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This commit is contained in:
Axel Kohlmeyer
2025-04-30 16:14:32 -04:00
parent 79ccd302c2
commit a83489e511
6 changed files with 12 additions and 12 deletions

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@ -881,7 +881,7 @@ Note that numeric *lo* and *hi* values are specified either as
absolute numbers or as fractions (0.0 to 1.0) of the range, depending absolute numbers or as fractions (0.0 to 1.0) of the range, depending
on the "a" or "f" in the style setting for the color map. The lo/hi on the "a" or "f" in the style setting for the color map. The lo/hi
values in each sub-range must satisfy lo < hi. values in each sub-range must satisfy lo < hi.
Here is how the *N* entries are used to determine the color of an Here is how the *N* entries are used to determine the color of an
individual atom, based on the value :math:`X` of its atom attribute. individual atom, based on the value :math:`X` of its atom attribute.
The entries are scanned from first to last. The first time that *lo* The entries are scanned from first to last. The first time that *lo*

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@ -158,13 +158,13 @@ void ComputeRigidAtom::compute_peratom()
zero(i); zero(i);
continue; continue;
} }
ibody = fixrigid->atom2body[i]; ibody = fixrigid->atom2body[i];
if (ibody < 0) { if (ibody < 0) {
zero(i); zero(i);
continue; continue;
} }
body = &fixrigid->body[ibody]; body = &fixrigid->body[ibody];
if (nvalues == 1) ptr = &vector_atom[i]; if (nvalues == 1) ptr = &vector_atom[i];

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@ -986,7 +986,7 @@ void FixRigid::pre_neighbor()
//domain->remap(xcm[ibody],imagebody[ibody]); //domain->remap(xcm[ibody],imagebody[ibody]);
domain->remap(xcm[ibody],imagebody[ibody],vcm[ibody]); domain->remap(xcm[ibody],imagebody[ibody],vcm[ibody]);
} }
image_shift(); image_shift();
} }

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@ -798,7 +798,7 @@ void FixRigidSmall::initial_integrate(int vflag)
use domain->remap() in case xcm is far away from box use domain->remap() in case xcm is far away from box
due to first-time definition of rigid body in setup_bodies_static() due to first-time definition of rigid body in setup_bodies_static()
or due to box flip or due to box flip
also adjust imagebody = rigid body image flags, due to xcm remap also adjust imagebody = rigid body image flags, due to xcm remap
also remap vcm if xcm crosses periodic shearing boundary also remap vcm if xcm crosses periodic shearing boundary
then communicate bodies so other procs will know of changes to body xcm/vcm then communicate bodies so other procs will know of changes to body xcm/vcm
then adjust xcmimage flags of all atoms in bodies via image_shift() then adjust xcmimage flags of all atoms in bodies via image_shift()
@ -809,7 +809,7 @@ void FixRigidSmall::initial_integrate(int vflag)
around in-box xcm and stay close to simulation box around in-box xcm and stay close to simulation box
if just inferred unwrapped from atom image flags, if just inferred unwrapped from atom image flags,
then an unwrapped body could end up very far away from box then an unwrapped body could end up very far away from box
set_xv() would then compute huge displacements every step to set_xv() would then compute huge displacements every step to
reset coords of all body atoms to be back inside the box, reset coords of all body atoms to be back inside the box,
ditto for triclinic box flip which could cause numeric problems ditto for triclinic box flip which could cause numeric problems
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */

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@ -155,7 +155,7 @@ class FixRigidSmall : public Fix {
int deform_vremap; // 1 if fix deform with V_REMAP exists int deform_vremap; // 1 if fix deform with V_REMAP exists
// if so, add/sub bias around Langevin // if so, add/sub bias around Langevin
double vbias[3]; // store deformation bias for one body double vbias[3]; // store deformation bias for one body
int tstat_flag, pstat_flag; // 0/1 = no/yes thermostat/barostat int tstat_flag, pstat_flag; // 0/1 = no/yes thermostat/barostat
int t_chain, t_iter, t_order; int t_chain, t_iter, t_order;

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@ -1883,7 +1883,7 @@ int ColorMap::reset(int narg, char **arg)
} }
// error return if color string was not recognized // error return if color string was not recognized
if (mentry[i].color == nullptr) return 1; if (mentry[i].color == nullptr) return 1;
} }
@ -1962,19 +1962,19 @@ int ColorMap::minmax(double mindynamic, double maxdynamic)
// the color for a bin starting at highcurrent, // the color for a bin starting at highcurrent,
// more sensible to assign them color for bin ending at hicurrent // more sensible to assign them color for bin ending at hicurrent
// rounddown_flag is used in value2color() // rounddown_flag is used in value2color()
} else if (mstyle == SEQUENTIAL) { } else if (mstyle == SEQUENTIAL) {
// NOTE: need to formalize and pre-set these 2 epsilon constants // NOTE: need to formalize and pre-set these 2 epsilon constants
double epsbin; double epsbin;
if (mrange == ABSOLUTE) epsbin = (hicurrent-locurrent) * 1.0e-12; if (mrange == ABSOLUTE) epsbin = (hicurrent-locurrent) * 1.0e-12;
else epsbin = 1.0e-9; else epsbin = 1.0e-9;
int ibin = static_cast<int> ((hicurrent-locurrent) * mbinsizeinv); int ibin = static_cast<int> ((hicurrent-locurrent) * mbinsizeinv);
int jbin = static_cast<int> ((hicurrent-locurrent-epsbin) * mbinsizeinv); int jbin = static_cast<int> ((hicurrent-locurrent-epsbin) * mbinsizeinv);
if (jbin < ibin) rounddown_flag = 1; if (jbin < ibin) rounddown_flag = 1;
else rounddown_flag = 0; else rounddown_flag = 0;
} }
return 0; return 0;
} }