Warning
-Setting core affinity is often used to pin MPI tasks -and OpenMP threads to a core or group of cores so that memory access -can be uniform. Unless disabled at build time, affinity for MPI tasks -and OpenMP threads on the host (CPU) will be set by default on the -host when using offload to a coprocessor. In this case, it is -unnecessary to use other methods to control affinity (e.g. taskset, -numactl, I_MPI_PIN_DOMAIN, etc.). This can be disabled in an input -script with the no_affinity option to the package intel command or by disabling the option at build time -(by adding -DINTEL_OFFLOAD_NOAFFINITY to the CCFLAGS line of your -Makefile). Disabling this option is not recommended, especially when -running on a machine with hyperthreading disabled.
+Note
+Setting core affinity is often used to pin MPI tasks and OpenMP +threads to a core or group of cores so that memory access can be +uniform. Unless disabled at build time, affinity for MPI tasks and +OpenMP threads on the host (CPU) will be set by default on the host +when using offload to a coprocessor. In this case, it is unnecessary +to use other methods to control affinity (e.g. taskset, numactl, +I_MPI_PIN_DOMAIN, etc.). This can be disabled in an input script with +the no_affinity option to the package intel command +or by disabling the option at build time (by adding +-DINTEL_OFFLOAD_NOAFFINITY to the CCFLAGS line of your Makefile). +Disabling this option is not recommended, especially when running on a +machine with hyperthreading disabled.
Guidelines for best performance on an Intel(R) Xeon Phi(TM) coprocessor:
@@ -406,7 +407,7 @@ supported.- © Copyright . + © Copyright 2013 Sandia Corporation.
Warning
-For good performance of the KOKKOS package on GPUs, -you must have Kepler generation GPUs (or later). The Kokkos library -exploits texture cache options not supported by Telsa generation GPUs -(or older).
+Note
+For good performance of the KOKKOS package on GPUs, you must +have Kepler generation GPUs (or later). The Kokkos library exploits +texture cache options not supported by Telsa generation GPUs (or +older).
To build with Kokkos support for Intel Xeon Phi coprocessors, your sysmte must be configured to use them in “native” mode, not “offload” @@ -272,14 +272,13 @@ make cuda KOKKOS_DEVICES=Cuda
These examples set the KOKKOS-specific OMP, MIC, CUDA variables on the make command line which requires a GNU-compatible make command. Try “gmake” if your system’s standard make complains.
-Warning
-If you build using make line variables and re-build -LAMMPS twice with different KOKKOS options and the same target, -e.g. g++ in the first two examples above, then you must perform a -“make clean-all” or “make clean-machine” before each build. This is -to force all the KOKKOS-dependent files to be re-compiled with the new -options.
+Note
+If you build using make line variables and re-build LAMMPS twice +with different KOKKOS options and the same target, e.g. g++ in the +first two examples above, then you must perform a “make clean-all” +or “make clean-machine” before each build. This is to force all the +KOKKOS-dependent files to be re-compiled with the new options.
You can also hardwire these make variables in the specified machine makefile, e.g. src/MAKE/Makefile.g++ in the first two examples above, @@ -291,23 +290,22 @@ with a line like:
different KOKKOS options (defined in different machine makefiles), you do not have to worry about doing a “clean” in between. This is because the targets will be different. -Warning
-The 3rd example above for a GPU, uses a different -machine makefile, in this case src/MAKE/Makefile.cuda, which is -included in the LAMMPS distribution. To build the KOKKOS package for -a GPU, this makefile must use the NVIDA “nvcc” compiler. And it must -have a KOKKOS_ARCH setting that is appropriate for your NVIDIA -hardware and installed software. Typical values for KOKKOS_ARCH are given -below, as well -as other settings that must be included in the machine makefile, if -you create your own.
+Note
+The 3rd example above for a GPU, uses a different machine +makefile, in this case src/MAKE/Makefile.cuda, which is included in +the LAMMPS distribution. To build the KOKKOS package for a GPU, this +makefile must use the NVIDA “nvcc” compiler. And it must have a +KOKKOS_ARCH setting that is appropriate for your NVIDIA hardware and +installed software. Typical values for KOKKOS_ARCH are given below, +as well as other settings that must be included in the machine +makefile, if you create your own.
Warning
-Currently, there are no precision options with the -KOKKOS package. All compilation and computation is performed in -double precision.
+Note
+Currently, there are no precision options with the KOKKOS +package. All compilation and computation is performed in double +precision.
There are other allowed options when building with the KOKKOS package. As above, they can be set either as variables on the make command line @@ -508,13 +506,13 @@ threads/task to a smaller value. This is because using all the cores on a dual-socket node will incur extra cost to copy memory from the 2nd socket to the GPU.
Examples of mpirun commands that follow these rules are shown above.
-Warning
-When using a GPU, you will achieve the best -performance if your input script does not use any fix or compute -styles which are not yet Kokkos-enabled. This allows data to stay on -the GPU for multiple timesteps, without being copied back to the host -CPU. Invoking a non-Kokkos fix or compute, or performing I/O for +
Note
+When using a GPU, you will achieve the best performance if your +input script does not use any fix or compute styles which are not yet +Kokkos-enabled. This allows data to stay on the GPU for multiple +timesteps, without being copied back to the host CPU. Invoking a +non-Kokkos fix or compute, or performing I/O for thermo or dump output will cause data to be copied back to the CPU.
- © Copyright . + © Copyright 2013 Sandia Corporation.
Restrictions¶
@@ -283,7 +282,7 @@ issue.- © Copyright . + © Copyright 2013 Sandia Corporation.
- © Copyright . + © Copyright 2013 Sandia Corporation.
- © Copyright . + © Copyright 2013 Sandia Corporation.
- © Copyright . + © Copyright 2013 Sandia Corporation.
- © Copyright . + © Copyright 2013 Sandia Corporation.
- © Copyright . + © Copyright 2013 Sandia Corporation.
- © Copyright . + © Copyright 2013 Sandia Corporation.
- © Copyright . + © Copyright 2013 Sandia Corporation.
- © Copyright . + © Copyright 2013 Sandia Corporation.
- © Copyright . + © Copyright 2013 Sandia Corporation.
- © Copyright . + © Copyright 2013 Sandia Corporation.
The torque on the dipole can be obtained by differentiating the potential using the ‘chain rule’ as in appendix C.3 of -(Allen):
+(Allen):
Example: if gamma0 is set to 0 degrees, the torque generated by the potential will tend to align the dipole along the reference @@ -200,16 +200,16 @@ more instructions on how to use the accelerated styles effectively.
This angle style can only be used if LAMMPS was built with the USER-MISC package. See the Making LAMMPS section for more info on packages.
-Warning
-In the “Angles” section of the data file, the atom ID -‘j’ corresponding to the dipole to restrain must come before the atom -ID of the reference atom ‘i’. A third atom ID ‘k’ must also be -provided, although ‘k’ is just a ‘dummy’ atom which can be any atom; -it may be useful to choose a convention (e.g., ‘k’=’i’) and adhere to -it. For example, if ID=1 for the dipolar atom to restrain, and ID=2 -for the reference atom, the corresponding line in the “Angles” section -of the data file would read: X X 1 2 2
+Note
+In the “Angles” section of the data file, the atom ID ‘j’ +corresponding to the dipole to restrain must come before the atom ID +of the reference atom ‘i’. A third atom ID ‘k’ must also be provided, +although ‘k’ is just a ‘dummy’ atom which can be any atom; it may be +useful to choose a convention (e.g., ‘k’=’i’) and adhere to it. For +example, if ID=1 for the dipolar atom to restrain, and ID=2 for the +reference atom, the corresponding line in the “Angles” section of the +data file would read: X X 1 2 2
The “newton” command for intramolecular interactions must be “on” (which is the default).
@@ -237,7 +237,7 @@ Clarendon Press, Oxford, 1987.- © Copyright . + © Copyright 2013 Sandia Corporation.
- © Copyright . + © Copyright 2013 Sandia Corporation.
- © Copyright . + © Copyright 2013 Sandia Corporation.
- © Copyright . + © Copyright 2013 Sandia Corporation.
- © Copyright . + © Copyright 2013 Sandia Corporation.
- © Copyright . + © Copyright 2013 Sandia Corporation.
- © Copyright . + © Copyright 2013 Sandia Corporation.
- © Copyright . + © Copyright 2013 Sandia Corporation.
Warning
+Note
When both an angle and pair style is defined, the special_bonds command often needs to be used to turn off (or weight) the pairwise interaction that would otherwise @@ -222,7 +222,7 @@ package.
- © Copyright . + © Copyright 2013 Sandia Corporation.
- © Copyright . + © Copyright 2013 Sandia Corporation.
Warning
-Running a simulation with sorting on versus off should -not change the simulation results in a statistical sense. However, a +
Note
+Running a simulation with sorting on versus off should not +change the simulation results in a statistical sense. However, a different ordering will induce round-off differences, which will lead to diverging trajectories over time when comparing two simluations. Various commands, particularly those which use random numbers @@ -288,7 +288,7 @@ cutoff will be used to set the bin size.
- © Copyright . + © Copyright 2013 Sandia Corporation.
Warning
-It is possible to add some attributes, such as a -molecule ID, to atom styles that do not have them via the fix property/atom command. This command also +
Note
+It is possible to add some attributes, such as a molecule ID, to +atom styles that do not have them via the fix property/atom command. This command also allows new custom attributes consisting of extra integer or floating-point values to be added to atoms. See the fix property/atom doc page for examples of cases where this is useful and details on how to initialize, access, and @@ -325,8 +325,8 @@ can save memory for systems comprised of a large number of small molecules, all of a single type (or small number of types). See the paper by Grime and Voth, in (Grime), for examples of how this can be advantageous for large-scale coarse-grained systems.
-Warning
+Note
When using the template style with a molecule template that contains multiple molecules, you should
insure the atom types, bond types, angle_types, etc in all the
molecules are consistent. E.g. if one molecule represents H2O and
@@ -427,7 +427,7 @@ only enabled if LAMMPS was built with that package. See the
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
Warning
-Balancing is performed even if the imbalance factor -does not exceed the thresh parameter if a “grid” style is specified -when the current partitioning is “tiled”. The meaning of “grid” vs -“tiled” is explained below. This is to allow forcing of the -partitioning to “grid” so that the comm_style brick -command can then be used to replace a current comm_style tiled setting.
+Note
+Balancing is performed even if the imbalance factor does not +exceed the thresh parameter if a “grid” style is specified when the +current partitioning is “tiled”. The meaning of “grid” vs “tiled” is +explained below. This is to allow forcing of the partitioning to +“grid” so that the comm_style brick command can then +be used to replace a current comm_style tiled +setting.
When the balance command completes, it prints statistics about the result, including the change in the imbalance factor and the change in @@ -225,32 +226,30 @@ the maximum number of particles on any processor. For “grid” method (defined below) that create a logical 3d grid of processors, the positions of all cutting planes in each of the 3 dimensions (as fractions of the box length) are also printed.
-Warning
-This command attempts to minimize the imbalance -factor, as defined above. But depending on the method a perfect -balance (1.0) may not be achieved. For example, “grid” methods -(defined below) that create a logical 3d grid cannot achieve perfect -balance for many irregular distributions of particles. Likewise, if a -portion of the system is a perfect lattice, e.g. the intiial system is -generated by the create_atoms command, then “grid” -methods may be unable to achieve exact balance. This is because -entire lattice planes will be owned or not owned by a single -processor.
+Note
+This command attempts to minimize the imbalance factor, as +defined above. But depending on the method a perfect balance (1.0) +may not be achieved. For example, “grid” methods (defined below) that +create a logical 3d grid cannot achieve perfect balance for many +irregular distributions of particles. Likewise, if a portion of the +system is a perfect lattice, e.g. the intiial system is generated by +the create_atoms command, then “grid” methods may +be unable to achieve exact balance. This is because entire lattice +planes will be owned or not owned by a single processor.
Warning
-The imbalance factor is also an estimate of the -maximum speed-up you can hope to achieve by running a perfectly -balanced simulation versus an imbalanced one. In the example above, -the 10000 particle simulation could run up to 20% faster if it were -perfectly balanced, versus when imbalanced. However, computational -cost is not strictly proportional to particle count, and changing the -relative size and shape of processor sub-domains may lead to -additional computational and communication overheads, e.g. in the PPPM -solver used via the kspace_style command. Thus -you should benchmark the run times of a simulation before and after -balancing.
+Note
+The imbalance factor is also an estimate of the maximum speed-up +you can hope to achieve by running a perfectly balanced simulation +versus an imbalanced one. In the example above, the 10000 particle +simulation could run up to 20% faster if it were perfectly balanced, +versus when imbalanced. However, computational cost is not strictly +proportional to particle count, and changing the relative size and +shape of processor sub-domains may lead to additional computational +and communication overheads, e.g. in the PPPM solver used via the +kspace_style command. Thus you should benchmark +the run times of a simulation before and after balancing.
The method used to perform a load balance is specified by one of the @@ -374,16 +373,16 @@ plane gets closer to the target value.
Once the rebalancing is complete and final processor sub-domains assigned, particles are migrated to their new owning processor, and the balance procedure ends.
-Warning
-At each rebalance operation, the bisectioning for each -cutting plane (line in 2d) typcially starts with low and high bounds -separated by the extent of a processor’s sub-domain in one dimension. -The size of this bracketing region shrinks by 1/2 every iteration. -Thus if Niter is specified as 10, the cutting plane will typically -be positioned to 1 part in 1000 accuracy (relative to the perfect -target position). For Niter = 20, it will be accurate to 1 part in -a million. Thus there is no need ot set Niter to a large value. +
Note
+At each rebalance operation, the bisectioning for each cutting +plane (line in 2d) typcially starts with low and high bounds separated +by the extent of a processor’s sub-domain in one dimension. The size +of this bracketing region shrinks by 1/2 every iteration. Thus if +Niter is specified as 10, the cutting plane will typically be +positioned to 1 part in 1000 accuracy (relative to the perfect target +position). For Niter = 20, it will be accurate to 1 part in a +million. Thus there is no need ot set Niter to a large value. LAMMPS will check if the threshold accuracy is reached (in a dimension) is less iterations than Niter and exit early. However, Niter should also not be set too small, since it will take roughly @@ -488,7 +487,7 @@ appear in dimstr for the shift style.
