void
DisplayDevice::find_pbc_images (const VMDDisplayList *cmdList,
ResizeArray<Matrix4> &pbcImages)
{
if (cmdList->pbc == PBC_NONE)
{
pbcImages.append (Matrix4 ());
return;
}
ResizeArray<int> pbcCells;
find_pbc_cells (cmdList, pbcCells);
for (int i = 0; i < pbcCells.num (); i += 3)
{
int nx = pbcCells[i];
int ny = pbcCells[i + 1];
int nz = pbcCells[i + 2];
Matrix4 mat;
for (int i1 = 1; i1 <= nx; i1++)
mat.multmatrix (cmdList->transX);
for (int i2 = -1; i2 >= nx; i2--)
mat.multmatrix (cmdList->transXinv);
for (int i3 = 1; i3 <= ny; i3++)
mat.multmatrix (cmdList->transY);
for (int i4 = -1; i4 >= ny; i4--)
mat.multmatrix (cmdList->transYinv);
for (int i5 = 1; i5 <= nz; i5++)
mat.multmatrix (cmdList->transZ);
for (int i6 = -1; i6 >= nz; i6--)
mat.multmatrix (cmdList->transZinv);
pbcImages.append (mat);
}
}
void DisplayDevice::find_pbc_cells(const VMDDisplayList *cmdList,
ResizeArray<int> &pbcCells) {
int pbc = cmdList->pbc;
if (pbc == PBC_NONE) {
pbcCells.append(0);
pbcCells.append(0);
pbcCells.append(0);
} else {
int npbc = cmdList->npbc;
int nx = pbc & PBC_X ? npbc : 0;
int ny = pbc & PBC_Y ? npbc : 0;
int nz = pbc & PBC_Z ? npbc : 0;
int nox = pbc & PBC_OPX ? -npbc : 0;
int noy = pbc & PBC_OPY ? -npbc : 0;
int noz = pbc & PBC_OPZ ? -npbc : 0;
int i, j, k;
for (i=nox; i<=nx; i++) {
for (j=noy; j<=ny; j++) {
for (k=noz; k<=nz; k++) {
if (! (pbc & PBC_NOSELF && !i && !j && !k)) {
pbcCells.append(i);
pbcCells.append(j);
pbcCells.append(k);
}
}
}
}
}
}
static void mol_delete_cb(Fl_Widget *w, void *v) {
VMDApp *app = (VMDApp *)w->user_data();
MolBrowser *browser = (MolBrowser *)v;
ResizeArray<int> idlist;
for (int i=0; i<browser->size(); i++) {
if (browser->selected(i+1)) {
idlist.append(app->molecule_id(i));
}
}
for (int j=0; j<idlist.num(); j++)
app->molecule_delete(idlist[j]);
}
/* return the list of exclusions from the file */
void GromacsTopFile::getExclusions(int* atomi, int* atomj) const {
for(int i =0; i < exclusions_atom_i.size(); i++) {
atomi[i] = exclusions_atom_i[i];
atomj[i] = exclusions_atom_j[i];
}
return;
}
ResizeArray<JString *> *generic_get_names(const T &devList) {
ResizeArray<JString *> *names = SensorConfig::getnames();
ResizeArray<JString *> *devnames = new ResizeArray<JString *>;
for (int i=0; i<names->num(); i++) {
JString *jstr = (*names)[i];
SensorConfig config(*jstr);
const char *type = config.gettype();
if (devList.typecode(type) >= 0)
devnames->append(jstr);
else
delete jstr;
}
delete names;
return devnames;
}
void PSDisplayDevice::render(const VMDDisplayList *display_list) {
DepthSortObject depth_obj;
char *cmd_ptr;
int draw;
int tok;
int nc;
float a[3], b[3], c[3], d[3];
float cent[3];
float r;
Matrix4 ident;
float textsize=1.0f; // default text size
// first we want to clear the transformation matrix stack
while (transMat.num())
transMat.pop();
// push on the identity matrix
transMat.push(ident);
// load the display list's transformation matrix
super_multmatrix(display_list->mat.mat);
// Now we need to calculate the normalized position of the light
// so we can compute angles of surfaces to that light for shading
norm_light[0] = lightState[0].pos[0];
norm_light[1] = lightState[0].pos[1];
norm_light[2] = lightState[0].pos[2];
if (norm_light[0] || norm_light[1] || norm_light[2])
vec_normalize(norm_light);
// Computer periodic images
ResizeArray<Matrix4> pbcImages;
find_pbc_images(display_list, pbcImages);
int nimages = pbcImages.num();
for (int pbcimage = 0; pbcimage < nimages; pbcimage++) {
transMat.dup();
super_multmatrix(pbcImages[pbcimage].mat);
// Loop through the display list and add each object to our
// depth-sort list for final rendering.
VMDDisplayList::VMDLinkIter cmditer;
display_list->first(&cmditer);
while ((tok = display_list->next(&cmditer, cmd_ptr)) != DLASTCOMMAND) {
draw = 0;
nc = -1;
switch (tok) {
case DPOINT:
// allocate memory
depth_obj.points = (float *) malloc(sizeof(float) * 2);
if (!depth_obj.points) {
// memory error
if (!memerror) {
memerror = 1;
msgErr << "PSDisplayDevice: Out of memory. Some " <<
"objects were not drawn." << sendmsg;
}
break;
}
// copy data
depth_obj.npoints = 1;
depth_obj.color = colorIndex;
(transMat.top()).multpoint3d(((DispCmdPoint *) cmd_ptr)->pos, a);
memcpy(depth_obj.points, a, sizeof(float) * 2);
// compute the distance to the eye
depth_obj.dist = compute_dist(a);
// valid object to depth sort
draw = 1;
break;
case DSPHERE:
{
(transMat.top()).multpoint3d(((DispCmdSphere *) cmd_ptr)->pos_r, c);
r = scale_radius(((DispCmdSphere *) cmd_ptr)->pos_r[3]);
sphere_approx(c, r);
break;
}
case DSPHEREARRAY:
{
DispCmdSphereArray *sa = (DispCmdSphereArray *) cmd_ptr;
int cIndex, rIndex; // cIndex: index of colors & centers
// rIndex: index of radii.
float * centers;
float * radii;
float * colors;
sa->getpointers(centers, radii, colors);
set_sphere_res(sa->sphereres);
for (cIndex = 0, rIndex=0; rIndex < sa->numspheres;
cIndex+=3, rIndex++)
{
colorIndex = nearest_index(colors[cIndex],
colors[cIndex+1],
colors[cIndex+2]);
(transMat.top()).multpoint3d(¢ers[cIndex] , c);
r = scale_radius(radii[rIndex]);
sphere_approx(c, r);
}
break;
}
case DLINE:
// check for zero-length line (degenerate)
if (!memcmp(((DispCmdLine *) cmd_ptr)->pos1,
((DispCmdLine *) cmd_ptr)->pos2,
sizeof(float) * 3)) {
// degenerate line
break;
}
// allocate memory
depth_obj.points = (float *) malloc(sizeof(float) * 4);
if (!depth_obj.points) {
// memory error
if (!memerror) {
memerror = 1;
msgErr << "PSDisplayDevice: Out of memory. Some " <<
"objects were not drawn." << sendmsg;
}
break;
}
// copy data
depth_obj.npoints = 2;
depth_obj.color = colorIndex;
(transMat.top()).multpoint3d(((DispCmdLine *) cmd_ptr)->pos1, a);
(transMat.top()).multpoint3d(((DispCmdLine *) cmd_ptr)->pos2, b);
memcpy(depth_obj.points, a, sizeof(float) * 2);
memcpy(&depth_obj.points[2], b, sizeof(float) * 2);
// compute the centerpoint of the object
cent[0] = (a[0] + b[0]) / 2;
cent[1] = (a[1] + b[1]) / 2;
cent[2] = (a[2] + b[2]) / 2;
// compute the distance to the eye
depth_obj.dist = compute_dist(cent);
// valid object to depth sort
draw = 1;
break;
case DLINEARRAY:
{
// XXX much replicated code from DLINE
float *v = (float *)cmd_ptr;
int nlines = (int)v[0];
v++;
for (int i=0; i<nlines; i++) {
// check for degenerate line
if (!memcmp(v,v+3,3*sizeof(float)))
break;
// allocate memory
depth_obj.points = (float *) malloc(sizeof(float) * 4);
if (!depth_obj.points) {
// memory error
if (!memerror) {
memerror = 1;
msgErr << "PSDisplayDevice: Out of memory. Some " <<
"objects were not drawn." << sendmsg;
}
break;
}
// copy data
depth_obj.npoints = 2;
depth_obj.color = colorIndex;
(transMat.top()).multpoint3d(v, a);
(transMat.top()).multpoint3d(v+3, b);
memcpy(depth_obj.points, a, sizeof(float) * 2);
memcpy(&depth_obj.points[2], b, sizeof(float) * 2);
// compute the centerpoint of the object
cent[0] = (a[0] + b[0]) / 2;
cent[1] = (a[1] + b[1]) / 2;
cent[2] = (a[2] + b[2]) / 2;
// compute the distance to the eye
depth_obj.dist = compute_dist(cent);
// we'll add the object here, since we have multiple objects
draw = 0;
memusage += sizeof(float) * 2 * depth_obj.npoints;
points += depth_obj.npoints;
objects++;
depth_list.append(depth_obj);
v += 6;
}
}
break;
case DPOLYLINEARRAY:
{
// XXX much replicated code from DLINE / DLINEARRAY
float *v = (float *)cmd_ptr;
int nverts = (int)v[0];
v++;
for (int i=0; i<nverts-1; i++) {
// check for degenerate line
if (!memcmp(v,v+3,3*sizeof(float)))
break;
// allocate memory
depth_obj.points = (float *) malloc(sizeof(float) * 4);
if (!depth_obj.points) {
// memory error
if (!memerror) {
memerror = 1;
msgErr << "PSDisplayDevice: Out of memory. Some " <<
"objects were not drawn." << sendmsg;
}
break;
}
// copy data
depth_obj.npoints = 2;
depth_obj.color = colorIndex;
(transMat.top()).multpoint3d(v, a);
(transMat.top()).multpoint3d(v+3, b);
memcpy(depth_obj.points, a, sizeof(float) * 2);
memcpy(&depth_obj.points[2], b, sizeof(float) * 2);
// compute the centerpoint of the object
cent[0] = (a[0] + b[0]) / 2;
cent[1] = (a[1] + b[1]) / 2;
cent[2] = (a[2] + b[2]) / 2;
// compute the distance to the eye
depth_obj.dist = compute_dist(cent);
// we'll add the object here, since we have multiple objects
draw = 0;
memusage += sizeof(float) * 2 * depth_obj.npoints;
points += depth_obj.npoints;
objects++;
depth_list.append(depth_obj);
v += 3;
}
}
break;
case DCYLINDER:
{
int res;
(transMat.top()).multpoint3d((float *) cmd_ptr, a);
(transMat.top()).multpoint3d(&((float *) cmd_ptr)[3], b);
r = scale_radius(((float *) cmd_ptr)[6]);
res = (int) ((float *) cmd_ptr)[7];
cylinder_approx(a, b, r, res, (int) ((float *) cmd_ptr)[8]);
break;
}
case DCONE:
{
(transMat.top()).multpoint3d(((DispCmdCone *) cmd_ptr)->pos1, a);
(transMat.top()).multpoint3d(((DispCmdCone *) cmd_ptr)->pos2, b);
float r1 = scale_radius(((DispCmdCone *) cmd_ptr)->radius);
float r2 = scale_radius(((DispCmdCone *) cmd_ptr)->radius2);
// XXX current implementation can't draw truncated cones.
