mirror of https://github.com/lammps/lammps.git
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@637 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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doc/fix.html
14
doc/fix.html
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@ -68,7 +68,8 @@ made to the old fix via the <A HREF = "fix_modify.html">fix_modify</A> command.
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<LI><A HREF = "fix_ave_spatial.html">fix ave/spatial</A> - output per-atom quantities by layer
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<LI><A HREF = "fix_ave_time.html">fix ave/time</A> - output time-averaged compute quantities
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<LI><A HREF = "fix_com.html">fix com</A> - compute a center-of-mass
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<LI><A HREF = "fix_desosit.html">fix deposit</A> - add new atoms above a surface
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<LI><A HREF = "fix_deform.html">fix deform</A> - change the simulation box size/shape
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<LI><A HREF = "fix_deposit.html">fix deposit</A> - add new atoms above a surface
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<LI><A HREF = "fix_drag.html">fix drag</A> - drag atoms towards a defined coordinate
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<LI><A HREF = "fix_efield.html">fix efield</A> - impose electric field on system
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<LI><A HREF = "fix_enforce2d.html">fix enforce2d</A> - zero out z-dimension velocity and force
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@ -83,10 +84,15 @@ made to the old fix via the <A HREF = "fix_modify.html">fix_modify</A> command.
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<LI><A HREF = "fix_momentum.html">fix momentum</A> - zero the linear and/or angular momentum of a group of atoms
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<LI><A HREF = "fix_nph.html">fix nph</A> - constant NPH time integration via Nose/Hoover
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<LI><A HREF = "fix_npt.html">fix npt</A> - constant NPT time integration via Nose/Hoover
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<LI><A HREF = "fix_npt_asphere.html">fix npt/asphere</A> - NPT for aspherical particles
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<LI><A HREF = "fix_nve.html">fix nve</A> - constant NVE time integration
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<LI><A HREF = "fix_nve_gran.html">fix nve/gran</A> - NVE time integration for granular systems
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<LI><A HREF = "fix_nve_noforce.html">fix nve/noforce</A> - NVE integration without forces (v only)
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<LI><A HREF = "fix_nve_asphere.html">fix nve/asphere</A> - NVT for aspherical particles
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<LI><A HREF = "fix_nve_dipole.html">fix nve/dipole</A> - NVE for point dipolar particles
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<LI><A HREF = "fix_nve_gran.html">fix nve/gran</A> - NVE for granular particles
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<LI><A HREF = "fix_nve_noforce.html">fix nve/noforce</A> - NVE without forces (v only)
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<LI><A HREF = "fix_nvt.html">fix nvt</A> - constant NVT time integration via Nose/Hoover
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<LI><A HREF = "fix_nvt_asphere.html">fix nvt/asphere</A> - NVT for aspherical particles
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<LI><A HREF = "fix_nvt_sllod.html">fix nvt/sllod</A> - NVT for NEMD with SLLOD equations
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<LI><A HREF = "fix_orient_fcc.html">fix orient/fcc</A> - add grain boundary migration force
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<LI><A HREF = "fix_planeforce.html">fix planeforce</A> - constrain atoms to move in a plane
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<LI><A HREF = "fix_poems.html">fix poems</A> - constrain clusters of atoms to move as coupled rigid bodies
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@ -104,8 +110,8 @@ made to the old fix via the <A HREF = "fix_modify.html">fix_modify</A> command.
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<LI><A HREF = "fix_tmd.html">fix tmd</A> - guide a group of atoms to a new configuration
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<LI><A HREF = "fix_viscous.html">fix viscous</A> - viscous damping for granular simulations
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<LI><A HREF = "fix_wall_gran.html">fix wall/gran</A> - frictional wall(s) for granular simulations
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<LI><A HREF = "fix_wall_lj93.html">fix wall/lj93</A> - Lennard-Jones 9-3 wall
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<LI><A HREF = "fix_wall_lj126.html">fix wall/lj126</A> - Lennard-Jones 12-6 wall
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<LI><A HREF = "fix_wall_lj93.html">fix wall/lj93</A> - Lennard-Jones 9-3 wall
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<LI><A HREF = "fix_wall_reflect.html">fix wall/reflect</A> - reflecting wall(s)
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<LI><A HREF = "fix_wiggle.html">fix wiggle</A> - oscillate walls and frozen atoms
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</UL>
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15
doc/fix.txt
15
doc/fix.txt
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@ -65,7 +65,8 @@ Here is an alphabetic list of fix styles defined in LAMMPS:
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"fix ave/spatial"_fix_ave_spatial.html - output per-atom quantities by layer
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"fix ave/time"_fix_ave_time.html - output time-averaged compute quantities
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"fix com"_fix_com.html - compute a center-of-mass
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"fix deposit"_fix_desosit.html - add new atoms above a surface
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"fix deform"_fix_deform.html - change the simulation box size/shape
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"fix deposit"_fix_deposit.html - add new atoms above a surface
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"fix drag"_fix_drag.html - drag atoms towards a defined coordinate
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"fix efield"_fix_efield.html - impose electric field on system
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"fix enforce2d"_fix_enforce2d.html - zero out z-dimension velocity and force
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@ -82,11 +83,15 @@ Here is an alphabetic list of fix styles defined in LAMMPS:
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of a group of atoms
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"fix nph"_fix_nph.html - constant NPH time integration via Nose/Hoover
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"fix npt"_fix_npt.html - constant NPT time integration via Nose/Hoover
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"fix npt/asphere"_fix_npt_asphere.html - NPT for aspherical particles
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"fix nve"_fix_nve.html - constant NVE time integration
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"fix nve/gran"_fix_nve_gran.html - NVE time integration for \
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granular systems
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"fix nve/noforce"_fix_nve_noforce.html - NVE integration without forces (v only)
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"fix nve/asphere"_fix_nve_asphere.html - NVT for aspherical particles
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"fix nve/dipole"_fix_nve_dipole.html - NVE for point dipolar particles
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"fix nve/gran"_fix_nve_gran.html - NVE for granular particles
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"fix nve/noforce"_fix_nve_noforce.html - NVE without forces (v only)
