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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8226 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2012-06-06 22:47:51 +00:00
parent f46eb9dedb
commit ef9e700545
1408 changed files with 58053 additions and 57983 deletions
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102
src/fix_box_relax.cpp
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@ -5,7 +5,7 @@
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
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.
@ -59,9 +59,9 @@ FixBoxRelax::FixBoxRelax(LAMMPS *lmp, int narg, char **arg) :
deviatoric_flag = 0;
nreset_h0 = 0;
p_target[0] = p_target[1] = p_target[2] =
p_target[0] = p_target[1] = p_target[2] =
p_target[3] = p_target[4] = p_target[5] = 0.0;
p_flag[0] = p_flag[1] = p_flag[2] =
p_flag[0] = p_flag[1] = p_flag[2] =
p_flag[3] = p_flag[4] = p_flag[5] = 0;
// process keywords
@ -77,18 +77,18 @@ FixBoxRelax::FixBoxRelax(LAMMPS *lmp, int narg, char **arg) :
p_target[0] = p_target[1] = p_target[2] = atof(arg[iarg+1]);
p_flag[0] = p_flag[1] = p_flag[2] = 1;
if (dimension == 2) {
p_target[2] = 0.0;
p_flag[2] = 0;
p_target[2] = 0.0;
p_flag[2] = 0;
}
iarg += 2;
iarg += 2;
} else if (strcmp(arg[iarg],"aniso") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix box/relax command");
pcouple = NONE;
p_target[0] = p_target[1] = p_target[2] = atof(arg[iarg+1]);
p_flag[0] = p_flag[1] = p_flag[2] = 1;
if (dimension == 2) {
p_target[2] = 0.0;
p_flag[2] = 0;
p_target[2] = 0.0;
p_flag[2] = 0;
}
iarg += 2;
} else if (strcmp(arg[iarg],"tri") == 0) {
@ -99,8 +99,8 @@ FixBoxRelax::FixBoxRelax(LAMMPS *lmp, int narg, char **arg) :
p_target[3] = p_target[4] = p_target[5] = 0.0;
p_flag[3] = p_flag[4] = p_flag[5] = 1;
if (dimension == 2) {
p_target[2] = p_target[3] = p_target[4] = 0.0;
p_flag[2] = p_flag[3] = p_flag[4] = 0;
p_target[2] = p_target[3] = p_target[4] = 0.0;
p_flag[2] = p_flag[3] = p_flag[4] = 0;
}
iarg += 2;
@ -109,44 +109,44 @@ FixBoxRelax::FixBoxRelax(LAMMPS *lmp, int narg, char **arg) :
p_target[0] = atof(arg[iarg+1]);
p_flag[0] = 1;
deviatoric_flag = 1;
iarg += 2;
iarg += 2;
} else if (strcmp(arg[iarg],"y") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix box/relax command");
p_target[1] = atof(arg[iarg+1]);
p_flag[1] = 1;
deviatoric_flag = 1;
iarg += 2;
iarg += 2;
} else if (strcmp(arg[iarg],"z") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix box/relax command");
p_target[2] = atof(arg[iarg+1]);
p_flag[2] = 1;
deviatoric_flag = 1;
iarg += 2;
iarg += 2;
if (dimension == 2)
error->all(FLERR,"Invalid fix box/relax command for a 2d simulation");
error->all(FLERR,"Invalid fix box/relax command for a 2d simulation");
} else if (strcmp(arg[iarg],"yz") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix box/relax command");
p_target[3] = atof(arg[iarg+1]);
p_flag[3] = 1;
deviatoric_flag = 1;
iarg += 2;
iarg += 2;
if (dimension == 2)
error->all(FLERR,"Invalid fix box/relax command for a 2d simulation");
error->all(FLERR,"Invalid fix box/relax command for a 2d simulation");
} else if (strcmp(arg[iarg],"xz") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix box/relax command");
