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apply clang-format

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This commit is contained in:
Axel Kohlmeyer
2021-08-22 11:13:34 -04:00
parent ce71e45db0
commit 403ee3a85f
1 changed files with 223 additions and 264 deletions
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src/EXTRA-MOLECULE/dihedral_spherical.cpp
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@ -29,8 +29,8 @@
#include "memory.h" #include "memory.h"
#include "neighbor.h" #include "neighbor.h"
#include <cmath>
#include <cassert> #include <cassert>
#include <cmath>
using namespace LAMMPS_NS; using namespace LAMMPS_NS;
using namespace MathConst; using namespace MathConst;
@ -51,36 +51,36 @@ DihedralSpherical::~DihedralSpherical()
memory->destroy(setflag); memory->destroy(setflag);
memory->destroy(nterms); memory->destroy(nterms);
for (int i=1; i<= atom->ndihedraltypes; i++) { for (int i = 1; i <= atom->ndihedraltypes; i++) {
if (Ccoeff[i]) delete [] Ccoeff[i]; if (Ccoeff[i]) delete[] Ccoeff[i];
if (phi_mult[i]) delete [] phi_mult[i]; if (phi_mult[i]) delete[] phi_mult[i];
if (phi_shift[i]) delete [] phi_shift[i]; if (phi_shift[i]) delete[] phi_shift[i];
if (phi_offset[i]) delete [] phi_offset[i]; if (phi_offset[i]) delete[] phi_offset[i];
if (theta1_mult[i]) delete [] theta1_mult[i]; if (theta1_mult[i]) delete[] theta1_mult[i];
if (theta1_shift[i]) delete [] theta1_shift[i]; if (theta1_shift[i]) delete[] theta1_shift[i];
if (theta1_offset[i]) delete [] theta1_offset[i]; if (theta1_offset[i]) delete[] theta1_offset[i];
if (theta2_mult[i]) delete [] theta2_mult[i]; if (theta2_mult[i]) delete[] theta2_mult[i];
if (theta2_shift[i]) delete [] theta2_shift[i]; if (theta2_shift[i]) delete[] theta2_shift[i];
if (theta2_offset[i]) delete [] theta2_offset[i]; if (theta2_offset[i]) delete[] theta2_offset[i];
} }
delete [] Ccoeff; delete[] Ccoeff;
delete [] phi_mult; delete[] phi_mult;
delete [] phi_shift; delete[] phi_shift;
delete [] phi_offset; delete[] phi_offset;
delete [] theta1_mult; delete[] theta1_mult;
delete [] theta1_shift; delete[] theta1_shift;
delete [] theta1_offset; delete[] theta1_offset;
delete [] theta2_mult; delete[] theta2_mult;
delete [] theta2_shift; delete[] theta2_shift;
delete [] theta2_offset; delete[] theta2_offset;
} }
} }
static void norm3safe(double *v) { static void norm3safe(double *v)
double inv_scale = sqrt(v[0]*v[0]+v[1]*v[1]+v[2]*v[2]); {
double inv_scale = sqrt(v[0] * v[0] + v[1] * v[1] + v[2] * v[2]);
double scale = 1.0; double scale = 1.0;
if (inv_scale > 0.0) if (inv_scale > 0.0) scale = 1.0 / inv_scale;
scale = 1.0 / inv_scale;
v[0] *= scale; v[0] *= scale;
v[1] *= scale; v[1] *= scale;
v[2] *= scale; v[2] *= scale;
@ -89,35 +89,35 @@ static void norm3safe(double *v) {
// -------------------------------------------- // --------------------------------------------
// ------- Calculate the dihedral angle ------- // ------- Calculate the dihedral angle -------
// -------------------------------------------- // --------------------------------------------
static const int g_dim=3; static const int g_dim = 3;
static double Phi(double const *x1, //array holding x,y,z coords atom 1 static double Phi(double const *x1, //array holding x,y,z coords atom 1
double const *x2, // : : : : 2 double const *x2, // : : : : 2
double const *x3, // : : : : 3 double const *x3, // : : : : 3
double const *x4, // : : : : 4 double const *x4, // : : : : 4
Domain *domain, //<-periodic boundary information Domain *domain, //<-periodic boundary information
double *vb12, //<-preallocated vector will store x2-x1 double *vb12, //<-preallocated vector will store x2-x1
double *vb23, //<-preallocated vector will store x3-x2 double *vb23, //<-preallocated vector will store x3-x2
double *vb34, //<-preallocated vector will store x4-x3 double *vb34, //<-preallocated vector will store x4-x3
double *n123, //<-will store normal to plane x1,x2,x3 double *n123, //<-will store normal to plane x1,x2,x3
