forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@2609 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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@ -11,6 +11,10 @@
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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/* ----------------------------------------------------------------------
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Contributing author: Aidan Thompson (SNL)
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------------------------------------------------------------------------- */
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#include "math.h"
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#include "string.h"
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#include "stdlib.h"
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@ -96,18 +100,18 @@ FixBoxRelax::FixBoxRelax(LAMMPS *lmp, int narg, char **arg) :
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// error checks
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if (press_couple == XY && (p_flag[0] == 0 || p_flag[1] == 0))
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error->all("Invalid fix npt command");
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error->all("Invalid fix box/relax command");
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if (press_couple == YZ && (p_flag[1] == 0 || p_flag[2] == 0))
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error->all("Invalid fix npt command");
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error->all("Invalid fix box/relax command");
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if (press_couple == XZ && (p_flag[0] == 0 || p_flag[2] == 0))
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error->all("Invalid fix npt command");
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error->all("Invalid fix box/relax command");
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if (press_couple == XY && p_target[0] != p_target[1])
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error->all("Invalid fix npt command");
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error->all("Invalid fix box/relax command");
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if (press_couple == YZ && p_target[1] != p_target[2])
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error->all("Invalid fix npt command");
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error->all("Invalid fix box/relax command");
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if (press_couple == XZ && p_target[0] != p_target[2])
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error->all("Invalid fix npt command");
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error->all("Invalid fix box/relax command");
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if (p_flag[0] && domain->xperiodic == 0)
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error->all("Cannot use fix box/relax on a non-periodic dimension");
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@ -152,6 +156,7 @@ FixBoxRelax::FixBoxRelax(LAMMPS *lmp, int narg, char **arg) :
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delete [] newarg;
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pflag = 1;
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dimension = domain->dimension;
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nrigid = 0;
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rfix = 0;
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}
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@ -186,11 +191,11 @@ void FixBoxRelax::init()
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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) error->all("Temp ID for fix npt does not exist");
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if (icompute < 0) error->all("Temp ID for fix box/relax does not exist");
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temperature = modify->compute[icompute];
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icompute = modify->find_compute(id_press);
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if (icompute < 0) error->all("Press ID for fix npt does not exist");
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if (icompute < 0) error->all("Press ID for fix box/relax does not exist");
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pressure = modify->compute[icompute];
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// initial box dimensions
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@ -198,7 +203,7 @@ void FixBoxRelax::init()
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xprdinit = domain->xprd;
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yprdinit = domain->yprd;
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zprdinit = domain->zprd;
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if (domain->dimension == 3) volinit = domain->xprd*domain->yprd*domain->zprd;
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if (dimension == 3) volinit = domain->xprd*domain->yprd*domain->zprd;
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else volinit = domain->xprd*domain->yprd;
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pv2e = 1.0 / force->nktv2p;
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@ -225,7 +230,7 @@ void FixBoxRelax::init()
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double FixBoxRelax::min_energy(double *fextra)
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{
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double scale, scalex, scaley, scalez;
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double eng,scale,scalex,scaley,scalez;
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double t_current = temperature->compute_scalar();
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if (press_couple == XYZ) {
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@ -240,53 +245,54 @@ double FixBoxRelax::min_energy(double *fextra)
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pressure->addstep(update->ntimestep+1);
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// compute new energy, forces for each extra degree of freedom
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// PV must be in units of energy
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double eng;
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// compute energy, forces for each extra degree of freedom
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// returned eng = PV must be in units of energy
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// returned force = Ptarget - Pcurrent must be in units of
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if (press_couple == XYZ) {
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scale = domain->xprd/xprdinit;
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if (domain->dimension == 3) {
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if (dimension == 3) {
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eng = pv2e * p_target[0] * (scale*scale*scale-1.0)*volinit;
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fextra[0] = pv2e * (p_current[0] - p_target[0])*3.0*volinit*scale*scale;
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} else {
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eng = pv2e * p_target[0] * (scale*scale-1.0)*volinit;
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fextra[0] = pv2e * (p_current[0] - p_target[0])*2.0*volinit*scale;
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}
