int angledist_set_params(int bond_type, double bend, double phimin, double distmin, double phimax, double distmax)
{
if(bond_type < 0)
return ES_ERROR;
make_bond_type_exist(bond_type);
bonded_ia_params[bond_type].p.angledist.bend = bend;
bonded_ia_params[bond_type].p.angledist.phimin = phimin;
bonded_ia_params[bond_type].p.angledist.distmin = distmin;
bonded_ia_params[bond_type].p.angledist.phimax = phimax;
bonded_ia_params[bond_type].p.angledist.distmax = distmax;
#ifdef BOND_ANGLEDIST_COSINE
#error angledist not implemented for BOND_ANGLEDIST_COSINE
#endif
#ifdef BOND_ANGLEDIST_COSSQUARE
#error angledist not implemented for BOND_ANGLEDIST_COSSQUARE
#endif
bonded_ia_params[bond_type].type = BONDED_IA_ANGLEDIST;
bonded_ia_params[bond_type].num = 2;
/* broadcast interaction parameters */
mpi_bcast_ia_params(bond_type, -1);
return ES_OK;
}
int IBM_VolumeConservation_SetParams(const int bond_type, const int softID, const double kappaV)
{
// Create bond
make_bond_type_exist(bond_type);
// General bond parameters
bonded_ia_params[bond_type].type = BONDED_IA_IBM_VOLUME_CONSERVATION;
bonded_ia_params[bond_type].num = 1; // This means that Espresso requires one bond partner. Here we simply ignore it, but Espresso cannot handle 0.
// Specific stuff
if ( softID > MaxNumIBM) { printf("Error: softID (%d) is larger than MaxNumIBM (%d)\n", softID, MaxNumIBM); return ES_ERROR; }
if ( softID < 0) { printf("Error: softID (%d) must be non-negative\n", softID); return ES_ERROR; }
bonded_ia_params[bond_type].p.ibmVolConsParameters.softID = softID;
bonded_ia_params[bond_type].p.ibmVolConsParameters.kappaV = kappaV;
bonded_ia_params[bond_type].p.ibmVolConsParameters.volRef = 0;
// NOTE: We cannot compute the reference volume here because not all interactions are setup
// and thus we do not know which triangles belong to this softID
// Calculate it later in the init function
//Communicate this to whoever is interested
mpi_bcast_ia_params(bond_type, -1);
return ES_OK;
}
int hydrogen_bond_set_params(int bond_type, DoubleList *params) {
if(bond_type < 0)
return ES_ERROR;
make_bond_type_exist(bond_type);
bonded_ia_params[bond_type].p.hydrogen_bond.r0 = params->e[0];
bonded_ia_params[bond_type].p.hydrogen_bond.alpha = params->e[1];
bonded_ia_params[bond_type].p.hydrogen_bond.E0 = params->e[2];
bonded_ia_params[bond_type].p.hydrogen_bond.kd = params->e[3];
bonded_ia_params[bond_type].p.hydrogen_bond.sigma1 = params->e[4];
bonded_ia_params[bond_type].p.hydrogen_bond.sigma2 = params->e[5];
bonded_ia_params[bond_type].p.hydrogen_bond.psi10 = params->e[6];
bonded_ia_params[bond_type].p.hydrogen_bond.psi20 = params->e[7];
bonded_ia_params[bond_type].p.hydrogen_bond.E0sb = params->e[8];
bonded_ia_params[bond_type].p.hydrogen_bond.r0sb = params->e[9];
bonded_ia_params[bond_type].p.hydrogen_bond.alphasb = params->e[10];
bonded_ia_params[bond_type].p.hydrogen_bond.f2 = params->e[11];
bonded_ia_params[bond_type].p.hydrogen_bond.f3 = params->e[12];
bonded_ia_params[bond_type].type = BONDED_IA_CG_DNA_BASEPAIR;
bonded_ia_params[bond_type].num = 3;
mpi_bcast_ia_params(bond_type, -1);
return ES_OK;
}
// set out_direction parameters
int out_direction_set_params(int bond_type)
{
if(bond_type < 0)
return ES_ERROR;
make_bond_type_exist(bond_type);
bonded_ia_params[bond_type].type = BONDED_IA_OIF_OUT_DIRECTION;
bonded_ia_params[bond_type].num = 3;
mpi_bcast_ia_params(bond_type, -1);
return ES_OK;
}
int virtual_set_params(int bond_type)