double *n234) //<-will store normal to plane x2,x3,x4 double *n234) //<-will store normal to plane x2,x3,x4
{ {
for (int d=0; d < g_dim; ++d) { for (int d = 0; d < g_dim; ++d) {
vb12[d] = x2[d] - x1[d]; // 1st bond vb12[d] = x2[d] - x1[d]; // 1st bond
vb23[d] = x3[d] - x2[d]; // 2nd bond vb23[d] = x3[d] - x2[d]; // 2nd bond
vb34[d] = x4[d] - x3[d]; // 3rd bond vb34[d] = x4[d] - x3[d]; // 3rd bond
} }
//Consider periodic boundary conditions: //Consider periodic boundary conditions:
domain->minimum_image(vb12[0],vb12[1],vb12[2]); domain->minimum_image(vb12[0], vb12[1], vb12[2]);
domain->minimum_image(vb23[0],vb23[1],vb23[2]); domain->minimum_image(vb23[0], vb23[1], vb23[2]);
domain->minimum_image(vb34[0],vb34[1],vb34[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 --- //--- 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, vb12, n123); // <- n123=vb23 x vb12
cross3(vb23, vb34, n234); // <- n234=vb23 x vb34 cross3(vb23, vb34, n234); // <- n234=vb23 x vb34
norm3safe(n123); norm3safe(n123);
norm3safe(n234); norm3safe(n234);
@ -132,20 +132,18 @@ static double Phi(double const *x1, //array holding x,y,z coords atom 1
double phi = acos(cos_phi); double phi = acos(cos_phi);
if (dot3(n123, vb34) > 0.0) { if (dot3(n123, vb34) > 0.0) {
phi = -phi; //(Note: Negative dihedral angles are possible only in 3-D.) 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 phi += MY_2PI; //<- This insure phi is always in the range 0 to 2*PI
} }
return phi; return phi;
} // DihedralSpherical::Phi() } // DihedralSpherical::Phi()
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
void DihedralSpherical::compute(int eflag, int vflag) void DihedralSpherical::compute(int eflag, int vflag)
{ {
int i1,i2,i3,i4,n,type; int i1, i2, i3, i4, n, type;
double edihedral,f1[3],f2[3],f3[3],f4[3]; double edihedral, f1[3], f2[3], f3[3], f4[3];
double **x = atom->x; double **x = atom->x;
double **f = atom->f; double **f = atom->f;
@ -188,17 +186,17 @@ void DihedralSpherical::compute(int eflag, int vflag)
// x[i4] // x[i4]
// //
double vb12[g_dim]; // displacement vector from atom i1 towards atom i2 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) // 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 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) // 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 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) // vb34[d] = x[i4][d] - x[i3][d] (for d=0,1,2)
// n123 & n234: These two unit vectors are normal to the planes // n123 & n234: These two unit vectors are normal to the planes
// defined by atoms 1,2,3 and 2,3,4. // 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 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 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 // The next 4 vectors are needed to calculate dphi_dx = d phi / dx
double proj12on23[g_dim]; double proj12on23[g_dim];
@ -211,8 +209,7 @@ void DihedralSpherical::compute(int eflag, int vflag)
// perp34on23[d] = v34[d] - proj34on23[d] // perp34on23[d] = v34[d] - proj34on23[d]
edihedral = 0.0; edihedral = 0.0;
ev_init(eflag,vflag); ev_init(eflag, vflag);
for (n = 0; n < ndihedrallist; n++) { for (n = 0; n < ndihedrallist; n++) {
@ -229,13 +226,10 @@ void DihedralSpherical::compute(int eflag, int vflag)
// This function also calculates the vectors: // This function also calculates the vectors:
// vb12, vb23, vb34, n123, and n234, which we will need later. // 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);
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: // Step 2: Compute the gradients of phi, theta1, theta2 with atom position:
// ===================== Step2a) phi dependence: ======================== // ===================== Step2a) phi dependence: ========================
// //
// Gradient variables: // Gradient variables:
@ -243,29 +237,29 @@ void DihedralSpherical::compute(int eflag, int vflag)
// dphi_dx1, dphi_dx2, dphi_dx3, dphi_dx4 are the gradients of phi with // 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. // respect to the atomic positions of atoms i1, i2, i3, i4, respectively.
