diff --git a/src/USER-MISC/Install.sh b/src/USER-MISC/Install.sh index 5b86de208c..aa2fc00f95 100644 --- a/src/USER-MISC/Install.sh +++ b/src/USER-MISC/Install.sh @@ -14,6 +14,8 @@ if (test $1 = 1) then cp fix_addtorque.cpp .. cp fix_imd.cpp .. cp fix_smd.cpp .. + cp improper_cossq.cpp .. + cp improper_ring.cpp .. cp pair_cdeam.cpp .. cp pair_coul_diel.cpp .. cp pair_dipole_sf.cpp .. @@ -35,6 +37,8 @@ if (test $1 = 1) then cp fix_addtorque.h .. cp fix_imd.h .. cp fix_smd.h .. + cp improper_cossq.h .. + cp improper_ring.h .. cp pair_cdeam.h .. cp pair_coul_diel.h .. cp pair_dipole_sf.h .. @@ -58,6 +62,8 @@ elif (test $1 = 0) then rm -f ../fix_addtorque.cpp rm -f ../fix_imd.cpp rm -f ../fix_smd.cpp + rm -f ../improper_cossq.cpp + rm -f ../improper_ring.cpp rm -f ../pair_cdeam.cpp rm -f ../pair_coul_diel.cpp rm -f ../pair_dipole_sf.cpp @@ -79,6 +85,8 @@ elif (test $1 = 0) then rm -f ../fix_addtorque.h rm -f ../fix_imd.h rm -f ../fix_smd.h + rm -f ../improper_cossq.h + rm -f ../improper_ring.h rm -f ../pair_cdeam.h rm -f ../pair_coul_diel.h rm -f ../pair_dipole_sf.h diff --git a/src/USER-MISC/improper_cossq.cpp b/src/USER-MISC/improper_cossq.cpp new file mode 100644 index 0000000000..ac66f2af42 --- /dev/null +++ b/src/USER-MISC/improper_cossq.cpp @@ -0,0 +1,315 @@ +/* ---------------------------------------------------------------------- + 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) +------------------------------------------------------------------------- */ + +#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_cossq.h b/src/USER-MISC/improper_cossq.h new file mode 100644 index 0000000000..d4b7ca64a7 --- /dev/null +++ b/src/USER-MISC/improper_cossq.h @@ -0,0 +1,45 @@ +/* ---------------------------------------------------------------------- + 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. +------------------------------------------------------------------------- */ + +#ifdef IMPROPER_CLASS + +ImproperStyle(cossq,ImproperCossq) + +#else + +#ifndef LMP_IMPROPER_COSSQ_H +#define LMP_IMPROPER_COSSQ_H + +#include "stdio.h" +#include "improper.h" + +namespace LAMMPS_NS { + +class ImproperCossq : public Improper { + public: + ImproperCossq(class LAMMPS *); + virtual ~ImproperCossq(); + virtual void compute(int, int); + void coeff(int, char **); + void write_restart(FILE *); + void read_restart(FILE *); + + protected: + double *k, *chi; + void allocate(); +}; + +} + +#endif +#endif diff --git a/src/USER-MISC/improper_ring.cpp b/src/USER-MISC/improper_ring.cpp new file mode 100644 index 0000000000..3a0d2fb9d9 --- /dev/null +++ b/src/USER-MISC/improper_ring.cpp @@ -0,0 +1,344 @@ +/* ---------------------------------------------------------------------- + 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) +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + 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; +} diff --git a/src/USER-MISC/improper_ring.h b/src/USER-MISC/improper_ring.h new file mode 100644 index 0000000000..f68d5a6d21 --- /dev/null +++ b/src/USER-MISC/improper_ring.h @@ -0,0 +1,46 @@ +/* ---------------------------------------------------------------------- + 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. +------------------------------------------------------------------------- */ + +#ifdef IMPROPER_CLASS + +ImproperStyle(ring,ImproperRing) + +#else + +#ifndef LMP_IMPROPER_RING_H +#define LMP_IMPROPER_RING_H + +#include "stdio.h" +#include "improper.h" + +namespace LAMMPS_NS { + +class ImproperRing : public Improper { + public: + ImproperRing(class LAMMPS *); + virtual ~ImproperRing(); + virtual void compute(int, int); + void coeff(int, char **); + void write_restart(FILE *); + void read_restart(FILE *); + + protected: + double *k,*chi; + + void allocate(); +}; + +} + +#endif +#endif