int set_particle_torque_lab(int part, double torque_lab[3])
{
int pnode;
if (!particle_node)
build_particle_node();
if (part < 0 || part > max_seen_particle)
return ES_ERROR;
pnode = particle_node[part];
if (pnode == -1)
return ES_ERROR;
/* Internal functions require the body coordinates
so we need to convert to these from the lab frame */
double A[9];
double torque[3];
Particle particle;
get_particle_data(part, &particle);
define_rotation_matrix(&particle, A);
torque[0] = A[0 + 3*0]*torque_lab[0] + A[0 + 3*1]*torque_lab[1] + A[0 + 3*2]*torque_lab[2];
torque[1] = A[1 + 3*0]*torque_lab[0] + A[1 + 3*1]*torque_lab[1] + A[1 + 3*2]*torque_lab[2];
torque[2] = A[2 + 3*0]*torque_lab[0] + A[2 + 3*1]*torque_lab[1] + A[2 + 3*2]*torque_lab[2];
mpi_send_torque(pnode, part, torque);
return ES_OK;
}
int remove_particle(int part)
{
int pnode;
Particle *cur_par = (Particle *) malloc (sizeof(Particle));
if (get_particle_data(part, cur_par) == ES_ERROR )
return ES_ERROR;
int type = cur_par->p.type;
free(cur_par);
if (remove_id_type_array(part, type) == ES_ERROR )
return ES_ERROR;
if (!particle_node)
build_particle_node();
if (part > max_seen_particle)
return ES_ERROR;
pnode = particle_node[part];
if (pnode == -1)
return ES_ERROR;
particle_node[part] = -1;
mpi_remove_particle(pnode, part);
if (part == max_seen_particle) {
while (max_seen_particle >= 0 && particle_node[max_seen_particle] == -1)
max_seen_particle--;
mpi_bcast_parameter(FIELD_MAXPART);
}
return ES_OK;
}
int set_particle_type(int part, int type)
{
int pnode;
make_particle_type_exist(type);
if (!particle_node)
build_particle_node();
if (part < 0 || part > max_seen_particle)
return ES_ERROR;
pnode = particle_node[part];
if (pnode == -1)
return ES_ERROR;
// check if the particle exists already and the type is changed, then remove it from the list which contains it
Particle *cur_par = (Particle *) malloc( sizeof(Particle) );
if ( Type_array_init ) {
if ( cur_par != (Particle *) 0 ) {
if ( get_particle_data(part, cur_par) != ES_ERROR ) {
int prev_type = cur_par->p.type;
if ( prev_type != type ) {
// particle existed before so delete it from the list
remove_id_type_array(part, prev_type);
}
}
}
free(cur_par);
}
mpi_send_type(pnode, part, type);
#ifdef ADDITIONAL_CHECKS
if ( Type_array_init ) {
if ( add_particle_to_list(part, type) == ES_ERROR ){
//Tcl_AppendResult(interp, "gc particle add failed", (char *) NULL);
return ES_ERROR;
}
}
#endif
return ES_OK;
}
int tclcommand_analyze_parse_and_print_check_mol(Tcl_Interp *interp,int argc, char **argv){
int j,count=0;
double dist;
char buffer[TCL_DOUBLE_SPACE];
Particle p;
updatePartCfg(WITHOUT_BONDS);
for(j=0; j<n_total_particles; j++){
if (!ifParticleIsVirtual(&partCfg[j])) continue;
get_particle_data(j,&p);
//dist=min_distance(partCfg[j].r.p,p.r.p);
unfold_position(p.r.p,p.l.i);
dist=distance(partCfg[j].r.p,p.r.p);
if (dist > 0.01){
if (count==0) Tcl_AppendResult(interp,"BEGIN Particle Missmatch: \n", (char *)NULL);
sprintf(buffer,"%i",j);
Tcl_AppendResult(interp,"Particle ",buffer, (char *)NULL);
Tcl_PrintDouble(interp,partCfg[j].r.p[0] , buffer);
Tcl_AppendResult(interp," partCfg x ",buffer, (char *)NULL);
Tcl_PrintDouble(interp,partCfg[j].r.p[1] , buffer);
Tcl_AppendResult(interp," y ",buffer, (char *)NULL);
Tcl_PrintDouble(interp,partCfg[j].r.p[2] , buffer);
Tcl_AppendResult(interp," z ",buffer, (char *)NULL);