- © Copyright . + © Copyright 2013 Sandia Corporation.
- © Copyright . + © Copyright 2013 Sandia Corporation.
- © Copyright . + © Copyright 2013 Sandia Corporation.
- © Copyright . + © Copyright 2013 Sandia Corporation.
- © Copyright . + © Copyright 2013 Sandia Corporation.
- © Copyright . + © Copyright 2013 Sandia Corporation.
- © Copyright . + © Copyright 2013 Sandia Corporation.
- © Copyright . + © Copyright 2013 Sandia Corporation.
- © Copyright . + © Copyright 2013 Sandia Corporation.
- © Copyright . + © Copyright 2013 Sandia Corporation.
- © Copyright . + © Copyright 2013 Sandia Corporation.
- © Copyright . + © Copyright 2013 Sandia Corporation.
- © Copyright . + © Copyright 2013 Sandia Corporation.
- © Copyright . + © Copyright 2013 Sandia Corporation.
Warning
+Note
When both a bond and pair style is defined, the special_bonds command often needs to be used to turn off (or weight) the pairwise interaction that would otherwise @@ -230,7 +230,7 @@ package.
- © Copyright . + © Copyright 2013 Sandia Corporation.
- © Copyright . + © Copyright 2013 Sandia Corporation.
- © Copyright . + © Copyright 2013 Sandia Corporation.
- © Copyright . + © Copyright 2013 Sandia Corporation.
IMPORTANT_NOTE: This means that you cannot use the change_box command +
Note
+This means that you cannot use the change_box command to enlarge a shrink-wrapped box, e.g. to make room to insert more atoms via the create_atoms command, because the simulation box will be re-shrink-wrapped before the change_box command completes. Instead you could do something like this, assuming the simulation box is non-periodic and atoms extend from 0 to 20 in all dimensions:
+change_box all x final -10 20
create_atoms 1 single -5 5 5 # this will fail to insert an atom
Warning
-Unlike the earlier “displace_box” version of this -command, atom remapping is NOT performed by default. This command -allows remapping to be done in a more general way, exactly when you -specify it (zero or more times) in the sequence of transformations. -Thus if you do not use the remap keyword, atom coordinates will not -be changed even if the box size/shape changes. If a uniformly -strained state is desired, the remap keyword should be specified.
+Note
+Unlike the earlier “displace_box” version of this command, atom +remapping is NOT performed by default. This command allows remapping +to be done in a more general way, exactly when you specify it (zero or +more times) in the sequence of transformations. Thus if you do not +use the remap keyword, atom coordinates will not be changed even if +the box size/shape changes. If a uniformly strained state is desired, +the remap keyword should be specified.
Warning
-It is possible to lose atoms with this command. -E.g. by changing the box without remapping the atoms, and having atoms -end up outside of non-periodic boundaries. It is also possible to -alter bonds between atoms straddling a boundary in bad ways. E.g. by +
Note
+It is possible to lose atoms with this command. E.g. by +changing the box without remapping the atoms, and having atoms end up +outside of non-periodic boundaries. It is also possible to alter +bonds between atoms straddling a boundary in bad ways. E.g. by converting a boundary from periodic to non-periodic. It is also possible when remapping atoms to put them (nearly) on top of each other. E.g. by converting a boundary from non-periodic to periodic. All of these will typically lead to bad dynamics and/or generate error messages.
Warning
-The simulation box size/shape can be changed by -arbitrarily large amounts by this command. This is not a problem, -except that the mapping of processors to the simulation box is not -changed from its initial 3d configuration; see the -processors command. Thus, if the box size/shape -changes dramatically, the mapping of processors to the simulation box -may not end up as optimal as the initial mapping attempted to be.
+Note
+The simulation box size/shape can be changed by arbitrarily +large amounts by this command. This is not a problem, except that the +mapping of processors to the simulation box is not changed from its +initial 3d configuration; see the processors +command. Thus, if the box size/shape changes dramatically, the +mapping of processors to the simulation box may not end up as optimal +as the initial mapping attempted to be.
Warning
-Because the keywords used in this command are applied -one at a time to the simulation box and the atoms in it, care must be -taken with triclinic cells to avoid exceeding the limits on skew after -each transformation in the sequence. If skew is exceeded before the -final transformation this can be avoided by changing the order of the +
Note
+Because the keywords used in this command are applied one at a +time to the simulation box and the atoms in it, care must be taken +with triclinic cells to avoid exceeding the limits on skew after each +transformation in the sequence. If skew is exceeded before the final +transformation this can be avoided by changing the order of the sequence, or breaking the transformation into two or more smaller transformations. For more information on the allowed limits for box skew see the discussion on triclinic boxes on this page.
@@ -317,10 +320,10 @@ keep the volume constant:change_box all x scale 1.1 z volume y scale 1.1 z volume
Warning
-For solids or liquids, when one dimension of the box -is expanded, it may be physically undesirable to hold the other 2 box +
Note
+For solids or liquids, when one dimension of the box is
+expanded, it may be physically undesirable to hold the other 2 box
lengths constant since that implies a density change. For solids,
adjusting the other dimensions via the volume style may make
physical sense (just as for a liquid), but may not be correct for
@@ -443,7 +446,7 @@ change_box command is issued, so long as an
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright . + © Copyright 2013 Sandia Corporation.
Warning
-These options apply to the currently defined comm -style. When you specify a comm_style command, all -communication settings are restored to their default values, including -those previously reset by a comm_modify command. Thus if your input -script specifies a comm_style command, you should use the comm_modify -command after it.
+Note
+These options apply to the currently defined comm style. When +you specify a comm_style command, all communication +settings are restored to their default values, including those +previously reset by a comm_modify command. Thus if your input script +specifies a comm_style command, you should use the comm_modify command +after it.
The mode keyword determines whether a single or multiple cutoff distances are used to determine which atoms to communicate.
@@ -228,14 +228,14 @@ atoms beyond the normal pairwise cutoff for some computation it performs (e.g. locate neighbors of ghost atoms in a multibody pair potential). Setting the ghost cutoff appropriately can insure it will find the needed atoms. -Warning
-In these scenarios, if you do not set the ghost cutoff -long enough, and if there is only one processor in a periodic -dimension (e.g. you are running in serial), then LAMMPS may “find” the -atom it is looking for (e.g. the partner atom in a bond), that is on -the far side of the simulation box, across a periodic boundary. This -will typically lead to bad dynamics (i.e. the bond length is now the +
Note
+In these scenarios, if you do not set the ghost cutoff long +enough, and if there is only one processor in a periodic dimension +(e.g. you are running in serial), then LAMMPS may “find” the atom it +is looking for (e.g. the partner atom in a bond), that is on the far +side of the simulation box, across a periodic boundary. This will +typically lead to bad dynamics (i.e. the bond length is now the simulation box length). To detect if this is happening, see the neigh_modify cluster command.
- © Copyright . + © Copyright 2013 Sandia Corporation.
- © Copyright . + © Copyright 2013 Sandia Corporation.
- © Copyright . + © Copyright 2013 Sandia Corporation.
- © Copyright . + © Copyright 2013 Sandia Corporation.
- © Copyright . + © Copyright 2013 Sandia Corporation.
Warning
-The coordinates of an atom contribute to the chunk’s -angular momentum in “unwrapped” form, by using the image flags -associated with each atom. See the dump custom command -for a discussion of “unwrapped” coordinates. See the Atoms section of -the read_data command for a discussion of image flags -and how they are set for each atom. You can reset the image flags +
Note
+The coordinates of an atom contribute to the chunk’s angular +momentum in “unwrapped” form, by using the image flags associated with +each atom. See the dump custom command for a discussion +of “unwrapped” coordinates. See the Atoms section of the +read_data command for a discussion of image flags and +how they are set for each atom. You can reset the image flags (e.g. to 0) before invoking this compute by using the set image command.
The simplest way to output the results of the compute angmom/chunk
@@ -215,7 +215,7 @@ mass-velocity-distance units
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright . + © Copyright 2013 Sandia Corporation.
- © Copyright . + © Copyright 2013 Sandia Corporation.
- © Copyright . + © Copyright 2013 Sandia Corporation.
- © Copyright . + © Copyright 2013 Sandia Corporation.
If the setting is every, which is the default, then chunk IDs are re-calculated on any timestep this compute is invoked.
-Warning
-If you want the persistent chunk-IDs calculated by -this compute to be continuous when running from a restart file, then you should use the same ID for this -compute, as in the original run. This is so that the fix this compute -creates to store per-atom quantities will also have the same ID, and -thus be initialized correctly with chunk IDs from the restart file.
+Note
+If you want the persistent chunk-IDs calculated by this compute +to be continuous when running from a restart file, +then you should use the same ID for this compute, as in the original +run. This is so that the fix this compute creates to store per-atom +quantities will also have the same ID, and thus be initialized +correctly with chunk IDs from the restart file.
The compress keyword applies to all chunk styles and affects how @@ -480,19 +481,19 @@ renumbered to (1,2,3,4,5). The original values (27,...,1000000) can be output to a file by the fix ave/chunk command, or by using the fix ave/time command in conjunction with the compute property/chunk command.
-Warning
-The compression operation requires global -communication across all processors to share their chunk ID values. -It can require large memory on every processor to store them, even -after they are compressed, if there are are a large number of unique -chunk IDs with atoms assigned to them. It uses a STL map to find -unique chunk IDs and store them in sorted order. Each time an atom is -assigned a compressed chunk ID, it must access the STL map. All of -this means that compression can be expensive, both in memory and CPU -time. The use of the limit keyword in conjunction with the -compress keyword can affect these costs, depending on which keyword -is used first. So use this option with care.
+Note
+The compression operation requires global communication across +all processors to share their chunk ID values. It can require large +memory on every processor to store them, even after they are +compressed, if there are are a large number of unique chunk IDs with +atoms assigned to them. It uses a STL map to find unique chunk IDs +and store them in sorted order. Each time an atom is assigned a +compressed chunk ID, it must access the STL map. All of this means +that compression can be expensive, both in memory and CPU time. The +use of the limit keyword in conjunction with the compress keyword +can affect these costs, depending on which keyword is used first. So +use this option with care.
The discard keyword applies to all chunk styles. It affects what @@ -613,7 +614,7 @@ the restarted simulation begins.
- © Copyright . + © Copyright 2013 Sandia Corporation.
Warning
+Note
If you have a bonded system, then the settings of special_bonds command can remove pairwise interactions between atoms in the same bond, angle, or dihedral. This @@ -205,7 +205,7 @@ LAMMPS output options.
- © Copyright . + © Copyright 2013 Sandia Corporation.
- © Copyright . + © Copyright 2013 Sandia Corporation.
A vector of three quantites is calculated by this compute, which are the x,y,z coordinates of the center of mass.
-Warning
-The coordinates of an atom contribute to the -center-of-mass in “unwrapped” form, by using the image flags -associated with each atom. See the dump custom command -for a discussion of “unwrapped” coordinates. See the Atoms section of -the read_data command for a discussion of image flags -and how they are set for each atom. You can reset the image flags +
Note
+The coordinates of an atom contribute to the center-of-mass in +“unwrapped” form, by using the image flags associated with each atom. +See the dump custom command for a discussion of +“unwrapped” coordinates. See the Atoms section of the +read_data command for a discussion of image flags and +how they are set for each atom. You can reset the image flags (e.g. to 0) before invoking this compute by using the set image command.
Output info:
@@ -189,7 +189,7 @@ distance units.- © Copyright . + © Copyright 2013 Sandia Corporation.
Warning
+Note
The coordinates of an atom contribute to the chunk’s center-of-mass in “unwrapped” form, by using the image flags associated with each atom. See the dump custom command @@ -213,7 +213,7 @@ distance units.
- © Copyright . + © Copyright 2013 Sandia Corporation.
- © Copyright . + © Copyright 2013 Sandia Corporation.
Warning
+Note
If you have a bonded system, then the settings of special_bonds command can remove pairwise interactions between atoms in the same bond, angle, or dihedral. This @@ -221,7 +221,7 @@ explained above.
- © Copyright . + © Copyright 2013 Sandia Corporation.
- © Copyright . + © Copyright 2013 Sandia Corporation.
- © Copyright . + © Copyright 2013 Sandia Corporation.
- © Copyright . + © Copyright 2013 Sandia Corporation.
The displacement of an atom is from its original position at the time the compute command was issued. The value of the displacement will be 0.0 for atoms not in the specified compute group.
-Warning
-Initial coordinates are stored in “unwrapped” form, by -using the image flags associated with each atom. See the dump custom command for a discussion of “unwrapped” coordinates. +
Note
+Initial coordinates are stored in “unwrapped” form, by using the +image flags associated with each atom. See the dump custom command for a discussion of “unwrapped” coordinates. See the Atoms section of the read_data command for a discussion of image flags and how they are set for each atom. You can reset the image flags (e.g. to 0) before invoking this compute by using the set image command.
Warning
-If you want the quantities calculated by this compute -to be continuous when running from a restart file, -then you should use the same ID for this compute, as in the original -run. This is so that the fix this compute creates to store per-atom +
Note
+If you want the quantities calculated by this compute to be +continuous when running from a restart file, then +you should use the same ID for this compute, as in the original run. +This is so that the fix this compute creates to store per-atom quantities will also have the same ID, and thus be initialized correctly with time=0 atom coordinates from the restart file.
- © Copyright . + © Copyright 2013 Sandia Corporation.
Warning
-For 2d models, ellipsoidal particles -are treated as ellipsoids, not ellipses, meaning their moments of -inertia will be the same as in 3d.
