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dihedral_spherical.cpp
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Andrew Jewett (Caltech)
[ using code borrowed from Loukas D. Peristeras (Scienomics SARL)
and Paul Crozier (SNL) ]
------------------------------------------------------------------------- */
#include <mpi.h>
#include <cmath>
#include <cstdlib>
#include <cassert>
#include "atom.h"
#include "comm.h"
#include "neighbor.h"
#include "domain.h"
#include "force.h"
#include "pair.h"
#include "update.h"
#include "math_const.h"
#include "math_extra.h"
#include "memory.h"
#include "error.h"
#include "dihedral_spherical.h"
using namespace std;
using namespace LAMMPS_NS;
using namespace MathConst;
using namespace MathExtra;
/* ---------------------------------------------------------------------- */
DihedralSpherical::DihedralSpherical(LAMMPS *lmp) : Dihedral(lmp) {}
/* ---------------------------------------------------------------------- */
DihedralSpherical::~DihedralSpherical()
{
if (allocated && !copymode) {
memory->destroy(setflag);
memory->destroy(nterms);
for (int i=1; i<= atom->ndihedraltypes; i++) {
if ( Ccoeff[i] ) delete [] Ccoeff[i];
if ( phi_mult[i] ) delete [] phi_mult[i];
if ( phi_shift[i] ) delete [] phi_shift[i];
if ( phi_offset[i] ) delete [] phi_offset[i];
if ( theta1_mult[i] ) delete [] theta1_mult[i];
if ( theta1_shift[i] ) delete [] theta1_shift[i];
if ( theta1_offset[i] ) delete [] theta1_offset[i];
if ( theta2_mult[i] ) delete [] theta2_mult[i];
if ( theta2_shift[i] ) delete [] theta2_shift[i];
if ( theta2_offset[i] ) delete [] theta2_offset[i];
}
delete [] Ccoeff;
delete [] phi_mult;
delete [] phi_shift;
delete [] phi_offset;
delete [] theta1_mult;
delete [] theta1_shift;
delete [] theta1_offset;
delete [] theta2_mult;
delete [] theta2_shift;
delete [] theta2_offset;
}
}
static void norm3safe(double *v) {
double inv_scale = sqrt(v[0]*v[0]+v[1]*v[1]+v[2]*v[2]);
double scale = 1.0;
if (inv_scale > 0.0)
scale = 1.0 / inv_scale;
v[0] *= scale;
v[1] *= scale;
v[2] *= scale;
}
// --------------------------------------------
// ------- Calculate the dihedral angle -------
// --------------------------------------------
static const int g_dim=3;
static double Phi(double const *x1, //array holding x,y,z coords atom 1
double const *x2, // : : : : 2
double const *x3, // : : : : 3
double const *x4, // : : : : 4
Domain *domain, //<-periodic boundary information
double *vb12, //<-preallocated vector will store x2-x1
double *vb23, //<-preallocated vector will store x3-x2
double *vb34, //<-preallocated vector will store x4-x3
double *n123, //<-will store normal to plane x1,x2,x3
double *n234) //<-will store normal to plane x2,x3,x4
{
for (int d=0; d < g_dim; ++d) {
vb12[d] = x2[d] - x1[d]; // 1st bond
vb23[d] = x3[d] - x2[d]; // 2nd bond
vb34[d] = x4[d] - x3[d]; // 3rd bond
}
//Consider periodic boundary conditions:
domain->minimum_image(vb12[0],vb12[1],vb12[2]);
domain->minimum_image(vb23[0],vb23[1],vb23[2]);
domain->minimum_image(vb34[0],vb34[1],vb34[2]);
//--- Compute the normal to the planes formed by atoms 1,2,3 and 2,3,4 ---
cross3(vb23, vb12, n123); // <- n123=vb23 x vb12
cross3(vb23, vb34, n234); // <- n234=vb23 x vb34
norm3safe(n123);
norm3safe(n234);
double cos_phi = -dot3(n123, n234);
if (cos_phi > 1.0)
cos_phi = 1.0;
else if (cos_phi < -1.0)
cos_phi = -1.0;
double phi = acos(cos_phi);
if (dot3(n123, vb34) > 0.0) {
phi = -phi; //(Note: Negative dihedral angles are possible only in 3-D.)