// As an example, consider dphi_dx1. The d'th element is: // As an example, consider dphi_dx1. The d'th element is:
double dphi_dx1[g_dim]; // d phi double dphi_dx1[g_dim]; // d phi
double dphi_dx2[g_dim]; // dphi_dx1[d] = ---------- (partial derivatives) double dphi_dx2[g_dim]; // dphi_dx1[d] = ---------- (partial derivatives)
double dphi_dx3[g_dim]; // d x[i1][d] 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 dphi_dx4[g_dim]; //where d=0,1,2 corresponds to x,y,z (g_dim==3)
double dot123 = dot3(vb12, vb23); double dot123 = dot3(vb12, vb23);
double dot234 = dot3(vb23, vb34); double dot234 = dot3(vb23, vb34);
double L23sqr = dot3(vb23, vb23); double L23sqr = dot3(vb23, vb23);
double L23 = sqrt(L23sqr); // (central bond length) double L23 = sqrt(L23sqr); // (central bond length)
double inv_L23sqr = 0.0; double inv_L23sqr = 0.0;
double inv_L23 = 0.0; double inv_L23 = 0.0;
if (L23sqr != 0.0) { if (L23sqr != 0.0) {
inv_L23sqr = 1.0 / L23sqr; inv_L23sqr = 1.0 / L23sqr;
inv_L23 = 1.0 / L23; inv_L23 = 1.0 / L23;
} }
double neg_inv_L23 = -inv_L23; double neg_inv_L23 = -inv_L23;
double dot123_over_L23sqr = dot123 * inv_L23sqr; double dot123_over_L23sqr = dot123 * inv_L23sqr;
double dot234_over_L23sqr = dot234 * inv_L23sqr; double dot234_over_L23sqr = dot234 * inv_L23sqr;
for (int d=0; d < g_dim; ++d) { for (int d = 0; d < g_dim; ++d) {
// See figure above for a visual definitions of these vectors: // See figure above for a visual definitions of these vectors:
proj12on23[d] = vb23[d] * dot123_over_L23sqr; proj12on23[d] = vb23[d] * dot123_over_L23sqr;
proj34on23[d] = vb23[d] * dot234_over_L23sqr; proj34on23[d] = vb23[d] * dot234_over_L23sqr;
@ -287,7 +281,7 @@ void DihedralSpherical::compute(int eflag, int vflag)
double inv_perp34on23 = 0.0; double inv_perp34on23 = 0.0;
if (perp34on23_len != 0.0) inv_perp34on23 = 1.0 / perp34on23_len; if (perp34on23_len != 0.0) inv_perp34on23 = 1.0 / perp34on23_len;
for (int d=0; d < g_dim; ++d) { for (int d = 0; d < g_dim; ++d) {
dphi_dx1[d] = n123[d] * inv_perp12on23; dphi_dx1[d] = n123[d] * inv_perp12on23;
dphi_dx4[d] = n234[d] * inv_perp34on23; dphi_dx4[d] = n234[d] * inv_perp34on23;
} }
@ -331,17 +325,16 @@ void DihedralSpherical::compute(int eflag, int vflag)
double dphi234_dx3_coef = neg_inv_L23 * (L23 + proj34on23_len); double dphi234_dx3_coef = neg_inv_L23 * (L23 + proj34on23_len);
double dphi123_dx3_coef = inv_L23 * proj12on23_len; double dphi123_dx3_coef = inv_L23 * proj12on23_len;
for (int d=0; d < g_dim; ++d) { for (int d = 0; d < g_dim; ++d) {
// Recall that the n123 and n234 plane normal vectors are proportional to // Recall that the n123 and n234 plane normal vectors are proportional to
// the dphi/dx1 and dphi/dx2 gradients vectors // the dphi/dx1 and dphi/dx2 gradients vectors
// It turns out we can save slightly more CPU cycles by expressing // 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 // dphi/dx2 and dphi/dx3 as linear combinations of dphi/dx1 and dphi/dx2
// which we computed already (instead of n123 & n234). // which we computed already (instead of n123 & n234).
dphi_dx2[d] = dphi123_dx2_coef*dphi_dx1[d] + dphi234_dx2_coef*dphi_dx4[d]; 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]; dphi_dx3[d] = dphi123_dx3_coef * dphi_dx1[d] + dphi234_dx3_coef * dphi_dx4[d];
} }
// ============= Step2b) theta1 and theta2 dependence: ============= // ============= Step2b) theta1 and theta2 dependence: =============
// --- Compute the gradient vectors dtheta1/dx1 and dtheta2/dx4: --- // --- Compute the gradient vectors dtheta1/dx1 and dtheta2/dx4: ---
@ -349,25 +342,25 @@ void DihedralSpherical::compute(int eflag, int vflag)
// These two gradients point in the direction of n123 and n234, // 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. // and are scaled by the distances of atoms 1 and 4 from the central axis.
// Distance of atom 1 to central axis: // Distance of atom 1 to central axis:
double dth1_dx1[g_dim]; // d theta1 (partial double dth1_dx1[g_dim]; // d theta1 (partial
double dth1_dx2[g_dim]; // dth1_dx1[d] = ---------- derivative) double dth1_dx2[g_dim]; // dth1_dx1[d] = ---------- derivative)
