diff --git a/src/USER-MISC/improper_cossq.cpp b/src/USER-MISC/improper_cossq.cpp index ac66f2af4..a7684017d 100644 --- a/src/USER-MISC/improper_cossq.cpp +++ b/src/USER-MISC/improper_cossq.cpp @@ -1,315 +1,316 @@ /* ---------------------------------------------------------------------- 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: Georgios G. Vogiatzis (CoMSE, NTU Athens) + Contributing author: Georgios G. Vogiatzis (CoMSE, NTU Athens), + gvog@chemeng.ntua.gr ------------------------------------------------------------------------- */ #include "lmptype.h" #include "mpi.h" #include "math.h" #include "stdlib.h" #include "improper_cossq.h" #include "atom.h" #include "comm.h" #include "neighbor.h" #include "domain.h" #include "force.h" #include "update.h" #include "memory.h" #include "error.h" #include "math_const.h" using namespace LAMMPS_NS; using namespace MathConst; #define TOLERANCE 0.05 #define SMALL 0.001 /* ---------------------------------------------------------------------- */ ImproperCossq::ImproperCossq(LAMMPS *lmp) : Improper(lmp) {} /* ---------------------------------------------------------------------- */ ImproperCossq::~ImproperCossq() { if (allocated) { memory->destroy(setflag); memory->destroy(k); memory->destroy(chi); } } /* ---------------------------------------------------------------------- */ void ImproperCossq::compute(int eflag, int vflag) { int i1,i2,i3,i4,m,n,type; double vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z ; double eimproper,f1[3],f2[3],f3[3],f4[3]; double rjisq, rji, rlksq, rlk, cosphi, angfac; double cjiji, clkji, clklk, cfact1, cfact2, cfact3; eimproper = 0.0; if (eflag || vflag) ev_setup(eflag,vflag); else evflag = 0; double **x = atom->x; double **f = atom->f; int **improperlist = neighbor->improperlist; int nimproperlist = neighbor->nimproperlist; int nlocal = atom->nlocal; int newton_bond = force->newton_bond; for (n = 0; n < nimproperlist; n++) { /* Ask the improper list for the atom types. */ i1 = improperlist[n][0]; i2 = improperlist[n][1]; i3 = improperlist[n][2]; i4 = improperlist[n][3]; type = improperlist[n][4]; /* separation vector between i1 and i2, (i2-i1) */ vb1x = x[i2][0] - x[i1][0]; vb1y = x[i2][1] - x[i1][1]; vb1z = x[i2][2] - x[i1][2]; domain->minimum_image(vb1x,vb1y,vb1z); rjisq = vb1x*vb1x + vb1y*vb1y + vb1z*vb1z ; rji = sqrt(rjisq); /* separation vector between i2 and i3 (i3-i2) */ vb2x = x[i3][0] - x[i2][0]; vb2y = x[i3][1] - x[i2][1]; vb2z = x[i3][2] - x[i2][2]; domain->minimum_image(vb2x,vb2y,vb2z); /* separation vector between i3 and i4, (i4-i3) */ vb3x = x[i4][0] - x[i3][0]; vb3y = x[i4][1] - x[i3][1]; vb3z = x[i4][2] - x[i3][2]; domain->minimum_image(vb3x,vb3y,vb3z); rlksq = vb3x*vb3x + vb3y*vb3y + vb3z*vb3z ; rlk = sqrt(rlksq); cosphi = (vb3x*vb1x + vb3y*vb1y + vb3z*vb1z)/(rji * rlk); /* Check that cos(phi) is in the correct limits. */ if (cosphi > 1.0 + TOLERANCE || cosphi < (-1.0 - TOLERANCE)) { int me; MPI_Comm_rank(world,&me); if (screen) { char str[128]; sprintf(str,"Improper problem: %d " BIGINT_FORMAT " %d %d %d %d", me,update->ntimestep,atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]); error->warning(FLERR,str,0); fprintf(screen," 1st atom: %d %g %g %g\n",me,x[i1][0],x[i1][1],x[i1][2]); fprintf(screen," 