{
if(bond_type < 0)
return ES_ERROR;
make_bond_type_exist(bond_type);
bonded_ia_params[bond_type].type = BONDED_IA_VIRTUAL_BOND;
bonded_ia_params[bond_type].num = 1;
/* broadcast interaction parameters */
mpi_bcast_ia_params(bond_type, -1);
return ES_OK;
}
int bonded_coulomb_set_params(int bond_type, double prefactor)
{
if(bond_type < 0)
return ES_ERROR;
make_bond_type_exist(bond_type);
bonded_ia_params[bond_type].p.bonded_coulomb.prefactor = prefactor;
bonded_ia_params[bond_type].type = BONDED_IA_BONDED_COULOMB;
bonded_ia_params[bond_type].num = 1;
/* broadcast interaction parameters */
mpi_bcast_ia_params(bond_type, -1);
return ES_OK;
}
/// set dihedral parameters
int dihedral_set_params(int bond_type, int mult, double bend, double phase)
{
if(bond_type < 0)
return ES_ERROR;
make_bond_type_exist(bond_type);
bonded_ia_params[bond_type].type = BONDED_IA_DIHEDRAL;
bonded_ia_params[bond_type].num = 3;
bonded_ia_params[bond_type].p.dihedral.mult = mult;
bonded_ia_params[bond_type].p.dihedral.bend = bend;
bonded_ia_params[bond_type].p.dihedral.phase = phase;
mpi_bcast_ia_params(bond_type, -1);
return ES_OK;
}
int subt_lj_set_params(int bond_type, double k, double r)
{
if(bond_type < 0)
return ES_ERROR;
make_bond_type_exist(bond_type);
bonded_ia_params[bond_type].p.subt_lj.k = k;
bonded_ia_params[bond_type].p.subt_lj.r = r;
bonded_ia_params[bond_type].type = BONDED_IA_SUBT_LJ;
bonded_ia_params[bond_type].p.subt_lj.r2 = SQR(bonded_ia_params[bond_type].p.subt_lj.r);
bonded_ia_params[bond_type].num = 1;
mpi_bcast_ia_params(bond_type, -1);
return ES_OK;
}
/// set the parameters for the stretching_force potential
int stretching_force_set_params(int bond_type, double r0, double ks)
{
if(bond_type < 0)
return ES_ERROR;
make_bond_type_exist(bond_type);
bonded_ia_params[bond_type].p.stretching_force.ks = ks;
bonded_ia_params[bond_type].p.stretching_force.r0 = r0;
bonded_ia_params[bond_type].type = BONDED_IA_STRETCHING_FORCE;
bonded_ia_params[bond_type].num = 1;
/* broadcast interaction parameters */
mpi_bcast_ia_params(bond_type, -1);
return ES_OK;
}
/*****************************************************************************
* setting parameters
*****************************************************************************/
int rigid_bond_set_params(int bond_type, double d, double p_tol, double v_tol)
{
if(bond_type < 0)
return ES_ERROR;
make_bond_type_exist(bond_type);
bonded_ia_params[bond_type].p.rigid_bond.d2 = d*d;
bonded_ia_params[bond_type].p.rigid_bond.p_tol = 2.0*p_tol;
bonded_ia_params[bond_type].p.rigid_bond.v_tol = v_tol*time_step;
bonded_ia_params[bond_type].type = BONDED_IA_RIGID_BOND;
bonded_ia_params[bond_type].num = 1;
n_rigidbonds += 1;
mpi_bcast_ia_params(bond_type, -1);
mpi_bcast_parameter(FIELD_RIGIDBONDS);
return ES_OK;
}
/** set parameters for the angle potential.
\todo The type of the angle potential
is chosen via config.hpp and cannot be changed at runtime.
*/
int angle_harmonic_set_params(int bond_type, double bend, double phi0)
{
if(bond_type < 0)
return ES_ERROR;
make_bond_type_exist(bond_type);
bonded_ia_params[bond_type].p.angle_harmonic.bend = bend;
bonded_ia_params[bond_type].p.angle_harmonic.phi0 = phi0;
bonded_ia_params[bond_type].type = BONDED_IA_ANGLE_HARMONIC;
bonded_ia_params[bond_type].num = 2;
/* broadcast interaction parameters */
mpi_bcast_ia_params(bond_type, -1);
return ES_OK;
}
/** set parameters for the AREA_FORCE_GLOBAL potential.
