git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8226 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
@ -5,7 +5,7 @@
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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@ -68,62 +68,62 @@ FixPressBerendsen::FixPressBerendsen(LAMMPS *lmp, int narg, char **arg) :
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while (iarg < narg) {
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if (strcmp(arg[iarg],"iso") == 0) {
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if (iarg+4 > narg)
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error->all(FLERR,"Illegal fix press/berendsen command");
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if (iarg+4 > narg)
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error->all(FLERR,"Illegal fix press/berendsen command");
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pcouple = XYZ;
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p_start[0] = p_start[1] = p_start[2] = atof(arg[iarg+1]);
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p_stop[0] = p_stop[1] = p_stop[2] = atof(arg[iarg+2]);
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p_period[0] = p_period[1] = p_period[2] = atof(arg[iarg+3]);
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p_flag[0] = p_flag[1] = p_flag[2] = 1;
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if (dimension == 2) {
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p_start[2] = p_stop[2] = p_period[2] = 0.0;
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p_flag[2] = 0;
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p_start[2] = p_stop[2] = p_period[2] = 0.0;
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p_flag[2] = 0;
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}
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iarg += 4;
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iarg += 4;
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} else if (strcmp(arg[iarg],"aniso") == 0) {
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if (iarg+4 > narg)
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error->all(FLERR,"Illegal fix press/berendsen command");
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if (iarg+4 > narg)
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error->all(FLERR,"Illegal fix press/berendsen command");
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pcouple = NONE;
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p_start[0] = p_start[1] = p_start[2] = atof(arg[iarg+1]);
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p_stop[0] = p_stop[1] = p_stop[2] = atof(arg[iarg+2]);
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p_period[0] = p_period[1] = p_period[2] = atof(arg[iarg+3]);
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p_flag[0] = p_flag[1] = p_flag[2] = 1;
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if (dimension == 2) {
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p_start[2] = p_stop[2] = p_period[2] = 0.0;
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p_flag[2] = 0;
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p_start[2] = p_stop[2] = p_period[2] = 0.0;
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p_flag[2] = 0;
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}
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iarg += 4;
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} else if (strcmp(arg[iarg],"x") == 0) {
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if (iarg+4 > narg)
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error->all(FLERR,"Illegal fix press/berendsen command");
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error->all(FLERR,"Illegal fix press/berendsen command");
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p_start[0] = atof(arg[iarg+1]);
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p_stop[0] = atof(arg[iarg+2]);
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p_period[0] = atof(arg[iarg+3]);
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p_flag[0] = 1;
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iarg += 4;
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iarg += 4;
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} else if (strcmp(arg[iarg],"y") == 0) {
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if (iarg+4 > narg)
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error->all(FLERR,"Illegal fix press/berendsen command");
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error->all(FLERR,"Illegal fix press/berendsen command");
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p_start[1] = atof(arg[iarg+1]);
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p_stop[1] = atof(arg[iarg+2]);
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p_period[1] = atof(arg[iarg+3]);
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p_flag[1] = 1;
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iarg += 4;
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iarg += 4;
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} else if (strcmp(arg[iarg],"z") == 0) {
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if (iarg+4 > narg)
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error->all(FLERR,"Illegal fix press/berendsen command");
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if (iarg+4 > narg)
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error->all(FLERR,"Illegal fix press/berendsen command");
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p_start[2] = atof(arg[iarg+1]);
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p_stop[2] = atof(arg[iarg+2]);
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p_period[2] = atof(arg[iarg+3]);
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p_flag[2] = 1;
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iarg += 4;
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iarg += 4;
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if (dimension == 2)
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error->all(FLERR,"Invalid fix press/berendsen for a 2d simulation");
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error->all(FLERR,"Invalid fix press/berendsen for a 2d simulation");
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} else if (strcmp(arg[iarg],"couple") == 0) {
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if (iarg+2 > narg)
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error->all(FLERR,"Illegal fix press/berendsen command");
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if (iarg+2 > narg)