double dth1_dx3[g_dim]; // d x[i1][d] double dth1_dx3[g_dim]; // d x[i1][d]
//Note dth1_dx4 = 0 //Note dth1_dx4 = 0
//Note dth2_dx1 = 0 //Note dth2_dx1 = 0
double dth2_dx2[g_dim]; // d theta2 (partial double dth2_dx2[g_dim]; // d theta2 (partial
double dth2_dx3[g_dim]; // dth2_dx1[d] = ---------- derivative) double dth2_dx3[g_dim]; // dth2_dx1[d] = ---------- derivative)
double dth2_dx4[g_dim]; // d x[i1][d] double dth2_dx4[g_dim]; // d x[i1][d]
//where d=0,1,2 corresponds to x,y,z (g_dim==3) //where d=0,1,2 corresponds to x,y,z (g_dim==3)
double L12sqr = dot3(vb12, vb12); double L12sqr = dot3(vb12, vb12);
double L12 = sqrt(L12sqr); double L12 = sqrt(L12sqr);
double L34sqr = dot3(vb34, vb34); double L34sqr = dot3(vb34, vb34);
double L34 = sqrt(L34sqr); double L34 = sqrt(L34sqr);
double inv_L12sqr = 0.0; double inv_L12sqr = 0.0;
double inv_L12 = 0.0; double inv_L12 = 0.0;
double inv_L34sqr = 0.0; double inv_L34sqr = 0.0;
double inv_L34 = 0.0; double inv_L34 = 0.0;
if (L12sqr != 0.0) { if (L12sqr != 0.0) {
inv_L12sqr = 1.0 / L12sqr; inv_L12sqr = 1.0 / L12sqr;
inv_L12 = 1.0 / L12; inv_L12 = 1.0 / L12;
@ -416,7 +409,7 @@ void DihedralSpherical::compute(int eflag, int vflag)
* x[i4] * x[i4]
*/ */
for (int d=0; d < g_dim; ++d) { for (int d = 0; d < g_dim; ++d) {
// See figure above for a visual definitions of these vectors: // See figure above for a visual definitions of these vectors:
proj23on12[d] = vb12[d] * dot123_over_L12sqr; proj23on12[d] = vb12[d] * dot123_over_L12sqr;
proj23on34[d] = vb34[d] * dot234_over_L34sqr; proj23on34[d] = vb34[d] * dot234_over_L34sqr;
@ -433,11 +426,11 @@ void DihedralSpherical::compute(int eflag, int vflag)
if (perp23on34_len != 0.0) inv_perp23on34 = 1.0 / perp23on34_len; if (perp23on34_len != 0.0) inv_perp23on34 = 1.0 / perp23on34_len;
double coeff_dth1_dx1 = -inv_perp23on12 * inv_L12; double coeff_dth1_dx1 = -inv_perp23on12 * inv_L12;
double coeff_dth1_dx3 = inv_perp12on23 * inv_L23; double coeff_dth1_dx3 = inv_perp12on23 * inv_L23;
double coeff_dth2_dx2 = -inv_perp34on23 * inv_L23; double coeff_dth2_dx2 = -inv_perp34on23 * inv_L23;
double coeff_dth2_dx4 = inv_perp23on34 * inv_L34; double coeff_dth2_dx4 = inv_perp23on34 * inv_L34;
for (int d=0; d < g_dim; ++d) { for (int d = 0; d < g_dim; ++d) {
dth1_dx1[d] = perp23on12[d] * coeff_dth1_dx1; dth1_dx1[d] = perp23on12[d] * coeff_dth1_dx1;
dth1_dx3[d] = perp12on23[d] * coeff_dth1_dx3; dth1_dx3[d] = perp12on23[d] * coeff_dth1_dx3;
dth1_dx2[d] = -(dth1_dx1[d] + dth1_dx3[d]); dth1_dx2[d] = -(dth1_dx1[d] + dth1_dx3[d]);
@ -450,24 +443,26 @@ void DihedralSpherical::compute(int eflag, int vflag)
} }
double ct1 = -dot123 * inv_L12 * inv_L23; double ct1 = -dot123 * inv_L12 * inv_L23;
if (ct1 < -1.0) ct1 = -1.0; if (ct1 < -1.0)
else if (ct1 > 1.0) ct1 = 1.0; ct1 = -1.0;
else if (ct1 > 1.0)
ct1 = 1.0;
double theta1 = acos(ct1); double theta1 = acos(ct1);
double ct2 = -dot234 * inv_L23 * inv_L34; double ct2 = -dot234 * inv_L23 * inv_L34;
if (ct2 < -1.0) ct2 = -1.0; if (ct2 < -1.0)
else if (ct2 > 1.0) ct2 = 1.0; ct2 = -1.0;
else if (ct2 > 1.0)
ct2 = 1.0;
double theta2 = acos(ct2); double theta2 = acos(ct2);
// - Step 3: Calculate the energy and force in the phi & theta1/2 directions // - Step 3: Calculate the energy and force in the phi & theta1/2 directions
double u=0.0; // u = energy double u = 0.0; // u = energy
double m_du_dth1 = 0.0; // m_du_dth1 = -du / d theta1 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_dth2 = 0.0; // m_du_dth2 = -du / d theta2
double m_du_dphi = 0.0; // m_du_dphi = -du / d phi double m_du_dphi = 0.0; // m_du_dphi = -du / d phi
u = CalcGeneralizedForces(type, u = CalcGeneralizedForces(type, phi, theta1, theta2, &m_du_dth1, &m_du_dth2, &m_du_dphi);
phi, theta1, theta2,
&m_du_dth1, &m_du_dth2, &m_du_dphi);
if (eflag) edihedral = u; if (eflag) edihedral = u;
@ -477,13 +472,13 @@ void DihedralSpherical::compute(int eflag, int vflag)
// d U d U d phi d U d theta1 d U d theta2 // d U d U d phi d U d theta1 d U d theta2
// -f = ----- = ----- * ----- + -------*------- + --------*-------- // -f = ----- = ----- * ----- + -------*------- + --------*--------
