double PmeKSpace::compute_energy(float *q_arr, const Lattice &lattice, double ewald, double *virial) {
double energy = 0.0;
double v0 = 0.;
double v1 = 0.;
double v2 = 0.;
double v3 = 0.;
double v4 = 0.;
double v5 = 0.;
int n;
int k1, k2, k3, ind;
int K1, K2, K3;
K1=myGrid.K1; K2=myGrid.K2; K3=myGrid.K3;
i_pi_volume = 1.0/(M_PI * lattice.volume());
piob = M_PI/ewald;
piob *= piob;
if ( lattice.orthogonal() ) {
// if ( 0 ) { // JCP FOR TESTING
//This branch is the usual call path.
#if USE_CKLOOP
int useCkLoop = Node::Object()->simParameters->useCkLoop;
if(useCkLoop>=CKLOOP_CTRL_PME_KSPACE){
return compute_energy_orthogonal_helper(q_arr, lattice, ewald, virial);
}
#endif
double recipx = lattice.a_r().x;
double recipy = lattice.b_r().y;
double recipz = lattice.c_r().z;
init_exp(exp1, K1, 0, K1, recipx);
init_exp(exp2, K2, k2_start, k2_end, recipy);
init_exp(exp3, K3, k3_start, k3_end, recipz);
ind = 0;
for ( k1=0; k1<K1; ++k1 ) {
double m1, m11, b1, xp1;
b1 = bm1[k1];
int k1_s = k1<=K1/2 ? k1 : k1-K1;
m1 = k1_s*recipx;
m11 = m1*m1;
xp1 = i_pi_volume*exp1[abs(k1_s)];
for ( k2=k2_start; k2<k2_end; ++k2 ) {
double m2, m22, b1b2, xp2;
b1b2 = b1*bm2[k2];
int k2_s = k2<=K2/2 ? k2 : k2-K2;
m2 = k2_s*recipy;
m22 = m2*m2;
xp2 = exp2[abs(k2_s)]*xp1;
k3 = k3_start;
if ( k1==0 && k2==0 && k3==0 ) {
q_arr[ind++] = 0.0;
q_arr[ind++] = 0.0;
++k3;
}
for ( ; k3<k3_end; ++k3 ) {
double m3, m33, xp3, msq, imsq, vir, fac;
double theta3, theta, q2, qr, qc, C;
theta3 = bm3[k3] *b1b2;
m3 = k3*recipz;
m33 = m3*m3;
xp3 = exp3[k3];
qr = q_arr[ind]; qc=q_arr[ind+1];
q2 = 2*(qr*qr + qc*qc)*theta3;
if ( (k3 == 0) || ( k3 == K3/2 && ! (K3 & 1) ) ) q2 *= 0.5;
msq = m11 + m22 + m33;
imsq = 1.0/msq;
C = xp2*xp3*imsq;
theta = theta3*C;
q_arr[ind] *= theta;
q_arr[ind+1] *= theta;
vir = -2*(piob+imsq);
fac = q2*C;
energy += fac;
v0 += fac*(1.0+vir*m11);
v1 += fac*vir*m1*m2;
v2 += fac*vir*m1*m3;
v3 += fac*(1.0+vir*m22);
v4 += fac*vir*m2*m3;
v5 += fac*(1.0+vir*m33);
ind += 2;
}
}
}
} else if ( cross(lattice.a(),lattice.b()).unit() == lattice.c().unit() ) {
// } else if ( 0 ) { // JCP FOR TESTING
Vector recip1 = lattice.a_r();
Vector recip2 = lattice.b_r();
Vector recip3 = lattice.c_r();
double recip3_x = recip3.x;
double recip3_y = recip3.y;
double recip3_z = recip3.z;
init_exp(exp3, K3, k3_start, k3_end, recip3.length());
ind = 0;
for ( k1=0; k1<K1; ++k1 ) {
double b1; Vector m1;
b1 = bm1[k1];
int k1_s = k1<=K1/2 ? k1 : k1-K1;
m1 = k1_s*recip1;
// xp1 = i_pi_volume*exp1[abs(k1_s)];
for ( k2=k2_start; k2<k2_end; ++k2 ) {
double xp2, b1b2, m2_x, m2_y, m2_z;