Tcl_PrintDouble(interp,p.r.p[0] , buffer);
Tcl_AppendResult(interp," my_partCfg x ",buffer, (char *)NULL);
Tcl_PrintDouble(interp,p.r.p[1] , buffer);
Tcl_AppendResult(interp," y ",buffer, (char *)NULL);
Tcl_PrintDouble(interp,p.r.p[2] , buffer);
Tcl_AppendResult(interp," z ",buffer, (char *)NULL);
Tcl_PrintDouble(interp, dist, buffer);
Tcl_AppendResult(interp," dist ",buffer,"\n", (char *)NULL);
count++;
}
}
if (count!=0){
Tcl_AppendResult(interp,"END Particle Missmatch\n", (char *)NULL);
return(TCL_ERROR);
}
return(TCL_OK);
}
int IBM_Tribend_SetParams(const int bond_type, const int ind1, const int ind2, const int ind3, const int ind4, const tBendingMethod method, const double kb, const bool flat)
{
// Create bond
make_bond_type_exist(bond_type);
// General parameters
bonded_ia_params[bond_type].type = BONDED_IA_IBM_TRIBEND;
// Specific parameters
bonded_ia_params[bond_type].p.ibm_tribend.method = method;
// Distinguish bending methods
if ( method == TriangleNormals )
{
double theta0;
if ( !flat )
{
// Compute theta0
Particle p1, p2, p3, p4;
get_particle_data(ind1, &p1);
get_particle_data(ind2, &p2);
get_particle_data(ind3, &p3);
get_particle_data(ind4, &p4);
//Get vectors of triangles
double dx1[3], dx2[3], dx3[3];
get_mi_vector(dx1, p1.r.p, p3.r.p);
get_mi_vector(dx2, p2.r.p, p3.r.p);
get_mi_vector(dx3, p4.r.p, p3.r.p);
//Get normals on triangle; pointing outwards by definition of indices sequence
double n1l[3], n2l[3];
vector_product(dx1, dx2, n1l);
vector_product(dx1, dx3, n2l);
// Wolfgang here had a minus. It seems to work, so leave it in
n2l[0] = -1*n2l[0];
n2l[1] = -1*n2l[1];
n2l[2] = -1*n2l[2];
double n1[3], n2[3];
unit_vector(n1l,n1);
unit_vector(n2l,n2);
//calculate theta by taking the acos of the scalar n1*n2
double sc = scalar(n1,n2);
if ( sc > 1.0) sc = 1.0;
theta0 = acos(sc);
double tmp[3];
vector_product(n1,n2,tmp);
const double desc = scalar(dx1,tmp);
if ( desc < 0) theta0 = 2.0*PI-theta0;
}
else theta0 = 0; // Flat
// Krüger always has three partners
bonded_ia_params[bond_type].num = 3;
bonded_ia_params[bond_type].p.ibm_tribend.theta0 = theta0;
// NOTE: This is the bare bending modulus used by the program.
// If triangle pairs appear only once, the total bending force should get a factor 2
// For the numerical model, a factor sqrt(3) should be added, see Gompper&Kroll J. Phys. 1996 and Krüger thesis
// This is an approximation, it holds strictly only for a sphere
bonded_ia_params[bond_type].p.ibm_tribend.kb = kb;
}
// Gompper
if ( method == NodeNeighbors )
{
// Interpret ind2 as number of partners
// Note: the actual partners are not set here, but must be set using the part command on the tcl level
if ( ind1 != 5 && ind1 != 6) { printf("Gompper bending with %d partners seems strange. Are you sure?\n", ind2); return ES_ERROR; }
bonded_ia_params[bond_type].num = ind1;
// Only flat eq possible, but actually this is ignored in the computation anyway
bonded_ia_params[bond_type].p.ibm_tribend.theta0 = 0;
bonded_ia_params[bond_type].p.ibm_tribend.kb = kb;
}
// Broadcast and return
mpi_bcast_ia_params(bond_type, -1);
return ES_OK;
}
// Setup the virtual_sites_relative properties of a particle so that the given virtaul particle will follow the given real particle
int vs_relate_to(int part_num, int relate_to)
{
// Get the data for the particle we act on and the one we wnat to relate
// it to.