if (r2 > 0.0f) {
msgWarn << "PSDisplayDevice) can't draw truncated cones"
<< sendmsg;
}
cone_approx(a, b, r1);
break;
}
case DTEXTSIZE:
textsize = ((DispCmdTextSize *)cmd_ptr)->size;
break;
case DTEXT:
{
float* pos = (float *)cmd_ptr;
#if 0
// thickness not implemented yet
float thickness = pos[3]; // thickness is stored in 4th slot
#endif
char* txt = (char *)(pos+4);
int txtlen = strlen(txt);
// allocate memory
depth_obj.points = (float *) malloc(sizeof(float) * 2);
depth_obj.text = (char *) malloc(sizeof(char) * (txtlen+1));
if ( !(depth_obj.points || depth_obj.text) ) {
// memory error
if (!memerror) {
memerror = 1;
msgErr << "PSDisplayDevice: Out of memory. Some " <<
"objects were not drawn." << sendmsg;
}
break;
}
// copy data
depth_obj.npoints = 1;
depth_obj.color = colorIndex;
(transMat.top()).multpoint3d(((DispCmdPoint *) cmd_ptr)->pos, a);
memcpy(depth_obj.points, a, sizeof(float) * 2);
strcpy(depth_obj.text , txt);
// note scale factor, stored into "light_scale", so we didn't
// have to add a new structure member just for this.
depth_obj.light_scale = textsize * 15;
// compute the distance to the eye
depth_obj.dist = compute_dist(a);
// valid object to depth sort
draw = 1;
break;
}
case DTRIANGLE:
// check for degenerate triangle
if (!memcmp(((DispCmdTriangle *) cmd_ptr)->pos1,
((DispCmdTriangle *) cmd_ptr)->pos2,
sizeof(float) * 3) ||
!memcmp(((DispCmdTriangle *) cmd_ptr)->pos2,
((DispCmdTriangle *) cmd_ptr)->pos3,
sizeof(float) * 3) ||
!memcmp(((DispCmdTriangle *) cmd_ptr)->pos2,
((DispCmdTriangle *) cmd_ptr)->pos3,
sizeof(float) * 3)) {
// degenerate triangle
break;
}
// allocate memory
depth_obj.points = (float *) malloc(sizeof(float) * 6);
if (!depth_obj.points) {
// memory error
if (!memerror) {
memerror = 1;
msgErr << "PSDisplayDevice: Out of memory. Some " <<
"objects were not drawn." << sendmsg;
}
break;
}
// copy data
depth_obj.npoints = 3;
depth_obj.color = (nc >= 0) ? nc : colorIndex;
(transMat.top()).multpoint3d(((DispCmdTriangle *) cmd_ptr)->pos1, a);
(transMat.top()).multpoint3d(((DispCmdTriangle *) cmd_ptr)->pos2, b);
(transMat.top()).multpoint3d(((DispCmdTriangle *) cmd_ptr)->pos3, c);
memcpy(depth_obj.points, a, sizeof(float) * 2);
memcpy(&depth_obj.points[2], b, sizeof(float) * 2);
memcpy(&depth_obj.points[4], c, sizeof(float) * 2);
// compute the centerpoint of the object
cent[0] = (a[0] + b[0] + c[0]) / 3;
cent[1] = (a[1] + b[1] + c[1]) / 3;
cent[2] = (a[2] + b[2] + c[2]) / 3;
// compute the distance to the eye for depth sorting
depth_obj.dist = compute_dist(cent);
// compute a light shading factor
depth_obj.light_scale = compute_light(a, b, c);
// valid object to depth sort
draw = 1;
break;
case DTRIMESH_C4F_N3F_V3F:
// call a separate routine to break up the mesh into
// its component triangles
decompose_mesh((DispCmdTriMesh *) cmd_ptr);
break;
case DTRISTRIP:
// call a separate routine to break up the strip into
// its component triangles
decompose_tristrip((DispCmdTriStrips *) cmd_ptr);
break;
case DSQUARE:
// check for degenerate quadrilateral
if (!memcmp(((DispCmdSquare *) cmd_ptr)->pos1,
((DispCmdSquare *) cmd_ptr)->pos2,
sizeof(float) * 3) ||
!memcmp(((DispCmdSquare *) cmd_ptr)->pos1,
((DispCmdSquare *) cmd_ptr)->pos3,
sizeof(float) * 3) ||
!memcmp(((DispCmdSquare *) cmd_ptr)->pos1,
((DispCmdSquare *) cmd_ptr)->pos4,
sizeof(float) * 3) ||
!memcmp(((DispCmdSquare *) cmd_ptr)->pos2,
((DispCmdSquare *) cmd_ptr)->pos3,
sizeof(float) * 3) ||
!memcmp(((DispCmdSquare *) cmd_ptr)->pos2,
((DispCmdSquare *) cmd_ptr)->pos4,
sizeof(float) * 3) ||
!memcmp(((DispCmdSquare *) cmd_ptr)->pos3,
((DispCmdSquare *) cmd_ptr)->pos4,
sizeof(float) * 3)) {
// degenerate quadrilateral
break;
}
// allocate memory
depth_obj.points = (float *) malloc(sizeof(float) * 8);
if (!depth_obj.points) {
// memory error
if (!memerror) {
memerror = 1;
msgErr << "PSDisplayDevice: Out of memory. Some " <<
"objects were not drawn." << sendmsg;
}
break;
}
// copy data
depth_obj.npoints = 4;
depth_obj.color = colorIndex;
(transMat.top()).multpoint3d(((DispCmdSquare *) cmd_ptr)->pos1, a);
(transMat.top()).multpoint3d(((DispCmdSquare *) cmd_ptr)->pos2, b);
(transMat.top()).multpoint3d(((DispCmdSquare *) cmd_ptr)->pos3, c);
(transMat.top()).multpoint3d(((DispCmdSquare *) cmd_ptr)->pos4, d);
memcpy(depth_obj.points, a, sizeof(float) * 2);
memcpy(&depth_obj.points[2], b, sizeof(float) * 2);
memcpy(&depth_obj.points[4], c, sizeof(float) * 2);
memcpy(&depth_obj.points[6], d, sizeof(float) * 2);
// compute the centerpoint of the object
cent[0] = (a[0] + b[0] + c[0] + d[0]) / 4;
cent[1] = (a[1] + b[1] + c[1] + d[1]) / 4;
cent[2] = (a[2] + b[2] + c[2] + d[2]) / 4;
// compute the distance to the eye for depth sorting
depth_obj.dist = compute_dist(cent);
// compute a light shading factor
depth_obj.light_scale = compute_light(a, b, c);
// valid object to depth sort
draw = 1;
break;
case DCOLORINDEX:
colorIndex = ((DispCmdColorIndex *) cmd_ptr)->color;
break;
case DSPHERERES:
set_sphere_res(((int *) cmd_ptr)[0]);
break;
default:
// unknown object, so just skip it
break;
}
// if we have a valid object to add to the depth sort list
if (draw && depth_obj.npoints) {
memusage += sizeof(float) * 2 * depth_obj.npoints;
if ( depth_obj.text )
memusage += sizeof(char) * (1+strlen(depth_obj.text));
points += depth_obj.npoints;
objects++;
depth_list.append(depth_obj);
}
depth_obj.npoints = 0;
depth_obj.points = NULL;
} // while (tok != DLASTCOMMAND)
transMat.pop();
} // end for() [periodic images]
}
extern "C" void * bondsearchthread(void *voidparms) {
int i, j, aindex;
int paircount = 0;
bondsearchthrparms *parms = (bondsearchthrparms *) voidparms;
const int threadid = parms->threadid;
const int threadcount = parms->threadcount;
wkf_mutex_t *pairlistmutex = parms->pairlistmutex;
const float *pos = parms->pos;
const float *radii = parms->radii;
const int totb = parms->totb;
const int **boxatom = (const int **) parms->boxatom;
const int *numinbox = parms->numinbox;
const int **nbrlist = (const int **) parms->nbrlist;
const int maxpairs = parms->maxpairs;
const float pairdist = parms->pairdist;
ResizeArray<int> *pairs = new ResizeArray<int>;
float sqdist = pairdist * pairdist;
wkfmsgtimer *msgt = wkf_msg_timer_create(5);
for (aindex = threadid; (aindex < totb) && (paircount < maxpairs); aindex+=threadcount) {
const int *tmpbox, *nbr;
tmpbox = boxatom[aindex];
int anbox = numinbox[aindex];
if (((aindex & 255) == 0) && wkf_msg_timer_timeout(msgt)) {
char tmpbuf[128];
sprintf(tmpbuf, "%6.2f", (100.0f * aindex) / (float) totb);
// XXX: we have to use printf here as msgInfo is not thread-safe.
// msgInfo << "vmd_gridsearch_bonds (thread " << threadid << "): "
// << tmpbuf << "% complete" << sendmsg;
printf("vmd_gridsearch_bonds (thread %d): %s %% complete\n",
threadid, tmpbuf);
}
for (nbr = nbrlist[aindex]; (*nbr != -1) && (paircount < maxpairs); nbr++) {
int nnbr=*nbr;
const int *nbrbox = boxatom[nnbr];
int nbox=numinbox[nnbr];
int self = (aindex == nnbr) ? 1 : 0;
for (i=0; (i<anbox) && (paircount < maxpairs); i++) {
int ind1 = tmpbox[i];
const float *p1 = pos + 3L*ind1;
// skip over self and already-tested atoms
int startj = (self) ? i+1 : 0;
for (j=startj; (j<nbox) && (paircount < maxpairs); j++) {
int ind2 = nbrbox[j];
const float *p2 = pos + 3L*ind2;
float dx = p1[0] - p2[0];
float dy = p1[1] - p2[1];
float dz = p1[2] - p2[2];
float ds2 = dx*dx + dy*dy + dz*dz;
// perform distance test, but ignore pairs between atoms
// with nearly identical coords
if ((ds2 > sqdist) || (ds2 < 0.001))
continue;
if (radii) { // Do atom-specific distance check
float cut = 0.6f * (radii[ind1] + radii[ind2]);
if (ds2 > cut*cut)
continue;
}
pairs->append(ind1);
pairs->append(ind2);
paircount++;
}
}
}
}
// setup results pairlist node
GridSearchPairlist *head;
head = (GridSearchPairlist *) malloc(sizeof(GridSearchPairlist));
head->next = NULL;
head->pairlist = pairs;
wkf_mutex_lock(pairlistmutex); // lock pairlist before update
parms->head = head;
wkf_mutex_unlock(pairlistmutex); // unlock pairlist after update
wkf_msg_timer_destroy(msgt);
return NULL;
}
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);
}
// To write an X3DOM-compatible scene file, we cannot include
// LineProperties nodes.
