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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7611 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2012-01-30 22:53:59 +00:00
parent 07973688a3
commit 12659b418f
5 changed files with 1161 additions and 3 deletions
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99
src/fix_deform.cpp
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@ -29,12 +29,14 @@
#include "modify.h"
#include "math_const.h"
#include "kspace.h"
#include "input.h"
#include "variable.h"
#include "error.h"
using namespace LAMMPS_NS;
using namespace MathConst;
enum{NONE,FINAL,DELTA,SCALE,VEL,ERATE,TRATE,VOLUME,WIGGLE};
enum{NONE,FINAL,DELTA,SCALE,VEL,ERATE,TRATE,VOLUME,WIGGLE,VARIABLE};
enum{ONE_FROM_ONE,ONE_FROM_TWO,TWO_FROM_ONE};
// same as domain.cpp, fix_nvt_sllod.cpp, compute_temp_deform.cpp
@ -58,6 +60,10 @@ FixDeform::FixDeform(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
set = new Set[6];
set[0].style = set[1].style = set[2].style =
set[3].style = set[4].style = set[5].style = NONE;
set[0].hstr = set[1].hstr = set[2].hstr =
set[3].hstr = set[4].hstr = set[5].hstr = NULL;
set[0].hratestr = set[1].hratestr = set[2].hratestr =
set[3].hratestr = set[4].hratestr = set[5].hratestr = NULL;
// parse arguments
@ -118,6 +124,22 @@ FixDeform::FixDeform(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
if (set[index].tperiod <= 0.0)
error->all(FLERR,"Illegal fix deform command");
iarg += 4;
} else if (strcmp(arg[iarg+1],"variable") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal fix deform command");
set[index].style = VARIABLE;
if (strstr(arg[iarg+2],"v_") != arg[iarg+2])
error->all(FLERR,"Illegal fix deform command");
if (strstr(arg[iarg+3],"v_") != arg[iarg+3])
error->all(FLERR,"Illegal fix deform command");
delete [] set[index].hstr;
delete [] set[index].hratestr;
int n = strlen(&arg[iarg+2][2]) + 1;
set[index].hstr = new char[n];
strcpy(set[index].hstr,&arg[iarg+2][2]);
n = strlen(&arg[iarg+3][2]) + 1;
set[index].hratestr = new char[n];
strcpy(set[index].hratestr,&arg[iarg+3][2]);
iarg += 4;
} else error->all(FLERR,"Illegal fix deform command");
} else if (strcmp(arg[iarg],"xy") == 0 ||
@ -164,6 +186,22 @@ FixDeform::FixDeform(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
if (set[index].tperiod <= 0.0)
error->all(FLERR,"Illegal fix deform command");
iarg += 4;
} else if (strcmp(arg[iarg+1],"variable") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal fix deform command");
set[index].style = VARIABLE;
if (strstr(arg[iarg+2],"v_") != arg[iarg+2])
error->all(FLERR,"Illegal fix deform command");
if (strstr(arg[iarg+3],"v_") != arg[iarg+3])
error->all(FLERR,"Illegal fix deform command");
delete [] set[index].hstr;
delete [] set[index].hratestr;
int n = strlen(&arg[iarg+2][2]) + 1;
set[index].hstr = new char[n];
strcpy(set[index].hstr,&arg[iarg+2][2]);
n = strlen(&arg[iarg+3][2]) + 1;
set[index].hratestr = new char[n];
strcpy(set[index].hratestr,&arg[iarg+3][2]);
iarg += 4;
} else error->all(FLERR,"Illegal fix deform command");
} else break;
@ -314,6 +352,10 @@ FixDeform::FixDeform(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
FixDeform::~FixDeform()
{
for (int i = 0; i < 6; i++) {
delete [] set[i].hstr;
delete [] set[i].hratestr;
}
delete [] set;
delete [] rfix;
@ -360,6 +402,22 @@ void FixDeform::init()
double delt = (update->endstep - update->beginstep) * update->dt;
// check variables for VARIABLE style
for (int i = 0; i < 6; i++) {
if (set[i].style != VARIABLE) continue;
set[i].hvar = input->variable->find(set[i].hstr);
if (set[i].hvar < 0)
error->all(FLERR,"Variable name for fix deform does not exist");
if (!input->variable->equalstyle(set[i].hvar))
error->all(FLERR,"Variable for fix deform is invalid style");
set[i].hratevar = input->variable->find(set[i].hratestr);
if (set[i].hratevar < 0)
error->all(FLERR,"Variable name for fix deform does not exist");
if (!input->variable->equalstyle(set[i].hratevar))
error->all(FLERR,"Variable for fix deform is invalid style");
}
// set start/stop values for box size and shape
// if single run, start is current values
// if multiple runs enabled via run start/stop settings,
@ -408,6 +466,13 @@ void FixDeform::init()
0.5*set[i].amplitude * sin(TWOPI*delt/set[i].tperiod);
set[i].hi_stop = set[i].hi_start +
0.5*set[i].amplitude * sin(TWOPI*delt/set[i].tperiod);
} else if (set[i].style == VARIABLE) {
bigint holdstep = update->ntimestep;
update->ntimestep = update->endstep;
double delta = input->variable->compute_equal(set[i].hvar);
update->ntimestep = holdstep;
set[i].lo_stop = set[i].lo_start - 0.5*delta;
set[i].hi_stop = set[i].hi_start + 0.5*delta;
}
}
@ -472,6 +537,13 @@ void FixDeform::init()
set[i].tilt_max = set[i].tilt_start + set[i].amplitude;
}
}
} else if (set[i].style == VARIABLE) {
bigint holdstep = update->ntimestep;
update->ntimestep = update->endstep;
double delta_tilt = input->variable->compute_equal(set[i].hvar);
update->ntimestep = holdstep;
set[i].tilt_stop = set[i].tilt_start + delta_tilt;
}
}
@ -482,7 +554,9 @@ void FixDeform::init()
error->all(FLERR,"Cannot use fix deform trate on a box with zero tilt");
// if yz changes and will cause box flip, then xy cannot be changing
// NOTE: is this comment correct, not what is tested below?