Particle p_current,p_relate_to;
if ((get_particle_data(relate_to,&p_relate_to)!=ES_OK) ||
(get_particle_data(part_num,&p_current)!=ES_OK)) {
char *errtxt = runtime_error(128 + 3*ES_INTEGER_SPACE);
ERROR_SPRINTF(errtxt, "Could not retrieve particle data for the given id");
return ES_ERROR;
}
// get teh distance between the particles
double d[3];
get_mi_vector(d, p_current.r.p,p_relate_to.r.p);
// Set the particle id of the particle we want to relate to and the distnace
if (set_particle_vs_relative(part_num, relate_to, sqrt(sqrlen(d))) == ES_ERROR) {
char *errtxt = runtime_error(128 + 3*ES_INTEGER_SPACE);
ERROR_SPRINTF(errtxt, "setting the vs_relative attributes failed");
return ES_ERROR;
}
// Check, if the distance between virtual and non-virtual particles is larger htan minimum global cutoff
// If so, warn user
double l=sqrt(sqrlen(d));
if (l>min_global_cut) {
char *errtxt = runtime_error(300 + 3*ES_INTEGER_SPACE);
ERROR_SPRINTF(errtxt, "Warning: The distance between virtual and non-virtual particle (%f) is\nlarger than the minimum global cutoff (%f). This may lead to incorrect simulations\nunder certain conditions. Use \"setmd min_global_cut\" to increase the minimum cutoff.\n",l,min_global_cut);
return ES_ERROR;
}
// Now, calculate the quaternions which specify the angle between
// the director of the particel we relate to and the vector
// (paritlce_we_relate_to - this_particle)
double quat[4];
// The vs_relative implemnation later obtains the direcotr by multiplying
// the quaternions representing the orientation of the real particle
// with those in the virtual particle. The re quulting quaternion is then
// converted to a director.
// Whe have quat_(real particle) *quat_(virtual particle)
// = quat_(obtained from desired director)
// Resolving this for the quat_(virtaul particle)
//Normalize desired director
int i;
for (i=0;i<3;i++)
d[i]/=l;
// Obtain quaternions from desired director
double quat_director[4];
convert_quatu_to_quat(d, quat_director);
// Define quat as described above:
double x=0;
for (i=0;i<4;i++)
x+=p_relate_to.r.quat[i]*p_relate_to.r.quat[i];
quat[0]=0;
for (i=0;i<4;i++)
quat[0] +=p_relate_to.r.quat[i]*quat_director[i];
quat[1] =-quat_director[0] *p_relate_to.r.quat[1]
+quat_director[1] *p_relate_to.r.quat[0]
+quat_director[2] *p_relate_to.r.quat[3]
-quat_director[3] *p_relate_to.r.quat[2];
quat[2] =p_relate_to.r.quat[1] *quat_director[3]
+ p_relate_to.r.quat[0] *quat_director[2]
- p_relate_to.r.quat[3] *quat_director[1]
- p_relate_to.r.quat[2] * quat_director[0];
quat[3] =quat_director[3] *p_relate_to.r.quat[0]
- p_relate_to.r.quat[3] *quat_director[0]
+ p_relate_to.r.quat[2] * quat_director[1]
- p_relate_to.r.quat[1] *quat_director[2];
for (i=0;i<4;i++)
quat[i]/=x;
// Verify result
double qtemp[4];
multiply_quaternions(p_relate_to.r.quat,quat,qtemp);
for (i=0;i<4;i++)
if (fabs(qtemp[i]-quat_director[i])>1E-9)
fprintf(stderr, "vs_relate_to: component %d: %f instead of %f\n",
i, qtemp[i], quat_director[i]);
// Save the quaternions in the particle
if (set_particle_quat(part_num, quat) == ES_ERROR) {
char *errtxt = runtime_error(128 + 3*ES_INTEGER_SPACE);
ERROR_SPRINTF(errtxt, "set particle position first");
return ES_ERROR;
}
return ES_OK;
}
int tclcommand_writemd(ClientData data, Tcl_Interp *interp,
int argc, char **argv)
{
static int end_num = -1;
char *row;
int p, i;
struct MDHeader header;
int tcl_file_mode;