p_target[4] = atof(arg[iarg+1]);
p_flag[4] = 1;
deviatoric_flag = 1;
iarg += 2;
iarg += 2;
if (dimension == 2)
error->all(FLERR,"Invalid fix box/relax command for a 2d simulation");
error->all(FLERR,"Invalid fix box/relax command for a 2d simulation");
} else if (strcmp(arg[iarg],"xy") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix box/relax command");
p_target[5] = atof(arg[iarg+1]);
p_flag[5] = 1;
deviatoric_flag = 1;
iarg += 2;
iarg += 2;
} else if (strcmp(arg[iarg],"couple") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix box/relax command");
@ -211,17 +211,17 @@ FixBoxRelax::FixBoxRelax(LAMMPS *lmp, int narg, char **arg) :
if (p_flag[3] && domain->zperiodic == 0)
error->all(FLERR,
"Cannot use fix box/relax on a 2nd non-periodic dimension");
"Cannot use fix box/relax on a 2nd non-periodic dimension");
if (p_flag[4] && domain->zperiodic == 0)
error->all(FLERR,
"Cannot use fix box/relax on a 2nd non-periodic dimension");
"Cannot use fix box/relax on a 2nd non-periodic dimension");
if (p_flag[5] && domain->yperiodic == 0)
error->all(FLERR,
"Cannot use fix box/relax on a 2nd non-periodic dimension");
"Cannot use fix box/relax on a 2nd non-periodic dimension");
if (!domain->triclinic && (p_flag[3] || p_flag[4] || p_flag[5]))
if (!domain->triclinic && (p_flag[3] || p_flag[4] || p_flag[5]))
error->all(FLERR,"Can not specify Pxy/Pxz/Pyz in "
"fix box/relax with non-triclinic box");
"fix box/relax with non-triclinic box");
if (pcouple == XYZ && dimension == 3 &&
(p_target[0] != p_target[1] || p_target[0] != p_target[2]))
@ -319,12 +319,12 @@ void FixBoxRelax::init()
// set temperature and pressure ptrs
int icompute = modify->find_compute(id_temp);
if (icompute < 0)
if (icompute < 0)
error->all(FLERR,"Temperature ID for fix box/relax does not exist");
temperature = modify->compute[icompute];
icompute = modify->find_compute(id_press);
if (icompute < 0)
if (icompute < 0)
error->all(FLERR,"Pressure ID for fix box/relax does not exist");
pressure = modify->compute[icompute];
@ -415,11 +415,11 @@ double FixBoxRelax::min_energy(double *fextra)
if (pstyle == TRICLINIC) {
fextra[3] = fextra[4] = fextra[5] = 0.0;
if (p_flag[3])
fextra[3] = pv2e*p_current[3]*scaley*yprdinit*scalex*xprdinit*yprdinit;
if (p_flag[4])
fextra[4] = pv2e*p_current[4]*scalex*xprdinit*scaley*yprdinit*xprdinit;
if (p_flag[5])
fextra[5] = pv2e*p_current[5]*scalex*xprdinit*scalez*zprdinit*xprdinit;
fextra[3] = pv2e*p_current[3]*scaley*yprdinit*scalex*xprdinit*yprdinit;
if (p_flag[4])
fextra[4] = pv2e*p_current[4]*scalex*xprdinit*scaley*yprdinit*xprdinit;
if (p_flag[5])
fextra[5] = pv2e*p_current[5]*scalex*xprdinit*scalez*zprdinit*xprdinit;
}
if (deviatoric_flag) {
@ -428,9 +428,9 @@ double FixBoxRelax::min_energy(double *fextra)
if (p_flag[1]) fextra[1] -= fdev[1]*yprdinit;
if (p_flag[2]) fextra[2] -= fdev[2]*zprdinit;
if (pstyle == TRICLINIC) {
if (p_flag[3]) fextra[3] -= fdev[3]*yprdinit;
if (p_flag[4]) fextra[4] -= fdev[4]*xprdinit;
if (p_flag[5]) fextra[5] -= fdev[5]*xprdinit;
if (p_flag[3]) fextra[3] -= fdev[3]*yprdinit;
if (p_flag[4]) fextra[4] -= fdev[4]*xprdinit;
if (p_flag[5]) fextra[5] -= fdev[5]*xprdinit;
}
eng += compute_strain_energy();