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}
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if (press_couple == ANISO) {
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} else if (press_couple == XY) {
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scale = domain->xprd/xprdinit;
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eng = pv2e * p_target[0] * (scale*scale-1.0)*volinit;
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fextra[0] = pv2e * (p_current[0] - p_target[0])*scale*volinit;
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if (p_flag[2]) {
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scale = domain->zprd/zprdinit;
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eng = pv2e * p_target[2] * (scale*scale-1.0)*volinit;
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fextra[1] = pv2e * (p_current[1] - p_target[1])*scale*volinit;
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}
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} else if (press_couple == YZ) {
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scale = domain->yprd/yprdinit;
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eng = pv2e * p_target[1] * (scale*scale-1.0)*volinit;
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fextra[1] = pv2e * (p_current[1] - p_target[1])*scale*volinit;
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fextra[0] = 0.0;
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} else if (press_couple == XZ) {
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scale = domain->xprd/xprdinit;
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eng = pv2e * p_target[0] * (scale*scale-1.0)*volinit;
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fextra[0] = pv2e * (p_current[0] - p_target[0])*scale*volinit;
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fextra[1] = 0.0;
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} else if (press_couple == ANISO) {
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scalex = domain->xprd/xprdinit;
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scaley = domain->yprd/yprdinit;
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scalez = domain->zprd/zprdinit;
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eng = pv2e * p_target[0] * (scalex*scaley*scalez-1.0)*volinit;
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fextra[0] = fextra[1] = fextra[2] = 0.0;
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if (p_flag[0]) {
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fextra[0] = pv2e * (p_current[0] - p_target[0])*scaley*scalez*volinit;
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}
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if (p_flag[1]) {
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fextra[1] = pv2e * (p_current[1] - p_target[1])*scalex*scalez*volinit;
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}
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if (p_flag[2]) {
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fextra[2] = pv2e * (p_current[2] - p_target[2])*scalex*scaley*volinit;
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}
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}
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if (press_couple == XY) {
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scale = domain->xprd/xprdinit;
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eng = pv2e * p_target[0] * (scale*scale-1.0)*volinit;
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fextra[0] = fextra[1] = pv2e * (p_current[0] - p_target[0])*scale*volinit;
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fextra[2] = 0.0;
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}
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if (press_couple == YZ) {
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scale = domain->yprd/yprdinit;
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eng = pv2e * p_target[1] * (scale*scale-1.0)*volinit;
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fextra[1] = fextra[2] = pv2e * (p_current[1] - p_target[1])*scale*volinit;
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fextra[0] = 0.0;
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}
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if (press_couple == XZ) {
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scale = domain->xprd/xprdinit;
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eng = pv2e * p_target[0] * (scale*scale-1.0)*volinit;
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fextra[0] = fextra[2] = pv2e * (p_current[0] - p_target[0])*scale*volinit;
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fextra[1] = 0.0;
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int i = 0;
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if (p_flag[0])
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fextra[i++] = pv2e * (p_current[0] - p_target[0])*scaley*scalez*volinit;
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if (p_flag[1])
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fextra[i++] = pv2e * (p_current[1] - p_target[1])*scalex*scalez*volinit;
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if (p_flag[2])
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fextra[i++] = pv2e * (p_current[2] - p_target[2])*scalex*scaley*volinit;
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}
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return eng;
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@ -294,6 +300,8 @@ double FixBoxRelax::min_energy(double *fextra)
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/* ----------------------------------------------------------------------
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store extra dof values for linesearch starting point
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boxlo0,boxhi0 = box dimensions
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s0 = ratio of current boxsize to initial boxsize
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------------------------------------------------------------------------- */
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void FixBoxRelax::min_store()
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@ -308,36 +316,27 @@ void FixBoxRelax::min_store()
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}
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/* ----------------------------------------------------------------------
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change the box dimensions by alpha from
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x0extra along linesearch direction fextra
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change the box dimensions by fraction ds = alpha*fextra
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------------------------------------------------------------------------- */
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void FixBoxRelax::min_step(double alpha, double *fextra)
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{
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double htmp;
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if (press_couple == XYZ) {
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ds[0] = alpha*fextra[0];
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ds[1] = alpha*fextra[0];
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ds[2] = alpha*fextra[0];
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}
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if (press_couple == ANISO) {
