Page Menu
Home
c4science
Search
Configure Global Search
Log In
Files
F81015354
dihedral_table_omp.cpp
No One
Temporary
Actions
Download File
Edit File
Delete File
View Transforms
Subscribe
Mute Notifications
Award Token
Subscribers
None
File Metadata
Details
File Info
Storage
Attached
Created
Tue, Sep 3, 19:18
Size
14 KB
Mime Type
text/x-c++
Expires
Thu, Sep 5, 19:18 (2 d)
Engine
blob
Format
Raw Data
Handle
20201581
Attached To
rLAMMPS lammps
dihedral_table_omp.cpp
View Options
/* ----------------------------------------------------------------------
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: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
#include <cmath>
#include <cstdlib>
#include <cstdio>
#include "dihedral_table_omp.h"
#include "atom.h"
#include "comm.h"
#include "neighbor.h"
#include "domain.h"
#include "force.h"
#include "update.h"
#include "error.h"
#include "math_const.h"
#include "math_extra.h"
#include "suffix.h"
using namespace LAMMPS_NS;
using namespace MathConst;
using namespace MathExtra;
#define TOLERANCE 0.05
#define SMALL 0.001
// --------------------------------------------
// ------- 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
// The following arrays are of doubles with g_dim elements.
// (g_dim is a constant known at compile time, usually 3).
// Their contents is calculated by this function.
// Space for these vectors must be allocated in advance.
// (This is not hidden internally because these vectors
// may be needed outside the function, later on.)
double *vb12, // will store x2-x1
double *vb23, // will store x3-x2
double *vb34, // 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
norm3(n123);
norm3(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;
} // DihedralTable::Phi()
/* ---------------------------------------------------------------------- */
DihedralTableOMP::DihedralTableOMP(class LAMMPS *lmp)
: DihedralTable(lmp), ThrOMP(lmp,THR_DIHEDRAL)
{
suffix_flag |= Suffix::OMP;
}
/* ---------------------------------------------------------------------- */
void DihedralTableOMP::compute(int eflag, int vflag)
{
if (eflag || vflag) {
ev_setup(eflag,vflag);
} else evflag = 0;
const int nall = atom->nlocal + atom->nghost;
const int nthreads = comm->nthreads;
const int inum = neighbor->ndihedrallist;
#if defined(_OPENMP)
#pragma omp parallel default(none) shared(eflag,vflag)
#endif
{
int ifrom, ito, tid;
loop_setup_thr(ifrom, ito, tid, inum, nthreads);
ThrData *thr = fix->get_thr(tid);
thr->timer(Timer::START);
ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
if (inum > 0) {
if (evflag) {
if (eflag) {
if (force->newton_bond) eval<1,1,1>(ifrom, ito, thr);
else eval<1,1,0>(ifrom, ito, thr);
} else {
if (force->newton_bond) eval<1,0,1>(ifrom, ito, thr);
else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_bond) eval<0,0,1>(ifrom, ito, thr);
else eval<0,0,0>(ifrom, ito, thr);
}
}
thr->timer(Timer::BOND);
reduce_thr(this, eflag, vflag, thr);
} // end of omp parallel region
}
template <int EVFLAG, int EFLAG, int NEWTON_BOND>
void DihedralTableOMP::eval(int nfrom, int nto, ThrData * const thr)
{
int i1,i2,i3,i4,n,type;
double edihedral,f1[3],f2[3],f3[3],f4[3];
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const int * const * const dihedrallist = neighbor->dihedrallist;
const int nlocal = atom->nlocal;
// 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-------->@ . . . . .
// /|\ /| \ |
// | / \ |
// | / \ |
// perp12vs23 / \ |
// | / \ perp34vs23
// | 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)
double proj12on23[g_dim];
// proj12on23[d] = (vb23[d]/|vb23|) * DotProduct(vb12,vb23)/|vb12|*|vb23|
double proj34on23[g_dim];
// proj34on23[d] = (vb34[d]/|vb23|) * DotProduct(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;
for (n = nfrom; n < nto; 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 gradient of phi with atomic position: ------
//
// 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 (if 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 forumula used in the 8 lines below explained here:
// "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];
}
// ----- Step 3: Calculate the energy and force in the phi direction -----
// tabulated force & energy
double u=0.0, m_du_dphi=0.0; //u = energy. m_du_dphi = "minus" du/dphi
uf_lookup(type, phi, u, m_du_dphi);
if (EFLAG) edihedral = u;
// ----- Step 4: Calculate the force direction in real space -----
// chain rule:
// d U d U d phi
// -f = ----- = ----- * -----
// d x d phi d x
for(int d=0; d < g_dim; ++d) {
f1[d] = m_du_dphi * dphi_dx1[d];
f2[d] = m_du_dphi * dphi_dx2[d];
f3[d] = m_du_dphi * dphi_dx3[d];
f4[d] = m_du_dphi * dphi_dx4[d];
}
// 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_thr(this,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],thr);
}
}
Event Timeline
Log In to Comment