2nd atom: %d %g %g %g\n",me,x[i2][0],x[i2][1],x[i2][2]); fprintf(screen," 3rd atom: %d %g %g %g\n",me,x[i3][0],x[i3][1],x[i3][2]); fprintf(screen," 4th atom: %d %g %g %g\n",me,x[i4][0],x[i4][1],x[i4][2]); } } /* Apply corrections to round-off errors. */ if (cosphi > 1.0) cosphi -= SMALL; if (cosphi < -1.0) cosphi += SMALL; /* Calculate the angle: */ double torangle = acos(cosphi); cosphi = cos(torangle - chi[type]); if (eflag) eimproper = 0.5 * k[type] * cosphi * cosphi; /* printf("The tags: %d-%d-%d-%d, of type %d .\n",atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4],type); printf("The ji vector: %f, %f, %f.\nThe lk vector: %f, %f, %f.\n", vb1x,vb1y,vb1z,vb3x,vb3y,vb3z); printf("The cosine of the angle: %-1.16e.\n", cosphi); printf("The energy of the improper: %-1.16e with prefactor %-1.16e.\n", eimproper, 0.5*k[type]); */ /* Work out forces. */ angfac = - k[type] * cosphi; cjiji = rjisq; clklk = rlksq; /*CLKJI = RXLK * RXJI + RYLK * RYJI + RZLK * RZJI */ clkji = vb3x*vb1x + vb3y*vb1y + vb3z*vb1z; /*CFACT1 = CLKLK * CJIJI CFACT1 = SQRT(CFACT1) CFACT1 = ANGFAC / CFACT1*/ cfact1 = angfac / sqrt(clklk * cjiji); /*CFACT2 = CLKJI / CLKLK*/ cfact2 = clkji / clklk; /*CFACT3 = CLKJI / CJIJI*/ cfact3 = clkji / cjiji; /*FIX = -RXLK + CFACT3 * RXJI FIY = -RYLK + CFACT3 * RYJI FIZ = -RZLK + CFACT3 * RZJI*/ f1[0] = - vb3x + cfact3 * vb1x; f1[1] = - vb3y + cfact3 * vb1y; f1[2] = - vb3z + cfact3 * vb1z; /*FJX = -FIX FJY = -FIY FJZ = -FIZ*/ f2[0] = - f1[0]; f2[1] = - f1[1]; f2[2] = - f1[2]; /*FKX = CFACT2 * RXLK - RXJI FKY = CFACT2 * RYLK - RYJI FKZ = CFACT2 * RZLK - RZJI*/ f3[0] = cfact2 * vb3x - vb1x; f3[1] = cfact2 * vb3y - vb1y; f3[2] = cfact2 * vb3z - vb1z; /*FLX = -FKX FLY = -FKY FLZ = -FKZ*/ f4[0] = - f3[0]; f4[1] = - f3[1]; f4[2] = - f3[2]; /*FIX = FIX * CFACT1 FIY = FIY * CFACT1 FIZ = FIZ * CFACT1*/ f1[0] *= cfact1; f1[1] *= cfact1; f1[2] *= cfact1; /*FJX = FJX * CFACT1 FJY = FJY * CFACT1 FJZ = FJZ * CFACT1*/ f2[0] *= cfact1; f2[1] *= cfact1; f2[2] *= cfact1; /*FKX = FKX * CFACT1 FKY = FKY * CFACT1 FKZ = FKZ * CFACT1*/ f3[0] *= cfact1; f3[1] *= cfact1; f3[2] *= cfact1; /*FLX = FLX * CFACT1 FLY = FLY * CFACT1 FLZ = FLZ * CFACT1*/ f4[0] *= cfact1; f4[1] *= cfact1; f4[2] *= cfact1; /* 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,eimproper,f1,f3,f4, -vb1x,-vb1y,-vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z); } } /* ---------------------------------------------------------------------- */ void ImproperCossq::allocate() { allocated = 1; int n = atom->nimpropertypes; memory->create(k,n+1,"improper:k"); memory->create(chi,n+1,"improper:chi"); memory->create(setflag,n+1,"improper:setflag"); for (int i = 1; i <= n; i++) setflag[i] = 0; } /* ---------------------------------------------------------------------- set coeffs for one type ------------------------------------------------------------------------- */ void ImproperCossq::coeff(int narg, char **arg) { /* Check whether there exist sufficient number of arguments. 