*/
int area_force_global_set_params(int bond_type, double A0_g, double ka_g)
{
if(bond_type < 0)
return ES_ERROR;
make_bond_type_exist(bond_type);
bonded_ia_params[bond_type].p.area_force_global.ka_g = ka_g;
bonded_ia_params[bond_type].p.area_force_global.A0_g = A0_g;
bonded_ia_params[bond_type].type = BONDED_IA_AREA_FORCE_GLOBAL;
bonded_ia_params[bond_type].num = 2;
/* broadcast interaction parameters */
mpi_bcast_ia_params(bond_type, -1);
return ES_OK;
}
int harmonic_set_params(int bond_type, double k, double r,double r_cut)
{
if(bond_type < 0)
return ES_ERROR;
make_bond_type_exist(bond_type);
bonded_ia_params[bond_type].p.harmonic.k = k;
bonded_ia_params[bond_type].p.harmonic.r = r;
bonded_ia_params[bond_type].p.harmonic.r_cut = r_cut;
bonded_ia_params[bond_type].type = BONDED_IA_HARMONIC;
bonded_ia_params[bond_type].num = 1;
/* broadcast interaction parameters */
mpi_bcast_ia_params(bond_type, -1);
return ES_OK;
}
/** set parameters for the angle potential.
\todo The type of the angle potential
is chosen via config.hpp and cannot be changed at runtime.
*/
int angle_cossquare_set_params(int bond_type, double bend, double phi0)
{
if(bond_type < 0)
return ES_ERROR;
make_bond_type_exist(bond_type);
bonded_ia_params[bond_type].p.angle_cossquare.bend = bend;
bonded_ia_params[bond_type].p.angle_cossquare.phi0 = phi0;
bonded_ia_params[bond_type].p.angle_cossquare.cos_phi0 = cos(phi0);
bonded_ia_params[bond_type].type = BONDED_IA_ANGLE_COSSQUARE;
bonded_ia_params[bond_type].num = 2;
/* broadcast interaction parameters */
mpi_bcast_ia_params(bond_type, -1);
return ES_OK;
}
int umbrella_set_params(int bond_type, double k,
int dir, double r)
{
if(bond_type < 0)
return ES_ERROR;
make_bond_type_exist(bond_type);
bonded_ia_params[bond_type].p.umbrella.k = k;
bonded_ia_params[bond_type].p.umbrella.dir = dir;
bonded_ia_params[bond_type].p.umbrella.r = r;
bonded_ia_params[bond_type].type = BONDED_IA_UMBRELLA;
bonded_ia_params[bond_type].num = 1;
/* broadcast interaction parameters */
mpi_bcast_ia_params(bond_type, -1);
return ES_OK;
}
/** set parameters for the OIF_GLOBAL_FORCES potential.
*/
int oif_global_forces_set_params(int bond_type, double A0_g, double ka_g, double V0, double kv)
{
if(bond_type < 0)
return ES_ERROR;
make_bond_type_exist(bond_type);
bonded_ia_params[bond_type].p.oif_global_forces.ka_g = ka_g;
bonded_ia_params[bond_type].p.oif_global_forces.A0_g = A0_g;
bonded_ia_params[bond_type].p.oif_global_forces.V0 = V0;
bonded_ia_params[bond_type].p.oif_global_forces.kv = kv;
bonded_ia_params[bond_type].type = BONDED_IA_OIF_GLOBAL_FORCES;
bonded_ia_params[bond_type].num = 2;
/* broadcast interaction parameters */
mpi_bcast_ia_params(bond_type, -1);
return ES_OK;
}
/// set the parameters for the fene potential
int fene_set_params(int bond_type, double k, double drmax, double r0)
{
if(bond_type < 0)
return ES_ERROR;
make_bond_type_exist(bond_type);
bonded_ia_params[bond_type].p.fene.k = k;
bonded_ia_params[bond_type].p.fene.drmax = drmax;
bonded_ia_params[bond_type].p.fene.r0 = r0;
bonded_ia_params[bond_type].p.fene.drmax2 = SQR(bonded_ia_params[bond_type].p.fene.drmax);
bonded_ia_params[bond_type].p.fene.drmax2i = 1.0/bonded_ia_params[bond_type].p.fene.drmax2;
bonded_ia_params[bond_type].type = BONDED_IA_FENE;
bonded_ia_params[bond_type].num = 1;
/* broadcast interaction parameters */
mpi_bcast_ia_params(bond_type, -1);
return ES_OK;
}