void X3DOMDisplayDevice::text(float *pos, float size, float thickness,
const char *str) {
float textpos[3];
float textsize;
hersheyhandle hh;
// transform the world coordinates
(transMat.top()).multpoint3d(pos, textpos);
textsize = size * 1.5f;
ResizeArray<int> idxs;
ResizeArray<float> pnts;
idxs.clear();
pnts.clear();
int idx=0;
while (*str != '\0') {
float lm, rm, x, y;
int draw;
x=y=0.0f;
draw=0;
hersheyDrawInitLetter(&hh, *str, &lm, &rm);
textpos[0] -= lm * textsize;
while (!hersheyDrawNextLine(&hh, &draw, &x, &y)) {
float pt[3];
if (draw) {
// add another connected point to the line strip
idxs.append(idx);
pt[0] = textpos[0] + textsize * x;
pt[1] = textpos[1] + textsize * y;
pt[2] = textpos[2];
pnts.append(pt[0]);
pnts.append(pt[1]);
pnts.append(pt[2]);
idx++;
} else {
idxs.append(-1); // pen-up, end of the line strip
}
}
idxs.append(-1); // pen-up, end of the line strip
textpos[0] += rm * textsize;
str++;
}
fprintf(outfile, "<Shape>\n");
fprintf(outfile, " ");
//
// Emit the line properties
//
fprintf(outfile, "<Appearance><Material ");
fprintf(outfile, "ambientIntensity='%g' ", mat_ambient);
fprintf(outfile, "diffuseColor='0 0 0' ");
const float *rgb = matData[colorIndex];
fprintf(outfile, "emissiveColor='%g %g %g' ",
mat_diffuse * rgb[0], mat_diffuse * rgb[1], mat_diffuse * rgb[2]);
fprintf(outfile, "/>");
#if 0
// XXX X3DOM v1.1 doesn't handle LineProperties nodes
// emit a line thickness directive, if needed
if (thickness < 0.99f || thickness > 1.01f) {
fprintf(outfile, " <LineProperties linewidthScaleFactor=\"%g\" "
"containerField=\"lineProperties\"/>\n",
(double) thickness);
}
#endif
fprintf(outfile, "</Appearance>\n");
//
// Emit the line set
//
fprintf(outfile, " <IndexedLineSet coordIndex='");
int i, cnt;
cnt = idxs.num();
for (i=0; i<cnt; i++) {
fprintf(outfile, "%d ", idxs[i]);
}
fprintf(outfile, "'>\n");
fprintf(outfile, " <Coordinate point='");
cnt = pnts.num();
for (i=0; i<cnt; i+=3) {
fprintf(outfile, "%c%g %g %g",
(i==0) ? ' ' : ',',
pnts[i], pnts[i+1], pnts[i+2]);
}
fprintf(outfile, "'/>\n");
fprintf(outfile, " </IndexedLineSet>\n");
fprintf(outfile, "</Shape>\n");
}
// draw a 3-D field lines that follow the volume gradient
void
DrawMolItem::draw_volume_field_lines (int volid, float seedval, float minlen,
float maxlen, float thickness)
{
const VolumetricData * v = NULL;
v = mol->get_volume_data (volid);
int printdonemesg = 0;
if (v == NULL)
{
msgInfo << "No volume data loaded at index " << volid << sendmsg;
return;
}
int seedcount = 0;
int pointcount = 0;
int totalpointcount = 0;
int usecolor;
ResizeArray<float> seeds;
append (DMATERIALOFF);
usecolor = draw_volume_get_colorid ();
cmdColorIndex.putdata (usecolor, cmdList);
seedcount = calcseeds_gradient_magnitude (v, &seeds, seedval * 0.5f,
seedval * 1.5f);
// Integrate field lines starting with each of the seeds to simulate
// particle advection.
// Uses Euler's approximation for solving the initial value problem.
// We could get a more accurate solution using a fourth order Runge-Kutta
// method, but with more math per iteration. We may want to implement
// the integrator as a user selected option.
// The choice of integration step size is currently arbitrary,
// but will become a user-defined parameter, since it affects speed
// and accuracy. A good default might be 0.25 times the smallest
// grid cell spacing axis.
float lx, ly, lz;
v->cell_lengths (&lx, &ly, &lz);
float mincelllen = lx;
mincelllen = (mincelllen < ly) ? mincelllen : ly;
mincelllen = (mincelllen < lz) ? mincelllen : lz;
float delta = mincelllen * 0.25f; // delta per step (compensates gradient magnitude)
// minimum gradient magnitude, before we consider that we've found
// a critical point in the dataset.
float mingmag = 0.0001f;
// max gradient magnitude, before we consider it a source/sink
float maxgmag = 5;
ResizeArray<float> points;
// For each seed point, integrate in both positive and
// negative directions for a field line length up to
// the maxlen criterion.
msgtimer *msgt = msg_timer_create (1);
int seed;
for (seed = 0; seed < seedcount; seed++)
{
// emit UI messages as integrator runs, for long calculations...
if (!(seed & 7) && msg_timer_timeout (msgt))
{
char tmpbuf[128];
sprintf (tmpbuf, "%6.2f %% complete",
(100.0f * seed) / (float) seedcount);
msgInfo << "integrating " << seedcount << " field lines: " << tmpbuf
<< sendmsg;
printdonemesg = 1;
}
int direction;
for (direction = -1; direction != 1; direction = 1)
{
float pos[3], comsum[3];
vec_copy (pos, &seeds[seed * 3]); // integration starting point is the seed
// init the arrays
points.clear ();
// main integration loop
pointcount = 0;
totalpointcount++;
float len = 0;
int iterations = 0;
float dir = (float) direction;
vec_zero (comsum); // clear center of mass accumulator
while ((len < maxlen) && (totalpointcount < 100000000))
{
float grad[3];
// sample gradient at the current position
v->voxel_gradient_interpolate_from_coord (pos, grad);
// Early-exit if we run out of bounds (gradient returned will
// be a vector of NANs), run into a critical point (zero gradient)
// or a huge gradient at a source/sink point in the dataset.
float gmag = norm (grad);
if (gmag < mingmag || gmag > maxgmag)
break;
// Draw the current point only after the gradient value
// has been checked, so we don't end up with out-of-bounds
// vertices.
// Only emit a fraction of integration points for display since
// the integrator stepsize needs to be small for more numerical
// accuracy, but the field lines themselves can be well
// represented with fewer sample points.
if (!(iterations & 1))
{
// Add a vertex for this field line
points.append (pos[0]);
points.append (pos[1]);
points.append (pos[2]);
vec_incr (comsum, pos);
pointcount++;
totalpointcount++;
}
// adjust integration stepsize so we never move more than
// the distance specified by delta at each step, to compensate
// for varying gradient magnitude
vec_scaled_add (pos, dir * delta / gmag, grad); // integrate position
len += delta; // accumulate distance
iterations++;
}
int drawfieldline = 1;
// only draw the field line for this seed if we have enough points.
// If we haven't reached the minimum field line length, we'll
// drop the whole field line.
if (pointcount < 2 || len < minlen)
drawfieldline = 0;
// only draw if bounding sphere diameter exceeds minlen
if (drawfieldline)
{
float com[3];
vec_scale (com, 1.0f / (float) pointcount, comsum);
float minlen2 = minlen * minlen;
drawfieldline = 0;
int p;
for (p = 0; p < pointcount; p++)
{
if ((2.0f * distance2 (com, &points[p * 3])) > minlen2)
{
drawfieldline = 1;
break;
}
}
}
// only draw the field line if it met all selection criteria
if (drawfieldline)
{
cmdLineType.putdata (SOLIDLINE, cmdList);
cmdLineWidth.putdata ((int) thickness, cmdList);
cmdColorIndex.putdata (usecolor, cmdList);
DispCmdPolyLineArray cmdPolyLineArray;
cmdPolyLineArray.putdata (&points[0], pointcount, cmdList);
}
}
}
msg_timer_destroy (msgt);
if (printdonemesg)
msgInfo << "field line integration complete." << sendmsg;
}
// read in the startup script, execute it, and then execute any other commands
// which might be necessary (i.e. to load any molecules at start)
// This searches for the startup file in the following
// places (and in this order), reading only the FIRST one found:
// 1. Current directory
// 2. Home directory
// 3. 'Default' directory (here, /usr/local/vmd)
// If a name was given in the -startup switch, that file is checked for ONLY.
void VMDreadStartup(VMDApp *app) {
char namebuf[512], *envtxt;
int found = FALSE;
FILE * tfp;
char *DataPath; // path of last resort to find a .vmdrc file
// These options were set by environment variables or command line options
app->display_set_screen_height(displayHeight);
app->display_set_screen_distance(displayDist);
app->set_eofexit(eofexit);
if (showTitle == TITLE_ON && which_display != DISPLAY_TEXT) {
app->display_titlescreen();
}
if((envtxt = getenv("VMDDIR")) != NULL)
DataPath = stringdup(envtxt);
else
DataPath = stringdup(DEF_VMDENVVAR);
stripslashes(DataPath); // strip out ending '/' chars.
// check if the file is available
if(startupFileStr) { // name specified by -startup
if((tfp = fopen(startupFileStr, "rb")) != NULL) {
found = TRUE;
fclose(tfp);
strcpy(namebuf, startupFileStr);
}
} else { // search in different directories, for default file
const char *def_startup = VMD_STARTUP;
// first, look in current dir
strcpy(namebuf, def_startup);
if((tfp = fopen(namebuf, "rb")) != NULL) {
found = TRUE;
fclose(tfp);
} else {
// not found in current dir; look in home dir
if((envtxt = getenv("HOME")) != NULL)
strcpy(namebuf,envtxt);
else
strcpy(namebuf,".");
strcat(namebuf,"/");
strcat(namebuf,def_startup);
if((tfp = fopen(namebuf, "rb")) != NULL) {
found = TRUE;
fclose(tfp);
} else {
// not found in home dir; look in default dir
strcpy(namebuf, DataPath);
strcat(namebuf,"/");
strcat(namebuf, def_startup);
if((tfp = fopen(namebuf, "rb")) != NULL) {
found = TRUE;
fclose(tfp);
}
}
}
}
delete [] DataPath; DataPath = NULL;
//
// execute any commands needed at start
//
// read in molecules requested via command-line switches
FileSpec spec;
spec.waitfor = -1; // wait for all files to load before proceeding
int molid = -1; // set sentinel value to determine if files were loaded
if (startNewMoleculeFlags.num() > 0) {
msgInfo << "File loading in progress, please wait." << sendmsg;
}
for (int i=0; i<startNewMoleculeFlags.num(); i++) {
const char *filename = initFilenames[i];
const char *filetype = initFiletypes[i];
if (!filetype) {
filetype = app->guess_filetype(filename);
if (!filetype) {
// assume pdb
msgErr << "Unable to determine file type for file '"
<< filename << "'. Assuming pdb." << sendmsg;
filetype = "pdb";
}
}
if (startNewMoleculeFlags[i]) {
molid = app->molecule_load(-1, filename, filetype, &spec);
} else {
molid = app->molecule_load(molid, filename, filetype, &spec);
}
if (molid < 0) {
msgErr << "Loading of startup molecule files aborted." << sendmsg;
break;
}
}
// if the startup file was found, read in the commands there
if(found) {
app->logfile_read(namebuf);
}
// Load the extension packages here, _after_ reading the .vmdrc file,
// so that the search path for extensions can be customized.
app->commandQueue->runcommand(
new TclEvalEvent("vmd_load_extension_packages"));
// Switch to Python if requested, before reading beginCmdFile
if (cmdFileUsesPython) {
if (!app->textinterp_change("python")) {
// bail out since Python scripts won't be readable by Tcl.
msgErr << "Skipping startup script because Python could not be started."
<< sendmsg;
return;
}
}
// after reading in startup file and loading any molecule, the file
// specified by the -e option is set up to be executed.
if(beginCmdFile) {
app->logfile_read(beginCmdFile);
}
}
// look for all environment variables VMD can use, and initialize the
// proper variables. If an env variable is not found, use a default value.
