diff --git a/src/USER-MISC/Install.sh b/src/USER-MISC/Install.sh index 4d9ac38c7d..7fe2688ac9 100644 --- a/src/USER-MISC/Install.sh +++ b/src/USER-MISC/Install.sh @@ -2,21 +2,41 @@ if (test $1 = 1) then + cp angle_cosineshift.cpp .. + cp angle_cosineshiftexp.cpp .. + cp bond_harmonic_shift.cpp .. + cp bond_harmonic_shift_cut.cpp .. cp compute_temp_rotate.cpp .. + cp dihedral_cosineshiftexp.cpp .. cp fix_addtorque.cpp .. cp pair_dipole_sf.cpp .. + cp angle_cosineshift.h .. + cp angle_cosineshiftexp.h .. + cp bond_harmonic_shift.h .. + cp bond_harmonic_shift_cut.h .. cp compute_temp_rotate.h .. + cp dihedral_cosineshiftexp.h .. cp fix_addtorque.h .. cp pair_dipole_sf.h .. elif (test $1 = 0) then + rm -f ../angle_cosineshift.cpp + rm -f ../angle_cosineshiftexp.cpp + rm -f ../bond_harmonic_shift.cpp + rm -f ../bond_harmonic_shift_cut.cpp rm -f ../compute_temp_rotate.cpp + rm -f ../dihedral_cosineshiftexp.cpp rm -f ../fix_addtorque.cpp rm -f ../pair_dipole_sf.cpp + rm -f ../angle_cosineshift.h + rm -f ../angle_cosineshiftexp.h + rm -f ../bond_harmonic_shift.h + rm -f ../bond_harmonic_shift_cut.h rm -f ../compute_temp_rotate.h + rm -f ../dihedral_cosineshiftexp.h rm -f ../fix_addtorque.h rm -f ../pair_dipole_sf.h diff --git a/src/USER-MISC/README b/src/USER-MISC/README index 575d31b569..cb3dc1fa64 100644 --- a/src/USER-MISC/README +++ b/src/USER-MISC/README @@ -16,6 +16,11 @@ feature or its code. ------------------------------------------------------------ -compute temp/rotate, Laurent Joly (U Lyon, France), ljoly.ulyon at gmail.com, 8Aug11 -fix addtorque, Laurent Joly (U Lyon, France), ljoly.ulyon at gmail.com, 8Aug11 -pair dipole/sf, Mario Orsi, orsimario at gmail.com, 8Aug11 +angle_style cosine/shift, Carsten Svaneborg, science at zqex.dk, 8 Aug 11 +angle_style cosine/shift/exp, Carsten Svaneborg, science at zqex.dk, 8 Aug 11 +bond_style harmonic/shift, Carsten Svaneborg, science at zqex.dk, 8 Aug 11 +bond_style harmonic/shift/cut, Carsten Svaneborg, science at zqex.dk, 8 Aug 11 +compute temp/rotate, Laurent Joly (U Lyon, France), ljoly.ulyon at gmail.com, 8 Aug 11 +dihedral_style cosine/shift/exp, Carsten Svaneborg, science at zqex.dk, 8 Aug 11 +fix addtorque, Laurent Joly (U Lyon, France), ljoly.ulyon at gmail.com, 8 Aug 11 +pair dipole/sf, Mario Orsi, orsimario at gmail.com, 8 Aug 11 diff --git a/src/USER-MISC/angle_cosineshift.cpp b/src/USER-MISC/angle_cosineshift.cpp new file mode 100644 index 0000000000..4e0d11d849 --- /dev/null +++ b/src/USER-MISC/angle_cosineshift.cpp @@ -0,0 +1,263 @@ +/* ---------------------------------------------------------------------- + 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: Carsten Svaneborg, science@zqex.dk +------------------------------------------------------------------------- */ + +#include "math.h" +#include "stdlib.h" +#include "angle_cosineshift.h" +#include "atom.h" +#include "neighbor.h" +#include "domain.h" +#include "comm.h" +#include "force.h" +#include "memory.h" +#include "error.h" + +using namespace LAMMPS_NS; + +#define SMALL 0.001 + +/* ---------------------------------------------------------------------- */ + +AngleCosineShift::AngleCosineShift(LAMMPS *lmp) : Angle(lmp) {} + +/* ---------------------------------------------------------------------- */ + +AngleCosineShift::~AngleCosineShift() +{ + if (allocated) { + memory->destroy(setflag); + memory->destroy(k); + memory->destroy(kcost); + memory->destroy(ksint); + memory->destroy(theta); + } +} + +/* ---------------------------------------------------------------------- */ + +void AngleCosineShift::compute(int eflag, int vflag) +{ + int i1,i2,i3,n,type; + double delx1,dely1,delz1,delx2,dely2,delz2; + double eangle,f1[3],f3[3]; + double rsq1,rsq2,r1,r2,c,s,cps,kcos,ksin,a11,a12,a22; + + eangle = 0.0; + if (eflag || vflag) ev_setup(eflag,vflag); + else evflag = 0; + + double **x = atom->x; + double **f = atom->f; + int **anglelist = neighbor->anglelist; + int nanglelist = neighbor->nanglelist; + int nlocal = atom->nlocal; + int newton_bond = force->newton_bond; + + for (n = 0; n < nanglelist; n++) { + i1 = anglelist[n][0]; + i2 = anglelist[n][1]; + i3 = anglelist[n][2]; + type = anglelist[n][3]; + + // 1st bond + + delx1 = x[i1][0] - x[i2][0]; + dely1 = x[i1][1] - x[i2][1]; + delz1 = x[i1][2] - x[i2][2]; + domain->minimum_image(delx1,dely1,delz1); + + rsq1 = delx1*delx1 + dely1*dely1 + delz1*delz1; + r1 = sqrt(rsq1); + + // 2nd bond + + delx2 = x[i3][0] - x[i2][0]; + dely2 = x[i3][1] - x[i2][1]; + delz2 = x[i3][2] - x[i2][2]; + domain->minimum_image(delx2,dely2,delz2); + + rsq2 = delx2*delx2 + dely2*dely2 + delz2*delz2; + r2 = sqrt(rsq2); + + // c = cosine of angle + c = delx1*delx2 + dely1*dely2 + delz1*delz2; + c /= r1*r2; + if (c > 1.0) c = 1.0; + if (c < -1.0) c = -1.0; + + // C= sine of angle + s = sqrt(1.0 - c*c); + if (s < SMALL) s = SMALL; + + // force & energy + if (eflag) eangle = -k[type]-kcos*c-ksin*s; + + kcos=kcost[type]; + ksin=ksint[type]; + cps = c/s; // NOTE absorbed one c + + a11 = (-kcos +ksin*cps )*c/ rsq1; + a12 = ( kcos -ksin*cps ) / (r1*r2); + a22 = (-kcos +ksin*cps )*c/ rsq2; + + f1[0] = a11*delx1 + a12*delx2; + f1[1] = a11*dely1 + a12*dely2; + f1[2] = a11*delz1 + a12*delz2; + f3[0] = a22*delx2 + a12*delx1; + f3[1] = a22*dely2 + a12*dely1; + f3[2] = a22*delz2 + a12*delz1; + + // apply force to each of 3 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] -= f1[0] + f3[0]; + f[i2][1] -= f1[1] + f3[1]; + f[i2][2] -= f1[2] + f3[2]; + } + + if (newton_bond || i3 < nlocal) { + f[i3][0] += f3[0]; + f[i3][1] += f3[1]; + f[i3][2] += f3[2]; + } + + if (evflag) ev_tally(i1,i2,i3,nlocal,newton_bond,eangle,f1,f3, + delx1,dely1,delz1,delx2,dely2,delz2); + } +} + +/* ---------------------------------------------------------------------- */ + +void AngleCosineShift::allocate() +{ + allocated = 1; + int n = atom->nangletypes; + + memory->create(k ,n+1,"Angle:k"); + memory->create(ksint ,n+1,"Angle:ksint"); + memory->create(kcost ,n+1,"Angle:kcost"); + memory->create(theta ,n+1,"Angle:theta"); + memory->create(setflag,n+1, "Angle:setflag"); + + for (int i = 1; i <= n; i++) setflag[i] = 0; +} + +/* ---------------------------------------------------------------------- + set coeffs for one type +------------------------------------------------------------------------- */ + +void AngleCosineShift::coeff(int narg, char **arg) +{ + if (narg != 3) error->all("Incorrect args for angle coefficients"); + if (!allocated) allocate(); + + int ilo,ihi; + force->bounds(arg[0],atom->nangletypes,ilo,ihi); + + double umin = force->numeric(arg[1]); + double theta0 = force->numeric(arg[2]); + +// k=Umin/2 + + int count = 0; + for (int i = ilo; i <= ihi; i++) { + k[i] = umin/2; + kcost[i] = umin/2*cos(theta0*3.14159265/180); + ksint[i] = umin/2*sin(theta0*3.14159265/180); + theta[i] = theta0*3.14159265/180; + + setflag[i] = 1; + count++; + } + + if (count == 0) error->all("Incorrect args for angle coefficients"); +} + +/* ---------------------------------------------------------------------- */ + +double AngleCosineShift::equilibrium_angle(int i) +{ + return theta[i]; +} + +/* ---------------------------------------------------------------------- + proc 0 writes out coeffs to restart file +------------------------------------------------------------------------- */ + +void AngleCosineShift::write_restart(FILE *fp) +{ + fwrite(&k[1],sizeof(double),atom->nangletypes,fp); + fwrite(&kcost[1],sizeof(double),atom->nangletypes,fp); + fwrite(&ksint[1],sizeof(double),atom->nangletypes,fp); + fwrite(&theta[1],sizeof(double),atom->nangletypes,fp); +} + +/* ---------------------------------------------------------------------- + proc 0 reads coeffs from restart file, bcasts them +------------------------------------------------------------------------- */ + +void AngleCosineShift::read_restart(FILE *fp) +{ + allocate(); + + if (comm->me == 0) + { + fread(&k[1],sizeof(double),atom->nangletypes,fp); + fread(&kcost[1],sizeof(double),atom->nangletypes,fp); + fread(&ksint[1],sizeof(double),atom->nangletypes,fp); + fread(&theta[1],sizeof(double),atom->nangletypes,fp); + } + MPI_Bcast(&k[1],atom->nangletypes,MPI_DOUBLE,0,world); + MPI_Bcast(&kcost[1],atom->nangletypes,MPI_DOUBLE,0,world); + MPI_Bcast(&ksint[1],atom->nangletypes,MPI_DOUBLE,0,world); + MPI_Bcast(&theta[1],atom->nangletypes,MPI_DOUBLE,0,world); + + for (int i = 1; i <= atom->nangletypes; i++) setflag[i] = 1; +} + +/* ---------------------------------------------------------------------- */ + +double AngleCosineShift::single(int type, int i1, int i2, int i3) +{ + double **x = atom->x; + + double delx1 = x[i1][0] - x[i2][0]; + double dely1 = x[i1][1] - x[i2][1]; + double delz1 = x[i1][2] - x[i2][2]; + domain->minimum_image(delx1,dely1,delz1); + double r1 = sqrt(delx1*delx1 + dely1*dely1 + delz1*delz1); + + double delx2 = x[i3][0] - x[i2][0]; + double dely2 = x[i3][1] - x[i2][1]; + double delz2 = x[i3][2] - x[i2][2]; + domain->minimum_image(delx2,dely2,delz2); + double r2 = sqrt(delx2*delx2 + dely2*dely2 + delz2*delz2); + + double c = delx1*delx2 + dely1*dely2 + delz1*delz2; + c /= r1*r2; + if (c > 1.0) c = 1.0; + if (c < -1.0) c = -1.0; + double s=sqrt(1.0-c*c); + + return -k[type]-kcost[type]*c-ksint[type]*s; +} diff --git a/src/USER-MISC/angle_cosineshift.h b/src/USER-MISC/angle_cosineshift.h new file mode 100644 index 0000000000..40f5fae122 --- /dev/null +++ b/src/USER-MISC/angle_cosineshift.h @@ -0,0 +1,67 @@ +/* ---------------------------------------------------------------------- + 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. +------------------------------------------------------------------------- */ + +/* + The angle is defined from (R1-R2) . (R3-R2) hence a straight + bond has costheta=180. + + U(theta,theta0,umin)= -Umin (1+cos[theta-theta0])/2 + + potential has minimum at theta=theta0 where U() = -Umin + potential has maximum at theta=theta0+180 where U() = 0 + + At the minimum U(theta,theta0,umin)=-Umin+Umin/4 (theta-theta0)^2+O( ()^4) + hence the effective spring constant is k=umin/2. + + to match U(theta,theta0,K)=K(theta-theta0)^2 at the minimum Umin=4*K +*/ + +#ifdef ANGLE_CLASS + +AngleStyle(cosineshift,AngleCosineShift) + +#else + +#ifndef LMP_ANGLE_COSINESHIFT_H +#define LMP_ANGLE_COSINESHIFT_H + +#include "stdio.h" +#include "angle.h" + +namespace LAMMPS_NS { + +class AngleCosineShift : public Angle { + public: + AngleCosineShift(class LAMMPS *); + ~AngleCosineShift(); + virtual void compute(int, int); + void coeff(int, char **); + double equilibrium_angle(int); + void write_restart(FILE *); + void read_restart(FILE *); + double single(int, int, int, int); + + private: + double *k; + double *a; + double *theta; + double *ksint; + double *kcost; + + void allocate(); +}; + +} + +#endif +#endif diff --git a/src/USER-MISC/angle_cosineshiftexp.cpp b/src/USER-MISC/angle_cosineshiftexp.cpp new file mode 100644 index 0000000000..f4a95ca7b0 --- /dev/null +++ b/src/USER-MISC/angle_cosineshiftexp.cpp @@ -0,0 +1,306 @@ +/* ---------------------------------------------------------------------- + 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: Carsten Svaneborg, science@zqex.dk +------------------------------------------------------------------------- */ + +#include "math.h" +#include "stdlib.h" +#include "angle_cosineshiftexp.h" +#include "atom.h" +#include "neighbor.h" +#include "domain.h" +#include "comm.h" +#include "force.h" +#include "memory.h" +#include "error.h" + +using namespace LAMMPS_NS; + +#define SMALL 0.001 + +/* ---------------------------------------------------------------------- */ + +AngleCosineShiftExp::AngleCosineShiftExp(LAMMPS *lmp) : Angle(lmp) {} + +/* ---------------------------------------------------------------------- */ + +AngleCosineShiftExp::~AngleCosineShiftExp() +{ + if (allocated) { + memory->destroy(setflag); + memory->destroy(umin); + memory->destroy(a); + memory->destroy(opt1); + memory->destroy(cost); + memory->destroy(sint); + memory->destroy(theta0); + memory->destroy(doExpansion); + } +} + +/* ---------------------------------------------------------------------- */ + +void AngleCosineShiftExp::compute(int eflag, int vflag) +{ + int i1,i2,i3,n,type; + double delx1,dely1,delz1,delx2,dely2,delz2; + double eangle,f1[3],f3[3],ff; + double rsq1,rsq2,r1,r2,c,s,cc,ss,a11,a12,a22; + double exp2,aa,uumin,cccpsss,cssmscc; + + eangle = 0.0; + if (eflag || vflag) ev_setup(eflag,vflag); + else evflag = 0; + + double **x = atom->x; + double **f = atom->f; + int **anglelist = neighbor->anglelist; + int nanglelist = neighbor->nanglelist; + int nlocal = atom->nlocal; + int newton_bond = force->newton_bond; + + for (n = 0; n < nanglelist; n++) { + i1 = anglelist[n][0]; + i2 = anglelist[n][1]; + i3 = anglelist[n][2]; + type = anglelist[n][3]; + + // 1st bond + + delx1 = x[i1][0] - x[i2][0]; + dely1 = x[i1][1] - x[i2][1]; + delz1 = x[i1][2] - x[i2][2]; + domain->minimum_image(delx1,dely1,delz1); + + rsq1 = delx1*delx1 + dely1*dely1 + delz1*delz1; + r1 = sqrt(rsq1); + + // 2nd bond + + delx2 = x[i3][0] - x[i2][0]; + dely2 = x[i3][1] - x[i2][1]; + delz2 = x[i3][2] - x[i2][2]; + domain->minimum_image(delx2,dely2,delz2); + + rsq2 = delx2*delx2 + dely2*dely2 + delz2*delz2; + r2 = sqrt(rsq2); + + // c = cosine of angle + c = delx1*delx2 + dely1*dely2 + delz1*delz2; + c /= r1*r2; + if (c > 1.0) c = 1.0; + if (c < -1.0) c = -1.0; + + // C= sine of angle + s = sqrt(1.0 - c*c); + if (s < SMALL) s = SMALL; + + // force & energy + + aa=a[type]; + uumin=umin[type]; + + cccpsss = c*cost[type]+s*sint[type]; + cssmscc = c*sint[type]-s*cost[type]; + + if (doExpansion[type]) + { // |a|<0.01 so use expansions relative precision <1e-5 +// std::cout << "Using expansion\n"; + if (eflag) eangle = -0.125*(1+cccpsss)*(4+aa*(cccpsss-1))*uumin; + ff=0.25*uumin*cssmscc*(2+aa*cccpsss)/s; + } + else + { +// std::cout << "Not using expansion\n"; + exp2=exp(0.5*aa*(1+cccpsss)); + if (eflag) eangle = opt1[type]*(1-exp2); + ff=0.5*a[type]*opt1[type]*exp2*cssmscc/s; + } + + a11 = ff*c/ rsq1; + a12 = -ff / (r1*r2); + a22 = ff*c/ rsq2; + + f1[0] = a11*delx1 + a12*delx2; + f1[1] = a11*dely1 + a12*dely2; + f1[2] = a11*delz1 + a12*delz2; + f3[0] = a22*delx2 + a12*delx1; + f3[1] = a22*dely2 + a12*dely1; + f3[2] = a22*delz2 + a12*delz1; + + // apply force to each of 3 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] -= f1[0] + f3[0]; + f[i2][1] -= f1[1] + f3[1]; + f[i2][2] -= f1[2] + f3[2]; + } + + if (newton_bond || i3 < nlocal) { + f[i3][0] += f3[0]; + f[i3][1] += f3[1]; + f[i3][2] += f3[2]; + } + + if (evflag) ev_tally(i1,i2,i3,nlocal,newton_bond,eangle,f1,f3, + delx1,dely1,delz1,delx2,dely2,delz2); + } +} + +/* ---------------------------------------------------------------------- */ + +void AngleCosineShiftExp::allocate() +{ + allocated = 1; + int n = atom->nangletypes; + + memory->create(doExpansion, n+1, "angle:doExpansion"); + memory->create(umin , n+1, "angle:umin"); + memory->create(a , n+1, "angle:a"); + memory->create(sint , n+1, "angle:sint"); + memory->create(cost , n+1, "angle:cost"); + memory->create(opt1 , n+1, "angle:opt1"); + memory->create(theta0 , n+1, "angle:theta0"); + memory->create(setflag , n+1, "angle:setflag"); + + for (int i = 1; i <= n; i++) setflag[i] = 0; +} + +/* ---------------------------------------------------------------------- + set coeffs for one type +------------------------------------------------------------------------- */ + +void AngleCosineShiftExp::coeff(int narg, char **arg) +{ + if (narg != 4) error->all("Incorrect args for angle coefficients"); + if (!allocated) allocate(); + + int ilo,ihi; + force->bounds(arg[0],atom->nangletypes,ilo,ihi); + + double umin_ = force->numeric(arg[1]); + double theta0_ = force->numeric(arg[2]); + double a_ = force->numeric(arg[3]); + + int count = 0; + for (int i = ilo; i <= ihi; i++) { + doExpansion[i]=(fabs(a_)<0.001); + umin[i] = umin_; + a[i] = a_; + cost[i] = cos(theta0_*3.14159265/180); + sint[i] = sin(theta0_*3.14159265/180); + theta0[i]= theta0_*3.14159265/180; + + if (!doExpansion[i]) opt1[i]=umin_/(exp(a_)-1); + + setflag[i] = 1; + count++; + } + + if (count == 0) error->all("Incorrect args for angle coefficients"); +} + +/* ---------------------------------------------------------------------- */ + +double AngleCosineShiftExp::equilibrium_angle(int i) +{ + return theta0[i]; +} + +/* ---------------------------------------------------------------------- + proc 