b1b2 = b1*bm2[k2];
int k2_s = k2<=K2/2 ? k2 : k2-K2;
m2_x = m1.x + k2_s*recip2.x;
m2_y = m1.y + k2_s*recip2.y;
m2_z = m1.z + k2_s*recip2.z;
// xp2 = exp2[abs(k2_s)]*xp1;
xp2 = i_pi_volume*exp(-piob*(m2_x*m2_x+m2_y*m2_y+m2_z*m2_z));
k3 = k3_start;
if ( k1==0 && k2==0 && k3==0 ) {
q_arr[ind++] = 0.0;
q_arr[ind++] = 0.0;
++k3;
}
for ( ; k3<k3_end; ++k3 ) {
double xp3, msq, imsq, vir, fac;
double theta3, theta, q2, qr, qc, C;
double m_x, m_y, m_z;
theta3 = bm3[k3] *b1b2;
m_x = m2_x + k3*recip3_x;
m_y = m2_y + k3*recip3_y;
m_z = m2_z + k3*recip3_z;
msq = m_x*m_x + m_y*m_y + m_z*m_z;
xp3 = exp3[k3];
qr = q_arr[ind]; qc=q_arr[ind+1];
q2 = 2*(qr*qr + qc*qc)*theta3;
if ( (k3 == 0) || ( k3 == K3/2 && ! (K3 & 1) ) ) q2 *= 0.5;
imsq = 1.0/msq;
C = xp2*xp3*imsq;
theta = theta3*C;
q_arr[ind] *= theta;
q_arr[ind+1] *= theta;
vir = -2*(piob+imsq);
fac = q2*C;
energy += fac;
v0 += fac*(1.0+vir*m_x*m_x);
v1 += fac*vir*m_x*m_y;
v2 += fac*vir*m_x*m_z;
v3 += fac*(1.0+vir*m_y*m_y);
v4 += fac*vir*m_y*m_z;
v5 += fac*(1.0+vir*m_z*m_z);
ind += 2;
}
}
}
} else {
Vector recip1 = lattice.a_r();
Vector recip2 = lattice.b_r();
Vector recip3 = lattice.c_r();
double recip3_x = recip3.x;
double recip3_y = recip3.y;
double recip3_z = recip3.z;
ind = 0;
for ( k1=0; k1<K1; ++k1 ) {
double b1; Vector m1;
b1 = bm1[k1];
int k1_s = k1<=K1/2 ? k1 : k1-K1;
m1 = k1_s*recip1;
// xp1 = i_pi_volume*exp1[abs(k1_s)];
for ( k2=k2_start; k2<k2_end; ++k2 ) {
double b1b2, m2_x, m2_y, m2_z;
b1b2 = b1*bm2[k2];
int k2_s = k2<=K2/2 ? k2 : k2-K2;
m2_x = m1.x + k2_s*recip2.x;
m2_y = m1.y + k2_s*recip2.y;
m2_z = m1.z + k2_s*recip2.z;
// xp2 = exp2[abs(k2_s)]*xp1;
k3 = k3_start;
if ( k1==0 && k2==0 && k3==0 ) {
q_arr[ind++] = 0.0;
q_arr[ind++] = 0.0;
++k3;
}
for ( ; k3<k3_end; ++k3 ) {
double xp3, msq, imsq, vir, fac;
double theta3, theta, q2, qr, qc, C;
double m_x, m_y, m_z;
theta3 = bm3[k3] *b1b2;
m_x = m2_x + k3*recip3_x;
m_y = m2_y + k3*recip3_y;
m_z = m2_z + k3*recip3_z;
msq = m_x*m_x + m_y*m_y + m_z*m_z;
// xp3 = exp3[k3];
xp3 = i_pi_volume*exp(-piob*msq);
qr = q_arr[ind]; qc=q_arr[ind+1];
q2 = 2*(qr*qr + qc*qc)*theta3;
if ( (k3 == 0) || ( k3 == K3/2 && ! (K3 & 1) ) ) q2 *= 0.5;
imsq = 1.0/msq;
C = xp3*imsq;
theta = theta3*C;
q_arr[ind] *= theta;
q_arr[ind+1] *= theta;
vir = -2*(piob+imsq);
fac = q2*C;
energy += fac;
v0 += fac*(1.0+vir*m_x*m_x);
v1 += fac*vir*m_x*m_y;
v2 += fac*vir*m_x*m_z;
v3 += fac*(1.0+vir*m_y*m_y);
v4 += fac*vir*m_y*m_z;
v5 += fac*(1.0+vir*m_z*m_z);
ind += 2;
}
}
}
}
virial[0] = 0.5 * v0;
virial[1] = 0.5 * v1;
virial[2] = 0.5 * v2;