// ENVIRONMENT VARIABLES USED BY VMD (default values set in config.h):
// VMDDIR directory with VMD data files and utility programs
// VMDTMPDIR directory in which to put temporary files (def: /tmp)
static void VMDGetOptions(int argc, char **argv) {
char *envtxt;
//
// VMDDISPLAYDEVICE: which display device to use by default
//
if((envtxt = getenv("VMDDISPLAYDEVICE"))) {
for(int i=0; i < NUM_DISPLAY_TYPES; i++) {
if(!strupcmp(envtxt, displayTypeNames[i])) {
which_display = i;
break;
}
}
}
//
// VMDTITLE: whether to enable the title screen
//
if((envtxt = getenv("VMDTITLE"))) {
for(int i=0; i < NUM_TITLE_TYPES; i++) {
if(!strupcmp(envtxt, titleTypeNames[i])) {
showTitle = i;
break;
}
}
}
//
// VMDSCRHEIGHT: height of the screen
//
if((envtxt = getenv("VMDSCRHEIGHT")))
displayHeight = (float) atof(envtxt);
//
// VMDSCRDIST: distance to the screen
//
if((envtxt = getenv("VMDSCRDIST")))
displayDist = (float) atof(envtxt);
//
// VMDSCRPOS: graphics window location
//
if((envtxt = getenv("VMDSCRPOS"))) {
char * dispStr = NULL;
char * dispArgv[64];
int dispArgc;
if((dispStr = str_tokenize(envtxt, &dispArgc, dispArgv)) != NULL
&& dispArgc == 2) {
displayLoc[0] = atoi(dispArgv[0]);
displayLoc[1] = atoi(dispArgv[1]);
} else {
msgErr << "Illegal VMDSCRPOS environment variable setting '"
<< envtxt << "'." << sendmsg;
}
if(dispStr) delete [] dispStr;
}
//
// VMDSCRSIZE: graphics window size
//
if((envtxt = getenv("VMDSCRSIZE"))) {
char * dispStr = NULL;
char * dispArgv[64];
int dispArgc;
if((dispStr = str_tokenize(envtxt, &dispArgc, dispArgv)) != NULL
&& dispArgc == 2) {
displaySize[0] = atoi(dispArgv[0]);
displaySize[1] = atoi(dispArgv[1]);
// force users to do something that makes sense
if (displaySize[0] < 100)
displaySize[0] = 100; // minimum sane width
if (displaySize[1] < 100)
displaySize[1] = 100; // minimum sane height
} else {
msgErr << "Illegal VMDSCRSIZE environment variable setting '"
<< envtxt << "'." << sendmsg;
}
if(dispStr) delete [] dispStr;
}
// initialize variables which indicate how VMD starts up, and
// parse the command-line options
// go through the arguments
int ev = 1;
while(ev < argc) {
if(!strupcmp(argv[ev], "-dist")) {
if(argc > (ev + 1)) {
displayDist = (float) atof(argv[++ev]);
} else
msgErr << "-dist must also specify a distance." << sendmsg;
} else if(!strupcmp(argv[ev], "-e")) {
if(argc > (ev + 1)) {
beginCmdFile = argv[++ev];
} else
msgErr << "-e must also specify a filename." << sendmsg;
} else if(!strupcmp(argv[ev], "-height")) {
if(argc > (ev + 1)) {
displayHeight = (float) atof(argv[++ev]);
} else
msgErr << "-height must also specify a distance." << sendmsg;
} else if(!strupcmp(argv[ev], "-pos")) {
if(argc > (ev + 2) && *(argv[ev+1]) != '-' && *(argv[ev+2]) != '-') {
displayLoc[0] = atoi(argv[++ev]);
displayLoc[1] = atoi(argv[++ev]);
} else
msgErr << "-pos must also specify an X Y pair." << sendmsg;
} else if(!strupcmp(argv[ev], "-size")) {
if(argc > (ev + 2) && *(argv[ev+1]) != '-' && *(argv[ev+2]) != '-') {
displaySize[0] = atoi(argv[++ev]);
displaySize[1] = atoi(argv[++ev]);
} else
msgErr << "-size must also specify an X Y pair." << sendmsg;
} else if(!strupcmp(argv[ev], "-startup")) {
// use next argument as startup config file name
if(argc > (ev + 1))
startupFileStr = argv[++ev];
else
msgErr << "-startup must also have a new file name specified."
<< sendmsg;
} else if(!strupcmp(argv[ev], "-nt")) {
// do not print out the program title
showTitle = TITLE_OFF;
} else if (!strupcmp(argv[ev], "-dispdev")) { // startup Display
ev++;
if (argc > ev) {
if (!strupcmp(argv[ev], "cave")) {
which_display = DISPLAY_CAVE; // use the CAVE
} else if (!strupcmp(argv[ev], "win")) {
which_display = DISPLAY_WIN; // use OpenGL, the default
} else if (!strupcmp(argv[ev], "opengl")) {
which_display = DISPLAY_WINOGL; // use OpenGL if available
} else if (!strupcmp(argv[ev], "text")) {
which_display = DISPLAY_TEXT; // use text console only
} else if (!strupcmp(argv[ev], "caveforms")) {
which_display = DISPLAY_CAVEFORMS; // use CAVE+Forms
} else if (!strupcmp(argv[ev], "freevr")) {
which_display = DISPLAY_FREEVR; // use FreeVR
} else if (!strupcmp(argv[ev], "freevrforms")) {
which_display = DISPLAY_FREEVRFORMS; // use FreeVR+Forms
} else if (!strupcmp(argv[ev], "none")) {
which_display = DISPLAY_TEXT; // use text console only
} else {
msgErr << "-dispdev options are 'win' (default), 'cave', 'caveforms', 'freevr', 'freevrforms', or 'text | none'" << sendmsg;
}
} else {
msgErr << "-dispdev options are 'win' (default), 'cave', 'caveforms', 'freevr', 'freevrforms', or 'text | none'" << sendmsg;
}
} else if (!strupcmp(argv[ev], "-h") || !strupcmp(argv[ev], "--help")) {
// print out command-line option summary
msgInfo << "Available command-line options:" << sendmsg;
msgInfo << "\t-dispdev <win | cave | text | none> Specify display device";
msgInfo << sendmsg;
msgInfo << "\t-dist <d> Distance from origin to screen";
msgInfo << sendmsg;
msgInfo << "\t-e <filename> Execute commands in <filename>\n";
msgInfo << "\t-python Use Python for -e file and subsequent text input\n";
msgInfo << "\t-eofexit Exit when end-of-file occurs on input\n";
msgInfo << "\t-h | --help Display this command-line summary\n";
msgInfo << "\t-height <h> Height of display screen";
msgInfo << sendmsg;
msgInfo << "\t-pos <X> <Y> Lower-left corner position of display";
msgInfo << sendmsg;
msgInfo << "\t-nt No title display at start" << sendmsg;
msgInfo << "\t-size <X> <Y> Size of display" << sendmsg;
msgInfo << "\t-startup <filename> Specify startup script file" << sendmsg;
msgInfo << "\t-m Load subsequent files as separate molecules\n";
msgInfo << "\t-f Load subsequent files into the same molecule\n";
msgInfo << "\t<filename> Load file using best-guess file type\n";
msgInfo << "\t-<type> <filename> Load file using specified file type\n";
msgInfo << "\t-args Pass subsequent arguments to text interpreter\n";
msgInfo << sendmsg;
just_print_help = 1;
} else if (!strupcmp(argv[ev], "-eofexit")) { // exit on EOF
eofexit = 1;
} else if (!strupcmp(argv[ev], "-node")) {
// start VMD process on a cluster node, next parm is node ID..
ev++; // skip node ID parm
} else if (!strupcmp(argv[ev], "-webhelper")) {
// Unix startup script doesn't run VMD in the background, so that
// web browsers won't delete files out from under us until it really
// exits. We don't do anything special inside VMD itself presently
// however.
} else if (!strupcmp(argv[ev], "-python")) {
cmdFileUsesPython = 1;
} else if (!strupcmp(argv[ev], "-args")) {
// pass the rest of the command line arguments, and only those,
// to the embedded text interpreters.
while (++ev < argc)
customArgv.append(argv[ev]);
} else if (!strupcmp(argv[ev], "-m")) {
loadAsMolecules = 1;
startNewMolecule = 1;
} else if (!strupcmp(argv[ev], "-f")) {
loadAsMolecules = 0;
startNewMolecule = 1;
#ifdef VMDMPI
} else if (!strupcmp(argv[ev], "-vmddir")) {
ev++; // skip VMDDIR directory parm, since we already handled this
// in MPI startup before we got to this loop...
#endif
} else {
// any other argument is treated either as a filename or as a
// filetype/filename pair of the form -filetype filename.
const char *filename, *filetype;
if (argv[ev][0] == '-') {
// must be filetype/filename pair
if (argc > ev+1) {
filetype = argv[ev]+1;
filename = argv[ev+1];
ev++;
} else {
msgErr << "filetype argument '" << argv[ev] << "' needs a filename."
<< sendmsg;
ev++; // because we skip past the ev++ at the bottom of the loop.
continue;
}
} else {
// Given just a filename. The filetype will have to be guessed.
filename = argv[ev];
filetype = NULL;
}
initFilenames.append(filename);
initFiletypes.append(filetype);
startNewMoleculeFlags.append(startNewMolecule);
if (!loadAsMolecules) startNewMolecule = 0;
}
ev++;
}
// command-line options have been parsed ... any init status variables that
// have been given initial values will have flags saying so, and their
// values will not be changed when the init file(s) is parsed.
}
int VMDinitialize(int *argc, char ***argv) {
int i;
#if defined VMDMPI
// hack to fix up env vars if necessary
for (i=0; i<(*argc); i++) {
if(!strupcmp((*argv)[i], "-vmddir")) {
if((*argc) > (i + 1)) {
setenv("VMDDIR", (*argv)[++i], 1);
} else {
msgErr << "-vmddir must specify a fully qualified path." << sendmsg;
}
}
}
vmd_mpi_init(argc, argv); // initialize MPI, fix up env vars, etc.
#endif
#if defined(_MSC_VER) && !defined(VMDSEPARATESTARTUP)
win32vmdstart(); // get registry info etc
#endif
#if !defined(VMDNOMACBUNDLE) && defined(__APPLE__)
macosxvmdstart(*argc, *argv); // get env variables etc
#endif
// Tell Tcl where the executable is located
const char *argv0 = vmd_initialize_tcl((*argv)[0]);
#ifdef VMDTCL
// register signal handler
tclhandler = Tcl_AsyncCreate(VMDTclAsyncProc, (ClientData)NULL);
signal(SIGINT, (sighandler_t) VMDTclSigHandler);
#endif
// Let people know who we are.
VMDtitle();
// Tell the user what we think about the hardware we're running on.
// If VMD is compiled for MPI, then we don't print any of the normal
// standalone startup messages and instead we use the special MPI-specific
// node scan startup messages only.
#if !defined(VMDMPI)
#if defined(VMDTHREADS)
int vmdnumcpus = wkf_thread_numprocessors();
msgInfo << "Multithreading available, " << vmdnumcpus <<
((vmdnumcpus > 1) ? " CPUs" : " CPU") << " detected."
<< sendmsg;
#endif
long vmdcorefree = vmd_get_avail_physmem_mb();
if (vmdcorefree >= 0) {
long vmdcorepcnt = vmd_get_avail_physmem_percent();
msgInfo << "Free system memory: " << vmdcorefree
<< "MB (" << vmdcorepcnt << "%)" << sendmsg;
}
#endif
// Read environment variables and command line options.
// Initialize customArgv with just argv0 to avoid problems with
// Tcl extension.
customArgv.append((char *)argv0);
VMDGetOptions(*argc, *argv);
#if (!defined(__APPLE__) && !defined(_MSC_VER)) && (defined(VMDOPENGL) || defined(VMDFLTK))
// If we're using X-windows, we autodetect if the DISPLAY environment
// variable is unset, and automatically switch back to text mode without
// requiring the user to pass the "-dispdev text" command line parameters
if ((which_display == DISPLAY_WIN) && (getenv("DISPLAY") == NULL)) {
which_display = DISPLAY_TEXT;
}
#endif
#if defined(VMDTKCON)
vmdcon_init();
msgInfo << "Using VMD Console redirection interface." << sendmsg;
// we default to a widget mode console, unless text mode is requested.
// we don't have an tcl interpreter registered yet, so it is set to NULL.
// flushing pending messages to the screen, is only in text mode possible.
if ((which_display == DISPLAY_TEXT) || just_print_help) {
vmdcon_use_text(NULL);
vmdcon_purge();
} else {
vmdcon_use_widget(NULL);
}
#endif
#ifdef VMDFLTK
// Do various special FLTK initialization stuff here
if ((which_display != DISPLAY_TEXT)) {
// Cause FLTK to to use 24-bit color for all windows if possible
// This must be done before any FLTK windows are shown for the first time.
if (!Fl::visual(FL_DOUBLE | FL_RGB8)) {
if (!Fl::visual(FL_RGB8)) {
Fl::visual(FL_RGB);
}
}
// Disable the use of the arrow keys for navigating buttons and other
// non-text widgets, we'll try it out and see how it pans out
Fl::visible_focus(0);
// Disable Drag 'n Drop since the only text field in VMD is the
// atomselection input and DND severely gets in the way there.