+Note
+For 2d models, ellipsoidal particles are +treated as ellipsoids, not ellipses, meaning their moments of inertia +will be the same as in 3d.
Output info:
This compute calculates a global scalar (the KE). This value can be @@ -195,7 +195,7 @@ particles.
- © Copyright . + © Copyright 2013 Sandia Corporation.
- © Copyright . + © Copyright 2013 Sandia Corporation.
The rotational energy is computed as 1/2 I w^2, where I is the moment of inertia for a sphere and w is the particle’s angular velocity.
-Warning
-For 2d models, particles are treated -as spheres, not disks, meaning their moment of inertia will be the -same as in 3d.
+Note
+For 2d models, particles are treated as +spheres, not disks, meaning their moment of inertia will be the same +as in 3d.
Output info:
This compute calculates a global scalar (the KE). This value can be @@ -187,7 +187,7 @@ contribute to the rotational energy.
- © Copyright . + © Copyright 2013 Sandia Corporation.
The rotational energy is computed as 1/2 I w^2, where I is the moment of inertia for a sphere and w is the particle’s angular velocity.
-Warning
-For 2d models, particles are treated -as spheres, not disks, meaning their moment of inertia will be the -same as in 3d.
+Note
+For 2d models, particles are treated as +spheres, not disks, meaning their moment of inertia will be the same +as in 3d.
The value of the rotational kinetic energy will be 0.0 for atoms not in the specified compute group or for point particles with a radius = @@ -186,7 +186,7 @@ LAMMPS output options.
- © Copyright . + © Copyright 2013 Sandia Corporation.
- © Copyright . + © Copyright 2013 Sandia Corporation.
IMPORTANT NOTES: This compute command does not take kinetic energy -into account, therefore the masses of the particles should not be -modified between the reference and perturbed states, or along the -alchemical transformation route. This compute command does not change -bond lengths or other internal coordinates (Boresch, Karplus).
+NOTES: This compute command does not take kinetic energy into account, +therefore the masses of the particles should not be modified between +the reference and perturbed states, or along the alchemical +transformation route. This compute command does not change bond +lengths or other internal coordinates (Boresch, Karplus).
The pair attribute enables various parameters of potentials defined by the pair_style and pair_coeff @@ -392,7 +392,7 @@ Liquids, Oxford University Press (1987)
- © Copyright . + © Copyright 2013 Sandia Corporation.
- © Copyright . + © Copyright 2013 Sandia Corporation.
Warning
-The coordinates of an atom contribute to Rg in -“unwrapped” form, by using the image flags associated with each atom. -See the dump custom command for a discussion of -“unwrapped” coordinates. See the Atoms section of the -read_data command for a discussion of image flags and -how they are set for each atom. You can reset the image flags -(e.g. to 0) before invoking this compute by using the set image command.
+Note
+The coordinates of an atom contribute to Rg in “unwrapped” form, +by using the image flags associated with each atom. See the dump custom command for a discussion of “unwrapped” coordinates. +See the Atoms section of the read_data command for a +discussion of image flags and how they are set for each atom. You can +reset the image flags (e.g. to 0) before invoking this compute by +using the set image command.
Output info:
This compute calculates a global scalar (Rg) and a global vector of @@ -202,7 +201,7 @@ distance^2 units re
- © Copyright . + © Copyright 2013 Sandia Corporation.
Warning
-The coordinates of an atom contribute to Rg in -“unwrapped” form, by using the image flags associated with each atom. -See the dump custom command for a discussion of -“unwrapped” coordinates. See the Atoms section of the -read_data command for a discussion of image flags and -how they are set for each atom. You can reset the image flags -(e.g. to 0) before invoking this compute by using the set image command.
+Note
+The coordinates of an atom contribute to Rg in “unwrapped” form, +by using the image flags associated with each atom. See the dump custom command for a discussion of “unwrapped” coordinates. +See the Atoms section of the read_data command for a +discussion of image flags and how they are set for each atom. You can +reset the image flags (e.g. to 0) before invoking this compute by +using the set image command.
The simplest way to output the results of the compute gyration/chunk calculation to a file is to use the fix ave/time @@ -233,7 +232,7 @@ represented by the formula above.
- © Copyright . + © Copyright 2013 Sandia Corporation.
Warning
-The compute pe/atom and -compute stress/atom commands have options -for which terms to include in their calculation (pair, bond, etc). -The heat flux calculation will thus include exactly the same terms. -Normally you should use compute stress/atom virial so as not to include a kinetic energy -term in the heat flux.
+Note
+The compute pe/atom and compute stress/atom commands have options for which +terms to include in their calculation (pair, bond, etc). The heat +flux calculation will thus include exactly the same terms. Normally +you should use compute stress/atom virial +so as not to include a kinetic energy term in the heat flux.
This compute calculates 6 quantities and stores them in a 6-component vector. The first 3 components are the x, y, z components of the full @@ -316,7 +315,7 @@ print "average conductivity: $k[W/mK] @ $T K, ${ndens} /A^3"
- © Copyright . + © Copyright 2013 Sandia Corporation.
Warning
+Note
If you have a bonded system, then the settings of special_bonds command can remove pairwise interactions between atoms in the same bond, angle, or dihedral. This is the default setting for the special_bonds command, and means those pairwise interactions do not appear in the neighbor list. Because this fix uses the neighbor list, it also means -those pairs will not be included in the order parameter. This difficulty -can be circumvented by writing a dump file, and using the -rerun command to compute the order parameter for snapshots -in the dump file. The rerun script can use a +those pairs will not be included in the order parameter. This +difficulty can be circumvented by writing a dump file, and using the +rerun command to compute the order parameter for +snapshots in the dump file. The rerun script can use a special_bonds command that includes all pairs in the neighbor list.
- © Copyright . + © Copyright 2013 Sandia Corporation.
- © Copyright . + © Copyright 2013 Sandia Corporation.
Warning
-The coordinates of an atom contribute to the chunk’s -inertia tensor in “unwrapped” form, by using the image flags -associated with each atom. See the dump custom command -for a discussion of “unwrapped” coordinates. See the Atoms section of -the read_data command for a discussion of image flags -and how they are set for each atom. You can reset the image flags +
Note
+The coordinates of an atom contribute to the chunk’s inertia +tensor in “unwrapped” form, by using the image flags associated with +each atom. See the dump custom command for a discussion +of “unwrapped” coordinates. See the Atoms section of the +read_data command for a discussion of image flags and +how they are set for each atom. You can reset the image flags (e.g. to 0) before invoking this compute by using the set image command.
The simplest way to output the results of the compute inertia/chunk
@@ -214,7 +214,7 @@ mass*distance^2 units
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright . + © Copyright 2013 Sandia Corporation.
- © Copyright . + © Copyright 2013 Sandia Corporation.
Warning
-The temperature in eFF should be monitored via the -compute temp/eff command, which can be printed -with thermodynamic output by using the -thermo_modify command, as shown in the following -example:
+Note
+The temperature in eFF should be monitored via the compute temp/eff command, which can be printed with +thermodynamic output by using the thermo_modify +command, as shown in the following example:
compute effTemp all temp/eff
thermo_style custom step etotal pe ke temp press
@@ -206,7 +204,7 @@ LAMMPS was built with that package. See the
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright . + © Copyright 2013 Sandia Corporation.
- © Copyright . + © Copyright 2013 Sandia Corporation.
- © Copyright . + © Copyright 2013 Sandia Corporation.
- © Copyright . + © Copyright 2013 Sandia Corporation.
- © Copyright . + © Copyright 2013 Sandia Corporation.
- © Copyright . + © Copyright 2013 Sandia Corporation.
Warning
-Initial coordinates are stored in “unwrapped” form, by -using the image flags associated with each atom. See the dump custom command for a discussion of “unwrapped” coordinates. +
Note
+Initial coordinates are stored in “unwrapped” form, by using the +image flags associated with each atom. See the dump custom command for a discussion of “unwrapped” coordinates. See the Atoms section of the read_data command for a discussion of image flags and how they are set for each atom. You can reset the image flags (e.g. to 0) before invoking this compute by using the set image command.
Warning
-If you want the quantities calculated by this compute -to be continuous when running from a restart file, -then you should use the same ID for this compute, as in the original -run. This is so that the fix this compute creates to store per-atom +
Note
+If you want the quantities calculated by this compute to be +continuous when running from a restart file, then +you should use the same ID for this compute, as in the original run. +This is so that the fix this compute creates to store per-atom quantities will also have the same ID, and thus be initialized -correctly with atom reference positions from the restart file. -When average is set to yes, then the atom reference positions -are restored correctly, but not the number of samples used -obtain them. As a result, the reference positions from the restart -file are combined with subsequent positions as if they were from a -single sample, instead of many, which will change the values of msd -somewhat.
+correctly with atom reference positions from the restart file. When +average is set to yes, then the atom reference positions are +restored correctly, but not the number of samples used obtain them. As +a result, the reference positions from the restart file are combined +with subsequent positions as if they were from a single sample, +instead of many, which will change the values of msd somewhat.Output info:
This compute calculates a global vector of length 4, which can be @@ -245,7 +244,7 @@ distance^2 units.
- © Copyright . + © Copyright 2013 Sandia Corporation.
The displacement of the center-of-mass of the chunk is from its original center-of-mass position, calculated on the timestep this compute command was first invoked.
-Warning
-The number of chunks Nchunk calculated by the -compute chunk/atom command must remain -constant each time this compute is invoked, so that the displacement -for each chunk from its original position can be computed -consistently. If Nchunk does not remain constant, an error will be -generated. If needed, you can enforce a constant Nchunk by using -the nchunk once or ids once options when specifying the compute chunk/atom command.
+Note
+The number of chunks Nchunk calculated by the compute chunk/atom command must remain constant each +time this compute is invoked, so that the displacement for each chunk +from its original position can be computed consistently. If Nchunk +does not remain constant, an error will be generated. If needed, you +can enforce a constant Nchunk by using the nchunk once or ids +once options when specifying the compute chunk/atom command.
Warning
+Note
This compute stores the original position (of the center-of-mass) of each chunk. When a displacement is calculated on a later timestep, it is assumed that the same atoms are assigned to the @@ -192,22 +191,22 @@ case, though you can use the ids once option when specifying the this is not the case, the MSD calculation does not have a sensible meaning.
Warning
-The initial coordinates of the atoms in each chunk are -stored in “unwrapped” form, by using the image flags associated with -each atom. See the dump custom command for a discussion -of “unwrapped” coordinates. See the Atoms section of the +
Note
+The initial coordinates of the atoms in each chunk are stored in +“unwrapped” form, by using the image flags associated with each atom. +See the dump custom command for a discussion of +“unwrapped” coordinates. See the Atoms section of the read_data command for a discussion of image flags and how they are set for each atom. You can reset the image flags (e.g. to 0) before invoking this compute by using the set image command.
Warning
-Unlike the compute msd command, -this compute does not store the initial center-of-mass coorindates of -its molecules in a restart file. Thus you cannot continue the MSD per -chunk calculation of this compute when running from a restart file.
+Note
+Unlike the compute msd command, this compute +does not store the initial center-of-mass coorindates of its molecules +in a restart file. Thus you cannot continue the MSD per chunk +calculation of this compute when running from a restart file.
The simplest way to output the results of the compute com/msd calculation to a file is to use the fix ave/time @@ -249,7 +248,7 @@ distance^2 units.
- © Copyright . + © Copyright 2013 Sandia Corporation.
If the com option is set to yes then the effect of any drift in the center-of-mass of the group of atoms is subtracted out before the displacment of each atom is calcluated.
-See the compute msd doc page for further IMPORTANT -NOTES, which also apply to this compute.
+See the compute msd doc page for further important +NOTEs, which also apply to this compute.
Output info:
This compute calculates a global vector of length 3, which can be
accessed by indices 1-3 by any command that uses global vector values
@@ -205,7 +205,7 @@ was built with that package. See the
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
Warning
-The coordinates of an atom contribute to the chunk’s -angular velocity in “unwrapped” form, by using the image flags -associated with each atom. See the dump custom command -for a discussion of “unwrapped” coordinates. See the Atoms section of -the read_data command for a discussion of image flags -and how they are set for each atom. You can reset the image flags +
Note
+The coordinates of an atom contribute to the chunk’s angular +velocity in “unwrapped” form, by using the image flags associated with +each atom. See the dump custom command for a discussion +of “unwrapped” coordinates. See the Atoms section of the +read_data command for a discussion of image flags and +how they are set for each atom. You can reset the image flags (e.g. to 0) before invoking this compute by using the set image command.
The simplest way to output the results of the compute omega/chunk
@@ -215,7 +215,7 @@ velocity/distance units
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
Warning
+Note
If you have a bonded system, then the settings of special_bonds command can remove pairwise interactions between atoms in the same bond, angle, or dihedral. This is the default setting for the special_bonds command, and means those pairwise interactions do not appear in the neighbor list. Because this fix uses the neighbor list, it also means -those pairs will not be included in the order parameter. This difficulty -can be circumvented by writing a dump file, and using the -rerun command to compute the order parameter for snapshots -in the dump file. The rerun script can use a +those pairs will not be included in the order parameter. This +difficulty can be circumvented by writing a dump file, and using the +rerun command to compute the order parameter for +snapshots in the dump file. The rerun script can use a special_bonds command that includes all pairs in the neighbor list.
- © Copyright . + © Copyright 2013 Sandia Corporation.
- © Copyright . + © Copyright 2013 Sandia Corporation.