int drude_set_params(int bond_type, double temp_core, double gamma_core, double temp_drude, double gamma_drude, double k, double mass_drude, double r_cut)
{
if(bond_type < 0)
return ES_ERROR;
make_bond_type_exist(bond_type);
bonded_ia_params[bond_type].p.drude.temp_core = temp_core;
bonded_ia_params[bond_type].p.drude.gamma_core = gamma_core;
bonded_ia_params[bond_type].p.drude.temp_drude = temp_drude;
bonded_ia_params[bond_type].p.drude.gamma_drude = gamma_drude;
bonded_ia_params[bond_type].p.drude.k = k;
bonded_ia_params[bond_type].p.drude.mass_drude = mass_drude;
bonded_ia_params[bond_type].p.drude.r_cut = r_cut;
bonded_ia_params[bond_type].type = BONDED_IA_DRUDE;
bonded_ia_params[bond_type].num = 1;
mpi_bcast_ia_params(bond_type, -1);
return ES_OK;
}
int oif_local_forces_set_params(int bond_type, double r0, double ks, double kslin, double phi0, double kb, double A01, double A02, double kal)
{
if(bond_type < 0)
return ES_ERROR;
make_bond_type_exist(bond_type);
bonded_ia_params[bond_type].p.oif_local_forces.phi0 = phi0;
bonded_ia_params[bond_type].p.oif_local_forces.kb = kb;
bonded_ia_params[bond_type].p.oif_local_forces.r0 = r0;
bonded_ia_params[bond_type].p.oif_local_forces.ks = ks;
bonded_ia_params[bond_type].p.oif_local_forces.kslin = kslin;
bonded_ia_params[bond_type].p.oif_local_forces.A01 = A01;
bonded_ia_params[bond_type].p.oif_local_forces.A02 = A02;
bonded_ia_params[bond_type].p.oif_local_forces.kal = kal;
bonded_ia_params[bond_type].type = BONDED_IA_OIF_LOCAL_FORCES;
bonded_ia_params[bond_type].num = 3;
mpi_bcast_ia_params(bond_type, -1);
return ES_OK;
}
int endangledist_set_params(int bond_type, double bend, double phi0 ,double distmin, double distmax)
{
if(bond_type < 0)
return ES_ERROR;
make_bond_type_exist(bond_type);
bonded_ia_params[bond_type].p.endangledist.bend = bend;
bonded_ia_params[bond_type].p.endangledist.phi0 = phi0;
bonded_ia_params[bond_type].p.endangledist.distmin = distmin;
bonded_ia_params[bond_type].p.endangledist.distmax = distmax;
bonded_ia_params[bond_type].type = BONDED_IA_ENDANGLEDIST;
/* Normally LENGTH=1 ANGLE=2 DIHEDRAL=3
* Here angle only requires one particle (other reference is wall constraint)
*/
bonded_ia_params[bond_type].num = 1;
/* broadcast interaction parameters */
mpi_bcast_ia_params(bond_type, -1);
return ES_OK;
}
int overlapped_bonded_set_params(int bond_type, int overlap_type,
char * filename)
{
int i, scan_success = 0, size;
FILE* fp;
if(bond_type < 0)
return 1;
make_bond_type_exist(bond_type);
/* set types */
bonded_ia_params[bond_type].type = BONDED_IA_OVERLAPPED;
bonded_ia_params[bond_type].p.overlap.type = overlap_type;
/* set number of interaction partners */
if(overlap_type == OVERLAP_BOND_LENGTH) bonded_ia_params[bond_type].num = 1;
if(overlap_type == OVERLAP_BOND_ANGLE) bonded_ia_params[bond_type].num = 2;
if(overlap_type == OVERLAP_BOND_DIHEDRAL) bonded_ia_params[bond_type].num = 3;
/* set max bondlength of between two beads, in Unit Angstrom */
bonded_ia_params[bond_type].p.overlap.maxval = 6.0;
/* copy filename */
size = strlen(filename);
bonded_ia_params[bond_type].p.overlap.filename = (char*)malloc((size+1)*sizeof(char));
strcpy(bonded_ia_params[bond_type].p.overlap.filename,filename);
fp = fopen( filename , "r");
if ( !fp )
return 2;
/* Read in size of overlapps from file */
scan_success = fscanf( fp , "%d ", &size);
if ( scan_success < 1 ) {
fclose(fp);
return 3;
}
bonded_ia_params[bond_type].p.overlap.noverlaps = size;
/* allocate overlapped funciton parameter arrays */
