Loading src/XTC/dump_xtc.cpp +5 −5 Original line number Diff line number Diff line Loading @@ -229,18 +229,18 @@ int DumpXTC::pack() /* ---------------------------------------------------------------------- */ void DumpXTC::write_data(int n, double *buf) void DumpXTC::write_data(int n, double *mybuf) { float *xyz; int j,tag; int m = 0; for (int i = 0; i < n; i++) { tag = static_cast<int> (buf[m]) - 1; tag = static_cast<int> (mybuf[m]) - 1; j = 3*tag; coords[j++] = buf[m+1]; coords[j++] = buf[m+2]; coords[j] = buf[m+3]; coords[j++] = mybuf[m+1]; coords[j++] = mybuf[m+2]; coords[j] = mybuf[m+3]; m += size_one; } Loading src/compute_com_molecule.cpp +1 −1 Original line number Diff line number Diff line Loading @@ -150,7 +150,7 @@ void ComputeCOMMolecule::compute_array() double ComputeCOMMolecule::memory_usage() { double bytes = 2*nmolecules * sizeof(double); if (molmap) bytes += nmolecules * sizeof(int); if (molmap) bytes += (idhi-idlo+1) * sizeof(int); bytes += 2*nmolecules*3 * sizeof(double); return bytes; } src/compute_gyration_molecule.cpp +1 −1 Original line number Diff line number Diff line Loading @@ -180,7 +180,7 @@ void ComputeGyrationMolecule::compute_vector() double ComputeGyrationMolecule::memory_usage() { double bytes = 4*nmolecules * sizeof(double); if (molmap) bytes += nmolecules * sizeof(int); if (molmap) bytes += (idhi-idlo+1) * sizeof(int); bytes += 2*nmolecules*3 * sizeof(double); return bytes; } src/compute_msd.cpp +8 −19 Original line number Diff line number Diff line Loading @@ -118,6 +118,7 @@ void ComputeMSD::compute_vector() double cm[3]; if (comflag) group->xcm(igroup,masstotal,cm); else cm[0] = cm[1] = cm[2] = 0.0; // dx,dy,dz = displacement of atom from original position // original unwrapped position is stored by fix Loading Loading @@ -148,15 +149,9 @@ void ComputeMSD::compute_vector() xbox = (image[i] & 1023) - 512; ybox = (image[i] >> 10 & 1023) - 512; zbox = (image[i] >> 20) - 512; if (comflag) { dx = x[i][0] + xbox*xprd - cm[0] - xoriginal[i][0]; dy = x[i][1] + ybox*yprd - cm[1] - xoriginal[i][1]; dz = x[i][2] + zbox*zprd - cm[2] - xoriginal[i][2]; } else { 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]; } msd[0] += dx*dx; msd[1] += dy*dy; msd[2] += dz*dz; Loading @@ -169,16 +164,10 @@ void ComputeMSD::compute_vector() xbox = (image[i] & 1023) - 512; ybox = (image[i] >> 10 & 1023) - 512; zbox = (image[i] >> 20) - 512; if (comflag) { dx = x[i][0] + h[0]*xbox + h[5]*ybox + h[4]*zbox - cm[0] - xoriginal[i][0]; dy = x[i][1] + h[1]*ybox + h[3]*zbox - cm[1] - xoriginal[i][1]; dz = x[i][2] + h[2]*zbox - cm[2] - xoriginal[i][2]; } else { dx = x[i][0] + h[0]*xbox + h[5]*ybox + h[4]*zbox - xoriginal[i][0]; dy = x[i][1] + h[1]*ybox + h[3]*zbox - xoriginal[i][1]; dz = x[i][2] + h[2]*zbox - xoriginal[i][2]; } msd[0] += dx*dx; msd[1] += dy*dy; msd[2] += dz*dz; Loading src/compute_msd_molecule.cpp +1 −1 Original line number Diff line number Diff line Loading @@ -183,7 +183,7 @@ void ComputeMSDMolecule::compute_array() double ComputeMSDMolecule::memory_usage() { double bytes = 2*nmolecules * sizeof(double); if (molmap) bytes += nmolecules * sizeof(int); if (molmap) bytes += (idhi-idlo+1) * sizeof(int); bytes += 2*nmolecules*3 * sizeof(double); bytes += nmolecules*4 * sizeof(double); return bytes; Loading Loading