phi += MY_2PI; //<- This insure phi is always in the range 0 to 2*PI
}
return phi;
} // DihedralSpherical::Phi()
/* ---------------------------------------------------------------------- */
void DihedralSpherical::compute(int eflag, int vflag)
{
int i1,i2,i3,i4,n,type;
double edihedral,f1[3],f2[3],f3[3],f4[3];
double **x = atom->x;
double **f = atom->f;
int **dihedrallist = neighbor->dihedrallist;
int ndihedrallist = neighbor->ndihedrallist;
int nlocal = atom->nlocal;
int newton_bond = force->newton_bond;
// The dihedral angle "phi" is the angle between n123 and n234
// the planes defined by atoms i1,i2,i3, and i2,i3,i4.
//
// Definitions of vectors: vb12, vb23, vb34, perp12on23
// proj12on23, perp43on32, proj43on32
//
// Note: The positions of the 4 atoms are labeled x[i1], x[i2], x[i3], x[i4]
// (which are also vectors)
//
// proj12on23 proj34on23
// ---------> ----------->
//
//
//
// x[i2] x[i3]
// . __@----------vb23-------->@ .
// /|\ /| \ |
// | / \ |
// | / \ |
// perp12on23 / \ |
// | / \ perp34on23
// | vb12 \ |
// | / vb34 |
// | / \ |
// | / \ |
// | / \ |
// @ \ |
// _\| \|/
// x[i1] @
//
// x[i4]
//
double vb12[g_dim]; // displacement vector from atom i1 towards atom i2
// vb12[d] = x[i2][d] - x[i1][d] (for d=0,1,2)
double vb23[g_dim]; // displacement vector from atom i2 towards atom i3
// vb23[d] = x[i3][d] - x[i2][d] (for d=0,1,2)
double vb34[g_dim]; // displacement vector from atom i3 towards atom i4
// vb34[d] = x[i4][d] - x[i3][d] (for d=0,1,2)
// n123 & n234: These two unit vectors are normal to the planes
// defined by atoms 1,2,3 and 2,3,4.
double n123[g_dim]; //n123=vb23 x vb12 / |vb23 x vb12| ("x" is cross product)
double n234[g_dim]; //n234=vb23 x vb34 / |vb23 x vb34| ("x" is cross product)
// The next 4 vectors are needed to calculate dphi_dx = d phi / dx
double proj12on23[g_dim];
// proj12on23[d] = (vb23[d]/|vb23|) * dot3(vb12,vb23)/|vb12|*|vb23|
double proj34on23[g_dim];
// proj34on23[d] = (vb34[d]/|vb23|) * dot3(vb34,vb23)/|vb34|*|vb23|
double perp12on23[g_dim];
// perp12on23[d] = v12[d] - proj12on23[d]
double perp34on23[g_dim];
// perp34on23[d] = v34[d] - proj34on23[d]
edihedral = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = 0;
for (n = 0; n < ndihedrallist; n++) {
i1 = dihedrallist[n][0];
i2 = dihedrallist[n][1];
i3 = dihedrallist[n][2];
i4 = dihedrallist[n][3];
type = dihedrallist[n][4];
// ------ Step 1: Compute the dihedral angle "phi" ------
//
// Phi() calculates the dihedral angle.
// This function also calculates the vectors:
// vb12, vb23, vb34, n123, and n234, which we will need later.
double phi = Phi(x[i1], x[i2], x[i3], x[i4], domain,
vb12, vb23, vb34, n123, n234);
// Step 2: Compute the gradients of phi, theta1, theta2 with atom position:
// ===================== Step2a) phi dependence: ========================
//
// Gradient variables:
//
// dphi_dx1, dphi_dx2, dphi_dx3, dphi_dx4 are the gradients of phi with
// respect to the atomic positions of atoms i1, i2, i3, i4, respectively.