@ -586,7 +586,7 @@ void FixBoxRelax::remap()
{
int i,n;
double ctr;
// ctr = geometric center of box in a dimension
// rescale simulation box from linesearch starting point
// scale atom coords for all atoms or only for fix group atoms
@ -601,7 +601,7 @@ void FixBoxRelax::remap()
else {
for (i = 0; i < n; i++)
if (mask[i] & groupbit)
domain->x2lamda(x[i],x[i]);
domain->x2lamda(x[i],x[i]);
}
if (nrigid)
@ -618,7 +618,7 @@ void FixBoxRelax::remap()
domain->boxlo[i] = currentBoxLo0 + (currentBoxLo0-ctr)*ds[i]/s0[i];
domain->boxhi[i] = currentBoxHi0 + (currentBoxHi0-ctr)*ds[i]/s0[i];
if (domain->boxlo[i] >= domain->boxhi[i])
error->all(FLERR,"Fix box/relax generated negative box length");
error->all(FLERR,"Fix box/relax generated negative box length");
}
if (pstyle == TRICLINIC) {
@ -636,7 +636,7 @@ void FixBoxRelax::remap()
else {
for (i = 0; i < n; i++)
if (mask[i] & groupbit)
domain->lamda2x(x[i],x[i]);
domain->lamda2x(x[i],x[i]);
}
if (nrigid)
@ -673,8 +673,8 @@ void FixBoxRelax::couple()
p_current[2] = tensor[2];
}
// switch order from xy-xz-yz to Voigt
// switch order from xy-xz-yz to Voigt
if (pstyle == TRICLINIC) {
p_current[3] = tensor[5];
p_current[4] = tensor[4];
@ -698,20 +698,20 @@ int FixBoxRelax::modify_param(int narg, char **arg)
strcpy(id_temp,arg[1]);
int icompute = modify->find_compute(arg[1]);
if (icompute < 0)
if (icompute < 0)
error->all(FLERR,"Could not find fix_modify temperature ID");
temperature = modify->compute[icompute];
if (temperature->tempflag == 0)
error->all(FLERR,
"Fix_modify temperature ID does not compute temperature");
"Fix_modify temperature ID does not compute temperature");
if (temperature->igroup != 0 && comm->me == 0)
error->warning(FLERR,"Temperature for fix modify is not for group all");
// reset id_temp of pressure to new temperature ID
icompute = modify->find_compute(id_press);
if (icompute < 0)
if (icompute < 0)
error->all(FLERR,"Pressure ID for fix modify does not exist");
modify->compute[icompute]->reset_extra_compute_fix(id_temp);
@ -769,7 +769,7 @@ void FixBoxRelax::compute_sigma()
h0_inv[3] = domain->h_inv[3];
h0_inv[4] = domain->h_inv[4];
h0_inv[5] = domain->h_inv[5];
htmp[0][0] = h0[0];
htmp[1][1] = h0[1];
htmp[2][2] = h0[2];
@ -835,26 +835,26 @@ void FixBoxRelax::compute_sigma()
double FixBoxRelax::compute_strain_energy()
{
// compute strain energy = 0.5*Tr(sigma*h*h^t) in energy units
// compute strain energy = 0.5*Tr(sigma*h*h^t) in energy units
double* h = domain->h;
double d0,d1,d2;
if (dimension == 3) {
d0 =
d0 =
sigma[0]*(h[0]*h[0]+h[5]*h[5]+h[4]*h[4]) +
sigma[5]*( h[1]*h[5]+h[3]*h[4]) +
sigma[4]*( h[2]*h[4]);
d1 =
d1 =
sigma[5]*( h[5]*h[1]+h[4]*h[3]) +
sigma[1]*( h[1]*h[1]+h[3]*h[3]) +
sigma[3]*( h[2]*h[3]);
d2 =
d2 =
sigma[4]*( h[4]*h[2]) +
sigma[3]*( h[3]*h[2]) +
sigma[2]*( h[2]*h[2]);
} else {
d0 = sigma[0]*(h[0]*h[0]+h[5]*h[5]) + sigma[5]*h[1]*h[5];
d0 = sigma[0]*(h[0]*h[0]+h[5]*h[5]) + sigma[5]*h[1]*h[5];
d1 = sigma[5]*h[5]*h[1] + sigma[1]*h[1]*h[1];
d2 = 0.0;
}
@ -870,7 +870,7 @@ double FixBoxRelax::compute_strain_energy()
void FixBoxRelax::compute_deviatoric()
{
double* h = domain->h;
// [ 0 5 4 ] [ 0 5 4 ] [ 0 5 4 ]
// [ 5 1 3 ] = [ - 1 3 ] [ 5 1 3 ]
// [ 4 3 2 ] [ - - 2 ] [ 4 3 2 ]