src/XTC/dump_xtc.cpp +5 −5 Original line number Diff line number Diff line Loading @@ -229,18 +229,18 @@ int DumpXTC::pack() /* ---------------------------------------------------------------------- */ void DumpXTC::write_data(int n, double *buf) void DumpXTC::write_data(int n, double *mybuf) { float *xyz; int j,tag; int m = 0; for (int i = 0; i < n; i++) { tag = static_cast<int> (buf[m]) - 1; tag = static_cast<int> (mybuf[m]) - 1; j = 3*tag; coords[j++] = buf[m+1]; coords[j++] = buf[m+2]; coords[j] = buf[m+3]; coords[j++] = mybuf[m+1]; coords[j++] = mybuf[m+2]; coords[j] = mybuf[m+3]; m += size_one; } Loading
src/compute_com_molecule.cpp +1 −1 Original line number Diff line number Diff line Loading @@ -150,7 +150,7 @@ void ComputeCOMMolecule::compute_array() double ComputeCOMMolecule::memory_usage() { double bytes = 2*nmolecules * sizeof(double); if (molmap) bytes += nmolecules * sizeof(int); if (molmap) bytes += (idhi-idlo+1) * sizeof(int); bytes += 2*nmolecules*3 * sizeof(double); return bytes; }
src/compute_gyration_molecule.cpp +1 −1 Original line number Diff line number Diff line Loading @@ -180,7 +180,7 @@ void ComputeGyrationMolecule::compute_vector() double ComputeGyrationMolecule::memory_usage() { double bytes = 4*nmolecules * sizeof(double); if (molmap) bytes += nmolecules * sizeof(int); if (molmap) bytes += (idhi-idlo+1) * sizeof(int); bytes += 2*nmolecules*3 * sizeof(double); return bytes; }
src/compute_msd.cpp +8 −19 Original line number Diff line number Diff line Loading @@ -118,6 +118,7 @@ void ComputeMSD::compute_vector() double cm[3]; if (comflag) group->xcm(igroup,masstotal,cm); else cm[0] = cm[1] = cm[2] = 0.0; // dx,dy,dz = displacement of atom from original position // original unwrapped position is stored by fix Loading Loading @@ -148,15 +149,9 @@ void ComputeMSD::compute_vector() xbox = (image[i] & 1023) - 512; ybox = (image[i] >> 10 & 1023) - 512; zbox = (image[i] >> 20) - 512; if (comflag) { dx = x[i][0] + xbox*xprd - cm[0] - xoriginal[i][0]; dy = x[i][1] + ybox*yprd - cm[1] - xoriginal[i][1]; dz = x[i][2] + zbox*zprd - cm[2] - xoriginal[i][2]; } else { 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]; } msd[0] += dx*dx; msd[1] += dy*dy; msd[2] += dz*dz; Loading @@ -169,16 +164,10 @@ void ComputeMSD::compute_vector() xbox = (image[i] & 1023) - 512; ybox = (image[i] >> 10 & 1023) - 512; zbox = (image[i] >> 20) - 512; if (comflag) { dx = x[i][0] + h[0]*xbox + h[5]*ybox + h[4]*zbox - cm[0] - xoriginal[i][0]; dy = x[i][1] + h[1]*ybox + h[3]*zbox - cm[1] - xoriginal[i][1]; dz = x[i][2] + h[2]*zbox - cm[2] - xoriginal[i][2]; } else { dx = x[i][0] + h[0]*xbox + h[5]*ybox + h[4]*zbox - xoriginal[i][0]; dy = x[i][1] + h[1]*ybox + h[3]*zbox - xoriginal[i][1]; dz = x[i][2] + h[2]*zbox - xoriginal[i][2]; } msd[0] += dx*dx; msd[1] += dy*dy; msd[2] += dz*dz; Loading
src/compute_msd_molecule.cpp +1 −1 Original line number Diff line number Diff line Loading @@ -183,7 +183,7 @@ void ComputeMSDMolecule::compute_array() double ComputeMSDMolecule::memory_usage() { double bytes = 2*nmolecules * sizeof(double); if (molmap) bytes += nmolecules * sizeof(int); if (molmap) bytes += (idhi-idlo+1) * sizeof(int); bytes += 2*nmolecules*3 * sizeof(double); bytes += nmolecules*4 * sizeof(double); return bytes; Loading