0 writes out coeffs to restart file +------------------------------------------------------------------------- */ + +void AngleCosineShiftExp::write_restart(FILE *fp) +{ + fwrite(&umin[1],sizeof(double),atom->nangletypes,fp); + fwrite(&a[1],sizeof(double),atom->nangletypes,fp); + fwrite(&cost[1],sizeof(double),atom->nangletypes,fp); + fwrite(&sint[1],sizeof(double),atom->nangletypes,fp); + fwrite(&theta0[1],sizeof(double),atom->nangletypes,fp); +} + +/* ---------------------------------------------------------------------- + proc 0 reads coeffs from restart file, bcasts them +------------------------------------------------------------------------- */ + +void AngleCosineShiftExp::read_restart(FILE *fp) +{ + allocate(); + + if (comm->me == 0) + { + fread(&umin[1],sizeof(double),atom->nangletypes,fp); + fread(&a[1],sizeof(double),atom->nangletypes,fp); + fread(&cost[1],sizeof(double),atom->nangletypes,fp); + fread(&sint[1],sizeof(double),atom->nangletypes,fp); + fread(&theta0[1],sizeof(double),atom->nangletypes,fp); + } + MPI_Bcast(&umin[1],atom->nangletypes,MPI_DOUBLE,0,world); + MPI_Bcast(&a[1],atom->nangletypes,MPI_DOUBLE,0,world); + MPI_Bcast(&cost[1],atom->nangletypes,MPI_DOUBLE,0,world); + MPI_Bcast(&sint[1],atom->nangletypes,MPI_DOUBLE,0,world); + MPI_Bcast(&theta0[1],atom->nangletypes,MPI_DOUBLE,0,world); + + for (int i = 1; i <= atom->nangletypes; i++) + { + setflag[i] = 1; + doExpansion[i]=(fabs(a[i])<0.01); + if (!doExpansion[i]) opt1[i]=umin[i]/(exp(a[i])-1); + } +} + +/* ---------------------------------------------------------------------- */ + +double AngleCosineShiftExp::single(int type, int i1, int i2, int i3) +{ + double **x = atom->x; + + double delx1 = x[i1][0] - x[i2][0]; + double dely1 = x[i1][1] - x[i2][1]; + double delz1 = x[i1][2] - x[i2][2]; + domain->minimum_image(delx1,dely1,delz1); + double r1 = sqrt(delx1*delx1 + dely1*dely1 + delz1*delz1); + + double delx2 = x[i3][0] - x[i2][0]; + double dely2 = x[i3][1] - x[i2][1]; + double delz2 = x[i3][2] - x[i2][2]; + domain->minimum_image(delx2,dely2,delz2); + double r2 = sqrt(delx2*delx2 + dely2*dely2 + delz2*delz2); + + double c = delx1*delx2 + dely1*dely2 + delz1*delz2; + c /= r1*r2; + if (c > 1.0) c = 1.0; + if (c < -1.0) c = -1.0; + double s=sqrt(1.0-c*c); + + double cccpsss=c*cost[type]+s*sint[type]; + double cssmscc=c*sint[type]-s*cost[type]; + + if (doExpansion[type]) + { + return -0.125*(1+cccpsss)*(4+a[type]*(cccpsss-1))*umin[type]; + } + else + { + return opt1[type]*(1-exp(0.5*a[type]*(1+cccpsss))); + } +} diff --git a/src/USER-MISC/angle_cosineshiftexp.h b/src/USER-MISC/angle_cosineshiftexp.h new file mode 100644 index 0000000000..d481de9c26 --- /dev/null +++ b/src/USER-MISC/angle_cosineshiftexp.h @@ -0,0 +1,72 @@ +/* ---------------------------------------------------------------------- + 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. +------------------------------------------------------------------------- */ + +/* + The angle is defined from Cos(theta)= b1.b2 / |b1||b2| where b1=(R1-R2) and + b2=(R3-R2) a straight bond has costheta=180. + + U(theta,theta0,umin,a) = -Umin[Exp(-a U)-1]/[[Exp(a)-1]] + with U = (-1-cos[theta-theta0])/2 = -Cos((theta-theta0)/2)^2 + + potential has minimum at theta=theta0 where U() = -Umin + potential has maximum at theta=theta0+180 where U() = 0 + + The spring constant around the minimum is controlled by a and + is given by k = a exp(a) Umin/[ 2(Exp[a]-1) ] for a=0 + the spring constant is k=Umin/2 and the potential reduces to + the cosineshifted potential. + + The potential is implemented such that for a<0.001 a series + expansion to linear order is used instead of the expression + above. This ensures a precision of about 1e-5 or better for + energies and forces, and ensures the potential is well + behaved for a=0 +*/ + +#ifdef ANGLE_CLASS +AngleStyle(cosineshiftexp,AngleCosineShiftExp) +#else + +#ifndef LMP_ANGLE_COSINESHIFTEXP_H +#define LMP_ANGLE_COSINESHIFTEXP_H + +#include "stdio.h" +#include "angle.h" + +namespace LAMMPS_NS { + +class AngleCosineShiftExp : public Angle { + public: + AngleCosineShiftExp(class LAMMPS *); + ~AngleCosineShiftExp(); + void compute(int, int); + void coeff(int, char **); + double equilibrium_angle(int); + void write_restart(FILE *); + void read_restart(FILE *); + double single(int, int, int, int); + + private: + bool *doExpansion; + double *umin,*a,*opt1; + double *theta0; + double *sint; + double *cost; + + void allocate(); +}; + +} + +#endif +#endif diff --git a/src/USER-MISC/bond_harmonic_shift.cpp b/src/USER-MISC/bond_harmonic_shift.cpp new file mode 100644 index 0000000000..b051c7dff5 --- /dev/null +++ b/src/USER-MISC/bond_harmonic_shift.cpp @@ -0,0 +1,199 @@ +/* ---------------------------------------------------------------------- + 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: Carsten Svaneborg, science@zqex.dk +------------------------------------------------------------------------- */ + +#include "math.h" +#include "stdlib.h" +#include "bond_harmonic_shift.h" +#include "atom.h" +#include "neighbor.h" +#include "domain.h" +#include "comm.h" +#include "force.h" +#include "memory.h" +#include "error.