Fl::dnd_text_ops(0);
}
#endif
// Quit now if the user just wanted a list of command line options.
if (just_print_help) {
vmd_sleep(10); // This is here so that the user can see the message
// before the terminal/shell exits...
return 0;
}
// Set up default allocators; these may be overridden by cave or freevr.
vmd_alloc = malloc; // system malloc() in the default case
vmd_dealloc = free; // system free() in the default case
vmd_realloc = realloc; // system realloc(), set to NULL when not available
// check for a CAVE display
if (DISPLAY_USES_CAVE(which_display)) {
#ifdef VMDCAVE
// allocate shared memory pool used to communicate with child renderers
int megs = 2048;
if (getenv("VMDCAVEMEM") != NULL) {
megs = atoi(getenv("VMDCAVEMEM"));
}
msgInfo << "Attempting to get " << megs <<
"MB of CAVE Shared Memory" << sendmsg;
grab_CAVE_memory(megs);
CAVEConfigure(argc, *argv, NULL); // configure cave walls and memory use
// point VMD shared memory allocators to CAVE routines
vmd_alloc = malloc_from_CAVE_memory;
vmd_dealloc = free_to_CAVE_memory;
vmd_realloc = NULL; // no realloc() functionality is available presently
#else
msgErr << "Not compiled with the CAVE options set." << sendmsg;
which_display = DISPLAY_WIN;
#endif
}
// check for a FreeVR display
if (DISPLAY_USES_FREEVR(which_display)) {
#ifdef VMDFREEVR
int megs = 2048;
if (getenv("VMDFREEVRMEM") != NULL) {
megs = atoi(getenv("VMDFREEVRMEM"));
}
msgInfo << "Attempting to get " << megs <<
"MB of FreeVR Shared Memory" << sendmsg;
grab_FreeVR_memory(megs); // have to do this *before* vrConfigure() if
// we want more than the default shared mem.
vrConfigure(NULL, NULL, NULL); // configure FreeVR walls
// point shared memory allocators to FreeVR routines
vmd_alloc = malloc_from_FreeVR_memory;
vmd_dealloc = free_to_FreeVR_memory;
vmd_realloc = NULL; // no realloc() functionality is available presently
#else
msgErr << "Not compiled with the FREEVR options set." << sendmsg;
which_display = DISPLAY_WIN;
#endif
}
// return custom argc/argv
*argc = customArgv.num();
for (i=0; i<customArgv.num(); i++) {
(*argv)[i] = customArgv[i];
}
return 1; // successful startup
}
int text_cmd_mobile(ClientData cd, Tcl_Interp *interp, int argc,
const char *argv[]) {
VMDApp *app = (VMDApp *)cd;
if (argc < 3 || argc > 6) {
// if here, something went wrong, so return an error message
mobile_usage(interp);
return TCL_ERROR;
}
if (!strupncmp(argv[1], "mode", CMDLEN)) {
int m1 = Mobile::OFF;
// see if these are string values
if (!strupncmp(argv[2], "off", CMDLEN)) m1 = Mobile::OFF;
else if (!strupncmp(argv[2], "move", CMDLEN)) m1 = Mobile::MOVE;
else if (!strupncmp(argv[2], "animate", CMDLEN)) m1 = Mobile::ANIMATE;
else if (!strupncmp(argv[2], "tracker", CMDLEN)) m1 = Mobile::TRACKER;
else if (!strupncmp(argv[2], "user", CMDLEN)) m1 = Mobile::USER;
else mobile_usage(interp); // error
if (!app->mobile_set_mode(m1)) {
Tcl_AppendResult(interp, "Unable to set Mobile mode to ",
argv[2], argc > 3 ? argv[3] : NULL, NULL);
// if here, something went wrong, so return an error message
mobile_usage(interp);
return TCL_ERROR;
}
} else if(!strupncmp(argv[1], "port", CMDLEN)) {
int port;
if (sscanf(argv[2], "%d", &port) == 1) {
if (!app->mobile_network_port(port)) {
// if here, something went wrong, so return an error message
mobile_usage(interp);
return TCL_ERROR;
}
} else {
// if here, something went wrong, so return an error message
mobile_usage(interp);
return TCL_ERROR;
}
} else if(!strupncmp(argv[1], "get", CMDLEN)) {
if (!strupncmp(argv[2], "mode", CMDLEN))
{
Tcl_AppendResult(interp, Mobile::get_mode_str((Mobile::MoveMode)app->mobile_get_mode()), NULL);
} else if (!strupncmp(argv[2], "clientList", CMDLEN)) {
ResizeArray <JString *>* ip;
ResizeArray <JString *>* nick;
ResizeArray <bool>* active;
app->mobile_get_client_list( nick, ip, active);
for (int i=0; i<nick->num(); i++)
{
Tcl_AppendResult(interp, " {", NULL);
Tcl_AppendResult(interp, " {", NULL);
// here's what we've got..
// (const char *)(*(*nick)[i])
// now to explain it....
// (const char *) Tcl_AppendResult needs a char*
// (* ) We have a JString* in ResizeArray that we want to be a JString
// (*nick) we have a ResizeArray ptr that we want to be a ResizeArray
// [i] specific array elem
Tcl_AppendResult(interp, (const char *)(*(*nick)[i]), NULL);
Tcl_AppendResult(interp, "}", NULL);
Tcl_AppendResult(interp, " {", NULL);
Tcl_AppendResult(interp, (const char *)(*(*ip)[i]), NULL);
Tcl_AppendResult(interp, "}", NULL);
Tcl_AppendResult(interp, " {", NULL);
char tmp[10]; sprintf(tmp, "%d", (*active)[i]);
Tcl_AppendResult(interp, tmp, NULL);
Tcl_AppendResult(interp, "}", NULL);
Tcl_AppendResult(interp, " }", NULL);
}
} else if (!strupncmp(argv[2], "port", CMDLEN)) {
char tmpstr[20];
sprintf(tmpstr, "%d", app->mobile_get_network_port());
Tcl_AppendResult(interp, tmpstr, NULL);
} else if (!strupncmp(argv[2], "APIsupported", CMDLEN)) {
char tmpstr[20];
sprintf(tmpstr, "%d", app->mobile_get_APIsupported());
Tcl_AppendResult(interp, tmpstr, NULL);
} else mobile_usage(interp); // error
} else if(!strupncmp(argv[1], "sendMsg", CMDLEN)) {
if (argc >= 6)
{
if (!app->mobile_sendMsg(argv[2], argv[3], argv[4], argv[5])) {
// if here, something went wrong, so return an error message
mobile_usage(interp);
return TCL_ERROR;
}
} else mobile_usage(interp); // error
} else if(!strupncmp(argv[1], "set", CMDLEN)) {
if (!strupncmp(argv[2], "activeClient", CMDLEN))
{
if (argc >= 5)
{
if (!app->mobile_set_activeClient(argv[3], argv[4])) {
// Tcl_AppendResult(interp, "Unable to set activeClient to ",
// argv[2], argc > 3 ? argv[3] : NULL, NULL);
// if here, something went wrong, so return an error message
mobile_usage(interp);
return TCL_ERROR;
}
} else mobile_usage(interp); // error
} else mobile_usage(interp); // error
} else {
// if here, something went wrong, so return an error message
mobile_usage(interp);
return TCL_ERROR;
}
// if here, everything worked out ok
return TCL_OK;
}
int
DisplayDevice::pick (int dim, const float *pos, const VMDDisplayList *cmdList,
float &eyedist, int *unitcell, float window_size)
{
char *cmdptr = NULL;
int tok;
float newEyeDist, currEyeDist = eyedist;
int tag = (-1), inRegion, currTag;
int minX = 0, minY = 0, maxX = 0, maxY = 0;
float fminX = 0.0f, fminY = 0.0f, fminZ = 0.0f, fmaxX = 0.0f, fmaxY = 0.0f,
fmaxZ = 0.0f;
float pntpos[3];
long cpos[2];
if (!cmdList)
return (-1);
// initialize picking: find screen region to look for object
if (dim == 2)
{
fminX = pos[0] - window_size;
fmaxX = pos[0] + window_size;
fminY = pos[1] - window_size;
fmaxY = pos[1] + window_size;
abs_screen_pos (fminX, fminY);
abs_screen_pos (fmaxX, fmaxY);
minX = (int) fminX;
maxX = (int) fmaxX;
minY = (int) fminY;
maxY = (int) fmaxY;
}
else
{
fminX = pos[0] - window_size;
fmaxX = pos[0] + window_size;
fminY = pos[1] - window_size;
fmaxY = pos[1] + window_size;
fminZ = pos[2] - window_size;
fmaxZ = pos[2] + window_size;
}
// make sure we do not disturb the regular transformation matrix
transMat.dup ();
(transMat.top ()).multmatrix (cmdList->mat);
// Transform the current pick point for each periodic image
ResizeArray<Matrix4> pbcImages;
ResizeArray<int> pbcCells;
find_pbc_images (cmdList, pbcImages);
find_pbc_cells (cmdList, pbcCells);
int pbcimg;
for (pbcimg = 0; pbcimg < pbcImages.num (); pbcimg++)
{
transMat.dup ();
(transMat.top ()).multmatrix (pbcImages[pbcimg]);
// scan through the list, getting each command and executing it, until
// the end of commands token is found
VMDDisplayList::VMDLinkIter cmditer;
cmdList->first (&cmditer);
float *dataBlock = NULL;
while ((tok = cmdList->next (&cmditer, cmdptr)) != DLASTCOMMAND)
{
switch (tok)
{
case DDATABLOCK:
#ifdef VMDCAVE
dataBlock = (float *)cmdptr;
#else
dataBlock = ((DispCmdDataBlock *) cmdptr)->data;
#endif
break;
case DPICKPOINT:
case DPICKPOINT_I:
// calculate the transformed position of the point
if (tok == DPICKPOINT)
{
DispCmdPickPoint *cmd = (DispCmdPickPoint *) cmdptr;
(transMat.top ()).multpoint3d (cmd->postag, pntpos);
currTag = cmd->tag;
}
else
{
DispCmdPickPointIndex *cmd = (DispCmdPickPointIndex *) cmdptr;
(transMat.top ()).multpoint3d (dataBlock + cmd->pos, pntpos);
currTag = cmd->tag;
}
// check if in picking region ... different for 2D and 3D
if (dim == 2)
{
// convert the 3D world coordinate to 2D absolute screen coord
abs_screen_loc_3D (pntpos, cpos);
// check to see if the position falls in our picking region
inRegion = (cpos[0] >= minX && cpos[0] <= maxX && cpos[1] >= minY
&& cpos[1] <= maxY);
}
else
{
// just check to see if the position is in a box centered on our
// pointer. The pointer position should already be transformed.
inRegion = (pntpos[0] >= fminX && pntpos[0] <= fmaxX
&& pntpos[1] >= fminY && pntpos[1] <= fmaxY
&& pntpos[2] >= fminZ && pntpos[2] <= fmaxZ);
}
// has a hit occurred?
if (inRegion)
{
// yes, see if it is closer to the eye position than earlier objects
if (dim == 2)
newEyeDist = DTOEYE(pntpos[0], pntpos[1], pntpos[2]);
else
newEyeDist = DTOPOINT(pntpos[0],pntpos[1],pntpos[2]);
if (currEyeDist < 0.0 || newEyeDist < currEyeDist)
{
currEyeDist = newEyeDist;
tag = currTag;
if (unitcell)
{
unitcell[0] = pbcCells[3 * pbcimg];
unitcell[1] = pbcCells[3 * pbcimg + 1];
unitcell[2] = pbcCells[3 * pbcimg + 2];
}
}
}
break;
case DPICKPOINT_IARRAY:
// loop over all of the pick points in the pick point index array
DispCmdPickPointIndexArray *cmd =
(DispCmdPickPointIndexArray *) cmdptr;
float *pickpos;
int *indices;
cmd->getpointers (indices);
int i;
for (i = 0; i < cmd->numpicks; i++)
{
if (cmd->allselected)
{
pickpos = dataBlock + i * 3;
currTag = i;
}
else
{
pickpos = dataBlock + indices[i] * 3;
currTag = indices[i];
}
(transMat.top ()).multpoint3d (pickpos, pntpos);
// check if in picking region ... different for 2D and 3D
if (dim == 2)
{
// convert the 3D world coordinate to 2D absolute screen coord
abs_screen_loc_3D (pntpos, cpos);
// check to see if the position falls in our picking region
inRegion = (cpos[0] >= minX && cpos[0] <= maxX
&& cpos[1] >= minY && cpos[1] <= maxY);
}
else
{
// just check to see if the position is in a box centered on our
// pointer. The pointer position should already be transformed.