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error->all(FLERR,"Illegal fix press/berendsen command");
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if (strcmp(arg[iarg+1],"xyz") == 0) pcouple = XYZ;
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else if (strcmp(arg[iarg+1],"xy") == 0) pcouple = XY;
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else if (strcmp(arg[iarg+1],"yz") == 0) pcouple = YZ;
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@ -133,15 +133,15 @@ FixPressBerendsen::FixPressBerendsen(LAMMPS *lmp, int narg, char **arg) :
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iarg += 2;
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} else if (strcmp(arg[iarg],"modulus") == 0) {
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if (iarg+2 > narg)
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error->all(FLERR,"Illegal fix press/berendsen command");
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if (iarg+2 > narg)
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error->all(FLERR,"Illegal fix press/berendsen command");
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bulkmodulus = atof(arg[iarg+1]);
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if (bulkmodulus <= 0.0)
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error->all(FLERR,"Illegal fix press/berendsen command");
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if (bulkmodulus <= 0.0)
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error->all(FLERR,"Illegal fix press/berendsen command");
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iarg += 2;
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} else if (strcmp(arg[iarg],"dilate") == 0) {
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if (iarg+2 > narg)
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error->all(FLERR,"Illegal fix press/berendsen command");
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if (iarg+2 > narg)
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error->all(FLERR,"Illegal fix press/berendsen command");
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if (strcmp(arg[iarg+1],"all") == 0) allremap = 1;
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else if (strcmp(arg[iarg+1],"partial") == 0) allremap = 0;
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else error->all(FLERR,"Illegal fix press/berendsen command");
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@ -171,38 +171,38 @@ FixPressBerendsen::FixPressBerendsen(LAMMPS *lmp, int narg, char **arg) :
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if (p_flag[0] && domain->xperiodic == 0)
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error->all(FLERR,
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"Cannot use fix press/berendsen on a non-periodic dimension");
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"Cannot use fix press/berendsen on a non-periodic dimension");
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if (p_flag[1] && domain->yperiodic == 0)
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error->all(FLERR,
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"Cannot use fix press/berendsen on a non-periodic dimension");
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"Cannot use fix press/berendsen on a non-periodic dimension");
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if (p_flag[2] && domain->zperiodic == 0)
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error->all(FLERR,
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"Cannot use fix press/berendsen on a non-periodic dimension");
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"Cannot use fix press/berendsen on a non-periodic dimension");
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if (pcouple == XYZ && dimension == 3 &&
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(p_start[0] != p_start[1] || p_start[0] != p_start[2] ||
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p_stop[0] != p_stop[1] || p_stop[0] != p_stop[2] ||
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(p_start[0] != p_start[1] || p_start[0] != p_start[2] ||
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p_stop[0] != p_stop[1] || p_stop[0] != p_stop[2] ||
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p_period[0] != p_period[1] || p_period[0] != p_period[2]))
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error->all(FLERR,"Invalid fix press/berendsen pressure settings");
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if (pcouple == XYZ && dimension == 2 &&
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(p_start[0] != p_start[1] || p_stop[0] != p_stop[1] ||
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(p_start[0] != p_start[1] || p_stop[0] != p_stop[1] ||
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p_period[0] != p_period[1]))
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error->all(FLERR,"Invalid fix press/berendsen pressure settings");
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if (pcouple == XY &&
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(p_start[0] != p_start[1] || p_stop[0] != p_stop[1] ||
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if (pcouple == XY &&
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(p_start[0] != p_start[1] || p_stop[0] != p_stop[1] ||
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p_period[0] != p_period[1]))
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error->all(FLERR,"Invalid fix press/berendsen pressure settings");
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if (pcouple == YZ &&
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if (pcouple == YZ &&
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(p_start[1] != p_start[2] || p_stop[1] != p_stop[2] ||
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p_period[1] != p_period[2]))
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error->all(FLERR,"Invalid fix press/berendsen pressure settings");
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if (pcouple == XZ &&
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if (pcouple == XZ &&
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(p_start[0] != p_start[2] || p_stop[0] != p_stop[2] ||
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p_period[0] != p_period[2]))
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error->all(FLERR,"Invalid fix press/berendsen pressure settings");
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if ((p_flag[0] && p_period[0] <= 0.0) ||
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(p_flag[1] && p_period[1] <= 0.0) ||