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +BondHarmonicShift::BondHarmonicShift(LAMMPS *lmp) : Bond(lmp) {} + +/* ---------------------------------------------------------------------- */ + +BondHarmonicShift::~BondHarmonicShift() +{ + if (allocated) { + memory->destroy(setflag); + memory->destroy(k); + memory->destroy(r0); + memory->destroy(r1); + } +} + +/* ---------------------------------------------------------------------- */ + +void BondHarmonicShift::compute(int eflag, int vflag) +{ + int i1,i2,n,type; + double delx,dely,delz,ebond,fbond; + double rsq,r,dr,rk; + + ebond = 0.0; + if (eflag || vflag) ev_setup(eflag,vflag); + else evflag = 0; + + double **x = atom->x; + double **f = atom->f; + int **bondlist = neighbor->bondlist; + int nbondlist = neighbor->nbondlist; + int nlocal = atom->nlocal; + int newton_bond = force->newton_bond; + + for (n = 0; n < nbondlist; n++) { + i1 = bondlist[n][0]; + i2 = bondlist[n][1]; + type = bondlist[n][2]; + + delx = x[i1][0] - x[i2][0]; + dely = x[i1][1] - x[i2][1]; + delz = x[i1][2] - x[i2][2]; + domain->minimum_image(delx,dely,delz); + + rsq = delx*delx + dely*dely + delz*delz; + r = sqrt(rsq); + + dr = r - r0[type]; + rk = k[type] * dr; + + // force & energy + + if (r > 0.0) fbond = -2.0*rk/r; + else fbond = 0.0; + + if (eflag) ebond = k[type]*(dr*dr -(r0[type]-r1[type])*(r0[type]-r1[type]) ); + + // apply force to each of 2 atoms + + if (newton_bond || i1 < nlocal) { + f[i1][0] += delx*fbond; + f[i1][1] += dely*fbond; + f[i1][2] += delz*fbond; + } + + if (newton_bond || i2 < nlocal) { + f[i2][0] -= delx*fbond; + f[i2][1] -= dely*fbond; + f[i2][2] -= delz*fbond; + } + + if (evflag) ev_tally(i1,i2,nlocal,newton_bond,ebond,fbond,delx,dely,delz); + } +} + +/* ---------------------------------------------------------------------- */ + +void BondHarmonicShift::allocate() +{ + allocated = 1; + int n = atom->nbondtypes; + + memory->create(k , n+1,"bond:k"); + memory->create(r0, n+1,"bond:r0"); + memory->create(r1, n+1,"bond:r1"); + memory->create(setflag,n+1,"bond:setflag"); + + for (int i = 1; i <= n; i++) setflag[i] = 0; +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more types +------------------------------------------------------------------------- */ + +void BondHarmonicShift::coeff(int narg, char **arg) +{ + if (narg != 4) error->all("Incorrect args for bond coefficients"); + if (!allocated) allocate(); + + int ilo,ihi; + force->bounds(arg[0],atom->nbondtypes,ilo,ihi); + + double Umin = force->numeric(arg[1]); // energy at minimum + double r0_one = force->numeric(arg[2]); // position of minimum + double r1_one = force->numeric(arg[3]); // position where energy = 0 + + int count = 0; + for (int i = ilo; i <= ihi; i++) { + k[i] = Umin/((r0_one-r1_one)*(r0_one-r1_one)); + r0[i] = r0_one; + r1[i] = r1_one; + setflag[i] = 1; + count++; + } + + if (count == 0) error->all("Incorrect args for bond coefficients"); +} + +/* ---------------------------------------------------------------------- + return an equilbrium bond length +------------------------------------------------------------------------- */ + +double BondHarmonicShift::equilibrium_distance(int i) +{ + return r0[i]; +} + +/* ---------------------------------------------------------------------- + proc 0 writes out coeffs to restart file +------------------------------------------------------------------------- */ + +void BondHarmonicShift::write_restart(FILE *fp) +{ + fwrite(&k[1],sizeof(double),atom->nbondtypes,fp); + fwrite(&r0[1],sizeof(double),atom->nbondtypes,fp); + fwrite(&r1[1],sizeof(double),atom->nbondtypes,fp); +} + +/* ---------------------------------------------------------------------- + proc 0 reads coeffs from restart file, bcasts them +------------------------------------------------------------------------- */ + +void BondHarmonicShift::read_restart(FILE *fp) +{ + allocate(); + + if (comm->me == 0) { + fread(&k[1],sizeof(double),atom->nbondtypes,fp); + fread(&r0[1],sizeof(double),atom->nbondtypes,fp); + fread(&r1[1],sizeof(double),atom->nbondtypes,fp); + } + MPI_Bcast(&k[1],atom->nbondtypes,MPI_DOUBLE,0,world); + MPI_Bcast(&r0[1],atom->nbondtypes,MPI_DOUBLE,0,world); + MPI_Bcast(&r1[1],atom->nbondtypes,MPI_DOUBLE,0,world); + + for (int i = 1; i <= atom->nbondtypes; i++) setflag[i] = 1; +} + +/* ---------------------------------------------------------------------- */ + +double BondHarmonicShift::single(int type, double rsq, int i, int j) +{ + double r = sqrt(rsq); + double dr = r - r0[type]; + double dr2=r0[type]-r1[type]; + + return k[type]*(dr*dr - dr2*dr2); +} diff --git a/src/USER-MISC/bond_harmonic_shift.h b/src/USER-MISC/bond_harmonic_shift.h new file mode 100644 index 0000000000..3f5eb7ae50 --- /dev/null +++ b/src/USER-MISC/bond_harmonic_shift.h @@ -0,0 +1,48 @@ +/* ---------------------------------------------------------------------- + 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 BOND_CLASS + +BondStyle(harmonicshift,BondHarmonicShift) + +#else + +#ifndef LMP_BOND_HARMONICSHIFT_H +#define LMP_BOND_HARMONICSHIFT_H + +#include "stdio.h" +#include "bond.h" + +namespace LAMMPS_NS { + +class BondHarmonicShift : public Bond { + public: + BondHarmonicShift(class LAMMPS *); + ~BondHarmonicShift(); + void compute(int, int); + void coeff(int, char **); + double equilibrium_distance(int); + void write_restart(FILE *); + void read_restart(FILE *); + double single(int, double, int, int); + + private: + double *k,*r0,*r1; + + void allocate(); +}; + +} + +#endif +#endif diff --git a/src/USER-MISC/bond_harmonic_shift_cut.cpp b/src/USER-MISC/bond_harmonic_shift_cut.cpp new file mode 100644 index 0000000000..68f622488f --- /dev/null +++ b/src/USER-MISC/bond_harmonic_shift_cut.cpp @@ -0,0 +1,202 @@ +/* ---------------------------------------------------------------------- + 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: Carsten Svaneborg, science@zqex.dk +------------------------------------------------------------------------- */ + +#include "math.h" +#include "stdlib.h" +#include "bond_harmonic_shift_cut.h" +#include "atom.h" +#include "neighbor.h" +#include "domain.h" +#include "comm.h" +#include "force.h" +#include "memory.h" +#include "error.