whitespace
This commit is contained in:
@ -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*
|
||||||
|
|||||||
@ -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];
|
||||||
|
|||||||
@ -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();
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|||||||
@ -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
|
||||||
------------------------------------------------------------------------- */
|
------------------------------------------------------------------------- */
|
||||||
|
|||||||
@ -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;
|
||||||
|
|||||||
@ -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;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|||||||
Reference in New Issue
Block a user