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@ -711,13 +711,14 @@ or USER-AWPMD packages.
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</P>
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<P>For libraries without provided source code, see the
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src/package/Makefile.lammps file for information on where to find the
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library and how to build it. E.g. the file src/KIM/Makefile.lammps.
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This file serves the same purpose as the lib/package/Makefile.lammps
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file described above. It has settings needed when LAMMPS is built to
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link with the auxiliary library. Again, you MUST insure that the
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settings in src/package/Makefile.lammps are appropriate for your
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system and where you installed the auxiliary library. If they are
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not, the LAMMPS build will fail.
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library and how to build it. E.g. the file src/KIM/Makefile.lammps or
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src/VORONOI/Makefile.lammps or src/UESR-MOLFILE/Makefile.lammps.
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These files serve the same purpose as the lib/package/Makefile.lammps
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files described above. The files have settings needed when LAMMPS is
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built to link with the corresponding auxiliary library. Again, you
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MUST insure that the settings in src/package/Makefile.lammps are
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appropriate for your system and where you installed the auxiliary
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library. If they are not, the LAMMPS build will fail.
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</P>
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<HR>
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@ -705,13 +705,14 @@ or USER-AWPMD packages.
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For libraries without provided source code, see the
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src/package/Makefile.lammps file for information on where to find the
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library and how to build it. E.g. the file src/KIM/Makefile.lammps.
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This file serves the same purpose as the lib/package/Makefile.lammps
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file described above. It has settings needed when LAMMPS is built to
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link with the auxiliary library. Again, you MUST insure that the
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settings in src/package/Makefile.lammps are appropriate for your
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system and where you installed the auxiliary library. If they are
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not, the LAMMPS build will fail.
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library and how to build it. E.g. the file src/KIM/Makefile.lammps or
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src/VORONOI/Makefile.lammps or src/UESR-MOLFILE/Makefile.lammps.
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These files serve the same purpose as the lib/package/Makefile.lammps
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files described above. The files have settings needed when LAMMPS is
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built to link with the corresponding auxiliary library. Again, you
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MUST insure that the settings in src/package/Makefile.lammps are
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appropriate for your system and where you installed the auxiliary
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library. If they are not, the LAMMPS build will fail.
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:line
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@ -438,24 +438,52 @@ for atom_style hybrid dipole full would list "q" twice:
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</P>
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<PRE>atom-ID atom-type x y z q mux muy myz molecule-ID q
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</PRE>
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<P>Atom lines (all lines or none of them) can optionally list 3 trailing
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integer values: nx,ny,nz. For periodic dimensions, they specify which
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image of the simulation box the atom is considered to be in. An image
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of 0 means it is inside the box as defined. A value of 2 means add 2
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box lengths to get the true value. A value of -1 means subtract 1 box
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length to get the true value. LAMMPS updates these flags as atoms
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cross periodic boundaries during the simulation. The flags can be
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output with atom snapshots via the <A HREF = "dump.html">dump</A> command.
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<P>Atom lines specify the (x,y,z) coordinates of atoms. These can be
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inside or outside the simulation box. When the data file is read,
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LAMMPS wraps coordinates outside the box back into the box for
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dimensions that are periodic. As discussed above, if an atom is
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outside the box in a non-periodic dimension, it will be lost.
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</P>
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<P>If nx,ny,nz values are not set in the data file, LAMMPS initializes
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them to 0. If image information is needed for later analysis and they
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are not all initially 0, it's important to set them correctly in the
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data file. Also, if you plan to use the <A HREF = "replicate.html">replicate</A>
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command to generate a larger system, these flags must be listed
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correctly for bonded atoms when the bond crosses a periodic boundary.
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I.e. the values of the image flags should be different by 1 (in the
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appropriate dimension) for the two atoms in such a bond.
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<P>LAMMPS always stores atom coordinates as values which are inside the
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simulation box. It also stores 3 flags which indicate which image of
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the simulation box (in each dimension) the atom would be in if its
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coordinates were unwrapped across periodic boundaries. An image flag
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of 0 means the atom is still inside the box when unwrapped. A value
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of 2 means add 2 box lengths to get the unwrapped coordinate. A value
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of -1 means subtract 1 box length to get the unwrapped coordinate.
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LAMMPS updates these flags as atoms cross periodic boundaries during
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the simulation. The <A HREF = "dump.html">dump</A> command can output atom atom
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coordinates in wrapped or unwrapped form, as well as the 3 image
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flags.
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</P>
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<P>In the data file, atom lines (all lines or none of them) can
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optionally list 3 trailing integer values (nx,ny,nz), which are used
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to initialize the atom's image flags. If nx,ny,nz values are not
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listed in the data file, LAMMPS initializes them to 0. Note that the
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image flags are immediately updated if an atom's coordinates need to
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wrapped back into the simulation box.