Warning
-For pairs, if two atoms I,J are involved in 1-2, 1-3, -1-4 interactions within the molecular topology, their pairwise -interaction may be turned off, and thus they may not appear in the -neighbor list, and will not be part of the local data created by this -command. More specifically, this will be true of I,J pairs with a -weighting factor of 0.0; pairs with a non-zero weighting factor are -included. The weighting factors for 1-2, 1-3, and 1-4 pairwise -interactions are set by the special_bonds -command. An exception is if long-range Coulombics are being computed -via the kspace_style command, then atom pairs with +
Note
+For pairs, if two atoms I,J are involved in 1-2, 1-3, 1-4
+interactions within the molecular topology, their pairwise interaction
+may be turned off, and thus they may not appear in the neighbor list,
+and will not be part of the local data created by this command. More
+specifically, this will be true of I,J pairs with a weighting factor
+of 0.0; pairs with a non-zero weighting factor are included. The
+weighting factors for 1-2, 1-3, and 1-4 pairwise interactions are set
+by the special_bonds command. An exception is if
+long-range Coulombics are being computed via the
+kspace_style command, then atom pairs with
weighting factors of zero are still included in the neighbor list, so
that a portion of the long-range interaction contribution can be
computed in the pair style. Hence in that case, those atom pairs will
@@ -243,7 +243,7 @@ output for eng will be in energy
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright . + © Copyright 2013 Sandia Corporation.
Warning
-The per-atom energy does not any Lennard-Jones tail -corrections invoked by the pair_modify tail yes -command, since those are global contributions to the system energy.
+Note
+The per-atom energy does not any Lennard-Jones tail corrections +invoked by the pair_modify tail yes command, since +those are global contributions to the system energy.
Output info:
This compute calculates a per-atom vector, which can be accessed by @@ -215,7 +215,7 @@ LAMMPS output options.
- © Copyright . + © Copyright 2013 Sandia Corporation.
- © Copyright . + © Copyright 2013 Sandia Corporation.
Details of how LAMMPS computes the virial efficiently for the entire system, including the effects of periodic boundary conditions is -discussed in (Thompson).
+discussed in (Thompson).The temperature and kinetic energy tensor is not calculated by this compute, but rather by the temperature compute specified with the command. If the kinetic energy is not included in the pressure, than @@ -256,7 +256,7 @@ options.
- © Copyright . + © Copyright 2013 Sandia Corporation.
- © Copyright . + © Copyright 2013 Sandia Corporation.
- © Copyright . + © Copyright 2013 Sandia Corporation.
Warning
-For pairs, if two atoms I,J are involved in 1-2, 1-3, -1-4 interactions within the molecular topology, their pairwise -interaction may be turned off, and thus they may not appear in the -neighbor list, and will not be part of the local data created by this -command. More specifically, this may be true of I,J pairs with a -weighting factor of 0.0; pairs with a non-zero weighting factor are -included. The weighting factors for 1-2, 1-3, and 1-4 pairwise -interactions are set by the special_bonds -command.
+Note
+For pairs, if two atoms I,J are involved in 1-2, 1-3, 1-4 +interactions within the molecular topology, their pairwise interaction +may be turned off, and thus they may not appear in the neighbor list, +and will not be part of the local data created by this command. More +specifically, this may be true of I,J pairs with a weighting factor of +0.0; pairs with a non-zero weighting factor are included. The +weighting factors for 1-2, 1-3, and 1-4 pairwise interactions are set +by the special_bonds command.
The batom1 and batom2 attributes refer to the atom IDs of the 2 atoms in each bond. The btype attribute refers to @@ -266,7 +265,7 @@ specified attribute.
- © Copyright . + © Copyright 2013 Sandia Corporation.
Warning
+Note
If you have a bonded system, then the settings of special_bonds command can remove pairwise interactions between atoms in the same bond, angle, or dihedral. This @@ -167,13 +167,14 @@ is the default setting for the rerun command -to compute the RDF for snapshots in the dump file. The rerun script -can use a special_bonds command that includes all -pairs in the neighbor list.
+using long-range coulomb (coul/long, coul/msm, coul/wolf or +similar. One way to get around this would be to set special_bond +scaling factors to very tiny numbers that are not exactly zero +(e.g. 1.0e-50). Another workaround is to write a dump file, and use +the rerun command to compute the RDF for snapshots in the +dump file. The rerun script can use a +special_bonds command that includes all pairs in +the neighbor list.The itypeN and jtypeN arguments are optional. These arguments must come in pairs. If no pairs are listed, then a single histogram @@ -280,7 +281,7 @@ change from zero to one at the location of the spike in g(r).
- © Copyright . + © Copyright 2013 Sandia Corporation.
- © Copyright . + © Copyright 2013 Sandia Corporation.
- © Copyright . + © Copyright 2013 Sandia Corporation.
- © Copyright . + © Copyright 2013 Sandia Corporation.
- © Copyright . + © Copyright 2013 Sandia Corporation.
- © Copyright . + © Copyright 2013 Sandia Corporation.
- © Copyright . + © Copyright 2013 Sandia Corporation.
- © Copyright . + © Copyright 2013 Sandia Corporation.
- © Copyright . + © Copyright 2013 Sandia Corporation.
- © Copyright . + © Copyright 2013 Sandia Corporation.
- © Copyright . + © Copyright 2013 Sandia Corporation.
- © Copyright . + © Copyright 2013 Sandia Corporation.
- © Copyright . + © Copyright 2013 Sandia Corporation.
- © Copyright . + © Copyright 2013 Sandia Corporation.
- © Copyright . + © Copyright 2013 Sandia Corporation.
- © Copyright . + © Copyright 2013 Sandia Corporation.
- © Copyright . + © Copyright 2013 Sandia Corporation.
- © Copyright . + © Copyright 2013 Sandia Corporation.
- © Copyright . + © Copyright 2013 Sandia Corporation.
- © Copyright . + © Copyright 2013 Sandia Corporation.
- © Copyright . + © Copyright 2013 Sandia Corporation.
- © Copyright . + © Copyright 2013 Sandia Corporation.
- © Copyright . + © Copyright 2013 Sandia Corporation.
- © Copyright . + © Copyright 2013 Sandia Corporation.
The keyword switchflag can be used to turn off the switching function.
-Warning
+Note
If you have a bonded system, then the settings of special_bonds command can remove pairwise interactions between atoms in the same bond, angle, or dihedral. This @@ -341,7 +341,7 @@ of Angular Momentum, World Scientific, Singapore (1987).
- © Copyright . + © Copyright 2013 Sandia Corporation.
- © Copyright . + © Copyright 2013 Sandia Corporation.
- © Copyright . + © Copyright 2013 Sandia Corporation.
- © Copyright . + © Copyright 2013 Sandia Corporation.
Warning
-This choice for degrees of freedom (dof) assumes that -all finite-size aspherical or spherical particles in your model will +
Note
+This choice for degrees of freedom (dof) assumes that all
+finite-size aspherical or spherical particles in your model will
freely rotate, sampling all their rotational dof. It is possible to
use a combination of interaction potentials and fixes that induce no
torque or otherwise constrain some of all of your particles so that
@@ -191,11 +191,11 @@ by the compute temp
- Warning For 2d models, particles are treated
-as ellipsoids, not ellipses, meaning their moments of inertia will be
-the same as in 3d. Note For 2d models, particles are treated as
+ellipsoids, not ellipses, meaning their moments of inertia will be the
+same as in 3d. A kinetic energy tensor, stored as a 6-element vector, is also
calculated by this compute. The formula for the components of the
@@ -269,7 +269,7 @@ shape attribute.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
Warning Only atoms in the specified group contribute to the
-calculations performed by this compute. The compute chunk/atom command defines its own group;
+ Note Only atoms in the specified group contribute to the calculations
+performed by this compute. The compute chunk/atom command defines its own group;
atoms will have a chunk ID = 0 if they are not in that group,
signifying they are not assigned to a chunk, and will thus also not
contribute to this calculation. You can specify the “all” group for
@@ -342,7 +342,7 @@ system (2 or 3), and cdof = 0.0.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
Define a computation that calculates the temperature of a system based
on the center-of-mass velocity of atom pairs that are bonded to each
other. This compute is designed to be used with the adiabatic
-core/shell model of (Mitchell and Finchham). See
+core/shell model of (Mitchell and Finchham). See
Section_howto 25 of the manual for an
overview of the model as implemented in LAMMPS. Specifically, this
compute enables correct temperature calculation and thermostatting of
@@ -233,7 +233,7 @@ be used which generate new molecules or atoms during a simulation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
Warning Fix deform has an option for
-remapping either atom coordinates or velocities to the changing
-simulation box. When using this compute in conjunction with a
-deforming box, fix deform should NOT remap atom positions, but rather
-should let atoms respond to the changing box by adjusting their own
-velocities (or let fix deform remap the atom
-velocities, see it’s remap option). If fix deform does remap atom
-positions, then they appear to move with the box but their velocity is
-not changed, and thus they do NOT have the streaming velocity assumed
-by this compute. LAMMPS will warn you if fix deform is defined and
-its remap setting is not consistent with this compute. Note Fix deform has an option for remapping either
+atom coordinates or velocities to the changing simulation box. When
+using this compute in conjunction with a deforming box, fix deform
+should NOT remap atom positions, but rather should let atoms respond
+to the changing box by adjusting their own velocities (or let fix deform remap the atom velocities, see it’s remap
+option). If fix deform does remap atom positions, then they appear to
+move with the box but their velocity is not changed, and thus they do
+NOT have the streaming velocity assumed by this compute. LAMMPS will
+warn you if fix deform is defined and its remap setting is not
+consistent with this compute. After the streaming velocity has been subtracted from each atom, the
temperature is calculated by the formula KE = dim/2 N k T, where KE =
@@ -198,12 +197,12 @@ command that performs thermostatting then this bias will be subtracted
from each atom, thermostatting of the remaining thermal velocity will
be performed, and the bias will be added back in. Thermostatting
fixes that work in this way include fix nvt, fix temp/rescale, fix temp/berendsen, and fix langevin. Warning The temperature calculated by this compute is only
-accurate if the atoms are indeed moving with a stream velocity profile
-that matches the box deformation. If not, then the compute will
-subtract off an incorrect stream velocity, yielding a bogus thermal
+ Note The temperature calculated by this compute is only accurate if
+the atoms are indeed moving with a stream velocity profile that
+matches the box deformation. If not, then the compute will subtract
+off an incorrect stream velocity, yielding a bogus thermal
temperature. You should NOT assume that your atoms are streaming at
the same rate the box is deforming. Rather, you should monitor their
velocity profile, e.g. via the fix ave/spatial
@@ -256,7 +255,7 @@ vector values will be in energy
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
Warning For eFF models, in order to override the default
-temperature reported by LAMMPS in the thermodynamic quantities
-reported via the thermo command, the user should apply a
+ Note For eFF models, in order to override the default temperature
+reported by LAMMPS in the thermodynamic quantities reported via the
+thermo command, the user should apply a
thermo_modify command, as shown in the following
example:
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
Warning When using the out keyword with a value of bin,
-the calculated temperature for each bin does not include the
+ Note When using the out keyword with a value of bin, the
+calculated temperature for each bin does not include the
degrees-of-freedom adjustment described in the preceeding paragraph,
for fixes that constrain molecular motion. It does include the
adjustment due to the extra option, which is applied to each bin.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
Warning This choice for degrees of freedom (dof) assumes that
-all finite-size spherical particles in your model will freely rotate,
+ Note This choice for degrees of freedom (dof) assumes that all
+finite-size spherical particles in your model will freely rotate,
sampling all their rotational dof. It is possible to use a
combination of interaction potentials and fixes that induce no torque
or otherwise constrain some of all of your particles so that this is
@@ -180,11 +180,11 @@ accordingly. Warning For 2d models, particles are treated
-as spheres, not disks, meaning their moment of inertia will be the
-same as in 3d. Note For 2d models, particles are treated as
+spheres, not disks, meaning their moment of inertia will be the same
+as in 3d. A kinetic energy tensor, stored as a 6-element vector, is also
calculated by this compute. The formula for the components of the
@@ -257,7 +257,7 @@ particles with radius = 0.0.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
Warning The coordinates of an atom contribute to the chunk’s
-torque in “unwrapped” form, by using the image flags associated with
-each atom. See the dump custom command for a discussion
-of “unwrapped” coordinates. See the Atoms section of the
+ Note The coordinates of an atom contribute to the chunk’s torque in
+“unwrapped” form, by using the image flags associated with each atom.
+See the dump custom command for a discussion of
+“unwrapped” coordinates. See the Atoms section of the
read_data command for a discussion of image flags and
how they are set for each atom. You can reset the image flags
(e.g. to 0) before invoking this compute by using the set image command.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
Warning If you want the quantities calculated by this compute
-to be continuous when running from a restart file,
-then you should use the same ID for this compute, as in the original
-run. This is so that the fix this compute creates to store per-atom
+ Note If you want the quantities calculated by this compute to be
+continuous when running from a restart file, then
+you should use the same ID for this compute, as in the original run.
+This is so that the fix this compute creates to store per-atom
quantities will also have the same ID, and thus be initialized
correctly with time=0 atom velocities from the restart file.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
Warning The calculation of Voronoi volumes is performed by
-each processor for the atoms it owns, and includes the effect of ghost
+ Note The calculation of Voronoi volumes is performed by each
+processor for the atoms it owns, and includes the effect of ghost
atoms stored by the processor. This assumes that the Voronoi cells of
owned atoms are not affected by atoms beyond the ghost atom cut-off
distance. This is usually a good assumption for liquid and solid
@@ -249,16 +249,16 @@ processor is determined by the cutoff used for
pair_style interactions. The cutoff can be set
explicitly via the comm_modify cutoff command. Warning The Voro++ package performs its calculation in 3d.
-This should still work for a 2d LAMMPS simulation, to effectively
-compute Voronoi “areas”, so long as the z-dimension of the box is
-roughly the same (or smaller) compared to the separation of the atoms.