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ds[0] = ds[1] = ds[2] = 0.0;
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ds[0] = ds[1] = ds[2] = alpha*fextra[0];
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} else if (press_couple == XY) {
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ds[0] = ds[1] = alpha*fextra[0];
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if (p_flag[2]) ds[2] = alpha*fextra[1];
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} else if (press_couple == YZ) {
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ds[1] = ds[2] = alpha*fextra[0];
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if (p_flag[0]) ds[0] = alpha*fextra[1];
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} else if (press_couple == XZ) {
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ds[0] = ds[2] = alpha*fextra[0];
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if (p_flag[1]) ds[1] = alpha*fextra[1];
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} else if (press_couple == ANISO) {
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if (p_flag[0]) ds[0] = alpha*fextra[0];
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if (p_flag[1]) ds[1] = alpha*fextra[1];
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if (p_flag[2]) ds[2] = alpha*fextra[2];
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}
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if (press_couple == XY) {
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ds[0] = ds[1] = alpha*fextra[0];
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ds[2] = 0.0;
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}
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if (press_couple == XZ) {
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ds[0] = ds[2] = alpha*fextra[0];
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ds[1] = 0.0;
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}
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if (press_couple == YZ) {
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ds[1] = ds[2] = alpha*fextra[1];
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ds[0] = 0.0;
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}
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remap();
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}
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int FixBoxRelax::min_dof()
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{
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if (press_couple == XYZ) return 1;
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else return 3;
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else if (press_couple == XY) return (1 + p_flag[2]);
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else if (press_couple == YZ) return (1 + p_flag[0]);
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else if (press_couple == XZ) return (1 + p_flag[1]);
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else if (press_couple == ANISO) return (p_flag[0] + p_flag[1] + p_flag[2]);
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return 0;
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}
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/* ----------------------------------------------------------------------
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@ -364,11 +367,6 @@ void FixBoxRelax::remap()
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// ctr = geometric center of box in a dimension
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// rescale simulation box from linesearch starting point
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// scale atom coords for all atoms or only for fix group atoms
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// don't do anything if non-periodic or style is constant volume
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// we assume initially the atoms positions and box dimensions
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// are at linesearch starting point.
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// If not, atom positions will not be scaled correctly.
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double **x = atom->x;
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int *mask = atom->mask;
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@ -389,13 +387,12 @@ void FixBoxRelax::remap()
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// reset global and local box to new size/shape
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for (i = 0; i < 3; i++) {
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for (i = 0; i < 3; i++)
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if (p_flag[i]) {
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ctr = 0.5 * ( boxlo0[i] + boxhi0[i]);
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ctr = 0.5 * (boxlo0[i] + boxhi0[i]);
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domain->boxlo[i] = boxlo0[i] + (boxlo0[i]-ctr)*ds[i]/s0[i];
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domain->boxhi[i] = boxhi0[i] + (boxhi0[i]-ctr)*ds[i]/s0[i];
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}
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}
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domain->set_global_box();
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domain->set_local_box();
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@ -412,8 +409,6 @@ void FixBoxRelax::remap()
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if (nrigid)
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for (i = 0; i < nrigid; i++)
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modify->fix[rfix[i]]->deform(1);
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}
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/* ---------------------------------------------------------------------- */
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@ -32,15 +32,15 @@ class FixBoxRelax : public Fix {
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private:
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int p_flag[3];
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int press_couple,allremap;
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int dimension;
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double p_target[3],p_current[3];
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double dilation[3];
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double volinit,xprdinit,yprdinit,zprdinit;
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double pv2e;
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// These variables are for linesearch
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double boxlo0[3],boxhi0[3]; // x0extra box bounds
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double s0[6]; // x0extra scale matrix in Voigt notation
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double ds[6]; // increment in scale matrix in Voigt notation
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double boxlo0[3],boxhi0[3]; // box bounds at start of line search
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double s0[6]; // scale matrix in Voigt notation
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double ds[6]; // increment in scale matrix
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char *id_temp,*id_press;
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class Compute *temperature,*pressure;
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