These are pair styles contributed by users, which can be used if diff --git a/doc/Section_commands.txt b/doc/Section_commands.txt index ac2a2bb19d..fc8e881c27 100644 --- a/doc/Section_commands.txt +++ b/doc/Section_commands.txt @@ -627,6 +627,7 @@ potentials. Click on the style itself for a full description: "adp"_pair_adp.html, "airebo"_pair_airebo.html, "beck"_pair_beck.html, +"bop"_pair_bop.html, "born"_pair_born.html, "born/coul/long"_pair_born.html, "born/coul/wolf"_pair_born.html, diff --git a/doc/Section_start.html b/doc/Section_start.html index e071e8182b..eef8e51a83 100644 --- a/doc/Section_start.html +++ b/doc/Section_start.html @@ -223,11 +223,14 @@ Restrictions section of the dump command for details.
Use at most one of the -DLAMMPS_SMALLBIG, -DLAMMPS_BIGBIG, -D-DLAMMPS_SMALLSMALL settings. The default is -DLAMMPS_SMALLBIG. -These refer to use of 4-byte (small) vs 8-byte (big) integers within -LAMMPS, as described in src/lmptype.h. The only reason to use the -BIGBIG setting is to enable simulation of huge molecular systems with -more than 2 billion atoms. The only reason to use the SMALLSMALL -setting is if your machine does not support 64-bit integers. +These settings refer to use of 4-byte (small) vs 8-byte (big) integers +within LAMMPS, as specified in src/lmptype.h. The only reason to use +the BIGBIG setting is to enable simulation of huge molecular systems +with more than 2 billion atoms or to allow moving atoms to wrap back +through a periodic box more than 512 times. The only reason to use +the SMALLSMALL setting is if your machine does not support 64-bit +integers. See the Additional build tips section below +for more details.
The -DLAMMPS_LONGLONG_TO_LONG setting may be needed if your system or MPI version does not recognize "long long" data types. In this case a @@ -434,41 +437,46 @@ Obj_target where it stores the system-specific *.o files. files created when LAMMPS is built, for either all builds or for a particular machine.
-(3) Changing the size limits in src/lmptype.h +
(3) Changing the LAMMPS size limits via -DLAMMPS_SMALLBIG or +-DLAMMPS_BIBIG or -DLAMMPS_SMALLSMALL
-If you are running a very large problem (billions of atoms or more) -and get a run-time error about the system being too big, either on a -per-processor basis or in total size, then you may need to change one -or more settings in src/lmptype.h and re-compile LAMMPS. +
As explained above, any of these 3 settings can be specified on the +LMP_INC line in your low-level src/MAKE/Makefile.foo.
-As the documentation in that file explains, you have basically -two choices to make: +
The default is -DLAMMPS_SMALLBIG which allows for systems with up to +2^63 atoms and timesteps (about 9 billion billion). The atom limit is +for atomic systems that do not require atom IDs. For molecular +models, which require atom IDs, the limit is 2^31 atoms (about 2 +billion). With this setting, image flags are stored in 32-bit +integers, which means for 3 dimensions that atoms can only wrap around +a periodic box at most 512 times. If atoms move through the periodic +box more than this limit, the image flags will "roll over", e.g. from +511 to -512, which can cause diagnostics like the mean-squared +displacement, as calculated by the compute msd +command, to be faulty.
-The default for atom IDs is 4-byte integers since there is a memory -and communication cost for 8-byte integers. Non-molecular problems do -not need atom IDs so this does not restrict their size. Molecular -problems (which use IDs to define molecular topology), are limited to -about 2 billion atoms (2^31) with 4-byte IDs. With 8-byte IDs they -are effectively unlimited in size (2^63). +
To allow for larger molecular systems or larger image flags, compile +with -DLAMMPS_BIGBIG. This enables molecular systems with up to 2^63 +atoms (about 9 billion billion). And image flags will not "roll over" +until they reach 2^20 = 1048576.