// As an example, consider dphi_dx1. The d'th element is:
double dphi_dx1[g_dim]; // d phi
double dphi_dx2[g_dim]; // dphi_dx1[d] = ---------- (partial derivatives)
double dphi_dx3[g_dim]; // d x[i1][d]
double dphi_dx4[g_dim]; //where d=0,1,2 corresponds to x,y,z (g_dim==3)
double dot123 = dot3(vb12, vb23);
double dot234 = dot3(vb23, vb34);
double L23sqr = dot3(vb23, vb23);
double L23 = sqrt(L23sqr); // (central bond length)
double inv_L23sqr = 0.0;
double inv_L23 = 0.0;
if (L23sqr != 0.0) {
inv_L23sqr = 1.0 / L23sqr;
inv_L23 = 1.0 / L23;
}
double neg_inv_L23 = -inv_L23;
double dot123_over_L23sqr = dot123 * inv_L23sqr;
double dot234_over_L23sqr = dot234 * inv_L23sqr;
for (int d=0; d < g_dim; ++d) {
// See figure above for a visual definitions of these vectors:
proj12on23[d] = vb23[d] * dot123_over_L23sqr;
proj34on23[d] = vb23[d] * dot234_over_L23sqr;
perp12on23[d] = vb12[d] - proj12on23[d];
perp34on23[d] = vb34[d] - proj34on23[d];
}
// --- Compute the gradient vectors dphi/dx1 and dphi/dx4: ---
// These two gradients point in the direction of n123 and n234,
// and are scaled by the distances of atoms 1 and 4 from the central axis.
// Distance of atom 1 to central axis:
double perp12on23_len = sqrt(dot3(perp12on23, perp12on23));
// Distance of atom 4 to central axis:
double perp34on23_len = sqrt(dot3(perp34on23, perp34on23));
double inv_perp12on23 = 0.0;
if (perp12on23_len != 0.0) inv_perp12on23 = 1.0 / perp12on23_len;
double inv_perp34on23 = 0.0;
if (perp34on23_len != 0.0) inv_perp34on23 = 1.0 / perp34on23_len;
for (int d=0; d < g_dim; ++d) {
dphi_dx1[d] = n123[d] * inv_perp12on23;
dphi_dx4[d] = n234[d] * inv_perp34on23;
}
// --- Compute the gradient vectors dphi/dx2 and dphi/dx3: ---
//
// This is more tricky because atoms 2 and 3 are shared by both planes
// 123 and 234 (the angle between which defines "phi"). Moving either
// one of these atoms effects both the 123 and 234 planes
// Both the 123 and 234 planes intersect with the plane perpendicular to the
// central bond axis (vb23). The two lines where these intersections occur
// will shift when you move either atom 2 or atom 3. The angle between
// these lines is the dihedral angle, phi. We can define four quantities:
// dphi123_dx2 is the change in "phi" due to the movement of the 123 plane
// ...as a result of moving atom 2.
// dphi234_dx2 is the change in "phi" due to the movement of the 234 plane
// ...as a result of moving atom 2.
// dphi123_dx3 is the change in "phi" due to the movement of the 123 plane
// ...as a result of moving atom 3.
// dphi234_dx3 is the change in "phi" due to the movement of the 234 plane
// ...as a result of moving atom 3.
double proj12on23_len = dot123 * inv_L23;
double proj34on23_len = dot234 * inv_L23;
// Interpretation:
//The magnitude of "proj12on23_len" is the length of the proj12on23 vector.
//The sign is positive if it points in the same direction as the central
//bond (vb23). Otherwise it is negative. The same goes for "proj34on23".
//(In the example figure in the comment above, both variables are positive.)
// The following 8 lines of code are used to calculate the gradient of phi
// with respect to the two "middle" atom positions (x[i2] and x[i3]).
// For an explanation of the formula used below, download the file
// "dihedral_table_2011-8-02.tar.gz" at the bottom of this post:
// http://lammps.sandia.gov/threads/msg22233.html
// Unpack it and go to this subdirectory:
// "supporting_information/doc/gradient_formula_explanation/"
double dphi123_dx2_coef = neg_inv_L23 * (L23 + proj12on23_len);
double dphi234_dx2_coef = inv_L23 * proj34on23_len;
double dphi234_dx3_coef = neg_inv_L23 * (L23 + proj34on23_len);
double dphi123_dx3_coef = inv_L23 * proj12on23_len;
for (int d=0; d < g_dim; ++d) {
// Recall that the n123 and n234 plane normal vectors are proportional to
// the dphi/dx1 and dphi/dx2 gradients vectors
// It turns out we can save slightly more CPU cycles by expressing
// dphi/dx2 and dphi/dx3 as linear combinations of dphi/dx1 and dphi/dx2
// which we computed already (instead of n123 & n234).
dphi_dx2[d] = dphi123_dx2_coef*dphi_dx1[d] + dphi234_dx2_coef*dphi_dx4[d];
dphi_dx3[d] = dphi123_dx3_coef*dphi_dx1[d] + dphi234_dx3_coef*dphi_dx4[d];
}
// ============= Step2b) theta1 and theta2 dependence: =============
// --- Compute the gradient vectors dtheta1/dx1 and dtheta2/dx4: ---
// These two gradients point in the direction of n123 and n234,
// and are scaled by the distances of atoms 1 and 4 from the central axis.