Tcl_Channel channel;
if (argc < 3) {
#if defined(ELECTROSTATICS) && defined(DIPOLES)
Tcl_AppendResult(interp, "wrong # args: should be \"",
argv[0], " <file> ?posx|posy|posz|q|mx|my|mz|vx|vy|vz|fx|fy|fz|type?* ...\"",
(char *) NULL);
#else
#ifdef ELECTROSTATICS
Tcl_AppendResult(interp, "wrong # args: should be \"",
argv[0], " <file> ?posx|posy|posz|q|vx|vy|vz|fx|fy|fz|type?* ...\"",
(char *) NULL);
#endif
#ifdef DIPOLES
Tcl_AppendResult(interp, "wrong # args: should be \"",
argv[0], " <file> ?posx|posy|posz|mx|my|mz|vx|vy|vz|fx|fy|fz|type?* ...\"",
(char *) NULL);
#endif
#endif
return (TCL_ERROR);
}
if ((channel = Tcl_GetChannel(interp, argv[1], &tcl_file_mode)) == NULL)
return (TCL_ERROR);
if (!(tcl_file_mode & TCL_WRITABLE)) {
Tcl_AppendResult(interp, "\"", argv[1], "\" not writeable", (char *) NULL);
return (TCL_ERROR);
}
/* tune channel to binary translation, e.g. none */
Tcl_SetChannelOption(interp, channel, "-translation", "binary");
/* assemble rows */
argc -= 2;
argv += 2;
row = (char*)malloc(sizeof(char)*argc);
for (i = 0; i < argc; i++) {
if (!strncmp(*argv, "posx", strlen(*argv))) {
row[i] = POSX;
}
else if (!strncmp(*argv, "posy", strlen(*argv))) {
row[i] = POSY;
}
else if (!strncmp(*argv, "posz", strlen(*argv))) {
row[i] = POSZ;
}
#ifdef MASS
else if (!strncmp(*argv, "mass", strlen(*argv))) {
row[i] = MASSES;
}
#endif
else if (!strncmp(*argv, "q", strlen(*argv))) {
row[i] = Q;
}
#ifdef DIPOLES
else if (!strncmp(*argv, "mx", strlen(*argv))) {
row[i] = MX;
}
else if (!strncmp(*argv, "my", strlen(*argv))) {
row[i] = MY;
}
else if (!strncmp(*argv, "mz", strlen(*argv))) {
row[i] = MZ;
}
#endif
else if (!strncmp(*argv, "vx", strlen(*argv))) {
row[i] = VX;
}
else if (!strncmp(*argv, "vy", strlen(*argv))) {
row[i] = VY;
}
else if (!strncmp(*argv, "vz", strlen(*argv))) {
row[i] = VZ;
}
else if (!strncmp(*argv, "fx", strlen(*argv))) {
row[i] = FX;
}
else if (!strncmp(*argv, "fy", strlen(*argv))) {
row[i] = FY;
}
else if (!strncmp(*argv, "fz", strlen(*argv))) {
row[i] = FZ;
}
else if (!strncmp(*argv, "type", strlen(*argv))) {
row[i] = TYPE;
}
else {
Tcl_AppendResult(interp, "no particle data field \"", *argv, "\"?",
(char *) NULL);
free(row);
return (TCL_ERROR);
}
argv++;
}
if (!particle_node)
build_particle_node();
/* write header and row data */
memmove(header.magic, MDMAGIC, 4*sizeof(char));
header.n_rows = argc;
Tcl_Write(channel, (char *)&header, sizeof(header));
Tcl_Write(channel, row, header.n_rows*sizeof(char));
for (p = 0; p <= max_seen_particle; p++) {
Particle data;
if (get_particle_data(p, &data) == ES_OK) {
unfold_position(data.r.p, data.m.v, data.l.i);
/* write particle index */
Tcl_Write(channel, (char *)&p, sizeof(int));
for (i = 0; i < header.n_rows; i++) {
switch (row[i]) {
case POSX: Tcl_Write(channel, (char *)&data.r.p[0], sizeof(double)); break;
case POSY: Tcl_Write(channel, (char *)&data.r.p[1], sizeof(double)); break;
case POSZ: Tcl_Write(channel, (char *)&data.r.p[2], sizeof(double)); break;
case VX: Tcl_Write(channel, (char *)&data.m.v[0], sizeof(double)); break;
case VY: Tcl_Write(channel, (char *)&data.m.v[1], sizeof(double)); break;
case VZ: Tcl_Write(channel, (char *)&data.m.v[2], sizeof(double)); break;
case FX: Tcl_Write(channel, (char *)&data.f.f[0], sizeof(double)); break;
case FY: Tcl_Write(channel, (char *)&data.f.f[1], sizeof(double)); break;
case FZ: Tcl_Write(channel, (char *)&data.f.f[2], sizeof(double)); break;