inRegion = (pntpos[0] >= fminX && pntpos[0] <= fmaxX
&& pntpos[1] >= fminY && pntpos[1] <= fmaxY
&& pntpos[2] >= fminZ && pntpos[2] <= fmaxZ);
}
// has a hit occurred?
if (inRegion)
{
// yes, see if it is closer to the eye than earlier hits
if (dim == 2)
newEyeDist = DTOEYE(pntpos[0], pntpos[1], pntpos[2]);
else
newEyeDist = DTOPOINT(pntpos[0],pntpos[1],pntpos[2]);
if (currEyeDist < 0.0 || newEyeDist < currEyeDist)
{
currEyeDist = newEyeDist;
tag = currTag;
if (unitcell)
{
unitcell[0] = pbcCells[3 * pbcimg];
unitcell[1] = pbcCells[3 * pbcimg + 1];
unitcell[2] = pbcCells[3 * pbcimg + 2];
}
}
}
}
break;
}
}
// Pop the PBC image transform
transMat.pop ();
} // end of loop over PBC images
// make sure we do not disturb the regular transformation matrix
transMat.pop ();
// return result; if tag >= 0, we found something
eyedist = currEyeDist;
return tag;
}
static PyObject *sasa(PyObject *self, PyObject *args, PyObject *keywds) {
int molid = -1, frame = -1;
float srad = 0;
PyObject *selobj = NULL, *restrictobj = NULL;
int samples = -1;
const int *sampleptr = NULL;
PyObject *pointsobj = NULL;
static char *kwlist[] = {
(char *)"srad", (char *)"molid", (char *)"frame", (char *)"selected",
(char *)"samples", (char *)"points", (char *)"restrict"
};
if (!PyArg_ParseTupleAndKeywords(args, keywds,
(char *)"fiiO!|iO!O!:atomselection.sasa", kwlist,
&srad, &molid, &frame, &PyTuple_Type, &selobj,
&samples, &PyList_Type, &pointsobj, &PyTuple_Type, &restrictobj))
return NULL;
// validate srad
if (srad < 0) {
PyErr_SetString(PyExc_ValueError, (char *)"atomselect.sasa: srad must be non-negative.");
return NULL;
}
// validate selection
VMDApp *app = get_vmdapp();
AtomSel *sel = sel_from_py(molid, frame, selobj, app);
if (!sel) return NULL;
// fetch the radii and coordinates
const float *radii =
app->moleculeList->mol_from_id(sel->molid())->extraflt.data("radius");
const float *coords = sel->coordinates(app->moleculeList);
// if samples was given and is valid, use it
if (samples > 1) sampleptr = &samples;
// if restrict is given, validate it
AtomSel *restrictsel = NULL;
if (restrictobj) {
if (!(restrictsel = sel_from_py(molid, frame, restrictobj, app))) {
delete sel;
return NULL;
}
}
// if points are requested, fetch them
ResizeArray<float> sasapts;
ResizeArray<float> *sasaptsptr = pointsobj ? &sasapts : NULL;
// go!
float sasa = 0;
int rc = measure_sasa(sel, coords, radii, srad, &sasa,
sasaptsptr, restrictsel, sampleptr);
delete sel;
delete restrictsel;
if (rc) {
PyErr_SetString(PyExc_ValueError, (char *)measure_error(rc));
return NULL;
}
// append surface points to the provided list object.
if (pointsobj) {
for (int i=0; i<sasapts.num(); i++) {
PyList_Append(pointsobj, PyFloat_FromDouble(sasapts[i]));
}
}
// return the total SASA.
return PyFloat_FromDouble(sasa);
}
GromacsTopFile::GromacsTopFile(char *filename) {
fudgeLJ = fudgeQQ = 1.0;
/* open the file */
FILE *f = fopen(filename,"r");
char buf[LINESIZE];
char modename[20];
int mode;
if(f==NULL) {
sprintf(buf,"Error opening file '%s'",filename);
NAMD_die(buf);
}
/* really bad parser XXX probably just works on the files we
happen to have REWRITE THIS SOON. It should allow for \- line
continuations, check for errors in the file, etc. */
while(fgets(buf,LINESIZE-1,f)) {
char testchar;
int i,j;
/* defaults */
int nbfunc, combrule;
char genpairs[20];
/* atom buffers */
int num, resnum, chargegp, typenum;
char type[NAMESIZE+1], restype[NAMESIZE+1], atomname[NAMESIZE+1];
char particletype[NAMESIZE+1];
float charge, mass, c6, c12, junkf;
/* moltype buffers */
int nrexcl;
char molname[LONGNAMESIZE+1];
/* molInst buffers */
int copies;
MolInst *moleculeinstance;
/* general atomset buffers */
int atomi, atomj, atomk, atoml;
char typea[NAMESIZE+1],typeb[NAMESIZE+1],
typec[NAMESIZE+1],typed[NAMESIZE+1];
const char *tmptypea,*tmptypeb,*tmptypec,*tmptyped;
int funct, index;
float c0,c1;
/* bonds */
float b0,kB,th0,kth;
/* dihedrals */
float c[6];
int mult=0;
/* check for comments */
if(sscanf(buf," %c",&testchar)==1) {
if(testchar == ';') continue;
}
else { /* this is a blank line */
continue;
}
/* check for a new mode */
if(sscanf(buf," [ %19[^] ] ]",modename)==1) {
/* switch the mode */
if(0==strcmp(modename,"atoms")) mode = ATOMS;
else if(0==strcmp(modename,"atomtypes")) mode = ATOMTYPES;
else if(0==strcmp(modename,"moleculetype")) mode = MOLECULETYPE;
else if(0==strcmp(modename,"molecules")) mode = MOLECULES;
else if(0==strcmp(modename,"system")) mode = SYSTEM;
else if(0==strcmp(modename,"bonds")) mode = BONDS;
else if(0==strcmp(modename,"bondtypes")) mode = BONDTYPES;
else if(0==strcmp(modename,"angles")) mode = ANGLES;
else if(0==strcmp(modename,"angletypes")) mode = ANGLETYPES;
else if(0==strcmp(modename,"dihedrals")) mode = DIHEDRALS;
else if(0==strcmp(modename,"dihedraltypes")) mode = DIHEDRALTYPES;
else if(0==strcmp(modename,"defaults")) mode = DEFAULTS;
else if(0==strcmp(modename,"nonbond_params")) mode = NONBOND;
// JLai
else if(0==strcmp(modename,"pairs")) mode = PAIRS;
else if(0==strcmp(modename,"exclusions")) mode = EXCLUSIONS;
else {
fprintf(stderr,"Warning: unknown mode %s\n",modename);
mode = UNKNOWN;
}
continue;
}
/* now do the appropriate thing based on the current mode */
switch(mode) {
case SYSTEM:
systemName = strdup(buf);
break;
case DEFAULTS:
i = sscanf(buf," %d %d %20s %f %f",
&nbfunc,&combrule,genpairs,&fudgeLJ,&fudgeQQ);
if(i < 3) { // didn't get enough parameters
fprintf(stderr,"syntax error in DEFAULTS\n");
exit(1);
}
if(nbfunc != 1) { // I don't know how it works with nbfunc=2
fprintf(stderr,"Non-bonded function != 1 unsupported in DEFAULTS\n");
exit(1);
}
if(combrule != 1) { // same here
fprintf(stderr,"Combination rule != 1 unsupported in DEFAULTS\n");
exit(1);
}
if(0==strcmp(genpairs,"yes")) {
genPairs=1;
if(i!=5) {
fprintf(stderr,"syntax error in DEFAULTS\n");
exit(1);
}
// else fudgeLJ and fudgeQQ got written automatically
}
else genPairs=0;
break;
case NONBOND:
if(5 != sscanf(buf," %5s %5s %d %f %f",
typea, typeb, &funct, &c6, &c12)) {
fprintf(stderr,"Syntax error in NONBOND\n");
exit(1);
}
// convert kJ/mol*nm6 to kcal/mol*A6 and ..12 ..12
c6 = c6/JOULES_PER_CALORIE*1E6;
c12= c12/JOULES_PER_CALORIE*1E12;
vdwTable.addType(typea,typeb,c6,c12);
break;
case BONDS:
i = sscanf(buf," %d %d %d %f %f",
&atomi,&atomj,&funct,&c0,&c1);
atomi--; // shift right away to a zero-indexing
atomj--;
if(i==3) {
tmptypea = genericMols[genericMols.size()-1]->getAtom(atomi)->getType();
tmptypeb = genericMols[genericMols.size()-1]->getAtom(atomj)->getType();
/* find the index and parameters */
index = bondTable.getParams(tmptypea, tmptypeb, funct, &b0, &kB);
if(index==-1) {
fprintf(stderr,"Required bondtype %s--%s (function %d) not found.\n",
tmptypea,tmptypeb,funct);
exit(1);
}
}
else if(i==5) {
/* first set the values of b0 and kB correctly */
b0 = c0*ANGSTROMS_PER_NM; /* convert nm to A */
if(funct==1) { /* harmonic potential */
/* convert kJ/nm2 to kcal/A2 and use E=kx2 instead of half that. */
kB = c1/JOULES_PER_CALORIE/100/2;
}
else if(funct==2) { /* special fourth-order potential */
/* convert to the normal harmonic constant and kJ/nm2 to kcal/A2 */
kB = 2*c1*c0*c0/JOULES_PER_CALORIE/100;
kB /= 2; /* use the NAMD system where E=kx2 */
}
else {
fprintf(stderr,"I don't know what funct=%d means in BONDS\n",funct);
exit(1);
}
/* look up the index */
index = bondTable.getIndex(b0,kB,funct);
}
else {
fprintf(stderr,"Syntax error in BONDS\n");
exit(1);
}
genericMols[genericMols.size()-1]->addBond(atomi,atomj,index);
break;
case BONDTYPES:
if(5 != sscanf(buf," %5s %5s %d %f %f",
typea,typeb,&funct,&c0,&c1)) {
fprintf(stderr,"Syntax error in BONDTYPES\n");
exit(1);
}
/* first set the values of b0 and kB correctly */
b0 = c0*10; /* convert nm to A */
if(funct==1) { /* harmonic potential */
/* convert kJ/nm2 to kcal/A2 and use E=kx2 instead of half that. */
kB = c1/JOULES_PER_CALORIE/100/2;
}
else if(funct==2) { /* special fourth-order potential */
/* convert to the normal harmonic constant and kJ/nm2 to kcal/A2 */
kB = 2*c1*c0*c0/JOULES_PER_CALORIE/100;
kB /= 2; /* use the NAMD system where E=kx2 */
}
else {
fprintf(stderr,"I don't know what funct=%d means in BONDTYPES\n",funct);
exit(1);
}
bondTable.addType(typea,typeb,b0,kB,funct);
break;
case ANGLES:
i = sscanf(buf," %d %d %d %d %f %f",
&atomi,&atomj,&atomk,&funct,&c0,&c1);
atomi--; // shift right away to a zero-indexing
atomj--;
atomk--;
if(i == 4) { /* we have to look up the last two parameters */
tmptypea = genericMols[genericMols.size()-1]->getAtom(atomi)->getType();
tmptypeb = genericMols[genericMols.size()-1]->getAtom(atomj)->getType();
tmptypec = genericMols[genericMols.size()-1]->getAtom(atomk)->getType();
/* find the index and parameters */
index = angleTable.getParams(tmptypea, tmptypeb, tmptypec,
funct, &th0, &kth);
if(index==-1) {
fprintf(stderr,
"Required angletype %s--%s--%s (function %d) not found.\n",
tmptypea,tmptypeb,tmptypec,funct);
exit(1);
}
}
else if(i == 6) {
/* first set the values of th0 and kth correctly */
if(funct == 1) {
th0 = c0; /* both are in degrees */
kth = c1/JOULES_PER_CALORIE/2; /* convert kJ/rad2 to kcal/rad2 and use E=kx2 */
}
else if(funct == 2) {
th0 = c0; /* both are in degrees */
/* convert G96 kJ to kcal/rad2 and use E=kx2 */
kth = sin(th0*PI/180)*sin(th0*PI/180)*c1/JOULES_PER_CALORIE/2;
}
else {
fprintf(stderr,"I don't know what funct=%d means in ANGLES\n",funct);
exit(1);
}
/* add the angle type to our table */
index = angleTable.getIndex(th0,kth,funct);
}
else {
fprintf(stderr,"Syntax error (%d args) in ANGLES: %s\n",i,buf);
exit(1);
}
/* add the angle to our table */
genericMols[genericMols.size()-1]->addAngle(atomi,atomj,atomk,index);
break;
case ANGLETYPES:
if(6 != sscanf(buf," %5s %5s %5s %d %f %f",
typea,typeb,typec,&funct,&c0,&c1)) {
fprintf(stderr,"Syntax error in ANGLETYPES\n");
exit(1);
}
/* first set the values of th0 and kth correctly */
if(funct == 1) {
th0 = c0; /* both are in degrees */
kth = c1/JOULES_PER_CALORIE/2; /* convert kJ/rad2 to kcal/rad2 and use E=kx2 */
}
else if(funct == 2) {
th0 = c0; /* both are in degrees */
/* convert G96 kJ to kcal/rad2 and use E=kx2 */
kth = sin(th0*PI/180)*sin(th0*PI/180)*c1/JOULES_PER_CALORIE/2;
}
else {
fprintf(stderr,"I don't know what funct=%d means in ANGLETYPES\n",
funct);
exit(1);
}
angleTable.addType(typea,typeb,typec,th0,kth,funct);
break;
case DIHEDRALS:
i = sscanf(buf," %d %d %d %d %d %f %f %f %f %f %f",
&atomi,&atomj,&atomk,&atoml,&funct,
&c[0],&c[1],&c[2],&c[3],&c[4],&c[5]);
atomi--; // shift right away to a zero-indexing
atomj--;
atomk--;
atoml--;
if(i==5) { /* we have to look up the parameters */
tmptypea = genericMols[genericMols.size()-1]->getAtom(atomi)->getType();
tmptypeb = genericMols[genericMols.size()-1]->getAtom(atomj)->getType();
tmptypec = genericMols[genericMols.size()-1]->getAtom(atomk)->getType();
tmptyped = genericMols[genericMols.size()-1]->getAtom(atoml)->getType();
/* find the index and parameters */
index = dihedralTable.getParams(tmptypea, tmptypeb, tmptypec,
tmptyped, funct, c, &mult);
if(index==-1) {
fprintf(stderr,
"Required dihedraltype %s--%s--%s--%s (function %d) not found.\n",
tmptypea,tmptypeb,tmptypec,tmptyped,funct);
exit(1);
}
}
else if(i==7 || i==8 || i==11) { /* the parameters are given */
if(funct==1 || funct==2) { /* we should have two parameters */
if(i!=7+(funct==1)) { /* plus a multiplicity for funct==1 */
fprintf(stderr,"Must have 7 args for funct=1,2\n");
exit(1);
}
c[0] = c[0]; /* both in deg */
if(i==7) {
c[1] = c[1]/(2*JOULES_PER_CALORIE); /* convert kJ to kcal and still use E=kx2*/
} else if (i==8 || i==11) {
c[1] = c[1]/(1*JOULES_PER_CALORIE); /* convert kJ to kcal and still use E=kx2*/
}
//c[1] = c[1]/(2*JOULES_PER_CALORIE); /* convert kJ to kcal and still use E=kx2*/
/* for funct==1 these are both divided by rad^2 */
if(funct==1) {
mult=(int)(c[2]+0.5); /* round to nearest integer :p */
}
}
else if(funct==3) {
if(i!=11){
fprintf(stderr,"Must have 11 args for funct=3\n");
exit(1);
}
for(j=0;j<6;j++) {
c[j] = c[j]/JOULES_PER_CALORIE; /* convert kJ to kcal and E=Cn cos^n */
}
}
else {
fprintf(stderr,
"I don't know what funct=%d means in DIHEDRALS\n",funct);
exit(1);
}
index = dihedralTable.getIndex(c,mult,funct);
}
else {
fprintf(stderr,"Syntax error (%d args) in DIHEDRALS: %s\n",i,buf);
exit(1);
}
/* add the dihedrals to our table */
genericMols[genericMols.size()-1]->addDihedral(atomi,atomj,atomk,atoml,
index);
break;
case DIHEDRALTYPES:
i = sscanf(buf," %5s %5s %d %f %f %f %f %f %f",
typea,typeb,&funct,&c[0],&c[1],&c[2],&c[3],&c[4],&c[5]);
if(funct == 1 || funct == 2) {
if(i!=5+(funct==1)) { /* 6 for f=2, 5 for f=1 */
fprintf(stderr,"Syntax error in DIHEDRALTYPES: %s\n",buf);
exit(1);
}
c[0] = c[0]; /* both in deg */
c[1] = c[1]/JOULES_PER_CALORIE; /* convert kJ to kcal and still use E=kx2*/
/* for funct==1 these are both divided by rad^2 */
if(funct==1) {
mult=(int)(c[2]+0.5); /* round to nearest integer :p */
}
}
else if(funct == 3) {
if(i!=9) {
fprintf(stderr,"Syntax error in DIHEDRALTYPES\n");
exit(1);
}
for(j=0;j<6;j++) {
c[j] = c[j]/JOULES_PER_CALORIE; /* convert kJ to kcal and E=Cn cos^n */
}
}
else {
fprintf(stderr,"I don't know what funct=%d means in DIHEDRALTYPES\n",
funct);
exit(1);
}
dihedralTable.addType(typea,typeb,c,mult,funct);
break;
case ATOMS:
i = sscanf(buf," %d %5s %d %5s %5s %d %f %f",
&num, type, &resnum, restype,
atomname, &chargegp, &charge, &mass);
if(i==7) { /* XXX temporary - I should be able to get more
params */
typenum = atomTable.getParams(type,&mass,&junkf,&junkf,&junkf);
i=8;
}
else {
if(i!=8) {
fprintf(stderr,"Syntax error in ATOMS\n");
exit(1);
}
// just get the type number
typenum = atomTable.getParams(type,&junkf,&junkf,&junkf,&junkf);
}
genericMols[genericMols.size()-1]->addAtom(type,typenum,resnum,
restype,atomname,charge,mass);
break;
case ATOMTYPES:
if(6 != sscanf(buf," %5s %f %f %5s %f %f",type,&mass,&charge,
particletype,&c6,&c12)) {
fprintf(stderr,"Syntax error in ATOMTYPES: %s\n",buf);
exit(1);
}
/* conversions:
c6 - kJ/mol nm6 -> kcal/mol A6
c12 - kJ/mol nm12 -> kcal/mol A12 */
atomTable.addType(type,mass,charge,
c6/(JOULES_PER_CALORIE)*1E6,
c12/(JOULES_PER_CALORIE)*1E12);
break;
case MOLECULETYPE:
if(2!=sscanf(buf," %20s %d",molname,&nrexcl)) {
fprintf(stderr,"Syntax error in MOLECULETYPE: %s\n",buf);
exit(1);
}
/* add another generic molecule holder */
genericMols.add(new GenericMol(molname));
break;
case MOLECULES:
if(2!=sscanf(buf," %20s %d",molname,&copies)) {
fprintf(stderr,"Syntax error in MOLECULES: %s\n",buf);
exit(1);
}
/* search for the specified molecule and make a molInst of it*/
moleculeinstance = NULL;
for(i=0;i<genericMols.size();i++) {
if(0==strcmp(molname,genericMols[i]->getName())) {
moleculeinstance = new MolInst(genericMols[i],copies);
break;
}
}
if(moleculeinstance==NULL) {
fprintf(stderr,"Molecule %s undefined.\n",molname);
exit(1);
}
/* put it at the end of the list */
molInsts.add(moleculeinstance);
break;
case PAIRS:
int indexA;
int indexB;
int pairFunction;
Real fA;
Real fB;
Real fC;
Real fD;
Real fE;
Real fF;
int countVariables;
countVariables = sscanf(buf," %d %d %d %f %f %f %f %f %f",&indexA,&indexB,&pairFunction,&fA,&fB,&fC,&fD,&fE,&fF);
if ((countVariables >= 4 && countVariables >= 10)) {
fprintf(stderr,"Syntax error in PAIRS: %s\n",buf);
exit(1);
}
// Shift the atom indices to be zero-based
indexA--;
indexB--;
// Make sure that the indexA is less than indexB
/*if ( indexA > indexB ) {
int tmpIndex = indexA;
indexB = indexA;
indexA = tmpIndex;
}*/
if (pairFunction == 1) {
// LJ code
fA = (fA/JOULES_PER_CALORIE)*1E6;
fB= (fB/JOULES_PER_CALORIE)*1E12;
pairTable.addPairLJType2(indexA,indexB,fA,fB);
} else if (pairFunction == 5){
// Bare Gaussian potential
fA = (fA/JOULES_PER_CALORIE); //-->gaussA
fB = (fB*ANGSTROMS_PER_NM); //-->gaussMu1
if(fC == 0) {
char buff[100];
sprintf(buff,"GromacsTopFile.C::Attempting to load zero into gaussSigma. Please check the pair: %s\n",buf);
NAMD_die(buff);
}
if(fC < 0 && !bool_negative_number_warning_flag) {
iout << iWARN << "Attempting to load a negative standard deviation into the gaussSigma. Taking the absolute value of the standard deviation.";
bool_negative_number_warning_flag = true;
}
fC = (fC*ANGSTROMS_PER_NM); //-->gaussSigma1
fC = 1.0/(2 * fC * fC); // Normalizes sigma
pairTable.addPairGaussType2(indexA,indexB,fA,fB,fC);
} else if (pairFunction == 6) {
// Combined Gaussian + repulsive r^-12 potential
fA = (fA/JOULES_PER_CALORIE); //-->gaussA
fB = (fB*ANGSTROMS_PER_NM); //-->gaussMu1
if(fC == 0) {
char buff[100];
sprintf(buff,"GromacsTopFile.C::Attempting to load zero into gaussSigma. Please check the pair: %s\n",buf);
NAMD_die(buff);
}
if(fC < 0 && !bool_negative_number_warning_flag) {
iout << iWARN << "Attempting to load a negative standard deviation into the gaussSigma. Taking the absolute value of the standard deviation.";
bool_negative_number_warning_flag = true;
}
fC = (fC*ANGSTROMS_PER_NM); //-->gaussSigma1
fC = 1.0/(2 * fC * fC); // Normalizes sigma
fD = (fD*ANGSTROMS_PER_NM); //-->gaussRepulsive
pairTable.addPairGaussType2(indexA,indexB,fA,fB,fC,fD);
} else if (pairFunction == 7) {
// Double well Guassian function
fA = (fA/JOULES_PER_CALORIE); //-->gaussA
fB = (fB*ANGSTROMS_PER_NM); //-->gaussMu1
if(fC == 0 || fE == 0) {
char buff[100];
sprintf(buff,"GromacsTopFile.C::Attempting to load zero into gaussSigma. Please check the pair: %s\n",buf);
NAMD_die(buff);
}
if((fC < 0 || fE < 0)&& !bool_negative_number_warning_flag) {
iout << iWARN << "Attempting to load a negative standard deviation into the gaussSigma. Taking the absolute value of the standard deviation.";
bool_negative_number_warning_flag = true;
}
fC = (fC*ANGSTROMS_PER_NM); //-->gaussSigma1
fC = 1.0/(2 * fC * fC); // Normalizes sigma
fD = (fD*ANGSTROMS_PER_NM); //-->gaussMu2
fE = (fE*ANGSTROMS_PER_NM); //-->gaussSigma2
fE = 1.0/(2 * fE * fE); // Normalizes sigma
fF = (fE*ANGSTROMS_PER_NM); //-->gaussRepulsive
pairTable.addPairGaussType2(indexA,indexB,fA,fB,fC,fD,fE,fF);
} else {
// Generic error statement
fprintf(stderr,"Unknown pairFunction in GromacsTopFile.C under the PAIRS section: %d\n",pairFunction);
}
break;
case EXCLUSIONS:
/* Start of JLai modifications August 16th, 2012 */
if(2 != sscanf(buf," %d %d ",&atomi,&atomj)) {
fprintf(stderr,"Syntax error in EXCLUSIONS: %s\n",buf);
exit(1);
}
// Shift the atom indices to be zero-based
atomi--;
atomj--;
/*Load exclusion information into file*/
exclusions_atom_i.add(atomi);
exclusions_atom_j.add(atomj);
numExclusion++;
/* Reading in exclusions information from file and loading */
break;
// End of JLai modifications August 16th, 2012
}
}
fclose(f);
}
int DisplayDevice::pick(int dim, const float *pos, const VMDDisplayList *cmdList,
float &eyedist, int *unitcell, float window_size) {
char *cmdptr = NULL;
int tok;
float newEyeDist, currEyeDist = eyedist;
int tag = (-1), inRegion, currTag;
float minX=0.0f, minY=0.0f, maxX=0.0f, maxY=0.0f;
float fminX=0.0f, fminY=0.0f, fminZ=0.0f, fmaxX=0.0f, fmaxY=0.0f, fmaxZ=0.0f;
float wpntpos[3], pntpos[3], cpos[3];
if(!cmdList)
return (-1);
// initialize picking: find screen region to look for object
if (dim == 2) {
fminX = pos[0] - window_size;
fmaxX = pos[0] + window_size;
fminY = pos[1] - window_size;
fmaxY = pos[1] + window_size;
abs_screen_pos(fminX, fminY);
abs_screen_pos(fmaxX, fmaxY);
#if defined(_MSC_VER)
// Win32 lacks the C99 round() routine
// Add +/- 0.5 then then round towards zero.