-Typical values for the z box dimensions in a 2d LAMMPS model are -0.5
-to 0.5, which satisfies the criterion for most units
-systems. Note that you define the z extent of the simulation box for
-2d simulations when using the create_box or
+ Note The Voro++ package performs its calculation in 3d. This should
+still work for a 2d LAMMPS simulation, to effectively compute Voronoi
+“areas”, so long as the z-dimension of the box is roughly the same (or
+smaller) compared to the separation of the atoms. Typical values for
+the z box dimensions in a 2d LAMMPS model are -0.5 to 0.5, which
+satisfies the criterion for most units systems. Note
+that you define the z extent of the simulation box for 2d simulations
+when using the create_box or
read_data commands. Output info:
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
Define a computation that calculates x-ray diffraction intensity as described
-in (Coleman) on a mesh of reciprocal lattice nodes defined
+in (Coleman) on a mesh of reciprocal lattice nodes defined
by the entire simulation domain (or manually) using a simulated radiation
of wavelength lambda. The x-ray diffraction intensity, I, at each reciprocal lattice point, k,
@@ -335,7 +335,7 @@ Volume C: Mathematical and Chemical Tables, 249-429 (2004).
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
Warning Particles generated by the random style will
-typically be highly overlapped which will cause many interatomic
-potentials to compute large energies and forces. Thus you should
-either perform an energy minimization or run dynamics
-with fix nve/limit to equilibrate such a system,
-before running normal dynamics. Note Particles generated by the random style will typically be
+highly overlapped which will cause many interatomic potentials to
+compute large energies and forces. Thus you should either perform an
+energy minimization or run dynamics with fix nve/limit to equilibrate such a system, before
+running normal dynamics. Note that this command adds particles to those that already exist.
This means it can be used to add particles to a system previously read
@@ -281,15 +280,15 @@ created in parallel. Also note that because of the random rotations, it may be important to
use a lattice with a large enough spacing that adjacent molecules will
not overlap, regardless of their relative orientations. Warning If the create_box command is used to
-create the simulation box, followed by the create_atoms command with
-its mol option for adding molecules, then you typically need to use
-the optional keywords allowed by the create_box
-command for extra bonds (angles,etc) or extra special neighbors. This
-is because by default, the create_box command sets
-up a non-molecular system which doesn’t allow molecules to be added. Note If the create_box command is used to create
+the simulation box, followed by the create_atoms command with its
+mol option for adding molecules, then you typically need to use the
+optional keywords allowed by the create_box command
+for extra bonds (angles,etc) or extra special neighbors. This is
+because by default, the create_box command sets up a
+non-molecular system which doesn’t allow molecules to be added. This is the meaning of the other allowed keywords.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
Warning If the system has no bonds to begin with, or if more
-bonds per atom are being added than currently exist, then you must
-insure that the number of bond types and the maximum number of bonds
-per atom are set to large enough values. Otherwise an error may occur
-when too many bonds are added to an atom. If the
-read_data command is used to define the system, these
-2 parameters can be set via the “bond types” and “extra bond per atom”
-fields in the header section of the data file. If the
-create_box command is used to define the system,
-these 2 parameters can be set via its optional “bond/types” and
-“extra/bond/per/atom” arguments. See the doc pages for the 2 commands
-for details. Note If the system has no bonds to begin with, or if more bonds per
+atom are being added than currently exist, then you must insure that
+the number of bond types and the maximum number of bonds per atom are
+set to large enough values. Otherwise an error may occur when too
+many bonds are added to an atom. If the read_data
+command is used to define the system, these 2 parameters can be set
+via the “bond types” and “extra bond per atom” fields in the header
+section of the data file. If the create_box command
+is used to define the system, these 2 parameters can be set via its
+optional “bond/types” and “extra/bond/per/atom” arguments. See the
+doc pages for the 2 commands for details.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
Warning If the system is non-periodic (in a dimension), then
-you should not make the lo/hi box dimensions (as defined in your
+ Note If the system is non-periodic (in a dimension), then you should
+not make the lo/hi box dimensions (as defined in your
region command) radically smaller/larger than the extent
of the atoms you eventually plan to create, e.g. via the
create_atoms command. For example, if your atoms
@@ -272,7 +272,7 @@ been previously defined to use this command.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
Warning The molecule deletion operation in invoked after all
-individual atoms have been deleted using the rules described above for
-each style. This means additional atoms may be deleted that are not
-in the group or region, that are not required by the overlap cutoff
+ Note The molecule deletion operation in invoked after all individual
+atoms have been deleted using the rules described above for each
+style. This means additional atoms may be deleted that are not in the
+group or region, that are not required by the overlap cutoff
criterion, or that will create a higher fraction of porosity than was
requested.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
Warning When comparing the formulas and coefficients for
-various LAMMPS dihedral styles with dihedral equations defined by
-other force fields, note that some force field implementations
-divide/multiply the energy prefactor K by the multiple number of
-torsions that contain the J-K bond in an I-J-K-L torsion. LAMMPS does
-not do this, i.e. the listed dihedral equation applies to each
-individual dihedral. Thus you need to define K appropriately to
-account for this difference if necessary. Note When comparing the formulas and coefficients for various LAMMPS
+dihedral styles with dihedral equations defined by other force fields,
+note that some force field implementations divide/multiply the energy
+prefactor K by the multiple number of torsions that contain the J-K
+bond in an I-J-K-L torsion. LAMMPS does not do this, i.e. the listed
+dihedral equation applies to each individual dihedral. Thus you need
+to define K appropriately to account for this difference if
+necessary. Here is an alphabetic list of dihedral styles defined in LAMMPS. Click on
@@ -235,7 +235,7 @@ set, either in the input script or in a data file.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
Warning Here are important points to take note of when
-defining LAMMPS dihedral coefficients for the harmonic style, so that
-they are compatible with how harmonic dihedrals are defined by other
-force fields: Note Here are important points to take note of when defining LAMMPS
+dihedral coefficients for the harmonic style, so that they are
+compatible with how harmonic dihedrals are defined by other force
+fields:
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
Warning Note When both a dihedral and pair style is defined, the
special_bonds command often needs to be used to
turn off (or weight) the pairwise interaction that would otherwise
@@ -180,16 +180,16 @@ is from left to right. Warning When comparing the formulas and coefficients for
-various LAMMPS dihedral styles with dihedral equations defined by
-other force fields, note that some force field implementations
-divide/multiply the energy prefactor K by the multiple number of
-torsions that contain the J-K bond in an I-J-K-L torsion. LAMMPS does
-not do this, i.e. the listed dihedral equation applies to each
-individual dihedral. Thus you need to define K appropriately via
-the dihedral_coeff command to account for this
+ Note When comparing the formulas and coefficients for various LAMMPS
+dihedral styles with dihedral equations defined by other force fields,
+note that some force field implementations divide/multiply the energy
+prefactor K by the multiple number of torsions that contain the J-K
+bond in an I-J-K-L torsion. LAMMPS does not do this, i.e. the listed
+dihedral equation applies to each individual dihedral. Thus you need
+to define K appropriately via the
+dihedral_coeff command to account for this
difference if necessary.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
See the discussion in Section_howto for
additional instructions on how to run 2d simulations. Warning Some models in LAMMPS treat particles as finite-size
-spheres or ellipsoids, as opposed to point particles. In 2d, the
-particles will still be spheres or ellipsoids, not circular disks or
-ellipses, meaning their moment of inertia will be the same as in 3d. Note Some models in LAMMPS treat particles as finite-size spheres or
+ellipsoids, as opposed to point particles. In 2d, the particles will
+still be spheres or ellipsoids, not circular disks or ellipses,
+meaning their moment of inertia will be the same as in 3d.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
Warning Care should be taken not to move atoms on top of other
-atoms. After the move, atoms are remapped into the periodic
-simulation box if needed, and any shrink-wrap boundary conditions (see
-the boundary command) are enforced which may change
-the box size. Other than this effect, this command does not change
-the size or shape of the simulation box. See the
+ Note Care should be taken not to move atoms on top of other atoms.
+After the move, atoms are remapped into the periodic simulation box if
+needed, and any shrink-wrap boundary conditions (see the
+boundary command) are enforced which may change the
+box size. Other than this effect, this command does not change the
+size or shape of the simulation box. See the
change_box command if that effect is desired. Warning Atoms can be moved arbitrarily long distances by this
-command. If the simulation box is non-periodic and shrink-wrapped
-(see the boundary command), this can change its size
-or shape. This is not a problem, except that the mapping of
-processors to the simulation box is not changed by this command from
-its initial 3d configuration; see the processors
-command. Thus, if the box size/shape changes dramatically, the
-mapping of processors to the simulation box may not end up as optimal
-as the initial mapping attempted to be. Note Atoms can be moved arbitrarily long distances by this command.
+If the simulation box is non-periodic and shrink-wrapped (see the
+boundary command), this can change its size or shape.
+This is not a problem, except that the mapping of processors to the
+simulation box is not changed by this command from its initial 3d
+configuration; see the processors command. Thus, if
+the box size/shape changes dramatically, the mapping of processors to
+the simulation box may not end up as optimal as the initial mapping
+attempted to be.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
As described below, the filename determines the kind of output (text
or binary or gzipped, one big file or one per timestep, one big file
or multiple smaller files). Warning Because periodic boundary conditions are enforced only
-on timesteps when neighbor lists are rebuilt, the coordinates of an
-atom written to a dump file may be slightly outside the simulation
-box. Note Because periodic boundary conditions are enforced only on
+timesteps when neighbor lists are rebuilt, the coordinates of an atom
+written to a dump file may be slightly outside the simulation box. Warning Unless the dump_modify sort option
-is invoked, the lines of atom information written to dump files
+ Note Unless the dump_modify sort option is
+invoked, the lines of atom information written to dump files
(typically one line per atom) will be in an indeterminate order for
each snapshot. This is even true when running on a single processor,
if the atom_modify sort option is on, which it is
@@ -716,7 +715,7 @@ machines.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
Warning Because periodic boundary conditions are enforced only
-on timesteps when neighbor lists are rebuilt, the coordinates of an
-atom written to a dump file may be slightly outside the simulation
-box. Note Because periodic boundary conditions are enforced only on
+timesteps when neighbor lists are rebuilt, the coordinates of an atom
+written to a dump file may be slightly outside the simulation box. Use from write_dump: It is possible to use this dump style with the
@@ -244,7 +243,7 @@ Comp. Phys. Comm. 185(6), 1546-1553 (2014) -
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
Warning Because periodic boundary conditions are enforced only
-on timesteps when neighbor lists are rebuilt, the coordinates of an
-atom in the image may be slightly outside the simulation box. Note Because periodic boundary conditions are enforced only on
+timesteps when neighbor lists are rebuilt, the coordinates of an atom
+in the image may be slightly outside the simulation box. Dumps are performed on timesteps that are a multiple of N (including
@@ -450,8 +450,8 @@ which is an orthographic rendering with no persepctive. A pfactor
value between 0.0 and 1.0 will introduce more perspective. A pfactor
value > 1 will create a highly skewed image with a large amount of
perspective. Warning Note The persp keyword is not yet supported as an option.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
Warning When using a file-style variable with the every
-keyword, the file of timesteps must list a first timestep that is
-beyond the current timestep (e.g. it cannot be 0). And it must list
-one or more timesteps beyond the length of the run you perform. This
-is because the dump command will generate an error if the next
-timestep it reads from the file is not a value greater than the
-current timestep. Thus if you wanted output on steps 0,15,100 of a
-100-timestep run, the file should contain the values 15,100,101 and
-you should also use the dump_modify first command. Any final value >
-100 could be used in place of 101. Note When using a file-style variable with the every keyword, the
+file of timesteps must list a first timestep that is beyond the
+current timestep (e.g. it cannot be 0). And it must list one or more
+timesteps beyond the length of the run you perform. This is because
+the dump command will generate an error if the next timestep it reads
+from the file is not a value greater than the current timestep. Thus
+if you wanted output on steps 0,15,100 of a 100-timestep run, the file
+should contain the values 15,100,101 and you should also use the
+dump_modify first command. Any final value > 100 could be used in
+place of 101. The first keyword determines whether a dump snapshot is written on
@@ -364,14 +364,14 @@ character in the format string. This option has no effect on the
for the cfg style, the first two fields (atom id and type) are not
actually written into the CFG file, though you must include formats
for them in the format string. Warning Any value written to a text-based dump file that is a
-per-atom quantity calculated by a compute or
-fix is stored internally as a floating-point value. If the
-value is actually an integer and you wish it to appear in the text
-dump file as a (large) integer, then you need to use an appropriate
-format. For example, these commands: Note Any value written to a text-based dump file that is a per-atom
+quantity calculated by a compute or fix is
+stored internally as a floating-point value. If the value is actually
+an integer and you wish it to appear in the text dump file as a
+(large) integer, then you need to use an appropriate format. For
+example, these commands: Warning Unless it is required by the dump style, sorting dump
-file output requires extra overhead in terms of CPU and communication
-cost, as well as memory, versus unsorted output. Note Unless it is required by the dump style, sorting dump file
+output requires extra overhead in terms of CPU and communication cost,
+as well as memory, versus unsorted output. The thresh keyword only applies to the dump custom, cfg,
@@ -697,10 +697,10 @@ compression and will result in higher quality movies. The quality is
also determined by the compression format and encoder. The default
setting is 2000 kbit/s, which will result in average quality with
older compression formats. Warning Not all movie file formats supported by dump movie
-allow the bitrate to be set. If not, the setting is silently ignored. Note Not all movie file formats supported by dump movie allow the
+bitrate to be set. If not, the setting is silently ignored. The boxcolor keyword sets the color of the simulation box drawn
@@ -990,7 +990,7 @@ Divide each value by 255 to get the equivalent 0.0 to 1.0 value.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
Warning Because periodic boundary conditions are enforced only
-on timesteps when neighbor lists are rebuilt, the coordinates of an
-atom written to a dump file may be slightly outside the simulation
-box. Note Because periodic boundary conditions are enforced only on
+timesteps when neighbor lists are rebuilt, the coordinates of an atom
+written to a dump file may be slightly outside the simulation box. The molfile plugin API has a few restrictions that have to be honored
by this dump style: the number of atoms must not change, the atoms
@@ -250,7 +249,7 @@ with a set of header files that are compatible with VMD 1.9 and 1.9.1
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
The ID of a fix can only contain alphanumeric characters and
underscores. Fixes can be deleted with the unfix command. Warning The unfix command is the only way to turn
-off a fix; simply specifying a new fix with a similar style will not
-turn off the first one. This is especially important to realize for
+ Note The unfix command is the only way to turn off a
+fix; simply specifying a new fix with a similar style will not turn
+off the first one. This is especially important to realize for
integration fixes. For example, using a fix nve
command for a second run after using a fix nvt command
for the first run, will not cancel out the NVT time integration
@@ -394,7 +394,7 @@ The doc pages for individual fixes tell if it is part of a package.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
Warning It is easy to add new potentials and their parameters
-to this list. All it typically takes is adding an extract() method to
-the pair_*.cpp file associated with the potential. Note It is easy to add new potentials and their parameters to this
+list. All it typically takes is adding an extract() method to the
+pair_*.cpp file associated with the potential. Some parameters are global settings for the pair style, e.g. the
viscosity setting “mu” for pair_style lubricate.
