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@ -881,7 +881,7 @@ Note that numeric *lo* and *hi* values are specified either as
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absolute numbers or as fractions (0.0 to 1.0) of the range, depending
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on the "a" or "f" in the style setting for the color map. The lo/hi
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values in each sub-range must satisfy lo < hi.
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Here is how the *N* entries are used to determine the color of an
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individual atom, based on the value :math:`X` of its atom attribute.
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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()
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zero(i);
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continue;
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}
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ibody = fixrigid->atom2body[i];
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if (ibody < 0) {
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zero(i);
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continue;
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}
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body = &fixrigid->body[ibody];
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if (nvalues == 1) ptr = &vector_atom[i];
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@ -986,7 +986,7 @@ void FixRigid::pre_neighbor()
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//domain->remap(xcm[ibody],imagebody[ibody]);
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domain->remap(xcm[ibody],imagebody[ibody],vcm[ibody]);
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}
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image_shift();
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}
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@ -798,7 +798,7 @@ void FixRigidSmall::initial_integrate(int vflag)
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use domain->remap() in case xcm is far away from box
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due to first-time definition of rigid body in setup_bodies_static()
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or due to box flip
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also adjust imagebody = rigid body image flags, due to xcm remap
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also adjust imagebody = rigid body image flags, due to xcm remap
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also remap vcm if xcm crosses periodic shearing boundary
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then communicate bodies so other procs will know of changes to body xcm/vcm
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then adjust xcmimage flags of all atoms in bodies via image_shift()
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@ -809,7 +809,7 @@ void FixRigidSmall::initial_integrate(int vflag)
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around in-box xcm and stay close to simulation box
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if just inferred unwrapped from atom image flags,
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then an unwrapped body could end up very far away from box
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set_xv() would then compute huge displacements every step to
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set_xv() would then compute huge displacements every step to
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reset coords of all body atoms to be back inside the box,
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ditto for triclinic box flip which could cause numeric problems
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------------------------------------------------------------------------- */
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@ -155,7 +155,7 @@ class FixRigidSmall : public Fix {
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int deform_vremap; // 1 if fix deform with V_REMAP exists
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// if so, add/sub bias around Langevin
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double vbias[3]; // store deformation bias for one body
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int tstat_flag, pstat_flag; // 0/1 = no/yes thermostat/barostat
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int t_chain, t_iter, t_order;
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@ -1883,7 +1883,7 @@ int ColorMap::reset(int narg, char **arg)
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}
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// error return if color string was not recognized
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if (mentry[i].color == nullptr) return 1;
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}
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@ -1962,19 +1962,19 @@ int ColorMap::minmax(double mindynamic, double maxdynamic)
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// the color for a bin starting at highcurrent,
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// more sensible to assign them color for bin ending at hicurrent
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// rounddown_flag is used in value2color()
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} else if (mstyle == SEQUENTIAL) {
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} else if (mstyle == SEQUENTIAL) {
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// NOTE: need to formalize and pre-set these 2 epsilon constants
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double epsbin;
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if (mrange == ABSOLUTE) epsbin = (hicurrent-locurrent) * 1.0e-12;
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else epsbin = 1.0e-9;
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int ibin = static_cast<int> ((hicurrent-locurrent) * mbinsizeinv);
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int jbin = static_cast<int> ((hicurrent-locurrent-epsbin) * mbinsizeinv);
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if (jbin < ibin) rounddown_flag = 1;
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else rounddown_flag = 0;
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}
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return 0;
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}
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