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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8391 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2012-06-25 16:42:20 +00:00
parent bee842bed7
commit e8ff810ee7
78 changed files with 396 additions and 474 deletions
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49
src/neigh_bond.cpp
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@ -15,6 +15,7 @@
#include "atom.h"
#include "force.h"
#include "update.h"
#include "domain.h"
#include "memory.h"
#include "error.h"
@ -53,7 +54,7 @@ void Neighbor::bond_all()
memory->grow(bondlist,maxbond,3,"neighbor:bondlist");
}
bondlist[nbondlist][0] = i;
bondlist[nbondlist][1] = atom1;
bondlist[nbondlist][1] = domain->closest_image(i,atom1);
bondlist[nbondlist][2] = bond_type[i][m];
nbondlist++;
}
@ -92,7 +93,7 @@ void Neighbor::bond_partial()
memory->grow(bondlist,maxbond,3,"neighbor:bondlist");
}
bondlist[nbondlist][0] = i;
bondlist[nbondlist][1] = atom1;
bondlist[nbondlist][1] = domain->closest_image(i,atom1);
bondlist[nbondlist][2] = bond_type[i][m];
nbondlist++;
}
@ -134,9 +135,9 @@ void Neighbor::angle_all()
maxangle += BONDDELTA;
memory->grow(anglelist,maxangle,4,"neighbor:anglelist");
}
anglelist[nanglelist][0] = atom1;
anglelist[nanglelist][1] = atom2;
anglelist[nanglelist][2] = atom3;
anglelist[nanglelist][0] = domain->closest_image(i,atom1);
anglelist[nanglelist][1] = domain->closest_image(i,atom2);
anglelist[nanglelist][2] = domain->closest_image(i,atom3);
anglelist[nanglelist][3] = angle_type[i][m];
nanglelist++;
}
@ -179,9 +180,9 @@ void Neighbor::angle_partial()
maxangle += BONDDELTA;
memory->grow(anglelist,maxangle,4,"neighbor:anglelist");
}
anglelist[nanglelist][0] = atom1;
anglelist[nanglelist][1] = atom2;
anglelist[nanglelist][2] = atom3;
anglelist[nanglelist][0] = domain->closest_image(i,atom1);
anglelist[nanglelist][1] = domain->closest_image(i,atom2);
anglelist[nanglelist][2] = domain->closest_image(i,atom3);
anglelist[nanglelist][3] = angle_type[i][m];
nanglelist++;
}
@ -227,10 +228,10 @@ void Neighbor::dihedral_all()
maxdihedral += BONDDELTA;
memory->grow(dihedrallist,maxdihedral,5,"neighbor:dihedrallist");
}
dihedrallist[ndihedrallist][0] = atom1;
dihedrallist[ndihedrallist][1] = atom2;
dihedrallist[ndihedrallist][2] = atom3;
dihedrallist[ndihedrallist][3] = atom4;
dihedrallist[ndihedrallist][0] = domain->closest_image(i,atom1);
dihedrallist[ndihedrallist][1] = domain->closest_image(i,atom2);
dihedrallist[ndihedrallist][2] = domain->closest_image(i,atom3);
dihedrallist[ndihedrallist][3] = domain->closest_image(i,atom4);
dihedrallist[ndihedrallist][4] = dihedral_type[i][m];
ndihedrallist++;
}
@ -277,10 +278,10 @@ void Neighbor::dihedral_partial()
maxdihedral += BONDDELTA;
memory->grow(dihedrallist,maxdihedral,5,"neighbor:dihedrallist");
}
dihedrallist[ndihedrallist][0] = atom1;
dihedrallist[ndihedrallist][1] = atom2;
dihedrallist[ndihedrallist][2] = atom3;
dihedrallist[ndihedrallist][3] = atom4;
dihedrallist[ndihedrallist][0] = domain->closest_image(i,atom1);
dihedrallist[ndihedrallist][1] = domain->closest_image(i,atom2);
dihedrallist[ndihedrallist][2] = domain->closest_image(i,atom3);
dihedrallist[ndihedrallist][3] = domain->closest_image(i,atom4);
dihedrallist[ndihedrallist][4] = dihedral_type[i][m];
ndihedrallist++;
}
@ -326,10 +327,10 @@ void Neighbor::improper_all()
maximproper += BONDDELTA;
memory->grow(improperlist,maximproper,5,"neighbor:improperlist");
}
improperlist[nimproperlist][0] = atom1;
improperlist[nimproperlist][1] = atom2;
improperlist[nimproperlist][2] = atom3;
improperlist[nimproperlist][3] = atom4;
improperlist[nimproperlist][0] = domain->closest_image(i,atom1);
improperlist[nimproperlist][1] = domain->closest_image(i,atom2);
improperlist[nimproperlist][2] = domain->closest_image(i,atom3);
improperlist[nimproperlist][3] = domain->closest_image(i,atom4);
improperlist[nimproperlist][4] = improper_type[i][m];
nimproperlist++;
}
@ -376,10 +377,10 @@ void Neighbor::improper_partial()
maximproper += BONDDELTA;
memory->grow(improperlist,maximproper,5,"neighbor:improperlist");
}
improperlist[nimproperlist][0] = atom1;
improperlist[nimproperlist][1] = atom2;
improperlist[nimproperlist][2] = atom3;
improperlist[nimproperlist][3] = atom4;
improperlist[nimproperlist][0] = domain->closest_image(i,atom1);
improperlist[nimproperlist][1] = domain->closest_image(i,atom2);
improperlist[nimproperlist][2] = domain->closest_image(i,atom3);
improperlist[nimproperlist][3] = domain->closest_image(i,atom4);
improperlist[nimproperlist][4] = improper_type[i][m];
nimproperlist++;
}