// Distance of atom 1 to central axis:
double dth1_dx1[g_dim]; // d theta1 (partial
double dth1_dx2[g_dim]; // dth1_dx1[d] = ---------- derivative)
double dth1_dx3[g_dim]; // d x[i1][d]
//Note dth1_dx4 = 0
//Note dth2_dx1 = 0
double dth2_dx2[g_dim]; // d theta2 (partial
double dth2_dx3[g_dim]; // dth2_dx1[d] = ---------- derivative)
double dth2_dx4[g_dim]; // d x[i1][d]
//where d=0,1,2 corresponds to x,y,z (g_dim==3)
double L12sqr = dot3(vb12, vb12);
double L12 = sqrt(L12sqr);
double L34sqr = dot3(vb34, vb34);
double L34 = sqrt(L34sqr);
double inv_L12sqr = 0.0;
double inv_L12 = 0.0;
double inv_L34sqr = 0.0;
double inv_L34 = 0.0;
if (L12sqr != 0.0) {
inv_L12sqr = 1.0 / L12sqr;
inv_L12 = 1.0 / L12;
}
if (L34sqr != 0.0) {
inv_L34sqr = 1.0 / L34sqr;
inv_L34 = 1.0 / L34;
}
// The next 2 vectors are needed for calculating dth1_dx = d theta1 / d x
double proj23on12[g_dim];
// proj23on12[d] = (vb12[d]/|vb12|) * dot3(vb23,vb12)/|vb23|*|vb12|
double perp23on12[g_dim];
// perp23on12[d] = v23[d] - proj23on12[d]
// The next 2 vectors are needed for calculating dth2_dx = d theta2 / d x
double proj23on34[g_dim];
// proj23on34[d] = (vb23[d]/|vb34|) * dot3(vb23,vb34)/|vb23|*|vb34|
double perp23on34[g_dim];
// perp23on34[d] = v23[d] - proj23on34[d]
double dot123_over_L12sqr = dot123 * inv_L12sqr;
double dot234_over_L34sqr = dot234 * inv_L34sqr;
/* __ .
* proj23on12 .\ .
* . . proj23on34
* . .
* . .
* x[i2] . _./ x[i3]
* __@----------vb23-------->@
* /| / \ \
* / theta1 theta2 \
* / <-' `-> \
* / \
* / \
* vb12 \
* / vb34
* / \
* / \
* / \
* @ \
* _\|
* x[i1] @
*
* x[i4]
*/
for (int d=0; d < g_dim; ++d) {
// See figure above for a visual definitions of these vectors:
proj23on12[d] = vb12[d] * dot123_over_L12sqr;
proj23on34[d] = vb34[d] * dot234_over_L34sqr;
perp23on12[d] = vb23[d] - proj23on12[d];
perp23on34[d] = vb23[d] - proj23on34[d];
}
double perp23on12_len = sqrt(dot3(perp23on12, perp23on12));
double perp23on34_len = sqrt(dot3(perp23on34, perp23on34));
double inv_perp23on12 = 0.0;
if (perp23on12_len != 0.0) inv_perp23on12 = 1.0 / perp23on12_len;
double inv_perp23on34 = 0.0;
if (perp23on34_len != 0.0) inv_perp23on34 = 1.0 / perp23on34_len;
double coeff_dth1_dx1 = -inv_perp23on12 * inv_L12;
double coeff_dth1_dx3 = inv_perp12on23 * inv_L23;
double coeff_dth2_dx2 = -inv_perp34on23 * inv_L23;
double coeff_dth2_dx4 = inv_perp23on34 * inv_L34;
for (int d=0; d < g_dim; ++d) {
dth1_dx1[d] = perp23on12[d] * coeff_dth1_dx1;
dth1_dx3[d] = perp12on23[d] * coeff_dth1_dx3;
dth1_dx2[d] = -(dth1_dx1[d] + dth1_dx3[d]);
//dtheta1_dx4 = 0
//dtheta2_dx1 = 0
dth2_dx2[d] = perp34on23[d] * coeff_dth2_dx2;
dth2_dx4[d] = perp23on34[d] * coeff_dth2_dx4;
dth2_dx3[d] = -(dth2_dx2[d] + dth2_dx4[d]);
}
double ct1 = -dot123 * inv_L12 * inv_L23;
if (ct1 < -1.0) ct1 = -1.0;
else if (ct1 > 1.0) ct1 = 1.0;