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if ((p_flag[0] && p_period[0] <= 0.0) ||
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(p_flag[1] && p_period[1] <= 0.0) ||
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(p_flag[2] && p_period[2] <= 0.0))
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error->all(FLERR,"Fix press/berendsen damping parameters must be > 0.0");
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@ -279,7 +279,7 @@ int FixPressBerendsen::setmask()
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void FixPressBerendsen::init()
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{
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if (domain->triclinic)
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if (domain->triclinic)
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error->all(FLERR,"Cannot use fix press/berendsen with triclinic box");
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// insure no conflict with fix deform
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@ -287,16 +287,16 @@ void FixPressBerendsen::init()
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for (int i = 0; i < modify->nfix; i++)
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if (strcmp(modify->fix[i]->style,"deform") == 0) {
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int *dimflag = ((FixDeform *) modify->fix[i])->dimflag;
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if ((p_flag[0] && dimflag[0]) || (p_flag[1] && dimflag[1]) ||
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(p_flag[2] && dimflag[2]))
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error->all(FLERR,"Cannot use fix press/berendsen and "
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"fix deform on same component of stress tensor");
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if ((p_flag[0] && dimflag[0]) || (p_flag[1] && dimflag[1]) ||
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(p_flag[2] && dimflag[2]))
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error->all(FLERR,"Cannot use fix press/berendsen and "
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"fix deform on same component of stress tensor");
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}
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// set temperature and pressure ptrs
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int icompute = modify->find_compute(id_temp);
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if (icompute < 0)
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if (icompute < 0)
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error->all(FLERR,"Temperature ID for fix press/berendsen does not exist");
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temperature = modify->compute[icompute];
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@ -331,7 +331,7 @@ void FixPressBerendsen::init()
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}
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/* ----------------------------------------------------------------------
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compute T,P before integrator starts
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compute T,P before integrator starts
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------------------------------------------------------------------------- */
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void FixPressBerendsen::setup(int vflag)
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@ -362,9 +362,9 @@ void FixPressBerendsen::end_of_step()
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for (int i = 0; i < 3; i++) {
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if (p_flag[i]) {
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p_target[i] = p_start[i] + delta * (p_stop[i]-p_start[i]);
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dilation[i] =
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pow(1.0 - update->dt/p_period[i] *
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(p_target[i]-p_current[i])/bulkmodulus,1.0/3.0);
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dilation[i] =
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pow(1.0 - update->dt/p_period[i] *
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(p_target[i]-p_current[i])/bulkmodulus,1.0/3.0);
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}
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}
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@ -430,7 +430,7 @@ void FixPressBerendsen::remap()
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else {
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for (i = 0; i < nlocal; i++)
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if (mask[i] & groupbit)
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domain->x2lamda(x[i],x[i]);
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domain->x2lamda(x[i],x[i]);
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}
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if (nrigid)
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@ -458,7 +458,7 @@ void FixPressBerendsen::remap()
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else {
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for (i = 0; i < nlocal; i++)
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if (mask[i] & groupbit)
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domain->lamda2x(x[i],x[i]);
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domain->lamda2x(x[i],x[i]);
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}
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if (nrigid)
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@ -491,9 +491,9 @@ int FixPressBerendsen::modify_param(int narg, char **arg)
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error->warning(FLERR,"Temperature for NPT is not for group all");
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// reset id_temp of pressure to new temperature ID
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icompute = modify->find_compute(id_press);
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if (icompute < 0)
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if (icompute < 0)
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error->all(FLERR,"Pressure ID for fix press/berendsen does not exist");
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modify->compute[icompute]->reset_extra_compute_fix(id_temp);
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