0: type of improper to be applied to 1: energetic constant 2: equilibrium angle in degrees */ if (narg != 3) error->all(FLERR,"Incorrect args for cossq improper coefficients"); if (!allocated) allocate(); int ilo,ihi; force->bounds(arg[0],atom->nimpropertypes,ilo,ihi); double k_one = force->numeric(arg[1]); double chi_one = force->numeric(arg[2]); int count = 0; for (int i = ilo; i <= ihi; i++) { k[i] = k_one; chi[i] = ((chi_one * MY_PI)/180.0); setflag[i] = 1; count++; } if (count == 0) error->all(FLERR,"Incorrect args for improper coefficients"); } /* ---------------------------------------------------------------------- proc 0 writes out coeffs to restart file ------------------------------------------------------------------------- */ void ImproperCossq::write_restart(FILE *fp) { fwrite(&k[1],sizeof(double),atom->nimpropertypes,fp); fwrite(&chi[1],sizeof(double),atom->nimpropertypes,fp); } /* ---------------------------------------------------------------------- proc 0 reads coeffs from restart file, bcasts them ------------------------------------------------------------------------- */ void ImproperCossq::read_restart(FILE *fp) { allocate(); if (comm->me == 0) { fread(&k[1],sizeof(double),atom->nimpropertypes,fp); fread(&chi[1],sizeof(double),atom->nimpropertypes,fp); } MPI_Bcast(&k[1],atom->nimpropertypes,MPI_DOUBLE,0,world); MPI_Bcast(&chi[1],atom->nimpropertypes,MPI_DOUBLE,0,world); for (int i = 1; i <= atom->nimpropertypes; i++) setflag[i] = 1; } diff --git a/src/USER-MISC/improper_ring.cpp b/src/USER-MISC/improper_ring.cpp index 3a0d2fb9d..0a93aeb5d 100644 --- a/src/USER-MISC/improper_ring.cpp +++ b/src/USER-MISC/improper_ring.cpp @@ -1,344 +1,343 @@ /* ---------------------------------------------------------------------- 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: Georgios G. Vogiatzis (NTU Athens) + Contributing author: Georgios G. Vogiatzis (NTU Athens), + gvog@chemeng.ntua.gr ------------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- Description: This file implements the improper potential introduced by Destree et al., in Equation 9 of: - M. Destree, F. Laupretre, A. Lyulin, and J.-P. Ryckaert, J. Chem. Phys. 112, 9632 (2000), and subsequently referred in: - A.V. Lyulin, M.A.J Michels, Macromolecules, 35, 1463, (2002) This potential does not affect small amplitude vibrations but is used in an ad hoc way to prevent the onset of accidentially large amplitude fluctuations leading to the occurrence of a planar conformation of the three bonds i, i + 1 and i', an intermediate conformation toward the chiral inversion of a methine carbon. In the "Impropers" section of data file four atoms: i, j, k and l are specified with i,j and l lying on the backbone of the chain and k specifying the chirality of j. ------------------------------------------------------------------------- */ #include "lmptype.h" #include "mpi.h" #include "math.h" #include "stdlib.h" #include "improper_ring.h" #include "atom.h" #include "comm.h" #include "neighbor.h" #include "domain.h" #include "force.h" #include "update.h" #include "math_const.h" #include "memory.h" #include "error.h" using namespace LAMMPS_NS; using namespace MathConst; #define TOLERANCE 0.05 #define SMALL 0.001 /* ---------------------------------------------------------------------- */ ImproperRing::ImproperRing(LAMMPS *lmp) : Improper(lmp) {} /* ---------------------------------------------------------------------- */ ImproperRing::~ImproperRing() { if (allocated) { memory->destroy(setflag); memory->destroy(k); memory->destroy(chi); } } /* ---------------------------------------------------------------------- */ void ImproperRing::compute(int eflag, int vflag) { - /* Be careful!: "chi" is the equilibrium angle in radians. */ int i1,i2,i3,i4,n,type; double eimproper ; /* Compatibility variables. */ double vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z; double f1[3], f3[3], f4[3]; /* Actual computation variables. */ int at1[3], at2[3], at3[3], icomb; double bvec1x[3], bvec1y[3], bvec1z[3], bvec2x[3], bvec2y[3], bvec2z[3], bvec1n[3], bvec2n[3], bend_angle[3]; double angle_summer, angfac, cfact1, cfact2, cfact3; double cjiji, ckjji, ckjkj, fix, fiy, fiz, fjx, fjy, fjz, fkx, fky, fkz; eimproper = 0.0; if (eflag || vflag) ev_setup(eflag,vflag); else evflag = 0; /* References to simulation data. */ double **x = atom->x; double **f = atom->f; int **improperlist = neighbor->improperlist; int nimproperlist = neighbor->nimproperlist; int nlocal = atom->nlocal; int newton_bond = force->newton_bond; /* A description of the potential can be found in Macromolecules 35, pp. 1463-1472 (2002). */ for (n = 0; n < nimproperlist; n++) { /* Take the ids of the atoms contributing to the improper potential. */ i1 = improperlist[n][0]; /* Atom "1" of Figure 1 from the above reference.*/ i2 = improperlist[n][1]; /* Atom "2" ... */ i3 = improperlist[n][2]; /* Atom "3" ... */ i4 = improperlist[n][3]; /* Atom "9" ... */ type = improperlist[n][4]; /* Calculate the necessary variables for LAMMPS implementation. if (evflag) ev_tally(i1,i2,i3,i4,nlocal,newton_bond,eimproper,f1,f3,f4, vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z); Although, they are irrelevant to the calculation of the potential, we keep them for maximal compatibility. */ vb1x = x[i1][0] - x[i2][0]; vb1y = x[i1][1] - x[i2][1]; vb1z = x[i1][2] - x[i2][2]; domain->minimum_image(vb1x,vb1y,vb1z); vb2x = x[i3][0] - x[i2][0]; vb2y = x[i3][1] - x[i2][1]; vb2z = x[i3][2] - x[i2][2]; domain->minimum_image(vb2x,vb2y,vb2z); vb3x = x[i4][0] - x[i3][0]; vb3y = x[i4][1] - x[i3][1]; vb3z = x[i4][2] - x[i3][2]; domain->minimum_image(vb3x,vb3y,vb3z); /* Pass the atom tags to form the necessary combinations. */ at1[0] = i1; at2[0] = i2; at3[0] = i4; /* ids: 1-2-9 */ at1[1] = i1; at2[1] = i2; at3[1] = i3; /* ids: 1-2-3 */ at1[2] = i4; at2[2] = i2; at3[2] = i3; /* ids: 9-2-3 */ /* Initialize the sum of the angles differences. */ angle_summer = 0.0; /* Take a loop over the three angles, defined by each triad: */ for (icomb = 0; icomb < 3; icomb ++) { /* Bond vector connecting the first and the second atom. */ bvec1x[icomb] = x[at2[icomb]][0] - x[at1[icomb]][0]; bvec1y[icomb] = x[at2[icomb]][1] - x[at1[icomb]][1]; bvec1z[icomb] = x[at2[icomb]][2] - x[at1[icomb]][2]; domain -> minimum_image(bvec1x[icomb], bvec1y[icomb], bvec1z[icomb]); /* also calculate the norm of the vector: */ bvec1n[icomb] = sqrt( bvec1x[icomb]*bvec1x[icomb] + bvec1y[icomb]*bvec1y[icomb] + bvec1z[icomb]*bvec1z[icomb]); /* Bond vector connecting the second and the third atom. */ bvec2x[icomb] = x[at3[icomb]][0] - x[at2[icomb]][0]; bvec2y[icomb] = x[at3[icomb]][1] - x[at2[icomb]][1]; bvec2z[icomb] = x[at3[icomb]][2] - x[at2[icomb]][2]; domain -> minimum_image(bvec2x[icomb], bvec2y[icomb], bvec2z[icomb]); /* also calculate the norm of the vector: */ bvec2n[icomb] = sqrt( bvec2x[icomb]*bvec2x[icomb] + bvec2y[icomb]*bvec2y[icomb] + bvec2z[icomb]*bvec2z[icomb]); /* Calculate the bending angle of the atom triad: */ bend_angle[icomb] = ( bvec2x[icomb]*bvec1x[icomb] + bvec2y[icomb]*bvec1y[icomb] + bvec2z[icomb]*bvec1z[icomb]); bend_angle[icomb] /= (bvec1n[icomb] * bvec2n[icomb]); if (bend_angle[icomb] > 1.0) bend_angle[icomb] -= SMALL; if (bend_angle[icomb] < -1.0) bend_angle[icomb] += SMALL; /* Append the current angle to the sum of angle differences. */ angle_summer += (bend_angle[icomb] - chi[type]); } if (eflag) eimproper = (1.0/6.0) *k[type] * pow(angle_summer,6); /* printf("The tags: %d-%d-%d-%d, of type %d .\n",atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4],type); // printf("The coordinates of the first: %f, %f, %f.\n", x[i1][0], x[i1][1], x[i1][2]); // printf("The coordinates of the second: %f, %f, %f.\n", x[i2][0], x[i2][1], x[i2][2]); // printf("The coordinates of the third: %f, %f, %f.\n", x[i3][0], x[i3][1], x[i3][2]); // printf("The coordinates of the fourth: %f, %f, %f.\n", x[i4][0], x[i4][1], x[i4][2]); printf("The angles are: %f / %f / %f equilibrium: %f.\n", bend_angle[0], bend_angle[1], bend_angle[2],chi[type]); printf("The energy of the improper: %f with prefactor %f.\n", eimproper,(1.0/6.0)*k[type]); printf("The sum of the angles: %f.\n", angle_summer); */ /* Force calculation acting on all atoms. Calculate the derivatives of the potential. */ angfac = k[type] * pow(angle_summer,5); f1[0] = 0.0; f1[1] = 0.0; f1[2] = 0.0; f3[0] = 0.0; f3[1] = 0.0; f3[2] = 0.0; f4[0] = 0.0; f4[1] = 0.0; f4[2] = 0.0; /* Take a loop over the three angles, defined by each triad: */ for (icomb = 0; icomb < 3; icomb ++) { /* Calculate the squares of the distances. */ cjiji = bvec1n[icomb] * bvec1n[icomb]; ckjkj = bvec2n[icomb] * bvec2n[icomb]; ckjji = bvec2x[icomb] * bvec1x[icomb] + bvec2y[icomb] * bvec1y[icomb] + bvec2z[icomb] * bvec1z[icomb] ; cfact1 = angfac / (sqrt(ckjkj * cjiji)); cfact2 = ckjji / ckjkj; cfact3 = ckjji / cjiji; /* Calculate the force acted on the thrid atom of the angle. */ fkx = cfact2 * bvec2x[icomb] - bvec1x[icomb]; fky = cfact2 * bvec2y[icomb] - bvec1y[icomb]; fkz = cfact2 * bvec2z[icomb] - bvec1z[icomb]; /* Calculate the force acted on the first atom of the angle. */ fix = bvec2x[icomb] - cfact3 * bvec1x[icomb]; fiy = bvec2y[icomb] - cfact3 * bvec1y[icomb]; fiz = bvec2z[icomb] - cfact3 * bvec1z[icomb]; /* Finally, calculate the force acted on the middle atom of the angle.*/ fjx = - fix - fkx; fjy = - fiy - fky; fjz = - fiz - fkz; /* Consider the appropriate scaling of the forces: */ fix *= cfact1; fiy *= cfact1; fiz *= cfact1; fjx *= cfact1; fjy *= cfact1; fjz *= cfact1; fkx *= cfact1; fky *= cfact1; fkz *= cfact1; if (at1[icomb] == i1) {f1[0] += fix; f1[1] += fiy; f1[2] += fiz;} else if (at2[icomb] == i1) {f1[0] += fjx; f1[1] += fjy; f1[2] += fjz;} else if (at3[icomb] == i1) {f1[0] += fkx; f1[1] += fky; f1[2] += fkz;} if (at1[icomb] == i3) {f3[0] += fix; f3[1] += fiy; f3[2] += fiz;} else if (at2[icomb] == i3) {f3[0] += fjx; f3[1] += fjy; f3[2] += fjz;} else if (at3[icomb] == i3) {f3[0] += fkx; f3[1] += fky; f3[2] += fkz;} if (at1[icomb] == i4) {f4[0] += fix; f4[1] += fiy; f4[2] += fiz;} else if (at2[icomb] == i4) {f4[0] += fjx; f4[1] += fjy; f4[2] += fjz;} else if (at3[icomb] == i4) {f4[0] += fkx; f4[1] += fky; f4[2] += fkz;} /* Store the contribution to the global arrays: */ /* Take the id of the atom from the at1[icomb] element, i1 = at1[icomb]. */ if (newton_bond || at1[icomb] < nlocal) { f[at1[icomb]][0] += fix; f[at1[icomb]][1] += fiy; f[at1[icomb]][2] += fiz; } /* Take the id of the atom from the at2[icomb] element, i2 = at2[icomb]. */ if (newton_bond || at2[icomb] < nlocal) { f[at2[icomb]][0] += fjx; f[at2[icomb]][1] += fjy; f[at2[icomb]][2] += fjz; } /* Take the id of the atom from the at3[icomb] element, i3 = at3[icomb]. */ if (newton_bond || at3[icomb] < nlocal) { f[at3[icomb]][0] += fkx; f[at3[icomb]][1] += fky; f[at3[icomb]][2] += fkz; } } if (evflag) ev_tally(i1,i2,i3,i4,nlocal,newton_bond,eimproper,f1,f3,f4, vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z); } } /* ---------------------------------------------------------------------- */ void ImproperRing::allocate() { allocated = 1; int n = atom->nimpropertypes; memory->create(k,n+1,"improper:k"); memory->create(chi,n+1,"improper:chi"); memory->create(setflag,n+1,"improper:setflag"); for (int i = 1; i <= n; i++) setflag[i] = 0; } /* ---------------------------------------------------------------------- set coeffs for one type ------------------------------------------------------------------------- */ void ImproperRing ::coeff(int narg, char **arg) { /* Check whether there exist sufficient number of arguments. 0: type of improper to be applied to 1: energetic constant 2: equilibrium angle in degrees */ if (narg != 3) error->all(FLERR,"Incorrect args for RING improper coefficients"); if (!allocated) allocate(); int ilo,ihi; force->bounds(arg[0],atom->nimpropertypes,ilo,ihi); double k_one = force->numeric(arg[1]); double chi_one = force->numeric(arg[2]); int count = 0; for (int i = ilo; i <= ihi; i++) { /* Read the k parameter in kcal/mol. */ k[i] = k_one; /* "chi_one" stores the equilibrium angle in degrees. Convert it to radians and store its cosine. */ chi[i] = cos((chi_one/180.0)*MY_PI); setflag[i] = 1; count++; } if (count == 0) error->all(FLERR,"Incorrect args for improper coefficients"); } /* ---------------------------------------------------------------------- proc 0 writes out coeffs to restart file ------------------------------------------------------------------------- */ void ImproperRing ::write_restart(FILE *fp) { fwrite(&k[1],sizeof(double),atom->nimpropertypes,fp); fwrite(&chi[1],sizeof(double),atom->nimpropertypes,fp); } /* ---------------------------------------------------------------------- proc 0 reads coeffs from restart file, bcasts them ------------------------------------------------------------------------- */ void ImproperRing::read_restart(FILE *fp) { allocate(); if (comm->me == 0) { fread(&k[1],sizeof(double),atom->nimpropertypes,fp); fread(&chi[1],sizeof(double),atom->nimpropertypes,fp); } MPI_Bcast(&k[1],atom->nimpropertypes,MPI_DOUBLE,0,world); MPI_Bcast(&chi[1],atom->nimpropertypes,MPI_DOUBLE,0,world); for (int i = 1; i <= atom->nimpropertypes; i++) setflag[i] = 1; }