// d x d phi d x d theta1 d X d theta2 d X // d x d phi d x d theta1 d X d theta2 d X
for (int d=0; d < g_dim; ++d) { for (int d = 0; d < g_dim; ++d) {
f1[d] = m_du_dphi*dphi_dx1[d]+m_du_dth1*dth1_dx1[d]; f1[d] = m_du_dphi * dphi_dx1[d] + m_du_dth1 * dth1_dx1[d];
//note: dth2_dx1[d]=0 //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]; 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]; 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]; f4[d] = m_du_dphi * dphi_dx4[d] + m_du_dth2 * dth2_dx4[d];
//note: dth1_dx4[d] = 0 //note: dth1_dx4[d] = 0
} }
// apply force to each of 4 atoms // apply force to each of 4 atoms
@ -513,26 +508,15 @@ void DihedralSpherical::compute(int eflag, int vflag)
} }
if (evflag) if (evflag)
ev_tally(i1,i2,i3,i4, ev_tally(i1, i2, i3, i4, nlocal, newton_bond, edihedral, f1, f3, f4, vb12[0], vb12[1],
nlocal,newton_bond,edihedral, vb12[2], vb23[0], vb23[1], vb23[2], vb34[0], vb34[1], vb34[2]);
f1,f3,f4,
vb12[0],vb12[1],vb12[2],
vb23[0],vb23[1],vb23[2],
vb34[0],vb34[1],vb34[2]);
} }
} // void DihedralSpherical::compute() } // void DihedralSpherical::compute()
// --- CalcGeneralizedForces() --- // --- CalcGeneralizedForces() ---
// --- Calculate the energy as a function of theta1, theta2, and phi --- // --- Calculate the energy as a function of theta1, theta2, and phi ---
// --- as well as its derivatives (with respect to 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 // The code above above is sufficiently general that it can work with any
// any function of the angles theta1, theta2, and phi. However the // any function of the angles theta1, theta2, and phi. However the
// function below calculates the energy and force according to this specific // function below calculates the energy and force according to this specific
@ -545,17 +529,9 @@ void DihedralSpherical::compute(int eflag, int vflag)
// \Theta_{2i}(\theta_2) = cos((\theta_2-b_i)L_i) + v_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 // \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 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; double energy = 0.0;
assert(m_du_dphi && m_du_dphi && m_du_dphi); assert(m_du_dphi && m_du_dphi && m_du_dphi);
@ -573,7 +549,7 @@ CalcGeneralizedForces(int type,
double cp = 1.0; double cp = 1.0;
double sp = 0.0; double sp = 0.0;
if (phi_mult[i][j] != 0.0) { if (phi_mult[i][j] != 0.0) {
double p = phi_mult[i][j] * (phi - phi_shift[i][j]); double p = phi_mult[i][j] * (phi - phi_shift[i][j]);
cp = cos(p); cp = cos(p);
sp = sin(p); sp = sin(p);
} }
@ -581,7 +557,7 @@ CalcGeneralizedForces(int type,
double ct1 = 1.0; double ct1 = 1.0;
double st1 = 0.0; double st1 = 0.0;
if (theta1_mult[i][j] != 0.0) { if (theta1_mult[i][j] != 0.0) {
double t1 = theta1_mult[i][j]*(theta1 - theta1_shift[i][j]); double t1 = theta1_mult[i][j] * (theta1 - theta1_shift[i][j]);
ct1 = cos(t1); ct1 = cos(t1);
st1 = sin(t1); st1 = sin(t1);
} }
@ -589,28 +565,23 @@ CalcGeneralizedForces(int type,
double ct2 = 1.0; double ct2 = 1.0;
double st2 = 0.0; double st2 = 0.0;
if (theta2_mult[i][j] != 0.0) { if (theta2_mult[i][j] != 0.0) {
double t2 = theta2_mult[i][j]*(theta2 - theta2_shift[i][j]); double t2 = theta2_mult[i][j] * (theta2 - theta2_shift[i][j]);
ct2 = cos(t2); ct2 = cos(t2);
st2 = sin(t2); st2 = sin(t2);
} }
energy += Ccoeff[i][j] * (phi_offset[i][j] - cp) * energy += Ccoeff[i][j] * (phi_offset[i][j] - cp) * (theta1_offset[i][j] - ct1) *
(theta1_offset[i][j] - ct1) * (theta2_offset[i][j] - ct2);
(theta2_offset[i][j] - ct2);
// Forces: // Forces:
*m_du_dphi += -Ccoeff[i][j] * sp * phi_mult[i][j] * *m_du_dphi += -Ccoeff[i][j] * sp * phi_mult[i][j] * (theta1_offset[i][j] - ct1) *
(theta1_offset[i][j] - ct1) * (theta2_offset[i][j] - ct2);
(theta2_offset[i][j] - ct2);
*m_du_dth1 += -Ccoeff[i][j] * (phi_offset[i][j] - cp) * *m_du_dth1 += -Ccoeff[i][j] * (phi_offset[i][j] - cp) * st1 * theta1_mult[i][j] *
st1 * theta1_mult[i][j] * (theta2_offset[i][j] - ct2);
(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];
*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: // Things to consider later:
// To speed up the computation, one could try to simplify the expansion: // To speed up the computation, one could try to simplify the expansion:
@ -622,35 +593,29 @@ CalcGeneralizedForces(int type,
// can be calculated more efficiently using polynomials of // can be calculated more efficiently using polynomials of
// cos(phi) and sin(phi) // cos(phi) and sin(phi)
} //for (int j = 0; j < nterms[i]; j++) { } //for (int j = 0; j < nterms[i]; j++) {
return energy; return energy;
} //CalcGeneralizedForces() } //CalcGeneralizedForces()
void DihedralSpherical::allocate() void DihedralSpherical::allocate()
{ {
allocated = 1; allocated = 1;
int n = atom->ndihedraltypes+1; int n = atom->ndihedraltypes + 1;
memory->create(nterms,n,"dihedral:nterms"); memory->create(nterms, n, "dihedral:nterms");
Ccoeff = new double * [n]; Ccoeff = new double *[n];
phi_mult = new double * [n]; phi_mult = new double *[n];
phi_shift = new double * [n]; phi_shift = new double *[n];
phi_offset = new double * [n]; phi_offset = new double *[n];
theta1_mult = new double * [n]; theta1_mult = new double *[n];
theta1_shift = new double * [n]; theta1_shift = new double *[n];
theta1_offset = new double * [n]; theta1_offset = new double *[n];
theta2_mult = new double * [n]; theta2_mult = new double *[n];
theta2_shift = new double * [n]; theta2_shift = new double *[n];
theta2_offset = new double * [n]; theta2_offset = new double *[n];
for (int i = 0; i < n; i++) { for (int i = 0; i < n; i++) {
Ccoeff[i] = nullptr; Ccoeff[i] = nullptr;
phi_mult[i] = nullptr; phi_mult[i] = nullptr;
@ -664,7 +629,7 @@ void DihedralSpherical::allocate()
theta2_offset[i] = nullptr; theta2_offset[i] = nullptr;
} }
memory->create(setflag,n,"dihedral:setflag"); memory->create(setflag, n, "dihedral:setflag");
for (int i = 1; i < n; i++) setflag[i] = 0; for (int i = 1; i < n; i++) setflag[i] = 0;
} }
@ -674,19 +639,18 @@ void DihedralSpherical::allocate()
void DihedralSpherical::coeff(int narg, char **arg) void DihedralSpherical::coeff(int narg, char **arg)
{ {
if (narg < 4) error->all(FLERR,"Incorrect args for dihedral coefficients"); if (narg < 4) error->all(FLERR, "Incorrect args for dihedral coefficients");
if (!allocated) allocate(); if (!allocated) allocate();
int ilo,ihi; int ilo, ihi;
utils::bounds(FLERR,arg[0],1,atom->ndihedraltypes,ilo,ihi,error); utils::bounds(FLERR, arg[0], 1, atom->ndihedraltypes, ilo, ihi, error);
int nterms_one = utils::inumeric(FLERR,arg[1],false,lmp); int nterms_one = utils::inumeric(FLERR, arg[1], false, lmp);
if (nterms_one < 1) if (nterms_one < 1) error->all(FLERR, "Incorrect number of terms arg for dihedral coefficients");
error->all(FLERR,"Incorrect number of terms arg for dihedral coefficients");
if (2+10*nterms_one < narg) if (2 + 10 * nterms_one < narg)
error->all(FLERR,"Incorrect number of arguments for dihedral coefficients"); error->all(FLERR, "Incorrect number of arguments for dihedral coefficients");
int count = 0; int count = 0;
for (int i = ilo; i <= ihi; i++) { for (int i = ilo; i <= ihi; i++) {
@ -701,34 +665,34 @@ void DihedralSpherical::coeff(int narg, char **arg)
delete[] theta2_mult[i]; delete[] theta2_mult[i];
delete[] theta2_shift[i]; delete[] theta2_shift[i];
delete[] theta2_offset[i]; delete[] theta2_offset[i];
Ccoeff[i] = new double [nterms_one]; Ccoeff[i] = new double[nterms_one];
phi_mult[i] = new double [nterms_one]; phi_mult[i] = new double[nterms_one];
phi_shift[i] = new double [nterms_one]; phi_shift[i] = new double[nterms_one];
phi_offset[i] = new double [nterms_one]; phi_offset[i] = new double[nterms_one];
theta1_mult[i] = new double [nterms_one]; theta1_mult[i] = new double[nterms_one];
theta1_shift[i] = new double [nterms_one]; theta1_shift[i] = new double[nterms_one];
theta1_offset[i] = new double [nterms_one]; theta1_offset[i] = new double[nterms_one];
theta2_mult[i] = new double [nterms_one]; theta2_mult[i] = new double[nterms_one];
theta2_shift[i] = new double [nterms_one]; theta2_shift[i] = new double[nterms_one];
theta2_offset[i] = new double [nterms_one]; theta2_offset[i] = new double[nterms_one];