@@ -357,11 +357,11 @@ specified as v_name, where name is the variable name. See the
discussion above describing the formulas associated with equal-style
variables. The new value is assigned to the corresponding attribute
for all atoms in the fix group. Warning The atom keyword works this way whether the scale
-keyword is set to no or yes. I.e. the use of scale yes is not yet
-supported by the atom keyword. Note The atom keyword works this way whether the scale keyword is
+set to no or yes. I.e. the use of scale yes is not yet supported
+by the atom keyword. If the atom parameter is diameter and per-atom density and per-atom
mass are defined for particles (e.g. atom_style granular), then the mass of each particle is also
@@ -411,7 +411,7 @@ parameters on the outermost rRESPA level.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
Warning It is easy to add new potentials and their parameters
-to this list. All it typically takes is adding an extract() method to
-the pair_*.cpp file associated with the potential. Note It is easy to add new potentials and their parameters to this
+list. All it typically takes is adding an extract() method to the
+pair_*.cpp file associated with the potential. Some parameters are global settings for the pair style, e.g. the
viscosity setting “mu” for pair_style lubricate.
@@ -410,7 +410,7 @@ This fix is not invoked during
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
Warning If you want the fictitious potential energy associated
-with the added forces to be included in the total potential energy of
-the system (the quantity being minimized), you MUST enable the
+ Note If you want the fictitious potential energy associated with the
+added forces to be included in the total potential energy of the
+system (the quantity being minimized), you MUST enable the
fix_modify energy option for this fix.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
Warning The x,y,z attributes are values that are re-wrapped
-inside the periodic box whenever an atom crosses a periodic boundary.
-Thus if you time average an atom that spends half its time on either
-side of the periodic box, you will get a value in the middle of the
-box. If this is not what you want, consider averaging unwrapped
-coordinates, which can be provided by the compute property/atom command via its xu,yu,zu
+ Note The x,y,z attributes are values that are re-wrapped inside the
+periodic box whenever an atom crosses a periodic boundary. Thus if
+you time average an atom that spends half its time on either side of
+the periodic box, you will get a value in the middle of the box. If
+this is not what you want, consider averaging unwrapped coordinates,
+which can be provided by the compute property/atom command via its xu,yu,zu
attributes. If a value begins with “c_”, a compute ID must follow which has been
@@ -265,7 +265,7 @@ the run command. Thi
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
IMPORTANT NOTE: NOTE: If you are trying to replace an older fix ave/spatial command with the
newer, more flexible fix ave/chunk and compute chunk/atom commands, you simply need to split
the fix ave/spatial arguments across the two new commands. For
@@ -240,17 +240,17 @@ ones that can be used with this fix since all other styles of variable
produce global quantities. The per-atom values of each input vector are summed and averaged
independently of the per-atom values in other input vectors. Warning This fix works by creating an array of size Nchunk
-by Nvalues on each processor. Nchunk is the number of chunks which
-is defined by the Note This fix works by creating an array of size Nchunk by Nvalues
+on each processor. Nchunk is the number of chunks which is defined
+by the The Nevery, Nrepeat, and Nfreq arguments specify on what
@@ -273,10 +273,10 @@ The way the averaging is done across the Nrepeat timesteps to
produce output on the Nfreq timesteps, and across multiple Nfreq
outputs, is determined by the norm and ave keyword settings, as
discussed below. Warning To perform per-chunk averaging within a Nfreq time
-window, the number of chunks Nchunk defined by the compute chunk/atom command must remain constant. If
+ Note To perform per-chunk averaging within a Nfreq time window, the
+number of chunks Nchunk defined by the compute chunk/atom command must remain constant. If
the ave keyword is set to running or window then Nchunk must
remain constant for the duration of the simulation. This fix forces
the chunk/atom compute specified by chunkID to hold Nchunk constant
@@ -527,7 +527,7 @@ title 1,2,3 = strings as described above.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
IMPORTANT NOTE: NOTE: The fix ave/spatial command has been replaced by the more flexible
fix ave/chunk and compute chunk/atom commands. The fix ave/spatial
command will be removed from LAMMPS sometime in the summer of 2015. Warning This fix works by creating an array of size Nbins by
-Nvalues on each processor. Nbins is the total number of bins; Nvalues
-is the number of input values specified. Each processor loops over
-its atoms, tallying its values to the appropriate bin. Then the
-entire array is summed across all processors. This means that using a
-large number of bins (easy to do for 2d or 3d bins) will incur an
-overhead in memory and computational cost (summing across processors),
-so be careful to use reasonable numbers of bins. Note This fix works by creating an array of size Nbins by Nvalues on
+each processor. Nbins is the total number of bins; Nvalues is the
+number of input values specified. Each processor loops over its
+atoms, tallying its values to the appropriate bin. Then the entire
+array is summed across all processors. This means that using a large
+number of bins (easy to do for 2d or 3d bins) will incur an overhead
+in memory and computational cost (summing across processors), so be
+careful to use reasonable numbers of bins. The Nevery, Nrepeat, and Nfreq arguments specify on what
@@ -512,7 +512,7 @@ output, and title 1,2,3 = strings as described above.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
Nbins specifies the number of spherical shells which will be created
between r_min and r_max centered at (origin_x, origin_y, origin_z). Warning This fix works by creating an array of size Nbins by
-Nvalues on each processor. Nbins is the total number of bins; Nvalues
-is the number of input values specified. Each processor loops over
-its atoms, tallying its values to the appropriate bin. Then the
-entire array is summed across all processors. This means that using a
-large number of bins will incur an overhead in memory and computational
-cost (summing across processors), so be careful to use reasonable numbers
+ Note This fix works by creating an array of size Nbins by Nvalues on
+each processor. Nbins is the total number of bins; Nvalues is the
+number of input values specified. Each processor loops over its
+atoms, tallying its values to the appropriate bin. Then the entire
+array is summed across all processors. This means that using a large
+number of bins will incur an overhead in memory and computational cost
+(summing across processors), so be careful to use reasonable numbers
of bins. Warning The lattice style may only be used if the lattice
-spacing is the same in each direction. Note The lattice style may only be used if the lattice spacing is
+the same in each direction. A reduced value means normalized unitless values between 0 and 1,
which represent the lower and upper faces of the simulation box
@@ -423,7 +423,7 @@ file output, and title 1,2,3 = strings as described above.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
Warning This command attempts to minimize the imbalance
-factor, as defined above. But depending on the method a perfect
-balance (1.0) may not be achieved. For example, “grid” methods
-(defined below) that create a logical 3d grid cannot achieve perfect
-balance for many irregular distributions of particles. Likewise, if a
-portion of the system is a perfect lattice, e.g. the initial system is
-generated by the create_atoms command, then “grid”
-methods may be unable to achieve exact balance. This is because
-entire lattice planes will be owned or not owned by a single
-processor. Note This command attempts to minimize the imbalance factor, as
+defined above. But depending on the method a perfect balance (1.0)
+may not be achieved. For example, “grid” methods (defined below) that
+create a logical 3d grid cannot achieve perfect balance for many
+irregular distributions of particles. Likewise, if a portion of the
+system is a perfect lattice, e.g. the initial system is generated by
+the create_atoms command, then “grid” methods may
+be unable to achieve exact balance. This is because entire lattice
+planes will be owned or not owned by a single processor. Warning The imbalance factor is also an estimate of the
-maximum speed-up you can hope to achieve by running a perfectly
-balanced simulation versus an imbalanced one. In the example above,
-the 10000 particle simulation could run up to 20% faster if it were
-perfectly balanced, versus when imbalanced. However, computational
-cost is not strictly proportional to particle count, and changing the
-relative size and shape of processor sub-domains may lead to
-additional computational and communication overheads, e.g. in the PPPM
-solver used via the kspace_style command. Thus
-you should benchmark the run times of a simulation before and after
-balancing. Note The imbalance factor is also an estimate of the maximum speed-up
+you can hope to achieve by running a perfectly balanced simulation
+versus an imbalanced one. In the example above, the 10000 particle
+simulation could run up to 20% faster if it were perfectly balanced,
+versus when imbalanced. However, computational cost is not strictly
+proportional to particle count, and changing the relative size and
+shape of processor sub-domains may lead to additional computational
+and communication overheads, e.g. in the PPPM solver used via the
+kspace_style command. Thus you should benchmark
+the run times of a simulation before and after balancing. The method used to perform a load balance is specified by one of the
@@ -343,13 +341,13 @@ so that you begin the run with a balanced system. Once the rebalancing is complete and final processor sub-domains
assigned, particles migrate to their new owning processor as part of
the normal reneighboring procedure. Warning At each rebalance operation, the bisectioning for each
-cutting plane (line in 2d) typcially starts with low and high bounds
-separated by the extent of a processor’s sub-domain in one dimension.
-The size of this bracketing region shrinks based on the local density,
-as described above, which should typically be 1/2 or more every
+ Note At each rebalance operation, the bisectioning for each cutting
+plane (line in 2d) typcially starts with low and high bounds separated
+by the extent of a processor’s sub-domain in one dimension. The size
+of this bracketing region shrinks based on the local density, as
+described above, which should typically be 1/2 or more every
iteration. Thus if Niter is specified as 10, the cutting plane will
typically be positioned to better than 1 part in 1000 accuracy
(relative to the perfect target position). For Niter = 20, it will
@@ -480,7 +478,7 @@ style.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
Warning One data structure that is not updated when a bond
-breaks are the molecule IDs stored by each atom. Even though
-one molecule becomes two moleclues due to the broken bond, all atoms
-in both new moleclues retain their original molecule IDs. Note One data structure that is not updated when a bond breaks are
+the molecule IDs stored by each atom. Even though one molecule
+becomes two moleclues due to the broken bond, all atoms in both new
+moleclues retain their original molecule IDs. Computationally, each timestep this fix operates, it loops over all
the bonds in the system and computes distances between pairs of bonded
@@ -213,14 +213,14 @@ presence of the bond and the settings of the
recognized. All of these operations increase the cost of a timestep.
Thus you should be cautious about invoking this fix too frequently. You can dump out snapshots of the current bond topology via the dump local command. Warning Breaking a bond typically alters the energy of a
-system. You should be careful not to choose bond breaking criteria
-that induce a dramatic change in energy. For example, if you define a
-very stiff harmonic bond and break it when 2 atoms are separated by a
-distance far from the equilibribum bond length, then the 2 atoms will
-be dramatically released when the bond is broken. More generally, you
+ Note Breaking a bond typically alters the energy of a system. You
+should be careful not to choose bond breaking criteria that induce a
+dramatic change in energy. For example, if you define a very stiff
+harmonic bond and break it when 2 atoms are separated by a distance
+far from the equilibribum bond length, then the 2 atoms will be
+dramatically released when the bond is broken. More generally, you
may need to thermostat your system to compensate for energy changes
resulting from broken bonds (and angles, dihedrals, impropers).
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
Warning One data structure that is not updated when a bond
-breaks are the molecule IDs stored by each atom. Even though two
-molecules become one moleclue due to the created bond, all atoms in
-the new moleclue retain their original molecule IDs. Note One data structure that is not updated when a bond breaks are
+the molecule IDs stored by each atom. Even though two molecules
+become one moleclue due to the created bond, all atoms in the new
+moleclue retain their original molecule IDs. If the atype keyword is used and if an angle potential is defined
via the Warning To create a new bond, the internal LAMMPS data
-structures that store this information must have space for it. When
-LAMMPS is initialized from a data file, the list of bonds is scanned
-and the maximum number of bonds per atom is tallied. If some atom
-will acquire more bonds than this limit as this fix operates, then the
+ Note To create a new bond, the internal LAMMPS data structures that
+store this information must have space for it. When LAMMPS is
+initialized from a data file, the list of bonds is scanned and the
+maximum number of bonds per atom is tallied. If some atom will
+acquire more bonds than this limit as this fix operates, then the
“extra bond per atom” parameter must be set to allow for it. Ditto
for “extra angle per atom”, “extra dihedral per atom”, and “extra
improper per atom” if angles, dihedrals, or impropers are being added
@@ -259,28 +259,28 @@ data file with no atoms can be used if you wish to add unbonded atoms
via the create atoms command, e.g. for a
percolation simulation. Warning LAMMPS stores and maintains a data structure with a
-list of the 1st, 2nd, and 3rd neighbors of each atom (within the bond
-topology of the system) for use in weighting pairwise interactions for
-bonded atoms. Note that adding a single bond always adds a new 1st
-neighbor but may also induce many new 2nd and 3rd neighbors,
-depending on the molecular topology of your system. The “extra
-special per atom” parameter must typically be set to allow for the new
-maximum total size (1st + 2nd + 3rd neighbors) of this per-atom list.
