/** convert a dipole moment to quaternions and dipolar strength */
int convert_dip_to_quat(double dip[3], double quat[4], double *dipm)
{
double dm;
// Calculate magnitude of dipole moment
dm = sqrt(dip[0]*dip[0] + dip[1]*dip[1] + dip[2]*dip[2]);
*dipm = dm;
convert_quatu_to_quat(dip,quat);
return 0;
}
// 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;
}
// 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;
}