virial[3] = 0.5 * v3;
virial[4] = 0.5 * v4;
virial[5] = 0.5 * v5;
return 0.5*energy;
}
void ComputeDPMEMaster::recvData(ComputeDPMEDataMsg *msg)
{
DebugM(4,"ComputeDPMEMaster::recvData() " << msg->numParticles
<< " particles from node " << msg->node << "\n");
{
homeNode.add(msg->node);
Pme2Particle *data_ptr = localData + numLocalAtoms;
for ( int j = 0; j < msg->numParticles; ++j, ++data_ptr ) {
*data_ptr = msg->particles[j];
}
numLocalAtoms += msg->numParticles;
endForNode.add(numLocalAtoms);
delete msg;
}
if ( homeNode.size() < numWorkingPes ) return; // messages outstanding
DebugM(4,"ComputeDPMEMaster::recvData() running serial code.\n");
// single processor version
Lattice lattice = host->getFlags()->lattice;
SimParameters * simParams = Node::Object()->simParameters;
int i;
AtomInfo atom_info;
atom_info.numatoms = numLocalAtoms;
atom_info.atompnt = 0; // not used
atom_info.freepnt = 0; // not used
atom_info.nlocal = numLocalAtoms;
atom_info.nother = 0;
if ( ! lattice.orthogonal() ) {
NAMD_die("DPME only supports orthogonal PBC's.");
}
BoxInfo box_info;
box_info.box.x = lattice.a().x;
box_info.box.y = lattice.b().y;
box_info.box.z = lattice.c().z;
box_info.box.origin = 0.; // why only one number?
box_info.prd.x = box_info.box.x;
box_info.prd.y = box_info.box.y;
box_info.prd.z = box_info.box.z;
box_info.prd2.x = 0.5 * box_info.box.x;
box_info.prd2.y = 0.5 * box_info.box.y;
box_info.prd2.z = 0.5 * box_info.box.z;
box_info.cutoff = simParams->cutoff;
box_info.rs = simParams->cutoff;
box_info.mc2.x = 2. * ( box_info.prd.x - box_info.cutoff );
box_info.mc2.y = 2. * ( box_info.prd.y - box_info.cutoff );
box_info.mc2.z = 2. * ( box_info.prd.z - box_info.cutoff );
box_info.ewaldcof = ComputeNonbondedUtil::ewaldcof;
box_info.dtol = simParams->PMETolerance;
for (i = 0; i <= 8; i++) {
box_info.recip[i] = 0.; /* assume orthogonal box */
}
box_info.recip[0] = 1.0/box_info.box.x;
box_info.recip[4] = 1.0/box_info.box.y;
box_info.recip[8] = 1.0/box_info.box.z;
GridInfo grid_info;
grid_info.order = simParams->PMEInterpOrder;
grid_info.nfftgrd.x = simParams->PMEGridSizeX;
grid_info.nfftgrd.y = simParams->PMEGridSizeY;
grid_info.nfftgrd.z = simParams->PMEGridSizeZ;
grid_info.nfft = 0;
grid_info.volume = lattice.volume();
PeInfo pe_info; // hopefully this isn't used for anything
pe_info.myproc.node = 0;
pe_info.myproc.nprocs = 1;
pe_info.myproc.ncube = 0;
pe_info.inst_node[0] = 0;
pe_info.igrid = 0;
PmeVector *localResults;
double recip_vir[6];
int time_count = 0;
int tsteps = 1;
double mytime = 0.;
// perform calculations