double theta1 = acos(ct1);
double ct2 = -dot234 * inv_L23 * inv_L34;
if (ct2 < -1.0) ct2 = -1.0;
else if (ct2 > 1.0) ct2 = 1.0;
double theta2 = acos(ct2);
// - Step 3: Calculate the energy and force in the phi & theta1/2 directions
double u=0.0; // u = energy
double m_du_dth1 = 0.0; // m_du_dth1 = -du / d theta1
double m_du_dth2 = 0.0; // m_du_dth2 = -du / d theta2
double m_du_dphi = 0.0; // m_du_dphi = -du / d phi
u = CalcGeneralizedForces(type,
phi, theta1, theta2,
&m_du_dth1, &m_du_dth2, &m_du_dphi);
if (eflag) edihedral = u;
// ----- Step 4: Calculate the force direction in real space -----
// chain rule:
// d U d U d phi d U d theta1 d U d theta2
// -f = ----- = ----- * ----- + -------*------- + --------*--------
// d x d phi d x d theta1 d X d theta2 d X
for(int d=0; d < g_dim; ++d) {
f1[d] = m_du_dphi*dphi_dx1[d]+m_du_dth1*dth1_dx1[d];
//note: dth2_dx1[d]=0
f2[d] = m_du_dphi*dphi_dx2[d]+m_du_dth1*dth1_dx2[d]+m_du_dth2*dth2_dx2[d];
f3[d] = m_du_dphi*dphi_dx3[d]+m_du_dth1*dth1_dx3[d]+m_du_dth2*dth2_dx3[d];
f4[d] = m_du_dphi*dphi_dx4[d] + m_du_dth2*dth2_dx4[d];
//note: dth1_dx4[d] = 0
}
// apply force to each of 4 atoms
if (newton_bond || i1 < nlocal) {
f[i1][0] += f1[0];
f[i1][1] += f1[1];
f[i1][2] += f1[2];
}
if (newton_bond || i2 < nlocal) {
f[i2][0] += f2[0];
f[i2][1] += f2[1];
f[i2][2] += f2[2];
}
if (newton_bond || i3 < nlocal) {
f[i3][0] += f3[0];
f[i3][1] += f3[1];
f[i3][2] += f3[2];
}
if (newton_bond || i4 < nlocal) {
f[i4][0] += f4[0];
f[i4][1] += f4[1];
f[i4][2] += f4[2];
}
if (evflag)
ev_tally(i1,i2,i3,i4,
nlocal,newton_bond,edihedral,
f1,f3,f4,
vb12[0],vb12[1],vb12[2],
vb23[0],vb23[1],vb23[2],
vb34[0],vb34[1],vb34[2]);
}
} // void DihedralSpherical::compute()
// --- CalcGeneralizedForces() ---
// --- Calculate the energy as a function of theta1, theta2, and phi ---
// --- as well as its derivatives (with respect to theta1, theta2, and phi) ---
// The code above above is sufficiently general that it can work with any
// any function of the angles theta1, theta2, and phi. However the
// function below calculates the energy and force according to this specific
// formula:
//
// E(\theta_1,\theta_2,\phi) =
// \sum_{i=1}^N C_i \Theta_{1i}(\theta_1) \Theta_{2i}(\theta_2) \Phi_i(\phi)
// where:
// \Theta_{1i}(\theta_1) = cos((\theta_1-a_i)K_i) + u_i
// \Theta_{2i}(\theta_2) = cos((\theta_2-b_i)L_i) + v_i
// \Phi_i(\phi) = cos((\phi - c_i)M_i) + w_i
double DihedralSpherical::
CalcGeneralizedForces(int type,
double phi,
double theta1,
double theta2,
double *m_du_dth1,
double *m_du_dth2,
double *m_du_dphi)
{
double energy = 0.0;
assert(m_du_dphi && m_du_dphi && m_du_dphi);
*m_du_dphi = 0.0;
*m_du_dth1 = 0.0;
*m_du_dth2 = 0.0;
int i = type;
for (int j = 0; j < nterms[i]; j++) {
// (It's common that some terms in an expansion have phi_multi[i][j]=0.