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</P>
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<P>It is only important to set image flags correctly in a data file if a
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simulation model relies on unwrapped coordinates for some calculation;
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otherwise they can be left unspecified. Examples of LAMMPS commands
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that use unwrapped coordinates internally are as follows:
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</P>
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<UL><LI>Atoms in a rigid body (see <A HREF = "fix_rigid.html">fix rigid</A>, <A HREF = "fix_rigid.html">fix
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rigid/small</A>) must have consistent image flags, so that
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when the atoms are unwrapped, they are near each other, i.e. as a
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single body.
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<LI>If the <A HREF = "replicate.html">replicate</A> command is used to generate a larger
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system, image flags must be consistent for bonded atoms when the bond
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crosses a periodic boundary. I.e. the values of the image flags
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should be different by 1 (in the appropriate dimension) for the two
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atoms in such a bond.
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<LI>If you plan to <A HREF = "dump.html">dump</A> image flags and perform post-analysis
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that will unwrap atom coordinates, it may be important that a
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continued run (restarted from a data file) begins with image flags
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that are consistent with the previous run.
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</UL>
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<P>Atom velocities and other atom quantities not defined above are set to
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0.0 when the <I>Atoms</I> section is read. Velocities can be set later by
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a <I>Velocities</I> section in the data file or by a
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@ -414,23 +414,51 @@ for atom_style hybrid dipole full would list "q" twice:
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atom-ID atom-type x y z q mux muy myz molecule-ID q :pre
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Atom lines (all lines or none of them) can optionally list 3 trailing
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integer values: nx,ny,nz. For periodic dimensions, they specify which
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image of the simulation box the atom is considered to be in. An image
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of 0 means it is inside the box as defined. A value of 2 means add 2
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box lengths to get the true value. A value of -1 means subtract 1 box
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length to get the true value. LAMMPS updates these flags as atoms
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cross periodic boundaries during the simulation. The flags can be
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output with atom snapshots via the "dump"_dump.html command.
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Atom lines specify the (x,y,z) coordinates of atoms. These can be
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inside or outside the simulation box. When the data file is read,
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LAMMPS wraps coordinates outside the box back into the box for
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dimensions that are periodic. As discussed above, if an atom is
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outside the box in a non-periodic dimension, it will be lost.
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If nx,ny,nz values are not set in the data file, LAMMPS initializes
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them to 0. If image information is needed for later analysis and they
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are not all initially 0, it's important to set them correctly in the
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data file. Also, if you plan to use the "replicate"_replicate.html
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command to generate a larger system, these flags must be listed
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correctly for bonded atoms when the bond crosses a periodic boundary.
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I.e. the values of the image flags should be different by 1 (in the
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appropriate dimension) for the two atoms in such a bond.
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LAMMPS always stores atom coordinates as values which are inside the
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simulation box. It also stores 3 flags which indicate which image of
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the simulation box (in each dimension) the atom would be in if its
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coordinates were unwrapped across periodic boundaries. An image flag
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of 0 means the atom is still inside the box when unwrapped. A value
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of 2 means add 2 box lengths to get the unwrapped coordinate. A value
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of -1 means subtract 1 box length to get the unwrapped coordinate.
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LAMMPS updates these flags as atoms cross periodic boundaries during
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the simulation. The "dump"_dump.html command can output atom atom
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coordinates in wrapped or unwrapped form, as well as the 3 image
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flags.
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In the data file, atom lines (all lines or none of them) can
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optionally list 3 trailing integer values (nx,ny,nz), which are used
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to initialize the atom's image flags. If nx,ny,nz values are not
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listed in the data file, LAMMPS initializes them to 0. Note that the
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image flags are immediately updated if an atom's coordinates need to
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wrapped back into the simulation box.
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It is only important to set image flags correctly in a data file if a
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simulation model relies on unwrapped coordinates for some calculation;
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otherwise they can be left unspecified. Examples of LAMMPS commands
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that use unwrapped coordinates internally are as follows:
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Atoms in a rigid body (see "fix rigid"_fix_rigid.html, "fix
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rigid/small"_fix_rigid.html) must have consistent image flags, so that
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when the atoms are unwrapped, they are near each other, i.e. as a
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single body. :ulb,l
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If the "replicate"_replicate.html command is used to generate a larger
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system, image flags must be consistent for bonded atoms when the bond
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crosses a periodic boundary. I.e. the values of the image flags
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should be different by 1 (in the appropriate dimension) for the two
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atoms in such a bond. :l
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If you plan to "dump"_dump.html image flags and perform post-analysis
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that will unwrap atom coordinates, it may be important that a
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continued run (restarted from a data file) begins with image flags
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that are consistent with the previous run. :l,ule
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Atom velocities and other atom quantities not defined above are set to
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0.0 when the {Atoms} section is read. Velocities can be set later by
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|
|
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