BigReal electEnergy = 0;
// calculate self energy
Pme2Particle *data_ptr = localData;
for(i=0; i<numLocalAtoms; ++i)
{
electEnergy += data_ptr->cg * data_ptr->cg;
++data_ptr;
}
electEnergy *= -1. * box_info.ewaldcof / SQRT_PI;
DebugM(4,"Ewald self energy: " << electEnergy << "\n");
DebugM(4,"Calling dpme_eval_recip().\n");
double pme_start_time = 0;
if ( runcount == 1 ) pme_start_time = CmiTimer();
electEnergy += dpme_eval_recip( atom_info, localData - 1, &localResults,
recip_vir, grid_info, box_info, pe_info,
time_count, tsteps, &mytime );
if ( runcount == 1 ) {
iout << iINFO << "PME reciprocal sum CPU time per evaluation: "
<< (CmiTimer() - pme_start_time) << "\n" << endi;
}
DebugM(4,"Returned from dpme_eval_recip().\n");
// REVERSE SIGN OF VIRIAL RETURNED BY DPME
for(i=0; i<6; ++i) recip_vir[i] *= -1.;
// send out reductions
DebugM(4,"Timestep : " << host->getFlags()->step << "\n");
DebugM(4,"Reciprocal sum energy: " << electEnergy << "\n");
DebugM(4,"Reciprocal sum virial: " << recip_vir[0] << " " <<
recip_vir[1] << " " << recip_vir[2] << " " << recip_vir[3] << " " <<
recip_vir[4] << " " << recip_vir[5] << "\n");
reduction->item(REDUCTION_ELECT_ENERGY_SLOW) += electEnergy;
reduction->item(REDUCTION_VIRIAL_SLOW_XX) += (BigReal)(recip_vir[0]);
reduction->item(REDUCTION_VIRIAL_SLOW_XY) += (BigReal)(recip_vir[1]);
reduction->item(REDUCTION_VIRIAL_SLOW_XZ) += (BigReal)(recip_vir[2]);
reduction->item(REDUCTION_VIRIAL_SLOW_YX) += (BigReal)(recip_vir[1]);
reduction->item(REDUCTION_VIRIAL_SLOW_YY) += (BigReal)(recip_vir[3]);
reduction->item(REDUCTION_VIRIAL_SLOW_YZ) += (BigReal)(recip_vir[4]);
reduction->item(REDUCTION_VIRIAL_SLOW_ZX) += (BigReal)(recip_vir[2]);
reduction->item(REDUCTION_VIRIAL_SLOW_ZY) += (BigReal)(recip_vir[4]);
reduction->item(REDUCTION_VIRIAL_SLOW_ZZ) += (BigReal)(recip_vir[5]);
reduction->submit();
PmeVector *results_ptr = localResults + 1;
numLocalAtoms = 0;
for ( i = 0; i < homeNode.size(); ++i ) {
ComputeDPMEResultsMsg *msg = new ComputeDPMEResultsMsg;
msg->node = homeNode[i];
msg->numParticles = endForNode[i] - numLocalAtoms;
msg->forces = new PmeVector[msg->numParticles];
for ( int j = 0; j < msg->numParticles; ++j, ++results_ptr ) {
msg->forces[j] = *results_ptr;
}
numLocalAtoms = endForNode[i];
host->comm->sendComputeDPMEResults(msg,homeNode[i]);
}
// reset
runcount += 1;
numLocalAtoms = 0;
homeNode.resize(0);
endForNode.resize(0);
}
void ComputeExtMgr::recvCoord(ExtCoordMsg *msg) {
if ( ! numSources ) {
numSources = (PatchMap::Object())->numNodesWithPatches();