// When this happens, perhaps it will speed up the calculation to avoid
// unnecessary calls to the cos() and sin() functions. Check this below)
// I also check whether theta1_mult[i][j] and theta2_mult[i][j] are 0.
double cp = 1.0;
double sp = 0.0;
if (phi_mult[i][j] != 0.0) {
double p = phi_mult[i][j] * (phi - phi_shift[i][j]);
cp = cos(p);
sp = sin(p);
}
double ct1 = 1.0;
double st1 = 0.0;
if (theta1_mult[i][j] != 0.0) {
double t1 = theta1_mult[i][j]*(theta1 - theta1_shift[i][j]);
ct1 = cos(t1);
st1 = sin(t1);
}
double ct2 = 1.0;
double st2 = 0.0;
if (theta2_mult[i][j] != 0.0) {
double t2 = theta2_mult[i][j]*(theta2 - theta2_shift[i][j]);
ct2 = cos(t2);
st2 = sin(t2);
}
energy += Ccoeff[i][j] * (phi_offset[i][j] - cp) *
(theta1_offset[i][j] - ct1) *
(theta2_offset[i][j] - ct2);
// Forces:
*m_du_dphi += -Ccoeff[i][j] * sp * phi_mult[i][j] *
(theta1_offset[i][j] - ct1) *
(theta2_offset[i][j] - ct2);
*m_du_dth1 += -Ccoeff[i][j] * (phi_offset[i][j] - cp) *
st1 * theta1_mult[i][j] *
(theta2_offset[i][j] - ct2);
*m_du_dth2 += -Ccoeff[i][j] * (phi_offset[i][j] - cp) *
(theta1_offset[i][j] - ct1) *
st2 * theta2_mult[i][j];
// Things to consider later:
// To speed up the computation, one could try to simplify the expansion:
// IE by factoring out common terms, and precomputing trig functions once:
// cos(K*theta1), sin(K*theta1),
// cos(L*theta2), sin(L*theta2), and
// cos(M*phi), sin(M*phi)
// Also: For integer K,L,M, the trig functions cos(M*phi) and sin(M*phi)
// can be calculated more efficiently using polynomials of
// cos(phi) and sin(phi)
} //for (int j = 0; j < nterms[i]; j++) {
return energy;
} //CalcGeneralizedForces()
void DihedralSpherical::allocate()
{
allocated = 1;
int n = atom->ndihedraltypes;
memory->create(nterms,n+1,"dihedral:nterms");
Ccoeff = new double * [n+1];
phi_mult = new double * [n+1];
phi_shift = new double * [n+1];
phi_offset = new double * [n+1];
theta1_mult = new double * [n+1];
theta1_shift = new double * [n+1];
theta1_offset = new double * [n+1];
theta2_mult = new double * [n+1];
theta2_shift = new double * [n+1];
theta2_offset = new double * [n+1];
for (int i = 1; i <= n; i++) {
Ccoeff[i] = NULL;
phi_mult[i] = NULL;
phi_shift[i] = NULL;
phi_offset[i] = NULL;
theta1_mult[i] = NULL;
theta1_shift[i] = NULL;
theta1_offset[i] = NULL;
theta2_mult[i] = NULL;
theta2_shift[i] = NULL;
theta2_offset[i] = NULL;
}
memory->create(setflag,n+1,"dihedral:setflag");
for (int i = 1; i <= n; i++) setflag[i] = 0;
}
/* ----------------------------------------------------------------------
set coeffs for one type
------------------------------------------------------------------------- */
void DihedralSpherical::coeff(int narg, char **arg)
{
if (narg < 4) error->all(FLERR,"Incorrect args for dihedral coefficients");
if (!allocated) allocate();
int ilo,ihi;
force->bounds(arg[0],atom->ndihedraltypes,ilo,ihi);
int nterms_one = force->inumeric(FLERR,arg[1]);
if (nterms_one < 1)
error->all(FLERR,"Incorrect number of terms arg for dihedral coefficients");
if (2+10*nterms_one < narg)
error->all(FLERR,"Incorrect number of arguments for dihedral coefficients");
