + zbox*zprd) - cm[2];
|
||||
domain->unmap(x[i],image[i],unwrap);
|
||||
dx = unwrap[0] - cm[0];
|
||||
dy = unwrap[1] - cm[1];
|
||||
dz = unwrap[2] - cm[2];
|
||||
if (rmass) massone = rmass[i];
|
||||
else massone = mass[type[i]];
|
||||
rg += (dx*dx + dy*dy + dz*dz) * massone;
|
||||
|
@ -1192,22 +1168,18 @@ void Group::angmom(int igroup, double *cm, double *lmom)
|
|||
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 unwrap[3];
|
||||
|
||||
double p[3];
|
||||
p[0] = p[1] = p[2] = 0.0;
|
||||
|
||||
for (int i = 0; i < nlocal; i++)
|
||||
if (mask[i] & groupbit) {
|
||||
xbox = (image[i] & IMGMASK) - IMGMAX;
|
||||
ybox = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
|
||||
zbox = (image[i] >> IMG2BITS) - IMGMAX;
|
||||
dx = (x[i][0] + xbox*xprd) - cm[0];
|
||||
dy = (x[i][1] + ybox*yprd) - cm[1];
|
||||
dz = (x[i][2] + zbox*zprd) - cm[2];
|
||||
domain->unmap(x[i],image[i],unwrap);
|
||||
dx = unwrap[0] - cm[0];
|
||||
dy = unwrap[1] - cm[1];
|
||||
dz = unwrap[2] - cm[2];
|
||||
if (rmass) massone = rmass[i];
|
||||
else massone = mass[type[i]];
|
||||
p[0] += massone * (dy*v[i][2] - dz*v[i][1]);
|
||||
|
@ -1238,22 +1210,18 @@ void Group::angmom(int igroup, double *cm, double *lmom, int iregion)
|
|||
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 unwrap[3];
|
||||
|
||||
double p[3];
|
||||
p[0] = p[1] = p[2] = 0.0;
|
||||
|
||||
for (int i = 0; i < nlocal; i++)
|
||||
if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) {
|
||||
xbox = (image[i] & IMGMASK) - IMGMAX;
|
||||
ybox = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
|
||||
zbox = (image[i] >> IMG2BITS) - IMGMAX;
|
||||
dx = (x[i][0] + xbox*xprd) - cm[0];
|
||||
dy = (x[i][1] + ybox*yprd) - cm[1];
|
||||
dz = (x[i][2] + zbox*zprd) - cm[2];
|
||||
domain->unmap(x[i],image[i],unwrap);
|
||||
dx = unwrap[0] - cm[0];
|
||||
dy = unwrap[1] - cm[1];
|
||||
dz = unwrap[2] - cm[2];
|
||||
if (rmass) massone = rmass[i];
|
||||
else massone = mass[type[i]];
|
||||
p[0] += massone * (dy*v[i][2] - dz*v[i][1]);
|
||||
|
@ -1280,22 +1248,18 @@ void Group::torque(int igroup, double *cm, double *tq)
|
|||
tagint *image = atom->image;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
int xbox,ybox,zbox;
|
||||
double dx,dy,dz;
|
||||
double xprd = domain->xprd;
|
||||
double yprd = domain->yprd;
|
||||
double zprd = domain->zprd;
|
||||
double unwrap[3];
|
||||
|
||||
double tlocal[3];
|
||||
tlocal[0] = tlocal[1] = tlocal[2] = 0.0;
|
||||
|
||||
for (int i = 0; i < nlocal; i++)
|
||||
if (mask[i] & groupbit) {
|
||||
xbox = (image[i] & IMGMASK) - IMGMAX;
|
||||
ybox = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
|
||||
zbox = (image[i] >> IMG2BITS) - IMGMAX;
|
||||
dx = (x[i][0] + xbox*xprd) - cm[0];
|
||||
dy = (x[i][1] + ybox*yprd) - cm[1];
|
||||
dz = (x[i][2] + zbox*zprd) - cm[2];
|
||||
domain->unmap(x[i],image[i],unwrap);
|
||||
dx = unwrap[0] - cm[0];
|
||||
dy = unwrap[1] - cm[1];
|
||||
dz = unwrap[2] - cm[2];
|
||||
tlocal[0] += dy*f[i][2] - dz*f[i][1];
|
||||
tlocal[1] += dz*f[i][0] - dx*f[i][2];
|
||||
tlocal[2] += dx*f[i][1] - dy*f[i][0];
|
||||
|
@ -1321,22 +1285,18 @@ void Group::torque(int igroup, double *cm, double *tq, int iregion)
|
|||
tagint *image = atom->image;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
int xbox,ybox,zbox;
|
||||
double dx,dy,dz;
|
||||
double xprd = domain->xprd;
|
||||
double yprd = domain->yprd;
|
||||
double zprd = domain->zprd;
|
||||
double unwrap[3];
|
||||
|
||||
double tlocal[3];
|
||||
tlocal[0] = tlocal[1] = tlocal[2] = 0.0;
|
||||
|
||||
for (int i = 0; i < nlocal; i++)
|
||||