for (int j = 0; j < nterms_one; j++) { for (int j = 0; j < nterms_one; j++) {
int offset = 1+10*j; int offset = 1 + 10 * j;
Ccoeff[i][j] = utils::numeric(FLERR,arg[offset+1],false,lmp); Ccoeff[i][j] = utils::numeric(FLERR, arg[offset + 1], false, lmp);
phi_mult[i][j] = utils::numeric(FLERR,arg[offset+2],false,lmp); phi_mult[i][j] = utils::numeric(FLERR, arg[offset + 2], false, lmp);
phi_shift[i][j] = utils::numeric(FLERR,arg[offset+3],false,lmp) * MY_PI/180.0; phi_shift[i][j] = utils::numeric(FLERR, arg[offset + 3], false, lmp) * MY_PI / 180.0;
phi_offset[i][j] = utils::numeric(FLERR,arg[offset+4],false,lmp); phi_offset[i][j] = utils::numeric(FLERR, arg[offset + 4], false, lmp);
theta1_mult[i][j] = utils::numeric(FLERR,arg[offset+5],false,lmp); theta1_mult[i][j] = utils::numeric(FLERR, arg[offset + 5], false, lmp);
theta1_shift[i][j] = utils::numeric(FLERR,arg[offset+6],false,lmp) * MY_PI/180.0; theta1_shift[i][j] = utils::numeric(FLERR, arg[offset + 6], false, lmp) * MY_PI / 180.0;
theta1_offset[i][j] = utils::numeric(FLERR,arg[offset+7],false,lmp); theta1_offset[i][j] = utils::numeric(FLERR, arg[offset + 7], false, lmp);
theta2_mult[i][j] = utils::numeric(FLERR,arg[offset+8],false,lmp); theta2_mult[i][j] = utils::numeric(FLERR, arg[offset + 8], false, lmp);
theta2_shift[i][j] = utils::numeric(FLERR,arg[offset+9],false,lmp) * MY_PI/180.0; theta2_shift[i][j] = utils::numeric(FLERR, arg[offset + 9], false, lmp) * MY_PI / 180.0;
theta2_offset[i][j] = utils::numeric(FLERR,arg[offset+10],false,lmp); theta2_offset[i][j] = utils::numeric(FLERR, arg[offset + 10], false, lmp);
} }
setflag[i] = 1; setflag[i] = 1;
count++; count++;
} }
if (count == 0) error->all(FLERR,"Incorrect args for dihedral coefficients"); if (count == 0) error->all(FLERR, "Incorrect args for dihedral coefficients");
} }
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
@ -737,18 +701,18 @@ void DihedralSpherical::coeff(int narg, char **arg)
void DihedralSpherical::write_restart(FILE *fp) void DihedralSpherical::write_restart(FILE *fp)
{ {
fwrite(&nterms[1],sizeof(int),atom->ndihedraltypes,fp); fwrite(&nterms[1], sizeof(int), atom->ndihedraltypes, fp);
for (int i = 1; i <= atom->ndihedraltypes; i++) { for (int i = 1; i <= atom->ndihedraltypes; i++) {
fwrite(Ccoeff[i],sizeof(double),nterms[i],fp); fwrite(Ccoeff[i], sizeof(double), nterms[i], fp);
fwrite(phi_mult[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_shift[i], sizeof(double), nterms[i], fp);
fwrite(phi_offset[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_mult[i], sizeof(double), nterms[i], fp);
fwrite(theta1_shift[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(theta1_offset[i], sizeof(double), nterms[i], fp);
fwrite(theta2_mult[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_shift[i], sizeof(double), nterms[i], fp);
fwrite(theta2_offset[i],sizeof(double),nterms[i],fp); fwrite(theta2_offset[i], sizeof(double), nterms[i], fp);
} }
} }
@ -761,58 +725,55 @@ void DihedralSpherical::read_restart(FILE *fp)
allocate(); allocate();
if (comm->me == 0) if (comm->me == 0)
utils::sfread(FLERR,&nterms[1],sizeof(int),atom->ndihedraltypes,fp,nullptr,error); utils::sfread(FLERR, &nterms[1], sizeof(int), atom->ndihedraltypes, fp, nullptr, error);
MPI_Bcast(&nterms[1],atom->ndihedraltypes,MPI_INT,0,world); MPI_Bcast(&nterms[1], atom->ndihedraltypes, MPI_INT, 0, world);
// allocate // allocate
for (int i=1; i<=atom->ndihedraltypes; i++) { for (int i = 1; i <= atom->ndihedraltypes; i++) {
Ccoeff[i] = new double [nterms[i]]; Ccoeff[i] = new double[nterms[i]];
phi_mult[i] = new double [nterms[i]]; phi_mult[i] = new double[nterms[i]];
phi_shift[i] = new double [nterms[i]]; phi_shift[i] = new double[nterms[i]];
phi_offset[i] = new double [nterms[i]]; phi_offset[i] = new double[nterms[i]];
theta1_mult[i] = new double [nterms[i]]; theta1_mult[i] = new double[nterms[i]];
theta1_shift[i] = new double [nterms[i]]; theta1_shift[i] = new double[nterms[i]];
theta1_offset[i] = new double [nterms[i]]; theta1_offset[i] = new double[nterms[i]];
theta2_mult[i] = new double [nterms[i]]; theta2_mult[i] = new double[nterms[i]];