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +BondHarmonicShiftCut::BondHarmonicShiftCut(LAMMPS *lmp) : Bond(lmp) {} + +/* ---------------------------------------------------------------------- */ + +BondHarmonicShiftCut::~BondHarmonicShiftCut() +{ + if (allocated) { + memory->destroy(setflag); + memory->destroy(k); + memory->destroy(r0); + memory->destroy(r1); + } +} + +/* ---------------------------------------------------------------------- */ + +void BondHarmonicShiftCut::compute(int eflag, int vflag) +{ + int i1,i2,n,type; + double delx,dely,delz,ebond,fbond; + double rsq,r,dr,rk; + + ebond = 0.0; + if (eflag || vflag) ev_setup(eflag,vflag); + else evflag = 0; + + double **x = atom->x; + double **f = atom->f; + int **bondlist = neighbor->bondlist; + int nbondlist = neighbor->nbondlist; + int nlocal = atom->nlocal; + int newton_bond = force->newton_bond; + + for (n = 0; n < nbondlist; n++) { + i1 = bondlist[n][0]; + i2 = bondlist[n][1]; + type = bondlist[n][2]; + + delx = x[i1][0] - x[i2][0]; + dely = x[i1][1] - x[i2][1]; + delz = x[i1][2] - x[i2][2]; + domain->minimum_image(delx,dely,delz); + + rsq = delx*delx + dely*dely + delz*delz; + r = sqrt(rsq); + + if (r>r1[type]) continue; + + dr = r - r0[type]; + rk = k[type] * dr; + + // force & energy + + if (r > 0.0) fbond = -2.0*rk/r; + else fbond = 0.0; + + if (eflag) ebond = k[type]*(dr*dr -(r0[type]-r1[type])*(r0[type]-r1[type]) ); + + // apply force to each of 2 atoms + + if (newton_bond || i1 < nlocal) { + f[i1][0] += delx*fbond; + f[i1][1] += dely*fbond; + f[i1][2] += delz*fbond; + } + + if (newton_bond || i2 < nlocal) { + f[i2][0] -= delx*fbond; + f[i2][1] -= dely*fbond; + f[i2][2] -= delz*fbond; + } + + if (evflag) ev_tally(i1,i2,nlocal,newton_bond,ebond,fbond,delx,dely,delz); + } +} + +/* ---------------------------------------------------------------------- */ + +void BondHarmonicShiftCut::allocate() +{ + allocated = 1; + int n = atom->nbondtypes; + + memory->create(k , n+1,"bond:k"); + memory->create(r0, n+1,"bond:r0"); + memory->create(r1, n+1,"bond:r1"); + memory->create(setflag,n+1,"bond:setflag"); + for (int i = 1; i <= n; i++) setflag[i] = 0; +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more types +------------------------------------------------------------------------- */ + +void BondHarmonicShiftCut::coeff(int narg, char **arg) +{ + if (narg != 4) error->all("Incorrect args for bond coefficients"); + if (!allocated) allocate(); + + int ilo,ihi; + force->bounds(arg[0],atom->nbondtypes,ilo,ihi); + + double Umin = force->numeric(arg[1]); // energy at minimum + double r0_one = force->numeric(arg[2]); // position of minimum + double r1_one = force->numeric(arg[3]); // position where energy = 0 = cutoff + + int count = 0; + for (int i = ilo; i <= ihi; i++) { + k[i] = Umin/((r0_one-r1_one)*(r0_one-r1_one)); + r0[i] = r0_one; + r1[i] = r1_one; + setflag[i] = 1; + count++; + } + + if (count == 0) error->all("Incorrect args for bond coefficients"); +} + +/* ---------------------------------------------------------------------- + return an equilbrium bond length +------------------------------------------------------------------------- */ + +double BondHarmonicShiftCut::equilibrium_distance(int i) +{ + return r0[i]; +} + +/* ---------------------------------------------------------------------- + proc 0 writes out coeffs to restart file +------------------------------------------------------------------------- */ + +void BondHarmonicShiftCut::write_restart(FILE *fp) +{ + fwrite(&k[1],sizeof(double),atom->nbondtypes,fp); + fwrite(&r0[1],sizeof(double),atom->nbondtypes,fp); + fwrite(&r1[1],sizeof(double),atom->nbondtypes,fp); +} + +/* ---------------------------------------------------------------------- + proc 0 reads coeffs from restart file, bcasts them +------------------------------------------------------------------------- */ + +void BondHarmonicShiftCut::read_restart(FILE *fp) +{ + allocate(); + + if (comm->me == 0) { + fread(&k[1],sizeof(double),atom->nbondtypes,fp); + fread(&r0[1],sizeof(double),atom->nbondtypes,fp); + fread(&r1[1],sizeof(double),atom->nbondtypes,fp); + } + MPI_Bcast(&k[1],atom->nbondtypes,MPI_DOUBLE,0,world); + MPI_Bcast(&r0[1],atom->nbondtypes,MPI_DOUBLE,0,world); + MPI_Bcast(&r1[1],atom->nbondtypes,MPI_DOUBLE,0,world); + + for (int i = 1; i <= atom->nbondtypes; i++) setflag[i] = 1; +} + +/* ---------------------------------------------------------------------- */ + +double BondHarmonicShiftCut::single(int type, double rsq, int i, int j) +{ + double r = sqrt(rsq); + + if (r>r1[type]) return 0; + + double dr = r - r0[type]; + double dr2=r0[type]-r1[type]; + return k[type]*(dr*dr - dr2*dr2); +} diff --git a/src/USER-MISC/bond_harmonic_shift_cut.h b/src/USER-MISC/bond_harmonic_shift_cut.h new file mode 100644 index 0000000000..37489a7006 --- /dev/null +++ b/src/USER-MISC/bond_harmonic_shift_cut.h @@ -0,0 +1,48 @@ +/* ---------------------------------------------------------------------- + 