coordMsgs = new ExtCoordMsg*[numSources];
for ( int i=0; i<numSources; ++i ) { coordMsgs[i] = 0; }
numArrived = 0;
numAtoms = Node::Object()->molecule->numAtoms;
coord = new ComputeExtAtom[numAtoms];
force = new ExtForce[numAtoms];
}
int i;
for ( i=0; i < msg->numAtoms; ++i ) {
coord[msg->coord[i].id] = msg->coord[i];
}
coordMsgs[numArrived] = msg;
++numArrived;
if ( numArrived < numSources ) return;
numArrived = 0;
// ALL DATA ARRIVED --- CALCULATE FORCES
Lattice lattice = msg->lattice;
SimParameters *simParams = Node::Object()->simParameters;
FILE *file;
int iret;
// write coordinates to file
//iout << "writing to file " << simParams->extCoordFilename << "\n" << endi;
file = fopen(simParams->extCoordFilename,"w");
if ( ! file ) { NAMD_die(strerror(errno)); }
for ( i=0; i<numAtoms; ++i ) {
int id = coord[i].id + 1;
double charge = coord[i].charge;
double x = coord[i].position.x;
double y = coord[i].position.y;
double z = coord[i].position.z;
iret = fprintf(file,"%d %f %f %f %f\n",id,charge,x,y,z);
if ( iret < 0 ) { NAMD_die(strerror(errno)); }
}
// write periodic cell lattice (0 0 0 if non-periodic)
Vector a = lattice.a(); if ( ! lattice.a_p() ) a = Vector(0,0,0);
Vector b = lattice.b(); if ( ! lattice.b_p() ) b = Vector(0,0,0);
Vector c = lattice.c(); if ( ! lattice.c_p() ) c = Vector(0,0,0);
iret = fprintf(file,"%f %f %f\n%f %f %f\n%f %f %f\n",
a.x, a.y, a.z, b.x, b.y, b.z, c.x, c.y, c.z);
if ( iret < 0 ) { NAMD_die(strerror(errno)); }
fclose(file);
// run user-specified command
//iout << "running command " << simParams->extForcesCommand << "\n" << endi;
iret = system(simParams->extForcesCommand);
if ( iret == -1 ) { NAMD_die(strerror(errno)); }
if ( iret ) { NAMD_die("Error running command for external forces."); }
// remove coordinate file
iret = remove(simParams->extCoordFilename);
if ( iret ) { NAMD_die(strerror(errno)); }
// read forces from file (overwrite positions)
//iout << "reading from file " << simParams->extForceFilename << "\n" << endi;
file = fopen(simParams->extForceFilename,"r");
if ( ! file ) { NAMD_die(strerror(errno)); }
for ( i=0; i<numAtoms; ++i ) {
int id, replace;
double x, y, z;
iret = fscanf(file,"%d %d %lf %lf %lf\n", &id, &replace, &x, &y, &z);
if ( iret != 5 ) { NAMD_die("Error reading external forces file."); }
if ( id != i + 1 ) { NAMD_die("Atom ID error in external forces file."); }
force[i].force.x = x; force[i].force.y = y; force[i].force.z = z;
force[i].replace = replace;
}
// read energy and virial if they are present
// virial used by NAMD is -'ve of normal convention, so reverse it!