#ifdef MASS
case MASSES: Tcl_Write(channel, (char *)&data.p.mass, sizeof(double)); break;
#endif
#ifdef ELECTROSTATICS
case Q: Tcl_Write(channel, (char *)&data.p.q, sizeof(double)); break;
#endif
#ifdef DIPOLES
case MX: Tcl_Write(channel, (char *)&data.r.dip[0], sizeof(double)); break;
case MY: Tcl_Write(channel, (char *)&data.r.dip[1], sizeof(double)); break;
case MZ: Tcl_Write(channel, (char *)&data.r.dip[2], sizeof(double)); break;
#endif
case TYPE: Tcl_Write(channel, (char *)&data.p.type, sizeof(int)); break;
}
}
free_particle(&data);
}
}
/* end marker */
Tcl_Write(channel, (char *)&end_num, sizeof(int));
free(row);
return TCL_OK;
}
// Setup the virtual_sites_relative properties of a particle so that the given virtaul particle will follow the given real particle
int vs_relate_to(int part_num, int relate_to)
{
// Get the data for the particle we act on and the one we wnat to relate
// it to.
Particle p_current,p_relate_to;
if ((get_particle_data(relate_to,&p_relate_to)!=TCL_OK) ||
(get_particle_data(part_num,&p_current)!=TCL_OK)) {
printf("Could not retrieve particle data for the given id.\n");
return TCL_ERROR;
}
// get teh distance between the particles
double d[3];
get_mi_vector(d, p_current.r.p,p_relate_to.r.p);
// Set the particle id of the particle we want to relate to and the distnace
if (set_particle_vs_relative(part_num, relate_to, sqrt(sqrlen(d))) == TCL_ERROR) {
printf("setting the vs_relative attributes failed.\n");
return TCL_ERROR;
}
// Now, calculate the quaternions which specify the angle between
// the director of the particel we relate to and the vector
// (paritlce_we_relate_to - this_particle)
double quat[4];
// The vs_relative implemnation later obtains the direcotr by multiplying
// the quaternions representing the orientation of the real particle
// with those in the virtual particle. The re quulting quaternion is then
// converted to a director.
// Whe have quat_(real particle) *quat_(virtual particle)
// = quat_(obtained from desired director)
// Resolving this for the quat_(virtaul particle)
//Normalize desired director
double l=sqrt(sqrlen(d));
int i;
for (i=0;i<3;i++)
d[i]/=l;
// Obtain quaternions from desired director
double quat_director[4];
convert_quatu_to_quat(d, quat_director);
// Define quat as described above:
double x=0;
for (i=0;i<4;i++)
x+=p_relate_to.r.quat[i]*p_relate_to.r.quat[i];
quat[0]=0;
for (i=0;i<4;i++)
quat[0] +=p_relate_to.r.quat[i]*quat_director[i];
quat[1] =-quat_director[0] *p_relate_to.r.quat[1]
+quat_director[1] *p_relate_to.r.quat[0]
+quat_director[2] *p_relate_to.r.quat[3]
-quat_director[3] *p_relate_to.r.quat[2];
quat[2] =p_relate_to.r.quat[1] *quat_director[3]
+ p_relate_to.r.quat[0] *quat_director[2]
- p_relate_to.r.quat[3] *quat_director[1]
- p_relate_to.r.quat[2] * quat_director[0];
quat[3] =quat_director[3] *p_relate_to.r.quat[0]
- p_relate_to.r.quat[3] *quat_director[0]
+ p_relate_to.r.quat[2] * quat_director[1]
- p_relate_to.r.quat[1] *quat_director[2];
for (i=0;i<4;i++)
quat[i]/=x;
// Verify result
double qtemp[4];
multiply_quaternions(p_relate_to.r.quat,quat,qtemp);
for (i=0;i<4;i++)
if (fabs(qtemp[i]-quat_director[i])>1E-9)
printf("Component %d: %f instead of %f\n",i,qtemp[i],quat_director[i]);
// Save the quaternions in the particle
if (set_particle_quat(part_num, quat) == TCL_ERROR) {
printf("set particle position first\n");
return TCL_ERROR;
}
return TCL_OK;
}