-There are 3 ways to do this. See the read_data or
+ Note LAMMPS stores and maintains a data structure with a list of the
+1st, 2nd, and 3rd neighbors of each atom (within the bond topology of
+the system) for use in weighting pairwise interactions for bonded
+atoms. Note that adding a single bond always adds a new 1st neighbor
+but may also induce many new 2nd and 3rd neighbors, depending on the
+molecular topology of your system. The “extra special per atom”
+parameter must typically be set to allow for the new maximum total
+size (1st + 2nd + 3rd neighbors) of this per-atom list. There are 3
+ways to do this. See the read_data or
create_box or “special_bonds extra” commands for
details. Warning Even if you do not use the atype, dtype, or
-itype keywords, the list of topological neighbors is updated for
-atoms affected by the new bond. This in turn affects which neighbors
-are considered for pairwise interactions, using the weighting rules
-set by the special_bonds command. Consider a new
-bond created between atoms I,J. If J has a bonded neighbor K, then K
+ Note Even if you do not use the atype, dtype, or itype
+keywords, the list of topological neighbors is updated for atoms
+affected by the new bond. This in turn affects which neighbors are
+considered for pairwise interactions, using the weighting rules set by
+the special_bonds command. Consider a new bond
+created between atoms I,J. If J has a bonded neighbor K, then K
becomes a 2nd neighbor of I. Even if the atype keyword is not used
to create angle I-J-K, the pairwise interaction between I and K will
be potentially turned off or weighted by the 1-3 weighting specified
@@ -309,16 +309,16 @@ excluded by the presence of the bond and the settings of the
recognized. All of these operations increase the cost of a timestep.
Thus you should be cautious about invoking this fix too frequently. You can dump out snapshots of the current bond topology via the dump local command. Warning Creating a bond typically alters the energy of a
-system. You should be careful not to choose bond creation criteria
-that induce a dramatic change in energy. For example, if you define a
-very stiff harmonic bond and create it when 2 atoms are separated by a
-distance far from the equilibribum bond length, then the 2 atoms will
-oscillate dramatically when the bond is formed. More generally, you
-may need to thermostat your system to compensate for energy changes
-resulting from created bonds (and angles, dihedrals, impropers). Note Creating a bond typically alters the energy of a system. You
+should be careful not to choose bond creation criteria that induce a
+dramatic change in energy. For example, if you define a very stiff
+harmonic bond and create it when 2 atoms are separated by a distance
+far from the equilibribum bond length, then the 2 atoms will oscillate
+dramatically when the bond is formed. More generally, you may need to
+thermostat your system to compensate for energy changes resulting from
+created bonds (and angles, dihedrals, impropers).
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
Warning If your simulation uses molecule IDs in the usual way,
-where all monomers on a single chain are assigned the same ID
-(different for each chain), then swaps will only occur within the same
-chain. If you assign the same molecule ID to all monomers in all
-chains then inter-chain swaps will occur, but they will not conserve
-chain length. Neither of these scenarios is probably what you want
-for this fix. Note If your simulation uses molecule IDs in the usual way, where all
+monomers on a single chain are assigned the same ID (different for
+each chain), then swaps will only occur within the same chain. If you
+assign the same molecule ID to all monomers in all chains then
+inter-chain swaps will occur, but they will not conserve chain length.
+Neither of these scenarios is probably what you want for this fix. Warning When a bond swap occurs the image flags of monomers in
-the new polymer chains can become inconsistent. See the
-dump command for a discussion of image flags. This is not
-an issue for running dynamics, but can affect calculation of some
-diagnostic quantities or the printing of unwrapped coordinates to a
-dump file. Note When a bond swap occurs the image flags of monomers in the new
+polymer chains can become inconsistent. See the dump
+command for a discussion of image flags. This is not an issue for
+running dynamics, but can affect calculation of some diagnostic
+quantities or the printing of unwrapped coordinates to a dump file. This fix computes a temperature each time it is invoked for use by the
@@ -304,7 +302,7 @@ cannot use a dihedral or improper potential.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
Warning Appling an external pressure to tilt dimensions xy,
-xz, yz can sometimes result in arbitrarily large values of the
-tilt factors, i.e. a dramatically deformed simulation box. This
-typically indicates that there is something badly wrong with how the
-simulation was constructed. The two most common sources of this error
-are applying a shear stress to a liquid system or specifying an
-external shear stress tensor that exceeds the yield stress of the
-solid. In either case the minimization may converge to a bogus
-conformation or not converge at all. Also note that if the box shape
-tilts to an extreme shape, LAMMPS will run less efficiently, due to
-the large volume of communication needed to acquire ghost atoms around
-a processor’s irregular-shaped sub-domain. For extreme values of
-tilt, LAMMPS may also lose atoms and generate an error. Note Appling an external pressure to tilt dimensions xy, xz, yz
+can sometimes result in arbitrarily large values of the tilt factors,
+i.e. a dramatically deformed simulation box. This typically indicates
+that there is something badly wrong with how the simulation was
+constructed. The two most common sources of this error are applying a
+shear stress to a liquid system or specifying an external shear stress
+tensor that exceeds the yield stress of the solid. In either case the
+minimization may converge to a bogus conformation or not converge at
+all. Also note that if the box shape tilts to an extreme shape,
+LAMMPS will run less efficiently, due to the large volume of
+communication needed to acquire ghost atoms around a processor’s
+irregular-shaped sub-domain. For extreme values of tilt, LAMMPS may
+also lose atoms and generate an error. Warning Performing a minimization with this fix is not a
-mathematically well-defined minimization problem. This is because the
-objective function being minimized changes if the box size/shape
-changes. In practice this means the minimizer can get “stuck” before
-you have reached the desired tolerance. The solution to this is to
-restart the minmizer from the new adjusted box size/shape, since that
-creates a new objective function valid for the new box size/shape.
-Repeat as necessary until the box size/shape has reached its new
-equilibrium. Note Performing a minimization with this fix is not a mathematically
+well-defined minimization problem. This is because the objective
+function being minimized changes if the box size/shape changes. In
+practice this means the minimizer can get “stuck” before you have
+reached the desired tolerance. The solution to this is to restart the
+minmizer from the new adjusted box size/shape, since that creates a
+new objective function valid for the new box size/shape. Repeat as
+necessary until the box size/shape has reached its new equilibrium. The couple keyword allows two or three of the diagonal components of
@@ -337,10 +336,10 @@ dimensions changes the objective function and gradients, which
sometimes causes the minimization to fail. This can be resolved by
changing the value of nreset, or simply continuing the minimization
from a restart file. Warning As normally computed, pressure includes a kinetic-
-energy or temperature-dependent component; see the compute pressure command. However, atom velocities are
+ Note As normally computed, pressure includes a kinetic- energy or
+temperature-dependent component; see the compute pressure command. However, atom velocities are
ignored during a minimization, and the applied pressure(s) specified
with this command are assumed to only be the virial component of the
pressure (the non-kinetic portion). Thus if atoms have a non-zero
@@ -352,19 +351,18 @@ monitoring the pressure without its kinetic component. The latter can
be done by outputting the pressure from the fix this command creates
(see below) or a pressure fix you define yourself. Warning Because pressure is often a very sensitive function of
-volume, it can be difficult for the minimizer to equilibrate the
-system the desired pressure with high precision, particularly for
-solids. Some techniques that seem to help are (a) use the
-“min_modify line quadratic” option when minimizing with box
-relaxations, (b) minimize several times in succession if need be,
-to drive the pressure closer to the target pressure, (c) relax
-the atom positions before relaxing the box, and (d) relax the box
-to the target hydrostatic pressure before relaxing to a target
-shear stress state. Also note that
-some systems (e.g. liquids) will not sustain a non-hydrostatic applied
+ Note Because pressure is often a very sensitive function of volume,
+it can be difficult for the minimizer to equilibrate the system the
+desired pressure with high precision, particularly for solids. Some
+techniques that seem to help are (a) use the “min_modify line
+quadratic” option when minimizing with box relaxations, (b) minimize
+several times in succession if need be, to drive the pressure closer
+to the target pressure, (c) relax the atom positions before relaxing
+the box, and (d) relax the box to the target hydrostatic pressure
+before relaxing to a target shear stress state. Also note that some
+systems (e.g. liquids) will not sustain a non-hydrostatic applied
pressure, which means the minimizer will not converge. Warning If both the temp and press keywords are used in a
-single thermo_modify command (or in two separate commands), then the
-order in which the keywords are specified is important. Note that a
-pressure compute defines its own temperature
-compute as an argument when it is specified. The temp keyword will
-override this (for the pressure compute being used by fix npt), but
-only if the temp keyword comes after the press keyword. If the
-temp keyword comes before the press keyword, then the new pressure
-compute specified by the press keyword will be unaffected by the
-temp setting. Note If both the temp and press keywords are used in a single
+thermo_modify command (or in two separate commands), then the order in
+which the keywords are specified is important. Note that a pressure compute defines its own temperature compute as
+an argument when it is specified. The temp keyword will override
+this (for the pressure compute being used by fix npt), but only if the
+temp keyword comes after the press keyword. If the temp keyword
+comes before the press keyword, then the new pressure compute
+specified by the press keyword will be unaffected by the temp
+setting. This fix computes a global scalar which can be accessed by various
output commands. The scalar is the
@@ -463,7 +460,7 @@ and if the tilt factor is not coupled to the barostat via keywords
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
Warning When non-equilibrium MD (NEMD) simulations are
-performed using this fix, the option “remap v” should normally be
-used. This is because fix nvt/sllod adjusts the
-atom positions and velocities to induce a velocity profile that
-matches the changing box size/shape. Thus atom coordinates should NOT
-be remapped by fix deform, but velocities SHOULD be when atoms cross
-periodic boundaries, since that is consistent with maintaining the
-velocity profile already created by fix nvt/sllod. LAMMPS will warn
-you if the remap setting is not consistent with fix nvt/sllod. Note When non-equilibrium MD (NEMD) simulations are performed using
+this fix, the option “remap v” should normally be used. This is
+because fix nvt/sllod adjusts the atom positions
+and velocities to induce a velocity profile that matches the changing
+box size/shape. Thus atom coordinates should NOT be remapped by fix
+deform, but velocities SHOULD be when atoms cross periodic boundaries,
+since that is consistent with maintaining the velocity profile already
+created by fix nvt/sllod. LAMMPS will warn you if the remap setting
+is not consistent with fix nvt/sllod. Warning For non-equilibrium MD (NEMD) simulations using “remap
-v” it is usually desirable that the fluid (or flowing material,
-e.g. granular particles) stream with a velocity profile consistent
-with the deforming box. As mentioned above, using a thermostat such
-as fix nvt/sllod or Note For non-equilibrium MD (NEMD) simulations using “remap v” it is
+usually desirable that the fluid (or flowing material, e.g. granular
+particles) stream with a velocity profile consistent with the
+deforming box. As mentioned above, using a thermostat such as fix nvt/sllod or Warning If a fix rigid is defined for rigid
-bodies, and remap is set to x, then the center-of-mass coordinates
-of rigid bodies will be remapped to the changing simulation box. This
-will be done regardless of whether atoms in the rigid bodies are in
-the fix deform group or not. The velocity of the centers of mass are
-not remapped even if remap is set to v, since fix nvt/sllod does not currently do anything special
+ Note If a fix rigid is defined for rigid bodies, and
+remap is set to x, then the center-of-mass coordinates of rigid
+bodies will be remapped to the changing simulation box. This will be
+done regardless of whether atoms in the rigid bodies are in the fix
+deform group or not. The velocity of the centers of mass are not
+remapped even if remap is set to v, since fix nvt/sllod does not currently do anything special
for rigid particles. If you wish to perform a NEMD simulation of
rigid particles, you can either thermostat them independently or
include a background fluid and thermostat the fluid via fix nvt/sllod.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
Warning LAMMPS checks that the specified region is wholly
-inside the simulation box. It can do this correctly for orthonormal
-simulation boxes. However for triclinic boxes, it only tests against the larger
-orthonormal box that bounds the tilted simulation box. If the
-specified region includes volume outside the tilted box, then an
-insertion will likely fail, leading to a “lost atoms” error. Thus for
-triclinic boxes you should insure the specified region is wholly
-inside the simulation box. Note LAMMPS checks that the specified region is wholly inside the
+simulation box. It can do this correctly for orthonormal simulation
+boxes. However for triclinic boxes, it
+only tests against the larger orthonormal box that bounds the tilted
+simulation box. If the specified region includes volume outside the
+tilted box, then an insertion will likely fail, leading to a “lost
+atoms” error. Thus for triclinic boxes you should insure the
+specified region is wholly inside the simulation box. Individual atoms are inserted, unless the mol keyword is used. It
specifies a template-ID previously defined using the
@@ -292,11 +292,11 @@ of the molecule. If this test fails, a new random position within the
insertion volume is chosen and another trial is made. Up to Q
attempts are made. If the particle is not successfully inserted,
LAMMPS prints a warning message. Warning If you are inserting finite size particles or a
-molecule or rigid body consisting of finite-size particles, then you
-should typically set R larger than the distance at which any inserted
+ Note If you are inserting finite size particles or a molecule or
+rigid body consisting of finite-size particles, then you should
+typically set R larger than the distance at which any inserted
particle may overlap with either a previouly inserted particle or an
existing particle. LAMMPS will issue a warning if R is smaller than
this value, based on the radii of existing and inserted particles. Warning If you are monitoring the temperature of a system
-where the atom count is changing due to adding particles, you
-typically should use the compute_modify dynamic yes command for the temperature compute you are
-using. Note If you are monitoring the temperature of a system where the atom
+count is changing due to adding particles, you typically should use
+the compute_modify dynamic yes command for the
+temperature compute you are using.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
Masses: begin{equation} M’ = M + m end{equation}