int count = 0;
for (int i = ilo; i <= ihi; i++) {
nterms[i] = nterms_one;
Ccoeff[i] = new double [nterms_one];
phi_mult[i] = new double [nterms_one];
phi_shift[i] = new double [nterms_one];
phi_offset[i] = new double [nterms_one];
theta1_mult[i] = new double [nterms_one];
theta1_shift[i] = new double [nterms_one];
theta1_offset[i] = new double [nterms_one];
theta2_mult[i] = new double [nterms_one];
theta2_shift[i] = new double [nterms_one];
theta2_offset[i] = new double [nterms_one];
for (int j = 0; j < nterms_one; j++) {
int offset = 1+10*j;
Ccoeff[i][j] = force->numeric(FLERR,arg[offset+1]);
phi_mult[i][j] = force->numeric(FLERR,arg[offset+2]);
phi_shift[i][j] = force->numeric(FLERR,arg[offset+3]) * MY_PI/180.0;
phi_offset[i][j] = force->numeric(FLERR,arg[offset+4]);
theta1_mult[i][j] = force->numeric(FLERR,arg[offset+5]);
theta1_shift[i][j] = force->numeric(FLERR,arg[offset+6]) * MY_PI/180.0;
theta1_offset[i][j] = force->numeric(FLERR,arg[offset+7]);
theta2_mult[i][j] = force->numeric(FLERR,arg[offset+8]);
theta2_shift[i][j] = force->numeric(FLERR,arg[offset+9]) * MY_PI/180.0;
theta2_offset[i][j] = force->numeric(FLERR,arg[offset+10]);
}
setflag[i] = 1;
count++;
}
if (count == 0) error->all(FLERR,"Incorrect args for dihedral coefficients");
}
/* ----------------------------------------------------------------------
proc 0 writes out coeffs to restart file
------------------------------------------------------------------------- */
void DihedralSpherical::write_restart(FILE *fp)
{
fwrite(&nterms[1],sizeof(int),atom->ndihedraltypes,fp);
for(int i = 1; i <= atom->ndihedraltypes; i++) {
fwrite(Ccoeff[i],sizeof(double),nterms[i],fp);
fwrite(phi_mult[i],sizeof(double),nterms[i],fp);
fwrite(phi_shift[i],sizeof(double),nterms[i],fp);
fwrite(phi_offset[i],sizeof(double),nterms[i],fp);
fwrite(theta1_mult[i],sizeof(double),nterms[i],fp);
fwrite(theta1_shift[i],sizeof(double),nterms[i],fp);
fwrite(theta1_offset[i],sizeof(double),nterms[i],fp);
fwrite(theta2_mult[i],sizeof(double),nterms[i],fp);
fwrite(theta2_shift[i],sizeof(double),nterms[i],fp);
fwrite(theta2_offset[i],sizeof(double),nterms[i],fp);
}
}
/* ----------------------------------------------------------------------
proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
void DihedralSpherical::read_restart(FILE *fp)
{
allocate();
if (comm->me == 0)
fread(&nterms[1],sizeof(int),atom->ndihedraltypes,fp);
MPI_Bcast(&nterms[1],atom->ndihedraltypes,MPI_INT,0,world);
// allocate
for (int i=1; i<=atom->ndihedraltypes; i++) {
Ccoeff[i] = new double [nterms[i]];
phi_mult[i] = new double [nterms[i]];
phi_shift[i] = new double [nterms[i]];
phi_offset[i] = new double [nterms[i]];
theta1_mult[i] = new double [nterms[i]];
theta1_shift[i] = new double [nterms[i]];
theta1_offset[i] = new double [nterms[i]];
theta2_mult[i] = new double [nterms[i]];
theta2_shift[i] = new double [nterms[i]];
theta2_offset[i] = new double [nterms[i]];
}
if (comm->me == 0) {
for (int i=1; i<=atom->ndihedraltypes; i++) {
fread(Ccoeff[i],sizeof(double),nterms[i],fp);