theta2_shift[i] = new double [nterms[i]]; theta2_shift[i] = new double[nterms[i]];
theta2_offset[i] = new double [nterms[i]]; theta2_offset[i] = new double[nterms[i]];
} }
if (comm->me == 0) { if (comm->me == 0) {
for (int i=1; i<=atom->ndihedraltypes; i++) { for (int i = 1; i <= atom->ndihedraltypes; i++) {
utils::sfread(FLERR,Ccoeff[i],sizeof(double),nterms[i],fp,nullptr,error); utils::sfread(FLERR, Ccoeff[i], sizeof(double), nterms[i], fp, nullptr, error);
utils::sfread(FLERR,phi_mult[i],sizeof(double),nterms[i],fp,nullptr,error); utils::sfread(FLERR, phi_mult[i], sizeof(double), nterms[i], fp, nullptr, error);
utils::sfread(FLERR,phi_shift[i],sizeof(double),nterms[i],fp,nullptr,error); utils::sfread(FLERR, phi_shift[i], sizeof(double), nterms[i], fp, nullptr, error);
utils::sfread(FLERR,phi_offset[i],sizeof(double),nterms[i],fp,nullptr,error); utils::sfread(FLERR, phi_offset[i], sizeof(double), nterms[i], fp, nullptr, error);
utils::sfread(FLERR,theta1_mult[i],sizeof(double),nterms[i],fp,nullptr,error); utils::sfread(FLERR, theta1_mult[i], sizeof(double), nterms[i], fp, nullptr, error);
utils::sfread(FLERR,theta1_shift[i],sizeof(double),nterms[i],fp,nullptr,error); utils::sfread(FLERR, theta1_shift[i], sizeof(double), nterms[i], fp, nullptr, error);
utils::sfread(FLERR,theta1_offset[i],sizeof(double),nterms[i],fp,nullptr,error); utils::sfread(FLERR, theta1_offset[i], sizeof(double), nterms[i], fp, nullptr, error);
utils::sfread(FLERR,theta2_mult[i],sizeof(double),nterms[i],fp,nullptr,error); utils::sfread(FLERR, theta2_mult[i], sizeof(double), nterms[i], fp, nullptr, error);
utils::sfread(FLERR,theta2_shift[i],sizeof(double),nterms[i],fp,nullptr,error); utils::sfread(FLERR, theta2_shift[i], sizeof(double), nterms[i], fp, nullptr, error);
utils::sfread(FLERR,theta2_offset[i],sizeof(double),nterms[i],fp,nullptr,error); utils::sfread(FLERR, theta2_offset[i], sizeof(double), nterms[i], fp, nullptr, error);
} }
} }
for (int i=1; i<=atom->ndihedraltypes; i++) { for (int i = 1; i <= atom->ndihedraltypes; i++) {
MPI_Bcast(Ccoeff[i],nterms[i],MPI_DOUBLE,0,world); MPI_Bcast(Ccoeff[i], nterms[i], MPI_DOUBLE, 0, world);
MPI_Bcast(phi_mult[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_shift[i], nterms[i], MPI_DOUBLE, 0, world);
MPI_Bcast(phi_offset[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_mult[i], nterms[i], MPI_DOUBLE, 0, world);
MPI_Bcast(theta1_shift[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(theta1_offset[i], nterms[i], MPI_DOUBLE, 0, world);
MPI_Bcast(theta2_mult[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_shift[i], nterms[i], MPI_DOUBLE, 0, world);
MPI_Bcast(theta2_offset[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; for (int i = 1; i <= atom->ndihedraltypes; i++) setflag[i] = 1;
} }
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
proc 0 writes to data file proc 0 writes to data file
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
@ -820,15 +781,14 @@ void DihedralSpherical::read_restart(FILE *fp)
void DihedralSpherical::write_data(FILE *fp) void DihedralSpherical::write_data(FILE *fp)
{ {
for (int i = 1; i <= atom->ndihedraltypes; i++) { for (int i = 1; i <= atom->ndihedraltypes; i++) {
fprintf(fp,"%d %d ", i , nterms[i]); fprintf(fp, "%d %d ", i, nterms[i]);
for (int j = 0; j < nterms[i]; j++) { for (int j = 0; j < nterms[i]; j++) {
fprintf(fp, "%g %g %g %g %g %g %g %g %g %g ", Ccoeff[i][j], fprintf(fp, "%g %g %g %g %g %g %g %g %g %g ", Ccoeff[i][j], phi_mult[i][j],
phi_mult[i][j], phi_shift[i][j]*180.0/MY_PI, phi_offset[i][j], phi_shift[i][j] * 180.0 / MY_PI, phi_offset[i][j], theta1_mult[i][j],
theta1_mult[i][j], theta1_shift[i][j]*180.0/MY_PI, theta1_shift[i][j] * 180.0 / MY_PI, theta1_offset[i][j], theta2_mult[i][j],
theta1_offset[i][j], theta2_mult[i][j], theta2_shift[i][j] * 180.0 / MY_PI, theta2_offset[i][j]);
theta2_shift[i][j]*180.0/MY_PI, theta2_offset[i][j]);
} }
fprintf(fp,"\n"); fprintf(fp, "\n");
} }
} }
@ -874,4 +834,3 @@ void DihedralSpherical::write_data(FILE *fp)
// &m_du_dth1, &m_du_dth2, &m_du_dphi); // &m_du_dth1, &m_du_dth2, &m_du_dphi);
// return u; // return u;
//} //}