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"fix nvt"_fix_nvt.html - constant NVT time integration via Nose/Hoover
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"fix nvt/asphere"_fix_nvt_asphere.html - NVT for aspherical particles
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"fix nvt/sllod"_fix_nvt_sllod.html - NVT for NEMD with SLLOD equations
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"fix orient/fcc"_fix_orient_fcc.html - add grain boundary migration force
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"fix planeforce"_fix_planeforce.html - constrain atoms to move in a plane
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"fix poems"_fix_poems.html - constrain clusters of atoms to move \
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@ -110,8 +115,8 @@ Here is an alphabetic list of fix styles defined in LAMMPS:
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"fix viscous"_fix_viscous.html - viscous damping for granular simulations
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"fix wall/gran"_fix_wall_gran.html - frictional wall(s) for \
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granular simulations
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"fix wall/lj93"_fix_wall_lj93.html - Lennard-Jones 9-3 wall
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"fix wall/lj126"_fix_wall_lj126.html - Lennard-Jones 12-6 wall
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"fix wall/lj93"_fix_wall_lj93.html - Lennard-Jones 9-3 wall
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"fix wall/reflect"_fix_wall_reflect.html - reflecting wall(s)
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"fix wiggle"_fix_wiggle.html - oscillate walls and frozen atoms :ul
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@ -169,7 +169,6 @@ void FixNPTASphere::final_integrate()
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v[i][0] = (v[i][0] + dtfm*f[i][0]) * factor[0];
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v[i][1] = (v[i][1] + dtfm*f[i][1]) * factor[1];
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v[i][2] = (v[i][2] + dtfm*f[i][2]) * factor[2];
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angmom[i][0] = (angmom[i][0] + dtf * torque[i][0]) * ang_factor;
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angmom[i][1] = (angmom[i][1] + dtf * torque[i][1]) * ang_factor;
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angmom[i][2] = (angmom[i][2] + dtf * torque[i][2]) * ang_factor;
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@ -76,7 +76,7 @@ PairGayBerne::~PairGayBerne()
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void PairGayBerne::compute(int eflag, int vflag)
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{
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int i,j,k,m,numneigh,itype,jtype;
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double one_eng,rsq,r2inv,r6inv,forcelj,phi;
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double one_eng,rsq,r2inv,r6inv,forcelj;
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double fforce[3],ttor[3],rtor[3],r12[3];
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double a1[3][3],b1[3][3],g1[3][3],a2[3][3],b2[3][3],g2[3][3],temp[3][3];
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int *neighs;
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@ -137,12 +137,14 @@ void PairGayBerne::compute(int eflag, int vflag)
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r6inv = r2inv*r2inv*r2inv;
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forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
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forcelj *= -r2inv;
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if (eflag) phi = r6inv*(r6inv*lj3[itype][jtype]-lj4[itype][jtype]) -
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if (eflag) one_eng =
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r6inv*(r6inv*lj3[itype][jtype]-lj4[itype][jtype]) -
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offset[itype][jtype];
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fforce[0] = r12[0]*forcelj;
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fforce[1] = r12[1]*forcelj;
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fforce[2] = r12[2]*forcelj;
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ttor[0] = ttor[1] = ttor[2] = 0.0;
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rtor[0] = rtor[1] = rtor[2] = 0.0;
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break;
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default:
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@ -399,7 +401,8 @@ void PairGayBerne::write_restart(FILE *fp)
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int i,j;
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for (i = 1; i <= atom->ntypes; i++) {
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fwrite(&well[i][0],sizeof(double),3,fp);
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fwrite(&setwell[i],sizeof(int),1,fp);
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if (setwell[i]) fwrite(&well[i][0],sizeof(double),3,fp);
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for (j = i; j <= atom->ntypes; j++) {
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fwrite(&setflag[i][j],sizeof(int),1,fp);
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if (setflag[i][j]) {
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@ -418,14 +421,17 @@ void PairGayBerne::write_restart(FILE *fp)
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void PairGayBerne::read_restart(FILE *fp)
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{
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read_restart_settings(fp);
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allocate();
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int i,j;
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int me = comm->me;
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for (i = 1; i <= atom->ntypes; i++) {
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if (me == 0) fread(&well[i][0],sizeof(double),3,fp);
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MPI_Bcast(&well[i][0],3,MPI_DOUBLE,0,world);
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if (me == 0) fread(&setwell[i],sizeof(int),1,fp);
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MPI_Bcast(&setwell[i],1,MPI_INT,0,world);
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if (setwell[i]) {
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if (me == 0) fread(&well[i][0],sizeof(double),3,fp);
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MPI_Bcast(&well[i][0],3,MPI_DOUBLE,0,world);
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}
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for (j = i; j <= atom->ntypes; j++) {
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if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
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MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
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@ -122,6 +122,8 @@ void Pair::init()
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if (tail_flag && domain->nonperiodic && comm->me == 0)
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error->warning("Using pair tail corrections with nonperiodic system");
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init_style();
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if (!allocated) error->all("All pair coeffs are not set");
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for (i = 1; i <= atom->ntypes; i++)
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@ -144,8 +146,6 @@ void Pair::init()
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}
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}
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}
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init_style();
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}
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/* ----------------------------------------------------------------------
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