if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) {
|
||||
xbox = (image[i] & IMGMASK) - IMGMAX;
|
||||
ybox = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
|
||||
zbox = (image[i] >> IMG2BITS) - IMGMAX;
|
||||
dx = (x[i][0] + xbox*xprd) - cm[0];
|
||||
dy = (x[i][1] + ybox*yprd) - cm[1];
|
||||
dz = (x[i][2] + zbox*zprd) - cm[2];
|
||||
domain->unmap(x[i],image[i],unwrap);
|
||||
dx = unwrap[0] - cm[0];
|
||||
dy = unwrap[1] - cm[1];
|
||||
dz = unwrap[2] - cm[2];
|
||||
tlocal[0] += dy*f[i][2] - dz*f[i][1];
|
||||
tlocal[1] += dz*f[i][0] - dx*f[i][2];
|
||||
tlocal[2] += dx*f[i][1] - dy*f[i][0];
|
||||
|
@ -1364,11 +1324,9 @@ void Group::inertia(int igroup, double *cm, double itensor[3][3])
|
|||
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 unwrap[3];
|
||||
|
||||
double ione[3][3];
|
||||
for (i = 0; i < 3; i++)
|
||||
for (j = 0; j < 3; j++)
|
||||
|
@ -1376,12 +1334,10 @@ void Group::inertia(int igroup, double *cm, double itensor[3][3])
|
|||
|
||||
for (i = 0; i < nlocal; i++)
|
||||
if (mask[i] & groupbit) {
|
||||
xbox = (image[i] & IMGMASK) - IMGMAX;
|
||||
ybox = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
|
||||
zbox = (image[i] >> IMG2BITS) - IMGMAX;
|
||||
dx = (x[i][0] + xbox*xprd) - cm[0];
|
||||
dy = (x[i][1] + ybox*yprd) - cm[1];
|
||||
dz = (x[i][2] + zbox*zprd) - cm[2];
|
||||
domain->unmap(x[i],image[i],unwrap);
|
||||
dx = unwrap[0] - cm[0];
|
||||
dy = unwrap[1] - cm[1];
|
||||
dz = unwrap[2] - cm[2];
|
||||
if (rmass) massone = rmass[i];
|
||||
else massone = mass[type[i]];
|
||||
ione[0][0] += massone * (dy*dy + dz*dz);
|
||||
|
@ -1418,11 +1374,9 @@ void Group::inertia(int igroup, double *cm, double itensor[3][3], int iregion)
|
|||
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 unwrap[3];
|
||||
|
||||
double ione[3][3];
|
||||
for (i = 0; i < 3; i++)
|
||||
for (j = 0; j < 3; j++)
|
||||
|
@ -1430,12 +1384,10 @@ void Group::inertia(int igroup, double *cm, double itensor[3][3], int iregion)
|
|||
|
||||
for (i = 0; i < nlocal; i++)
|
||||
if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) {
|
||||
xbox = (image[i] & IMGMASK) - IMGMAX;
|
||||
ybox = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
|
||||
zbox = (image[i] >> IMG2BITS) - IMGMAX;
|
||||
dx = (x[i][0] + xbox*xprd) - cm[0];
|
||||
dy = (x[i][1] + ybox*yprd) - cm[1];
|
||||
dz = (x[i][2] + zbox*zprd) - cm[2];
|
||||
domain->unmap(x[i],image[i],unwrap);
|
||||
dx = unwrap[0] - cm[0];
|
||||
dy = unwrap[1] - cm[1];
|
||||
dz = unwrap[2] - cm[2];
|
||||
if (rmass) massone = rmass[i];
|
||||
else massone = mass[type[i]];
|
||||
ione[0][0] += massone * (dy*dy + dz*dz);
|
||||
|
|
|
@ -718,20 +718,15 @@ void Velocity::zero_rotation()
|
|||
tagint *image = atom->image;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
int xbox,ybox,zbox;
|
||||
double dx,dy,dz;
|
||||
double xprd = domain->xprd;
|
||||
double yprd = domain->yprd;
|
||||
double zprd = domain->zprd;
|
||||
double unwrap[3];
|
||||
|
||||
for (i = 0; i < nlocal; i++)
|
||||
if (mask[i] & groupbit) {
|
||||
xbox = (image[i] & IMGMASK) - IMGMAX;
|
||||
ybox = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
|
||||
zbox = (image[i] >> IMG2BITS) - IMGMAX;
|
||||
dx = (x[i][0] + xbox*xprd) - xcm[0];
|
||||
dy = (x[i][1] + ybox*yprd) - xcm[1];
|
||||
dz = (x[i][2] + zbox*zprd) - xcm[2];
|
||||
domain->unmap(x[i],image[i],unwrap);
|
||||
dx = unwrap[0]- xcm[0];
|
||||
dy = unwrap[1] - xcm[1];
|
||||
dz = unwrap[2] - xcm[2];
|
||||
v[i][0] -= omega[1]*dz - omega[2]*dy;
|
||||
v[i][1] -= omega[2]*dx - omega[0]*dz;
|
||||
v[i][2] -= omega[0]*dy - omega[1]*dx;
|
||||
|
|
Loading…
Reference in New Issue