fread(phi_mult[i],sizeof(double),nterms[i],fp);
fread(phi_shift[i],sizeof(double),nterms[i],fp);
fread(phi_offset[i],sizeof(double),nterms[i],fp);
fread(theta1_mult[i],sizeof(double),nterms[i],fp);
fread(theta1_shift[i],sizeof(double),nterms[i],fp);
fread(theta1_offset[i],sizeof(double),nterms[i],fp);
fread(theta2_mult[i],sizeof(double),nterms[i],fp);
fread(theta2_shift[i],sizeof(double),nterms[i],fp);
fread(theta2_offset[i],sizeof(double),nterms[i],fp);
}
}
for (int i=1; i<=atom->ndihedraltypes; i++) {
MPI_Bcast(Ccoeff[i],nterms[i],MPI_DOUBLE,0,world);
MPI_Bcast(phi_mult[i],nterms[i],MPI_DOUBLE,0,world);
MPI_Bcast(phi_shift[i],nterms[i],MPI_DOUBLE,0,world);
MPI_Bcast(phi_offset[i],nterms[i],MPI_DOUBLE,0,world);
MPI_Bcast(theta1_mult[i],nterms[i],MPI_DOUBLE,0,world);
MPI_Bcast(theta1_shift[i],nterms[i],MPI_DOUBLE,0,world);
MPI_Bcast(theta1_offset[i],nterms[i],MPI_DOUBLE,0,world);
MPI_Bcast(theta2_mult[i],nterms[i],MPI_DOUBLE,0,world);
MPI_Bcast(theta2_shift[i],nterms[i],MPI_DOUBLE,0,world);
MPI_Bcast(theta2_offset[i],nterms[i],MPI_DOUBLE,0,world);
}
for (int i = 1; i <= atom->ndihedraltypes; i++) setflag[i] = 1;
}
/* ----------------------------------------------------------------------
proc 0 writes to data file
------------------------------------------------------------------------- */
void DihedralSpherical::write_data(FILE *fp)
{
for (int i = 1; i <= atom->ndihedraltypes; i++) {
fprintf(fp,"%d %d ", i , nterms[i]);
for (int j = 0; j < nterms[i]; j++) {
fprintf(fp, "%g %g %g %g %g %g %g %g %g ",
phi_mult[i][j], phi_shift[i][j], phi_offset[i][j],
theta1_mult[i][j], theta1_shift[i][j], theta1_offset[i][j],
theta2_mult[i][j], theta2_shift[i][j], theta2_offset[i][j]);
}
fprintf(fp,"\n");
}
}
// Not needed?
// single() calculates the dihedral-angle energy of atoms i1, i2, i3, i4.
//double DihedralSpherical::single(int type, int i1, int i2, int i3, int i4)
//{
// //variables we will need
// double vb12[g_dim];
// double vb23[g_dim];
// double vb34[g_dim];
//
// // Some functions calculate numbers we don't care about. Store in variables:
// double n123[g_dim]; // (will be ignored)
// double n234[g_dim]; // (will be ignored)
// double m_du_dth1; // (will be ignored)
// double m_du_dth2; // (will be ignored)
// double m_du_dphi; // (will be ignored)
//
// double **x = atom->x;
//
// // Calculate the 4-body angle: phi
// double phi = Phi(x[i1], x[i2], x[i3], x[i4], domain,
// vb12, vb23, vb34, n123, n234);
//
// // Calculate the 3-body angles: theta1 and theta2
// double L12 = sqrt(dot3(vb12, vb12));
// double L23 = sqrt(dot3(vb23, vb23));
// double L34 = sqrt(dot3(vb34, vb34));
//
// double ct1 = -dot3(vb12, vb23) / (L12 * L23);
// if (ct1 < -1.0) ct1 = -1.0;
// else if (ct1 > 1.0) ct1 = 1.0;
// double theta1 = acos(ct1);
//
// double ct2 = -dot3(vb23, vb34) / (L23 * L34);
// if (ct2 < -1.0) ct2 = -1.0;
// else if (ct2 > 1.0) ct2 = 1.0;
// double theta2 = acos(ct2);
//
// double u = CalcGeneralizedForces(type,
// phi, theta1, theta2,
// &m_du_dth1, &m_du_dth2, &m_du_dphi);
// return u;
//}

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