// virial[i][j] in file should be sum of -1 * f_i * r_j
double energy;
double virial[3][3];
iret = fscanf(file,"%lf\n", &energy);
if ( iret != 1 ) {
energy = 0;
for ( int k=0; k<3; ++k ) for ( int l=0; l<3; ++l ) virial[k][l] = 0;
} else {
iret = fscanf(file,"%lf %lf %lf\n%lf %lf %lf\n%lf %lf %lf\n",
&virial[0][0], &virial[0][1], &virial[0][2],
&virial[1][0], &virial[1][1], &virial[1][2],
&virial[2][0], &virial[2][1], &virial[2][2]);
if ( iret != 9 ) {
for ( int k=0; k<3; ++k ) for ( int l=0; l<3; ++l ) virial[k][l] = 0;
} else {
// virial used by NAMD is -'ve of normal convention, so reverse it!
for ( int k=0; k<3; ++k ) for ( int l=0; l<3; ++l ) virial[k][l] *= -1.0;
}
}
fclose(file);
// remove force file
iret = remove(simParams->extForceFilename);
if ( iret ) { NAMD_die(strerror(errno)); }
// distribute forces
for ( int j=0; j < numSources; ++j ) {
ExtCoordMsg *cmsg = coordMsgs[j];
coordMsgs[j] = 0;
ExtForceMsg *fmsg = new (cmsg->numAtoms, 0) ExtForceMsg;
for ( int i=0; i < cmsg->numAtoms; ++i ) {
fmsg->force[i] = force[cmsg->coord[i].id];
}
if ( ! j ) {
fmsg->energy = energy;
for ( int k=0; k<3; ++k ) for ( int l=0; l<3; ++l )
fmsg->virial[k][l] = virial[k][l];
} else {
fmsg->energy = 0;
for ( int k=0; k<3; ++k ) for ( int l=0; l<3; ++l )
fmsg->virial[k][l] = 0;
}
extProxy[cmsg->sourceNode].recvForce(fmsg);
delete cmsg;
}
}
void ComputeMsmSerialMgr::recvCoord(MsmSerialCoordMsg *msg) {
if ( ! numSources ) {
numSources = (PatchMap::Object())->numNodesWithPatches();
coordMsgs = new MsmSerialCoordMsg*[numSources];
for ( int i=0; i<numSources; ++i ) { coordMsgs[i] = 0; }
numArrived = 0;
numAtoms = Node::Object()->molecule->numAtoms;
coord = new ComputeMsmSerialAtom[numAtoms];
force = new MsmSerialForce[numAtoms];
}
int i;
for ( i=0; i < msg->numAtoms; ++i ) {
coord[msg->coord[i].id] = msg->coord[i];
}
coordMsgs[numArrived] = msg;
++numArrived;
if ( numArrived < numSources ) return;
numArrived = 0;
// ALL DATA ARRIVED --- CALCULATE FORCES
Lattice lattice = msg->lattice;
SimParameters *simParams = Node::Object()->simParameters;
double energy = 0;
double virial[3][3];
int rc = 0; // return code
if ( ! msmsolver ) {
//
// setup MSM solver
//
msmsolver = NL_msm_create();
if ( ! msmsolver ) NAMD_die("unable to create MSM solver");
double dielectric = simParams->dielectric;
double cutoff = simParams->cutoff;
double gridspacing = simParams->MSMGridSpacing;
double padding = simParams->MSMPadding;
int approx = simParams->MSMApprox;
int split = simParams->MSMSplit;
int nlevels = simParams->MSMLevels;
int msmflags = 0;
msmflags |= (lattice.a_p() ? NL_MSM_PERIODIC_VEC1 : 0);
msmflags |= (lattice.b_p() ? NL_MSM_PERIODIC_VEC2 : 0);
msmflags |= (lattice.c_p() ? NL_MSM_PERIODIC_VEC3 : 0);
msmflags |= NL_MSM_COMPUTE_LONG_RANGE; // compute only long-range part
//msmflags |= NL_MSM_COMPUTE_ALL;
//printf("msmflags = %x\n", msmflags);
rc = NL_msm_configure(msmsolver, gridspacing, approx, split, nlevels);