bonded_ia_params[bond_type].p.overlap.para_a = (double*)malloc(size*sizeof(double));
bonded_ia_params[bond_type].p.overlap.para_b = (double*)malloc(size*sizeof(double));
bonded_ia_params[bond_type].p.overlap.para_c = (double*)malloc(size*sizeof(double));
/* Read in the overlapped funciton parameter data */
for (i=0; i<size; i++) {
scan_success = fscanf(fp, "%lg ", &bonded_ia_params[bond_type].p.overlap.para_a[i]);
if ( scan_success < 1 ) {
fclose(fp);
return 3;
}
scan_success = fscanf( fp, "%lg ", &bonded_ia_params[bond_type].p.overlap.para_b[i]);
if ( scan_success < 1 ) {
fclose(fp);
return 3;
}
scan_success = fscanf( fp, "%lg ", &bonded_ia_params[bond_type].p.overlap.para_c[i]);
if ( scan_success < 1 ) {
fclose(fp);
return 3;
}
}
fclose(fp);
mpi_bcast_ia_params(bond_type, -1);
return 0;
}
int tabulated_bonded_set_params(int bond_type, int tab_type, char * filename)
{
int i, token = 0, size;
double dummr;
FILE* fp;
if(bond_type < 0)
return 1;
make_bond_type_exist(bond_type);
fp = fopen( filename , "r");
if ( !fp )
return 3;
/*Look for a line starting with # */
while ( token != EOF) {
token = fgetc(fp);
if ( token == '#' ) { break; } // magic number for # symbol
}
if ( token == EOF ) {
fclose(fp);
return 4;
}
/* set types */
bonded_ia_params[bond_type].type = BONDED_IA_TABULATED;
bonded_ia_params[bond_type].p.tab.type = tab_type;
/* set number of interaction partners */
if(tab_type == TAB_BOND_LENGTH) bonded_ia_params[bond_type].num = 1;
if(tab_type == TAB_BOND_ANGLE) bonded_ia_params[bond_type].num = 2;
if(tab_type == TAB_BOND_DIHEDRAL) bonded_ia_params[bond_type].num = 3;
/* copy filename */
size = strlen(filename);
bonded_ia_params[bond_type].p.tab.filename = (char*)malloc((size+1)*sizeof(char));
strcpy(bonded_ia_params[bond_type].p.tab.filename,filename);
/* read basic parameters from file */
if (fscanf( fp , "%d %lf %lf", &size,
&bonded_ia_params[bond_type].p.tab.minval,
&bonded_ia_params[bond_type].p.tab.maxval) != 3) return 5;
bonded_ia_params[bond_type].p.tab.npoints = size;
/* Check interval for angle and dihedral potentials. With adding
ROUND_ERROR_PREC to the upper boundary we make sure, that during
the calculation we do not leave the defined table!
*/
if(tab_type == TAB_BOND_ANGLE ) {
if( bonded_ia_params[bond_type].p.tab.minval != 0.0 ||
abs(bonded_ia_params[bond_type].p.tab.maxval-PI) > 1e-5 ) {
fclose(fp);
return 6;
}
bonded_ia_params[bond_type].p.tab.maxval = PI+ROUND_ERROR_PREC;
}
/* check interval for angle and dihedral potentials */
if(tab_type == TAB_BOND_DIHEDRAL ) {
if( bonded_ia_params[bond_type].p.tab.minval != 0.0 ||
abs(bonded_ia_params[bond_type].p.tab.maxval-(2*PI)) > 1e-5 ) {
fclose(fp);
return 6;
}
bonded_ia_params[bond_type].p.tab.maxval = (2*PI)+ROUND_ERROR_PREC;
}
/* calculate dependent parameters */
bonded_ia_params[bond_type].p.tab.invstepsize = (double)(size-1)/(bonded_ia_params[bond_type].p.tab.maxval-bonded_ia_params[bond_type].p.tab.minval);
/* allocate force and energy tables */
bonded_ia_params[bond_type].p.tab.f = (double*)malloc(size*sizeof(double));
bonded_ia_params[bond_type].p.tab.e = (double*)malloc(size*sizeof(double));
/* Read in the new force and energy table data */
for (i =0 ; i < size ; i++) {
if (fscanf(fp,"%lf %lf %lf", &dummr,
&bonded_ia_params[bond_type].p.tab.f[i],
&bonded_ia_params[bond_type].p.tab.e[i]) != 3) return 5;
}
fclose(fp);
mpi_bcast_ia_params(bond_type, -1);
return ES_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;
}