// test for WIGGLE is on min/max oscillation limit, not tilt_stop
// test for VARIABLE is error, since no way to calculate min/max limits
// this is b/c the flips would induce continuous changes in xz
// in order to keep the edge vectors of the flipped shape matrix
// an integer combination of the edge vectors of the unflipped shape matrix
@ -494,6 +568,10 @@ void FixDeform::init()
lo = set[3].tilt_min;
hi = set[3].tilt_max;
} else lo = hi = set[3].tilt_stop;
if (set[3].style == VARIABLE)
error->all(FLERR,"Fix deform is changing yz with xy variable");
// NOTE is this preceding error test and message correct?
// NOTE is this test on set[1] correct? which is y dim?
if (lo < -0.5*(set[1].hi_start-set[1].lo_start) ||
hi > 0.5*(set[1].hi_start-set[1].lo_start)) flag = 1;
if (set[1].style) {
@ -501,12 +579,13 @@ void FixDeform::init()
hi > 0.5*(set[1].hi_stop-set[1].lo_stop)) flag = 1;
}
if (flag)
error->all(FLERR,"Fix deform is changing yz by too much with changing xy");
error->all(FLERR,
"Fix deform is changing yz by too much with changing xy");
}
// set domain->h_rate values for use by domain and other fixes/computes
// initialize all rates to 0.0
// cannot set here for TRATE,VOLUME,WIGGLE styles since not constant
// cannot set here for TRATE,VOLUME,WIGGLE,VARIABLE since not constant
h_rate = domain->h_rate;
h_ratelo = domain->h_ratelo;
@ -596,6 +675,7 @@ void FixDeform::end_of_step()
// set new box size
// for TRATE, set target directly based on current time, also set h_rate
// for WIGGLE, set target directly based on current time, also set h_rate
// for VARIABLE, set target directly based on current time, also set h_rate
// for NONE, target is current box size
// for others except VOLUME, target is linear value between start and stop
@ -617,6 +697,14 @@ void FixDeform::end_of_step()
h_rate[i] = TWOPI/set[i].tperiod * set[i].amplitude *
cos(TWOPI*delt/set[i].tperiod);
h_ratelo[i] = -0.5*h_rate[i];
} else if (set[i].style == VARIABLE) {
// NOTE: worry about clearstep, addstep, maybe set on
// outside of loop with global varflag
double delta = input->variable->compute_equal(set[i].hvar);
set[i].lo_target = set[i].lo_start - 0.5*delta;
set[i].hi_target = set[i].hi_start + 0.5*delta;
h_rate[i] = input->variable->compute_equal(set[i].hratevar);
h_ratelo[i] = -0.5*h_rate[i];
} else if (set[i].style == NONE) {
set[i].lo_target = domain->boxlo[i];
set[i].hi_target = domain->boxhi[i];
@ -681,6 +769,7 @@ void FixDeform::end_of_step()
// for triclinic, set new box shape
// for TRATE, set target directly based on current time. also set h_rate
// for WIGGLE, set target directly based on current time. also set h_rate
// for VARIABLE, set target directly based on current time. also set h_rate
// for NONE, target is current tilt
// for other styles, target is linear value between start and stop values
@ -698,6 +787,10 @@ void FixDeform::end_of_step()
set[i].amplitude * sin(TWOPI*delt/set[i].tperiod);
h_rate[i] = TWOPI/set[i].tperiod * set[i].amplitude *
cos(TWOPI*delt/set[i].tperiod);
} else if (set[i].style == VARIABLE) {
double delta_tilt = input->variable->compute_equal(set[i].hvar);
set[i].tilt_target = set[i].tilt_start + delta_tilt;
h_rate[i] = input->variable->compute_equal(set[i].hratevar);
} else if (set[i].style == NONE) {
if (i == 5) set[i].tilt_target = domain->xy;
else if (i == 4) set[i].tilt_target = domain->xz;