Loading doc/src/Manual.txt +2 −2 Original line number Diff line number Diff line <!-- HTML_ONLY --> <HEAD> <TITLE>LAMMPS Users Manual</TITLE> <META NAME="docnumber" CONTENT="7 Mar 2017 version"> <META NAME="docnumber" CONTENT="10 Mar 2017 version"> <META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories"> <META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License."> </HEAD> Loading @@ -21,7 +21,7 @@ <H1></H1> LAMMPS Documentation :c,h3 7 Mar 2017 version :c,h4 10 Mar 2017 version :c,h4 Version info: :h4 Loading doc/src/PDF/colvars-refman-lammps.pdf +677 B (553 KiB) File changed.No diff preview for this file type. View original file View changed file doc/src/balance.txt +23 −15 Original line number Diff line number Diff line Loading @@ -286,24 +286,32 @@ above. It performs a recursive coordinate bisectioning (RCB) of the simulation domain. The basic idea is as follows. The simulation domain is cut into 2 boxes by an axis-aligned cut in the longest dimension, leaving one new box on either side of the cut. All the processors are also partitioned into 2 groups, half assigned to the box on the lower side of the cut, and half to the box on the upper side. (If the processor count is odd, one side gets an extra processor.) The cut is positioned so that the number of particles in the lower box is exactly the number that the processors assigned to that box should own for load balance to be perfect. This also makes load balance for the upper box perfect. The positioning is done iteratively, by a bisectioning method. Note that counting particles on either side of the cut requires communication between all processors at each iteration. one of the dimensions, leaving one new sub-box on either side of the cut. Which dimension is chosen for the cut depends on the particle (weight) distribution within the parent box. Normally the longest dimension of the box is cut, but if all (or most) of the particles are at one end of the box, a cut may be performed in another dimension to induce sub-boxes that are more cube-ish (3d) or square-ish (2d) in shape. After the cut is made, all the processors are also partitioned into 2 groups, half assigned to the box on the lower side of the cut, and half to the box on the upper side. (If the processor count is odd, one side gets an extra processor.) The cut is positioned so that the number of (weighted) particles in the lower box is exactly the number that the processors assigned to that box should own for load balance to be perfect. This also makes load balance for the upper box perfect. The positioning of the cut is done iteratively, by a bisectioning method (median search). Note that counting particles on either side of the cut requires communication between all processors at each iteration. That is the procedure for the first cut. Subsequent cuts are made recursively, in exactly the same manner. The subset of processors assigned to each box make a new cut in the longest dimension of that box, splitting the box, the subset of processors, and the particles in the box in two. The recursion continues until every processor is assigned a sub-box of the entire simulation domain, and owns the assigned to each box make a new cut in one dimension of that box, splitting the box, the subset of processors, and the particles in the box in two. The recursion continues until every processor is assigned a sub-box of the entire simulation domain, and owns the (weighted) particles in that sub-box. :line Loading doc/src/change_box.txt +2 −2 Original line number Diff line number Diff line Loading @@ -105,7 +105,7 @@ create_atoms 1 single -5 5 5 # this will fail to insert an atom :pre change_box all x final -10 20 boundary f s s create_atoms 1 single -5 5 5 change_box boundary s s s # this will work :pre change_box all boundary s s s # this will work :pre NOTE: Unlike the earlier "displace_box" version of this command, atom remapping is NOT performed by default. This command allows remapping Loading doc/src/create_atoms.txt +11 −0 Original line number Diff line number Diff line Loading @@ -134,6 +134,17 @@ not overlap existing atoms inappropriately, especially if molecules are being added. The "delete_atoms"_delete_atoms.html command can be used to remove overlapping atoms or molecules. NOTE: You cannot use any of the styles explained above to create atoms that are outside the simulation box; they will just be ignored by LAMMPS. This is true even if you are using shrink-wrapped box boundaries, as specified by the "boundary"_boundary.html command. However, you can first use the "change_box"_change_box.html command to temporarily expand the box, then add atoms via create_atoms, then finally use change_box command again if needed to re-shrink-wrap the new atoms. See the "change_box"_change_box.html doc page for an example of how to do this, using the create_atoms {single} style to insert a new atom outside the current simulation box. :line Individual atoms are inserted by this command, unless the {mol} Loading Loading