if (rc) NAMD_die("unable to configure MSM solver");
Vector u=lattice.a(), v=lattice.b(), w=lattice.c(), c=lattice.origin();
Vector ru=lattice.a_r(), rv=lattice.b_r(), rw=lattice.c_r();
if ((msmflags & NL_MSM_PERIODIC_ALL) != NL_MSM_PERIODIC_ALL) {
// called only if there is some non-periodic boundary
int isperiodic = (msmflags & NL_MSM_PERIODIC_ALL);
//printf("calling rescale\n");
rescale_nonperiodic_cell(u, v, w, c, ru, rv, rw,
isperiodic, numAtoms, coord, padding, gridspacing);
}
double vec1[3], vec2[3], vec3[3], center[3];
vec1[0] = u.x;
vec1[1] = u.y;
vec1[2] = u.z;
vec2[0] = v.x;
vec2[1] = v.y;
vec2[2] = v.z;
vec3[0] = w.x;
vec3[1] = w.y;
vec3[2] = w.z;
center[0] = c.x;
center[1] = c.y;
center[2] = c.z;
#if 0
printf("dielectric = %g\n", dielectric);
printf("vec1 = %g %g %g\n", vec1[0], vec1[1], vec1[2]);
printf("vec2 = %g %g %g\n", vec2[0], vec2[1], vec2[2]);
printf("vec3 = %g %g %g\n", vec3[0], vec3[1], vec3[2]);
printf("center = %g %g %g\n", center[0], center[1], center[2]);
printf("cutoff = %g\n", cutoff);
printf("numatoms = %d\n", numAtoms);
#endif
rc = NL_msm_setup(msmsolver, cutoff, vec1, vec2, vec3, center, msmflags);
if (rc) NAMD_die("unable to set up MSM solver");
msmcoord = new double[4*numAtoms];
msmforce = new double[3*numAtoms];
if (msmcoord==0 || msmforce==0) NAMD_die("can't allocate MSM atom buffers");
// scale charges - these won't change
double celec = sqrt(COULOMB / simParams->dielectric);
for (i = 0; i < numAtoms; i++) {
msmcoord[4*i+3] = celec * coord[i].charge;
}
}
// evaluate long-range MSM forces
for (i = 0; i < numAtoms; i++) {
msmcoord[4*i ] = coord[i].position.x;
msmcoord[4*i+1] = coord[i].position.y;
msmcoord[4*i+2] = coord[i].position.z;
}
for (i = 0; i < numAtoms; i++) {
msmforce[3*i ] = 0;
msmforce[3*i+1] = 0;
msmforce[3*i+2] = 0;
}
rc = NL_msm_compute_force(msmsolver, msmforce, &energy, msmcoord, numAtoms);
if (rc) NAMD_die("error evaluating MSM forces");
for (i = 0; i < numAtoms; i++) {
force[i].x = msmforce[3*i ];
force[i].y = msmforce[3*i+1];
force[i].z = msmforce[3*i+2];
}
// MSM does not yet calculate virial
for (int k=0; k < 3; k++) {
for (int l=0; l < 3; l++) {
virial[k][l] = 0;
}
}
// distribute forces
for (int j=0; j < numSources; j++) {
MsmSerialCoordMsg *cmsg = coordMsgs[j];
coordMsgs[j] = 0;
MsmSerialForceMsg *fmsg = new (cmsg->numAtoms, 0) MsmSerialForceMsg;
for (int i=0; i < cmsg->numAtoms; i++) {
fmsg->force[i] = force[cmsg->coord[i].id];
}
if ( ! j ) { // set virial and energy only for first message
fmsg->energy = energy;
for (int k=0; k < 3; k++) {
for (int l=0; l < 3; l++) {
fmsg->virial[k][l] = virial[k][l];
}
}
}
else { // set other messages to zero, add into reduction only once
fmsg->energy = 0;
for (int k=0; k < 3; k++) {
for (int l=0; l < 3; l++) {
fmsg->virial[k][l] = 0;
}
}
}
msmProxy[cmsg->sourceNode].recvForce(fmsg);
delete cmsg;
}
}
int ScriptTcl::Tcl_coorfile(ClientData clientData,
Tcl_Interp *interp, int argc, char *argv[]) {
ScriptTcl *script = (ScriptTcl *)clientData;