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 BOND_CLASS + +BondStyle(harmonicshiftcut,BondHarmonicShiftCut) + +#else + +#ifndef LMP_BOND_HARMONICSHIFTCUT_H +#define LMP_BOND_HARMONICSHIFTCUT_H + +#include "stdio.h" +#include "bond.h" + +namespace LAMMPS_NS { + +class BondHarmonicShiftCut : public Bond { + public: + BondHarmonicShiftCut(class LAMMPS *); + ~BondHarmonicShiftCut(); + void compute(int, int); + void coeff(int, char **); + double equilibrium_distance(int); + void write_restart(FILE *); + void read_restart(FILE *); + double single(int, double, int, int); + + private: + double *k,*r0,*r1; + + void allocate(); +}; + +} + +#endif +#endif diff --git a/src/USER-MISC/dihedral_cosineshiftexp.cpp b/src/USER-MISC/dihedral_cosineshiftexp.cpp new file mode 100644 index 0000000000..c3570d72d5 --- /dev/null +++ b/src/USER-MISC/dihedral_cosineshiftexp.cpp @@ -0,0 +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: Carsten Svaneborg, science@zqex.dk +------------------------------------------------------------------------- */ + +#include "lmptype.h" +#include "mpi.h" +#include "math.h" +#include "stdlib.h" +#include "dihedral_cosineshiftexp.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" + +using namespace LAMMPS_NS; + +#define TOLERANCE 0.05 +#define SMALL 0.001 + +/* ---------------------------------------------------------------------- */ + +DihedralCosShiftExp::DihedralCosShiftExp(LAMMPS *lmp) : Dihedral(lmp) {} + +/* ---------------------------------------------------------------------- */ + +DihedralCosShiftExp::~DihedralCosShiftExp() +{ + if (allocated) { + memory->destroy(setflag); + memory->destroy(umin); + memory->destroy(a); + memory->destroy(opt1); + memory->destroy(cost); + memory->destroy(sint); + memory->destroy(theta); + memory->destroy(doExpansion); + } +} + +/* ---------------------------------------------------------------------- */ + +void DihedralCosShiftExp::compute(int eflag, int vflag) +{ + int i1,i2,i3,i4,i,m,n,type; + double vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z,vb2xm,vb2ym,vb2zm; + double edihedral,f1[3],f2[3],f3[3],f4[3]; + double ax,ay,az,bx,by,bz,rasq,rbsq,rgsq,rg,rginv,ra2inv,rb2inv,rabinv; + double df,df1,ddf1,fg,hg,fga,hgb,gaa,gbb; + double dtfx,dtfy,dtfz,dtgx,dtgy,dtgz,dthx,dthy,dthz; + double c,s,p,sx2,sy2,sz2; + double cccpsss,cssmscc,exp2; + + edihedral = 0.0; + if (eflag || vflag) ev_setup(eflag,vflag); + else evflag = 0; + + double **x = atom->x; + double **f = atom->f; + int **dihedrallist = neighbor->dihedrallist; + int ndihedrallist = neighbor->ndihedrallist; + int nlocal = atom->nlocal; + int newton_bond = force->newton_bond; + + for (n = 0; n < ndihedrallist; n++) { + i1 = dihedrallist[n][0]; + i2 = dihedrallist[n][1]; + i3 = dihedrallist[n][2]; + i4 = dihedrallist[n][3]; + type = dihedrallist[n][4]; + + // 1st bond + + 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); + + // 2nd bond + + 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); + + vb2xm = -vb2x; + vb2ym = -vb2y; + vb2zm = -vb2z; + domain->minimum_image(vb2xm,vb2ym,vb2zm); + + // 3rd bond + + 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); + + // c,s calculation + + ax = vb1y*vb2zm - vb1z*vb2ym; + ay = vb1z*vb2xm - vb1x*vb2zm; + az = vb1x*vb2ym - vb1y*vb2xm; + bx = vb3y*vb2zm - vb3z*vb2ym; + by = vb3z*vb2xm - vb3x*vb2zm; + bz = vb3x*vb2ym - vb3y*vb2xm; + + rasq = ax*ax + ay*ay + az*az; + rbsq = bx*bx + by*by + bz*bz; + rgsq = vb2xm*vb2xm + vb2ym*vb2ym + vb2zm*vb2zm; + rg = sqrt(rgsq); + + rginv = ra2inv = rb2inv = 0.0; + if (rg > 0) rginv = 1.0/rg; + if (rasq > 0) ra2inv = 1.0/rasq; + if (rbsq > 0) rb2inv = 1.0/rbsq; + rabinv = sqrt(ra2inv*rb2inv); + + c = (ax*bx + ay*by + az*bz)*rabinv; + s = rg*rabinv*(ax*vb3x + ay*vb3y + az*vb3z); + + // error check + + if (c > 1.0 + TOLERANCE || c < (-1.0 - TOLERANCE)) { + int me; + MPI_Comm_rank(world,&me); + if (screen) { + char str[128]; + sprintf(str,"Dihedral 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(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]); + } + } + + if (c > 1.0) c = 1.0; + if (c < -1.0) c = -1.0; + + double aa=a[type]; + double uumin=umin[type]; + + cccpsss = c*cost[type]+s*sint[type]; + cssmscc = c*sint[type]-s*cost[type]; + + // eflag=1; + + if (doExpansion[type]) + { // |a|<0.001 so use expansions relative precision <1e-5 + if (eflag) edihedral = -0.125*(1+cccpsss)*(4+aa*(cccpsss-1))*uumin; + df=0.5*uumin*( cssmscc + 0.5*aa*cccpsss); + } + else + { + exp2=exp(0.5*aa*(1+cccpsss)); + if (eflag) edihedral = opt1[type]*(1-exp2); + df= 0.5*opt1[type]*aa* ( exp2*cssmscc ); + } + + fg = vb1x*vb2xm + vb1y*vb2ym + vb1z*vb2zm; + hg = vb3x*vb2xm + vb3y*vb2ym + vb3z*vb2zm; + fga = fg*ra2inv*rginv; + hgb = hg*rb2inv*rginv; + gaa = -ra2inv*rg; + gbb = rb2inv*rg; + + dtfx = gaa*ax; + dtfy = gaa*ay; + dtfz = gaa*az; + dtgx = fga*ax - hgb*bx; + dtgy = fga*ay - hgb*by; + dtgz = fga*az - hgb*bz; + dthx = gbb*bx; + dthy = gbb*by; + dthz = gbb*bz; + + sx2 = df*dtgx; + sy2 = df*dtgy; + sz2 = df*dtgz; + + f1[0] = df*dtfx; + f1[1] = df*dtfy; + f1[2] = df*dtfz; + + f2[0] = sx2 - f1[0]; + f2[1] = sy2 - f1[1]; + f2[2] = sz2 - f1[2]; + + f4[0] = df*dthx; + f4[1] = df*dthy; + f4[2] = df*dthz; + + f3[0] = -sx2 - f4[0]; + f3[1] = -sy2 - f4[1]; + f3[2] = -sz2 - f4[2]; + + // apply force to each of 4 atoms + + if (newton_bond || i1 < nlocal) { + f[i1][0] += f1[0]; + f[i1][1] += f1[1]; + f[i1][2] += f1[2]; + } + + if (newton_bond || i2 < nlocal) { + f[i2][0] += f2[0]; + f[i2][1] += f2[1]; + f[i2][2] += f2[2]; + } + + if (newton_bond || i3 < nlocal) { + f[i3][0] += f3[0]; + f[i3][1] += f3[1]; + f[i3][2] += f3[2]; + } + + if (newton_bond || i4 < nlocal) { + f[i4][0] += f4[0]; + f[i4][1] += f4[1]; + f[i4][2] += f4[2]; + } + + if (evflag) + ev_tally(i1,i2,i3,i4,nlocal,newton_bond,edihedral,f1,f3,f4, + vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z); + } +} + +/* ---------------------------------------------------------------------- */ + +void DihedralCosShiftExp::allocate() +{ + allocated = 1; + int n = atom->ndihedraltypes; + + memory->create(doExpansion, n+1, "dihedral:doExpansion"); + memory->create(umin,n+1,"dihedral:umin"); + memory->create(a,n+1,"dihedral:a"); + memory->create(sint,n+1,"dihedral:sind"); + memory->create(cost,n+1,"dihedral:cosd"); + memory->create(opt1,n+1,"dihedral:opt1"); + memory->create(theta,n+1,"dihedral:opt1"); + memory->create(setflag, n+1,"dihedral:setflag"); + for (int i = 1; i <= n; i++) setflag[i] = 0; + +} + +/* ---------------------------------------------------------------------- + set coeffs for one type +------------------------------------------------------------------------- */ + +void DihedralCosShiftExp::coeff(int narg, char **arg) +{ + if (narg != 4) error->all("Incorrect args for dihedral coefficients"); + if (!allocated) allocate(); + + int ilo,ihi; + force->bounds(arg[0],atom->ndihedraltypes,ilo,ihi); + + double umin_ = force->numeric(arg[1]); + double theta0_ = force->numeric(arg[2]); + double a_ = force->numeric(arg[3]); + + int count = 0; + for (int i = ilo; i <= ihi; i++) { + doExpansion[i]=(fabs(a_)<0.001); + umin[i] = umin_; + a[i] = a_; + cost[i] = cos(theta0_*3.14159265/180); + sint[i] = sin(theta0_*3.14159265/180); + theta[i] = theta0_*3.14159265/180; + + if (!doExpansion[i]) opt1[i]=umin_/(exp(a_)-1); + + setflag[i] = 1; + count++; + } + + if (count == 0) error->all("Incorrect args for dihedral coefficients"); +} + +/* ---------------------------------------------------------------------- + proc 0 writes out coeffs to restart file +------------------------------------------------------------------------- */ + +void DihedralCosShiftExp::write_restart(FILE *fp) +{ + fwrite(&umin[1],sizeof(double),atom->ndihedraltypes,fp); + fwrite(&a[1],sizeof(double),atom->ndihedraltypes,fp); + fwrite(&cost[1],sizeof(double),atom->ndihedraltypes,fp); + fwrite(&sint[1],sizeof(double),atom->ndihedraltypes,fp); + fwrite(&theta[1],sizeof(double),atom->ndihedraltypes,fp); +} + +/* ---------------------------------------------------------------------- + proc 0 reads coeffs from restart file, bcasts them +------------------------------------------------------------------------- */ + +void DihedralCosShiftExp::read_restart(FILE *fp) +{ + allocate(); + + if (comm->me == 0) { + fread(&umin[1],sizeof(double),atom->ndihedraltypes,fp); + fread(&a[1],sizeof(double),atom->ndihedraltypes,fp); + fread(&cost[1],sizeof(double),atom->ndihedraltypes,fp); + fread(&sint[1],sizeof(double),atom->ndihedraltypes,fp); + fread(&theta[1],sizeof(double),atom->ndihedraltypes,fp); + } + MPI_Bcast(&umin[1],atom->ndihedraltypes,MPI_DOUBLE,0,world); + MPI_Bcast(&a[1],atom->ndihedraltypes,MPI_DOUBLE,0,world); + MPI_Bcast(&cost[1],atom->ndihedraltypes,MPI_DOUBLE,0,world); + MPI_Bcast(&sint[1],atom->ndihedraltypes,MPI_DOUBLE,0,world); + MPI_Bcast(&theta[1],atom->ndihedraltypes,MPI_DOUBLE,0,world); + + for (int i = 1; i <= atom->ndihedraltypes; i++) { + setflag[i] = 1; + doExpansion[i]=(fabs(a[i])<0.01); + if (!doExpansion[i]) opt1[i]=umin[i]/(exp(a[i])-1); + } +} diff --git a/src/USER-MISC/dihedral_cosineshiftexp.h b/src/USER-MISC/dihedral_cosineshiftexp.h new file mode 100644 index 0000000000..4cd85e3f9c --- /dev/null +++ b/src/USER-MISC/dihedral_cosineshiftexp.h @@ -0,0 +1,71 @@ +/* ---------------------------------------------------------------------- + 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. +------------------------------------------------------------------------- */ + +/* + The torsion angle is defined such that a straight bond has costheta=180. + + U(theta,theta0,umin,a) = -Umin[Exp(-a U)-1]/[[Exp(a)-1]] + with U = (-1-cos[theta-theta0])/2 = -Cos((theta-theta0)/2)^2 + + potential has minimum at theta=theta0 where U() = -Umin + potential has maximum at theta=theta0+180 where U() = 0 + + The spring constant around the minimum is controlled by a and + is given by k = a exp(a) Umin/[ 2(Exp[a]-1) ] for a=0 + the spring constant is k=Umin/2 and the potential reduces to + the cosineshifted potential. + + The potential is implemented such that for a<0.001 a series + expansion to linear order is used instead of the expression + above. This ensures a precision of about 1e-5 or better for + energies and forces, and ensures the potential is well + behaved for a=0 +*/ + +#ifdef DIHEDRAL_CLASS + +DihedralStyle(cosineshiftexp,DihedralCosShiftExp) + +#else + +#ifndef LMP_DIHEDRAL_COSINESHIFTEDEXP_H +#define LMP_DIHEDRAL_COSINESHIFTEDEXP_H + +#include "stdio.h" +#include "dihedral.h" + +namespace LAMMPS_NS { + +class DihedralCosShiftExp : public Dihedral { + public: + DihedralCosShiftExp(class LAMMPS *); + ~DihedralCosShiftExp(); + void compute(int, int); + void coeff(int, char **); + void write_restart(FILE *); + void read_restart(FILE *); + + private: + bool *doExpansion; + double *umin,*a,*opt1; + double *sint; + double *cost; + double *theta; + + void allocate(); +}; + +} + +#endif +#endif