doc/src/Manual.txt +2 −2 Original line number Diff line number Diff line <!-- HTML_ONLY --> <HEAD> <TITLE>LAMMPS Users Manual</TITLE> <META NAME="docnumber" CONTENT="7 Mar 2017 version"> <META NAME="docnumber" CONTENT="10 Mar 2017 version"> <META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories"> <META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License."> </HEAD> Loading @@ -21,7 +21,7 @@ <H1></H1> LAMMPS Documentation :c,h3 7 Mar 2017 version :c,h4 10 Mar 2017 version :c,h4 Version info: :h4 Loading
doc/src/PDF/colvars-refman-lammps.pdf +677 B (553 KiB) File changed.No diff preview for this file type. View original file View changed file
doc/src/balance.txt +23 −15 Original line number Diff line number Diff line Loading @@ -286,24 +286,32 @@ above. It performs a recursive coordinate bisectioning (RCB) of the simulation domain. The basic idea is as follows. The simulation domain is cut into 2 boxes by an axis-aligned cut in the longest dimension, leaving one new box on either side of the cut. All the processors are also partitioned into 2 groups, half assigned to the box on the lower side of the cut, and half to the box on the upper side. (If the processor count is odd, one side gets an extra processor.) The cut is positioned so that the number of particles in the lower box is exactly the number that the processors assigned to that box should own for load balance to be perfect. This also makes load balance for the upper box perfect. The positioning is done iteratively, by a bisectioning method. Note that counting particles on either side of the cut requires communication between all processors at each iteration. one of the dimensions, leaving one new sub-box on either side of the cut. Which dimension is chosen for the cut depends on the particle (weight) distribution within the parent box. Normally the longest dimension of the box is cut, but if all (or most) of the particles are at one end of the box, a cut may be performed in another dimension to induce sub-boxes that are more cube-ish (3d) or square-ish (2d) in shape. After the cut is made, all the processors are also partitioned into 2 groups, half assigned to the box on the lower side of the cut, and half to the box on the upper side. (If the processor count is odd, one side gets an extra processor.) The cut is positioned so that the number of (weighted) particles in the lower box is exactly the number that the processors assigned to that box should own for load balance to be perfect. This also makes load balance for the upper box perfect. The positioning of the cut is done iteratively, by a bisectioning method (median search). Note that counting particles on either side of the cut requires communication between all processors at each iteration. That is the procedure for the first cut. Subsequent cuts are made recursively, in exactly the same manner. The subset of processors assigned to each box make a new cut in the longest dimension of that box, splitting the box, the subset of processors, and the particles in the box in two. The recursion continues until every processor is assigned a sub-box of the entire simulation domain, and owns the assigned to each box make a new cut in one dimension of that box, splitting the box, the subset of processors, and the particles in the box in two. The recursion continues until every processor is assigned a sub-box of the entire simulation domain, and owns the (weighted) particles in that sub-box. :line Loading
doc/src/change_box.txt +2 −2 Original line number Diff line number Diff line Loading @@ -105,7 +105,7 @@ create_atoms 1 single -5 5 5 # this will fail to insert an atom :pre change_box all x final -10 20 boundary f s s create_atoms 1 single -5 5 5 change_box boundary s s s # this will work :pre change_box all boundary s s s # this will work :pre NOTE: Unlike the earlier "displace_box" version of this command, atom remapping is NOT performed by default. This command allows remapping Loading
doc/src/create_atoms.txt +11 −0 Original line number Diff line number Diff line Loading @@ -134,6 +134,17 @@ not overlap existing atoms inappropriately, especially if molecules are being added. The "delete_atoms"_delete_atoms.html command can be used to remove overlapping atoms or molecules. NOTE: You cannot use any of the styles explained above to create atoms that are outside the simulation box; they will just be ignored by LAMMPS. This is true even if you are using shrink-wrapped box boundaries, as specified by the "boundary"_boundary.html command. However, you can first use the "change_box"_change_box.html command to temporarily expand the box, then add atoms via create_atoms, then finally use change_box command again if needed to re-shrink-wrap the new atoms. See the "change_box"_change_box.html doc page for an example of how to do this, using the create_atoms {single} style to insert a new atom outside the current simulation box. :line Individual atoms are inserted by this command, unless the {mol} Loading