script->initcheck();
if (argc == 4 && !strcmp(argv[1], "open")) {
if (strcmp(argv[2], "dcd")) {
NAMD_die("Sorry, coorfile presently supports only DCD files");
}
filehandle = dcdplugin->open_file_read(argv[3], "dcd", &numatoms);
if (!filehandle) {
Tcl_AppendResult(interp, "coorfile: Error opening file ", argv[3], NULL);
return TCL_ERROR;
}
if (numatoms != Node::Object()->pdb->num_atoms()) {
Tcl_AppendResult(interp, "Coordinate file ", argv[3],
"\ncontains the wrong number of atoms.", NULL);
return TCL_ERROR;
}
coords = new float[3*numatoms];
vcoords = new Vector[3*numatoms];
iout << iINFO << "Coordinate file " << argv[3] << " opened for reading.\n"
<< endi;
} else if (argc == 2 && !strcmp(argv[1], "read")) {
if (filehandle == NULL) {
Tcl_AppendResult(interp, "coorfile read: Error, no file open for reading",
NULL);
return TCL_ERROR;
}
molfile_timestep_t ts;
ts.coords = coords;
int rc = dcdplugin->read_next_timestep(filehandle, numatoms, &ts);
if (rc) { // EOF
Tcl_SetObjResult(interp, Tcl_NewIntObj(-1));
return TCL_OK;
}
iout << iINFO << "Reading timestep from file.\n" << endi;
Lattice lattice;
if (get_lattice_from_ts(&lattice, &ts)) {
iout << iINFO << "Updating unit cell from timestep.\n" << endi;
if ( lattice.a_p() && ! script->state->lattice.a_p() ||
lattice.b_p() && ! script->state->lattice.b_p() ||
lattice.c_p() && ! script->state->lattice.c_p() ) {
iout << iWARN << "Cell basis vectors should be specified before reading trajectory.\n" << endi;
}
// update Controller's lattice, but don't change the origin!
Vector a(0.); if ( script->state->lattice.a_p() ) a = lattice.a();
Vector b(0.); if ( script->state->lattice.b_p() ) b = lattice.b();
Vector c(0.); if ( script->state->lattice.c_p() ) c = lattice.c();
script->state->lattice.set(a,b,c);
SetLatticeMsg *msg = new SetLatticeMsg;
msg->lattice = script->state->lattice;
(CProxy_PatchMgr(CkpvAccess(BOCclass_group).patchMgr)).setLattice(msg);
script->barrier();
}
for (int i=0; i<numatoms; i++) {
vcoords[i].x = coords[3*i+0];
vcoords[i].y = coords[3*i+1];
vcoords[i].z = coords[3*i+2];
}
Node::Object()->pdb->set_all_positions(vcoords);
script->reinitAtoms();
Tcl_SetObjResult(interp, Tcl_NewIntObj(0));
} else if (argc == 2 && !strcmp(argv[1], "close")) {
if (!filehandle) {
Tcl_AppendResult(interp, "coorfile close: No file opened for reading!",
NULL);
return TCL_OK;
}
iout << iINFO << "Closing coordinate file.\n" << endi;
dcdplugin->close_file_read(filehandle);
filehandle = NULL;
delete [] coords;
delete [] vcoords;
} else if (argc ==2 && !strcmp(argv[1], "skip")) {
if (filehandle == NULL) {
Tcl_AppendResult(interp, "coorfile skip: Error, no file open for reading",
NULL);
return TCL_ERROR;
}
int rc = dcdplugin->read_next_timestep(filehandle, numatoms, NULL);
if (rc) { // EOF
Tcl_SetObjResult(interp, Tcl_NewIntObj(-1));
return TCL_OK;
}
Tcl_SetObjResult(interp, Tcl_NewIntObj(0));
} else {
NAMD_die("Unknown option passed to coorfile");
}
return TCL_OK;
}