#if 1
minX = (int) ((float) (fminX + (fminX >= 0.0f ? 0.5f : -0.5f)));
maxX = (int) ((float) (fmaxX + (fmaxX >= 0.0f ? 0.5f : -0.5f)));
minY = (int) ((float) (fminY + (fminY >= 0.0f ? 0.5f : -0.5f)));
maxY = (int) ((float) (fmaxY + (fmaxY >= 0.0f ? 0.5f : -0.5f)));
#else
minX = truncf(fminX + (fminX >= 0.0f ? 0.5f : -0.5f));
maxX = truncf(fmaxX + (fmaxX >= 0.0f ? 0.5f : -0.5f));
minY = truncf(fminY + (fminY >= 0.0f ? 0.5f : -0.5f));
maxY = truncf(fmaxY + (fmaxY >= 0.0f ? 0.5f : -0.5f));
// minX = floor(fminX + 0.5);
// maxX = floor(fmaxX + 0.5);
// minY = floor(fminY + 0.5);
// maxY = floor(fmaxY + 0.5);
#endif
#else
minX = round(fminX);
maxX = round(fmaxX);
minY = round(fminY);
maxY = round(fmaxY);
#endif
} else {
fminX = pos[0] - window_size;
fmaxX = pos[0] + window_size;
fminY = pos[1] - window_size;
fmaxY = pos[1] + window_size;
fminZ = pos[2] - window_size;
fmaxZ = pos[2] + window_size;
}
// make sure we do not disturb the regular transformation matrix
transMat.dup();
(transMat.top()).multmatrix(cmdList->mat);
// Transform the current pick point for each periodic image
ResizeArray<Matrix4> pbcImages;
ResizeArray<int> pbcCells;
find_pbc_images(cmdList, pbcImages);
find_pbc_cells(cmdList, pbcCells);
int pbcimg;
for (pbcimg=0; pbcimg<pbcImages.num(); pbcimg++) {
transMat.dup();
(transMat.top()).multmatrix(pbcImages[pbcimg]);
// scan through the list, getting each command and executing it, until
// the end of commands token is found
VMDDisplayList::VMDLinkIter cmditer;
cmdList->first(&cmditer);
while((tok = cmdList->next(&cmditer, cmdptr)) != DLASTCOMMAND) {
switch (tok) {
case DPICKPOINT:
// calculate the transformed position of the point
{
DispCmdPickPoint *cmd = (DispCmdPickPoint *)cmdptr;
vec_copy(wpntpos, cmd->postag);
currTag = cmd->tag;
}
(transMat.top()).multpoint3d(wpntpos, pntpos);
// check if in picking region ... different for 2D and 3D
if (dim == 2) {
// convert the 3D world coordinate to 2D (XY) absolute screen
// coordinate, and a normalized Z coordinate.
abs_screen_loc_3D(pntpos, cpos);
// check to see if the projected picking position falls within the
// view frustum, with the XY coords falling within the displayed
// window, and the Z coordinate falling within the view volume
// between the front and rear clipping planes.
inRegion = (cpos[0] >= minX && cpos[0] <= maxX &&
cpos[1] >= minY && cpos[1] <= maxY &&
cpos[2] >= 0.0 && cpos[2] <= 1.0);
} else {
// just check to see if the position is in a box centered on our
// pointer. The pointer position should already be transformed.
inRegion = (pntpos[0] >= fminX && pntpos[0] <= fmaxX &&
pntpos[1] >= fminY && pntpos[1] <= fmaxY &&
pntpos[2] >= fminZ && pntpos[2] <= fmaxZ);
}
// Clip still-viable pick points against all active clipping planes
if (inRegion) {
// We must perform a check against all of the active
// user-defined clipping planes to ensure that only pick points
// associated with visible geometry can be selected.
int cp;
for (cp=0; cp < VMD_MAX_CLIP_PLANE; cp++) {
// The final result is the intersection of all of the
// individual clipping plane tests...
if (cmdList->clipplanes[cp].mode) {
float cpdist[3];
vec_sub(cpdist, wpntpos, cmdList->clipplanes[cp].center);
inRegion &= (dot_prod(cpdist,
cmdList->clipplanes[cp].normal) > 0.0f);
}
}
}
// has a hit occurred?
if (inRegion) {
// yes, see if it is closer to the eye position than earlier objects
if(dim==2)
newEyeDist = DTOEYE(pntpos[0], pntpos[1], pntpos[2]);
else
newEyeDist = DTOPOINT(pntpos[0],pntpos[1],pntpos[2]);
if(currEyeDist < 0.0 || newEyeDist < currEyeDist) {
currEyeDist = newEyeDist;
tag = currTag;
if (unitcell) {
unitcell[0] = pbcCells[3*pbcimg ];
unitcell[1] = pbcCells[3*pbcimg+1];
unitcell[2] = pbcCells[3*pbcimg+2];
}
}
}
break;
case DPICKPOINT_ARRAY:
// loop over all of the pick points in the pick point index array
DispCmdPickPointArray *cmd = (DispCmdPickPointArray *)cmdptr;
float *pickpos=NULL;
float *crds=NULL;
int *indices=NULL;
cmd->getpointers(crds, indices);
int i;
for (i=0; i<cmd->numpicks; i++) {
pickpos = crds + i*3;
if (cmd->allselected) {
currTag = i + cmd->firstindex;
} else {
currTag = indices[i];
}
vec_copy(wpntpos, pickpos);
(transMat.top()).multpoint3d(pickpos, pntpos);
// check if in picking region ... different for 2D and 3D
if (dim == 2) {
// convert the 3D world coordinate to 2D absolute screen coord
abs_screen_loc_3D(pntpos, cpos);
// check to see if the position falls in our picking region
// including the clipping region (cpos[2])
inRegion = (cpos[0] >= minX && cpos[0] <= maxX &&
cpos[1] >= minY && cpos[1] <= maxY &&
cpos[2] >= 0.0 && cpos[2] <= 1.0);
} else {
// just check to see if the position is in a box centered on our
// pointer. The pointer position should already be transformed.
inRegion = (pntpos[0] >= fminX && pntpos[0] <= fmaxX &&
pntpos[1] >= fminY && pntpos[1] <= fmaxY &&
pntpos[2] >= fminZ && pntpos[2] <= fmaxZ);
}
// Clip still-viable pick points against all active clipping planes
if (inRegion) {
// We must perform a check against all of the active
// user-defined clipping planes to ensure that only pick points
// associated with visible geometry can be selected.
int cp;
for (cp=0; cp < VMD_MAX_CLIP_PLANE; cp++) {
// The final result is the intersection of all of the
// individual clipping plane tests...
if (cmdList->clipplanes[cp].mode) {
float cpdist[3];
vec_sub(cpdist, wpntpos, cmdList->clipplanes[cp].center);
inRegion &= (dot_prod(cpdist,
cmdList->clipplanes[cp].normal) > 0.0f);
}
}
}
// has a hit occurred?
if (inRegion) {
// yes, see if it is closer to the eye than earlier hits
if (dim==2)
newEyeDist = DTOEYE(pntpos[0], pntpos[1], pntpos[2]);
else
newEyeDist = DTOPOINT(pntpos[0],pntpos[1],pntpos[2]);
if (currEyeDist < 0.0 || newEyeDist < currEyeDist) {
currEyeDist = newEyeDist;
tag = currTag;
if (unitcell) {
unitcell[0] = pbcCells[3*pbcimg ];
unitcell[1] = pbcCells[3*pbcimg+1];
unitcell[2] = pbcCells[3*pbcimg+2];
}
}
}
}
break;
}
}
// Pop the PBC image transform
transMat.pop();
} // end of loop over PBC images
// make sure we do not disturb the regular transformation matrix
transMat.pop();
// return result; if tag >= 0, we found something
eyedist = currEyeDist;
return tag;
}
void
DrawMolItem::draw_volume_isosurface_lit_points (const VolumetricData * v,
float isovalue, int stepsize, int thickness)
{
int x, y, z;
float *addr;
float pos[3];
float xax[3], yax[3], zax[3];
ResizeArray<float> centers;
ResizeArray<float> normals;
ResizeArray<float> colors;
int i;
float vorigin[3];
for (i = 0; i < 3; i++)
{
vorigin[i] = float (v->origin[i]);
}
int pointcount = 0;
int usecolor;
append (DMATERIALON);
usecolor = draw_volume_get_colorid ();
const float *cp = scene->color_value (usecolor);
cmdColorIndex.putdata (usecolor, cmdList);
// calculate cell axes
v->cell_axes (xax, yax, zax);
for (z = 0; z < v->zsize; z += stepsize)
{
for (y = 0; y < v->ysize; y += stepsize)
{
addr = &(v->data[(z * (v->xsize * v->ysize)) + (y * v->xsize)]);
// loop through xsize - 1 rather than the full range
for (x = 0; x < (v->xsize - 1); x += stepsize)
{
float diff, isodiff;
// draw a point if the isovalue falls between neighboring X samples
diff = addr[x] - addr[x + 1];
isodiff = addr[x] - isovalue;
if ((fabs (diff) > fabs (isodiff)) && (MYSGN(diff) == MYSGN(isodiff)))
{
pos[0] = vorigin[0] + x * xax[0] + y * yax[0] + z * zax[0];
pos[1] = vorigin[1] + x * xax[1] + y * yax[1] + z * zax[1];
pos[2] = vorigin[2] + x * xax[2] + y * yax[2] + z * zax[2];
float norm[3];
vec_copy (norm,
&v->gradient[(z * v->xsize * v->ysize + y * v->xsize + x) * 3]);
// draw a point there.
centers.append (pos[0]);
centers.append (pos[1]);
centers.append (pos[2]);
normals.append (norm[0]);
normals.append (norm[1]);
normals.append (norm[2]);
colors.append (cp[0]);
colors.append (cp[1]);
colors.append (cp[2]);
pointcount++;
}
}
}
}
if (pointcount > 0)
{
DispCmdLitPointArray cmdLitPointArray;
cmdLitPointArray.putdata ((float *) ¢ers[0], (float *) &normals[0],
(float *) &colors[0], (float) thickness, pointcount, cmdList);
}
}