-The default for total system size quantities (like the number of atoms -or timesteps) is 8-byte integers by default which is effectively -unlimited in size (2^63). If your system or MPI implementation does -not support 8-byte integers, an error will be generated, and you will -need to set "bigint" to 4-byte integers. This restricts your total -system size to about 2 billion atoms or timesteps (2^31). +
IMPORTANT NOTE: As of 6/2012, the BIGBIG setting does not yet enable +molecular systems to grow as large as 2^63. Only the image flag roll +over is currently affected by this compile option. +
+If your system does not support 8-byte integers, you will need to +compile with the -DLAMMPS_SMALLSMALL setting. This will restrict your +total number of atoms (for atomic or molecular models) and timesteps +to 2^31 (about 2 billion). Image flags will roll over at 2^9 = 512.
Note that in src/lmptype.h there are also settings for the MPI data types associated with the integers that store atom IDs and total -system sizes, which need to be set consistent with the associated C -data types. +system sizes. These need to be consistent with the associated C data +types, or else LAMMPS will generate a run-time error.
In all cases, the size of problem that can be run on a per-processor -basis is limited by 4-byte integer storage to about 2 billion atoms -per processor (2^31), which should not normally be a restriction since +basis is limited by 4-byte integer storage to 2^31 atoms per processor +(about 2 billion). This should not normally be a restriction since such a problem would have a huge per-processor memory footprint due to neighbor lists and would run very slowly in terms of CPU secs/timestep. diff --git a/doc/Section_start.txt b/doc/Section_start.txt index 3d07fd2613..d0641e3097 100644 --- a/doc/Section_start.txt +++ b/doc/Section_start.txt @@ -217,11 +217,14 @@ Restrictions section of the "dump"_dump.html command for details. Use at most one of the -DLAMMPS_SMALLBIG, -DLAMMPS_BIGBIG, -D-DLAMMPS_SMALLSMALL settings. The default is -DLAMMPS_SMALLBIG. -These refer to use of 4-byte (small) vs 8-byte (big) integers within -LAMMPS, as described in src/lmptype.h. The only reason to use the -BIGBIG setting is to enable simulation of huge molecular systems with -more than 2 billion atoms. The only reason to use the SMALLSMALL -setting is if your machine does not support 64-bit integers. +These settings refer to use of 4-byte (small) vs 8-byte (big) integers +within LAMMPS, as specified in src/lmptype.h. The only reason to use +the BIGBIG setting is to enable simulation of huge molecular systems +with more than 2 billion atoms or to allow moving atoms to wrap back +through a periodic box more than 512 times. The only reason to use +the SMALLSMALL setting is if your machine does not support 64-bit +integers. See the "Additional build tips"_#start_2_4 section below +for more details. The -DLAMMPS_LONGLONG_TO_LONG setting may be needed if your system or MPI version does not recognize "long long" data types. In this case a @@ -428,41 +431,46 @@ Typing "make clean-all" or "make clean-foo" will delete *.o object files created when LAMMPS is built, for either all builds or for a particular machine. -(3) Changing the size limits in src/lmptype.h +(3) Changing the LAMMPS size limits via -DLAMMPS_SMALLBIG or +-DLAMMPS_BIBIG or -DLAMMPS_SMALLSMALL -If you are running a very large problem (billions of atoms or more) -and get a run-time error about the system being too big, either on a -per-processor basis or in total size, then you may need to change one -or more settings in src/lmptype.h and re-compile LAMMPS. +As explained above, any of these 3 settings can be specified on the +LMP_INC line in your low-level src/MAKE/Makefile.foo. -As the documentation in that file explains, you have basically -two choices to make: +The default is -DLAMMPS_SMALLBIG which allows for systems with up to +2^63 atoms and timesteps (about 9 billion billion). The atom limit is +for atomic systems that do not require atom IDs. For molecular +models, which require atom IDs, the limit is 2^31 atoms (about 2 +billion). With this setting, image flags are stored in 32-bit +integers, which means for 3 dimensions that atoms can only wrap around +a periodic box at most 512 times. If atoms move through the periodic +box more than this limit, the image flags will "roll over", e.g. from +511 to -512, which can cause diagnostics like the mean-squared +displacement, as calculated by the "compute msd"_compute_msd.html +command, to be faulty. -set the data type size of integer atom IDs to 4 or 8 bytes -set the data type size of integers that store the total system size to 4 or 8 bytes :ul +To allow for larger molecular systems or larger image flags, compile +with -DLAMMPS_BIGBIG. This enables molecular systems with up to 2^63 +atoms (about 9 billion billion). And image flags will not "roll over" +until they reach 2^20 = 1048576. -The default for atom IDs is 4-byte integers since there is a memory -and communication cost for 8-byte integers. Non-molecular problems do -not need atom IDs so this does not restrict their size. Molecular -problems (which use IDs to define molecular topology), are limited to -about 2 billion atoms (2^31) with 4-byte IDs. With 8-byte IDs they -are effectively unlimited in size (2^63). +IMPORTANT NOTE: As of 6/2012, the BIGBIG setting does not yet enable +molecular systems to grow as large as 2^63. Only the image flag roll +over is currently affected by this compile option. -The default for total system size quantities (like the number of atoms -or timesteps) is 8-byte integers by default which is effectively -unlimited in size (2^63). If your system or MPI implementation does -not support 8-byte integers, an error will be generated, and you will -need to set "bigint" to 4-byte integers. This restricts your total -system size to about 2 billion atoms or timesteps (2^31). +If your system does not support 8-byte integers, you will need to +compile with the -DLAMMPS_SMALLSMALL setting. This will restrict your +total number of atoms (for atomic or molecular models) and timesteps +to 2^31 (about 2 billion). Image flags will roll over at 2^9 = 512. Note that in src/lmptype.h there are also settings for the MPI data types associated with the integers that store atom IDs and total -system sizes, which need to be set consistent with the associated C -data types. +system sizes. These need to be consistent with the associated C data +types, or else LAMMPS will generate a run-time error. In all cases, the size of problem that can be run on a per-processor -basis is limited by 4-byte integer storage to about 2 billion atoms -per processor (2^31), which should not normally be a restriction since +basis is limited by 4-byte integer storage to 2^31 atoms per processor +(about 2 billion). This should not normally be a restriction since such a problem would have a huge per-processor memory footprint due to neighbor lists and would run very slowly in terms of CPU secs/timestep. diff --git a/doc/pair_airebo.html b/doc/pair_airebo.html index 42502af09d..2cb34a2195 100644 --- a/doc/pair_airebo.html +++ b/doc/pair_airebo.html @@ -92,6 +92,8 @@ would be 10.2 Angstroms.
The E_TORSION term is an explicit 4-body potential that describes various dihedral angle preferences in hydrocarbon configurations.
+Only a single pair_coeff command is used with the airebo or rebo style which specifies an AIREBO potential file with parameters for C and H. Note that the rebo style in LAMMPS uses the same diff --git a/doc/pair_airebo.txt b/doc/pair_airebo.txt index 0d76804a05..59313a27a5 100644 --- a/doc/pair_airebo.txt +++ b/doc/pair_airebo.txt @@ -86,6 +86,8 @@ would be 10.2 Angstroms. The E_TORSION term is an explicit 4-body potential that describes various dihedral angle preferences in hydrocarbon configurations. +:line + Only a single pair_coeff command is used with the {airebo} or {rebo} style which specifies an AIREBO potential file with parameters for C and H. Note that the {rebo} style in LAMMPS uses the same diff --git a/doc/pair_coeff.html b/doc/pair_coeff.html index 1f47c40b39..942428e17b 100644 --- a/doc/pair_coeff.html +++ b/doc/pair_coeff.html @@ -99,6 +99,7 @@ section of this page.