-begin{equation} m’ = frac {M, m } {M’} end{equation}
-Positions: begin{equation} X’ = frac {M, X + m, x} {M’}
-end{equation} begin{equation} x’ = x - X end{equation}
-Velocities: begin{equation} V’ = frac {M, V + m, v} {M’}
-end{equation} begin{equation} v’ = v - V end{equation}
-Forces: begin{equation} F’ = F + f end{equation}
-begin{equation} f’ = frac { M, f - m, F} {M’}
-end{equation} This transform conserves the total kinetic energy
-begin{equation} frac 1 2 , (M, V^2+ m, v^2)
-= frac 1 2 , (M’, V’^2+ m’, v’^2) end{equation}
-and the virial defined with absolute positions
-begin{equation} X, F + x, f = X’, F’ + x’, f’ end{equation} Masses: Positions: Velocities: Forces: This transform conserves the total kinetic energy and the virial defined with absolute positions This fix requires each atom know whether it is a Drude particle or
not. You must therefore use the fix drude command to
specify the Drude status of each atom type. Warning only the Drude core atoms need to be in the group
-specified for this fix. A Drude electron will be transformed together
-with its core even if it is not itself in the group. It is safe to
-include Drude electrons or non-polarizable atoms in the group. The
-non-polarizable atoms will simply not be transformed. Note only the Drude core atoms need to be in the group specified for
+this fix. A Drude electron will be transformed together with its core
+even if it is not itself in the group. It is safe to include Drude
+electrons or non-polarizable atoms in the group. The non-polarizable
+atoms will simply not be transformed. This fix does NOT perform time integration. It only transform masses,
@@ -199,12 +212,11 @@ integration fixes, like fi
atoms. In order to thermalize the reduced degrees of freedom at
different temperatures, two Nose-Hoover thermostats must be defined,
acting on two distinct groups. Warning The fix drude/transform/direct command must appear
-before any Nose-Hoover thermostating fixes. The fix
-drude/transform/inverse command must appear after any Nose-Hoover
-thermostating fixes. Note The fix drude/transform/direct command must appear before any
+Nose-Hoover thermostating fixes. The fix drude/transform/inverse
+command must appear after any Nose-Hoover thermostating fixes. Example:
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
Warning If you want the fictitious potential energy associated
-with the added forces to be included in the total potential energy of
-the system (the quantity being minimized), you MUST enable the
+ Note If you want the fictitious potential energy associated with the
+added forces to be included in the total potential energy of the
+system (the quantity being minimized), you MUST enable the
fix_modify energy option for this fix.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
Note that neighbor lists are re-built on timesteps that atoms are
removed. Thus you should not remove atoms too frequently or you will
incur overhead due to the cost of building neighbor lists. Warning If you are monitoring the temperature of a system
-where the atom count is changing due to evaporation, you typically
-should use the compute_modify dynamic yes
-command for the temperature compute you are using. Note If you are monitoring the temperature of a system where the atom
+count is changing due to evaporation, you typically should use the
+compute_modify dynamic yes command for the
+temperature compute you are using.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
The forces due to this fix are imposed during an energy minimization,
invoked by the minimize command. Warning If you want the fictitious potential energy associated
-with the added forces to be included in the total potential energy of
-the system (the quantity being minimized), you MUST enable the
+ Note If you want the fictitious potential energy associated with the
+added forces to be included in the total potential energy of the
+system (the quantity being minimized), you MUST enable the
fix_modify energy option for this fix.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
This fix performs grand canonical Monte Carlo (GCMC) exchanges of
atoms or molecules of the given type with an imaginary ideal gas reservoir at
the specified T and chemical potential (mu) as discussed in
-(Frenkel). If used with the fix nvt command,
+(Frenkel). If used with the fix nvt command,
simulations in the grand canonical ensemble (muVT, constant chemical
potential, constant volume, and constant temperature) can be
performed. Specific uses include computing isotherms in microporous
@@ -450,7 +450,7 @@ Academic Press, London, 2002.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
Warning Note While this fix bears many similarities to fix langevin, it has one significant
difference. Namely, fix gld performs time integration,
whereas fix langevin does NOT. To this end, the
@@ -268,7 +268,7 @@ was built with that package. See the
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
Warning If heat is subtracted from the system too aggressively
-so that the group’s kinetic energy would go to zero, or any individual
-atom’s kinetic energy would go to zero for the case where eflux is
-an atom-style variable, then LAMMPS will halt with an error message. Note If heat is subtracted from the system too aggressively so that
+the group’s kinetic energy would go to zero, or any individual atom’s
+kinetic energy would go to zero for the case where eflux is an
+atom-style variable, then LAMMPS will halt with an error message. Fix heat is different from a thermostat such as fix nvt
or fix temp/rescale in that energy is
@@ -249,7 +249,7 @@ the run command. Thi
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
Warning If you want the atom/indenter interaction energy to be
-included in the total potential energy of the system (the quantity
-being minimized), you must enable the fix_modify
-energy option for this fix. Note If you want the atom/indenter interaction energy to be included
+in the total potential energy of the system (the quantity being
+minimized), you must enable the fix_modify energy
+option for this fix.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
Warning Unlike the fix nvt command which
-performs Nose/Hoover thermostatting AND time integration, this fix
-does NOT perform time integration. It only modifies forces to effect
+ Note Unlike the fix nvt command which performs
+Nose/Hoover thermostatting AND time integration, this fix does NOT
+perform time integration. It only modifies forces to effect
thermostatting. Thus you must use a separate time integration fix,
like fix nve to actually update the velocities and
positions of atoms using the modified forces. Likewise, this fix
@@ -320,11 +320,11 @@ it is the energy exchanged between the infinite thermal reservoir and
the particles. As described below, this energy can then be printed
out or added to the potential energy of the system to monitor energy
conservation. Warning this accumulated energy does NOT include kinetic
-energy removed by the zero flag. LAMMPS will print a warning when
-both options are active. Note this accumulated energy does NOT include kinetic energy removed
+by the zero flag. LAMMPS will print a warning when both options are
+active. The keyword zero can be used to eliminate drift due to the
thermostat. Because the random forces on different atoms are
@@ -435,7 +435,7 @@ types, tally = no, zero = no, gjf = no.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
Velocities:
-begin{equation} V’ = frac {M, V + m, v} {M’} end{equation}
-begin{equation} v’ = v - V end{equation}
-Masses:
-begin{equation} M’ = M + m end{equation}
-begin{equation} m’ = frac {M, m } {M’} end{equation}
-The Langevin forces are computed as
-begin{equation} F’ = - frac {M’} {mathtt{damp_com}}, V’ + F_r’ end{equation}
-begin{equation} f’ = - frac {m’} {mathtt{damp_drude}}, v’ + f_r’ end{equation}
-(F_r’) is a random force proportional to
-(sqrt { frac {2, k_B mathtt{Tcom}, m’} } ). (f_r’) is a random force proportional to
-(sqrt { frac {2, k_B mathtt{Tdrude}, m’} } ). Then the real forces acting on the particles are computed from the inverse
-transform:
-begin{equation} F = frac M {M’}, F’ - f’ end{equation}
-begin{equation} f = frac m {M’}, F’ + f’ end{equation} Velocities: Masses: The Langevin forces are computed as \(F_r'\) is a random force proportional to
+\(\sqrt { \frac {2\, k_B \mathtt{Tcom}\, m'} {\mathrm dt\, \mathtt{damp\_com} } }\). :b:math:`f_r’` is a random force proportional to
+\(\sqrt { \frac {2\, k_B \mathtt{Tdrude}\, m'} {\mathrm dt\, \mathtt{damp\_drude} } }\).
+Then the real forces acting on the particles are computed from the inverse
+transform: This fix also thermostates non-polarizable atoms in the group at
temperature Tcom, as if they had a massless Drude partner. The
Drude particles themselves need not be in the group. The center of
@@ -207,15 +204,15 @@ important consideration if finite-size particles, which have
rotational degrees of freedom, are being thermostated. The
translational degrees of freedom can also have a bias velocity removed
from them before thermostating takes place; see the description below. Warning Like the fix langevin command,
-this fix does NOT perform time integration. It only modifies forces to
-effect thermostating. Thus you must use a separate time integration
-fix, like fix nve or fix nph to actually
-update the velocities and positions of atoms using the modified
-forces. Likewise, this fix should not normally be used on atoms that
-also have their temperature controlled by another fix - e.g. by fix nvt or fix temp/rescale commands. Note Like the fix langevin command, this fix does
+NOT perform time integration. It only modifies forces to effect
+thermostating. Thus you must use a separate time integration fix, like
+fix nve or fix nph to actually update the
+velocities and positions of atoms using the modified forces.
+Likewise, this fix should not normally be used on atoms that also have
+their temperature controlled by another fix - e.g. by fix nvt or fix temp/rescale commands. See this howto section of the manual for
a discussion of different ways to compute temperature and perform
@@ -224,20 +221,20 @@ thermostating. This fix requires each atom know whether it is a Drude particle or
not. You must therefore use the fix drude command to
specify the Drude status of each atom type. Warning only the Drude core atoms need to be in the group
-specified for this fix. A Drude electron will be transformed together
-with its cores even if it is not itself in the group. It is safe to
-include Drude electrons or non-polarizable atoms in the group. The
-non-polarizable atoms will simply be thermostatted as if they had
-a massless Drude partner (electron). Note only the Drude core atoms need to be in the group specified for
+this fix. A Drude electron will be transformed together with its cores
+even if it is not itself in the group. It is safe to include Drude
+electrons or non-polarizable atoms in the group. The non-polarizable
+atoms will simply be thermostatted as if they had a massless Drude
+partner (electron). Warning Ghost atoms need to know their velocity for this fix
-to act correctly. You must use the comm_modify
-command to enable this, e.g. Note Ghost atoms need to know their velocity for this fix to act
+correctly. You must use the comm_modify command to
+enable this, e.g.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
Warning while this fix applies the force of the particles on
-the fluid, it does not apply the force of the fluid to the particles.
-When the force coupling constant is set using the default method,
-there is only one option to include this hydrodynamic force on the
-particles, and that is through the use of the
-lb/viscous fix. This fix adds the hydrodynamic
-force to the total force acting on the particles, after which any of
-the built-in LAMMPS integrators can be used to integrate the particle
-motion. However, if the user specifies their own value for the force
-coupling constant, as mentioned in Mackay et al., the
-built-in LAMMPS integrators may prove to be unstable. Therefore, we
-have included our own integrators fix lb/rigid/pc/sphere, and fix lb/pc, to solve for the particle motion in these
+ Note while this fix applies the force of the particles on the fluid,
+it does not apply the force of the fluid to the particles. When the
+force coupling constant is set using the default method, there is only
+one option to include this hydrodynamic force on the particles, and
+that is through the use of the lb/viscous fix.
+This fix adds the hydrodynamic force to the total force acting on the
+particles, after which any of the built-in LAMMPS integrators can be
+used to integrate the particle motion. However, if the user specifies
+their own value for the force coupling constant, as mentioned in
+Mackay et al., the built-in LAMMPS integrators may prove to
+be unstable. Therefore, we have included our own integrators fix lb/rigid/pc/sphere, and fix lb/pc, to solve for the particle motion in these
cases. These integrators should not be used with the
lb/viscous fix, as they add hydrodynamic forces
to the particles directly. In addition, they can not be used if the
force coupling constant has been set the default way. Warning if the force coupling constant is set using the
-default method, and the lb/viscous fix is NOT
-used to add the hydrodynamic force to the total force acting on the
-particles, this physically corresponds to a situation in which an
-infinitely massive particle is moving through the fluid (since
-collisions between the particle and the fluid do not act to change the
-particle’s velocity). Therefore, the user should set the mass of the
-particle to be significantly larger than the mass of the fluid at the
-particle location, in order to approximate an infinitely massive
-particle (see the dragforce test run for an example). Note if the force coupling constant is set using the default method,
+and the lb/viscous fix is NOT used to add the
+hydrodynamic force to the total force acting on the particles, this
+physically corresponds to a situation in which an infinitely massive
+particle is moving through the fluid (since collisions between the
+particle and the fluid do not act to change the particle’s velocity).
+Therefore, the user should set the mass of the particle to be
+significantly larger than the mass of the fluid at the particle
+location, in order to approximate an infinitely massive particle (see
+the dragforce test run for an example). Inside the fix, parameters are scaled by the lattice-Boltzmann
@@ -285,11 +284,11 @@ equal to 1.0, and dx is chosen so that tau/(dt) =
(3*eta*dt)/(rho*dx^2) is approximately equal to 1. However, the user
has the option of specifying their own values for dm, and dx, by using
the optional keywords dm, and dx respectively. Warning Care must be taken when choosing both a value for dx,
-and a simulation domain size. This fix uses the same subdivision of
-the simulation domain among processors as the main LAMMPS program. In
+ Note Care must be taken when choosing both a value for dx, and a
+simulation domain size. This fix uses the same subdivision of the
+simulation domain among processors as the main LAMMPS program. In
order to uniformly cover the simulation domain with lattice sites, the
lengths of the individual LAMMPS subdomains must all be evenly
divisible by dx. If the simulation domain size is cubic, with equal
@@ -351,10 +350,10 @@ integer, N, a binary restart file is printed every N LB timesteps.
This restart file only contains information about the fluid.
Therefore, a LAMMPS restart file should also be written in order to
print out full details of the simulation. Warning When a large number of lattice grid points are used,
-the restart files may become quite large. Note When a large number of lattice grid points are used, the restart
+files may become quite large. In order to restart the fluid portion of the simulation, the keyword
read_restart is specified, followed by the name of the binary
@@ -443,7 +442,7 @@ If walls are present, they are assumed to be stationary.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
This fix adds a force, F = - Gamma*(velocity-fluid_velocity), to each
atom, where Gamma is the force coupling constant described in the fix lb/fluid command (which applies an equal and
opposite force to the fluid). Warning This fix should only be used in conjunction with one
-of the built in LAMMPS integrators; it should not be used with the
-fix lb/pc or fix lb/rigid/pc/sphere integrators, which
+ Note This fix should only be used in conjunction with one of the
+built in LAMMPS integrators; it should not be used with the fix lb/pc or fix lb/rigid/pc/sphere integrators, which
already include the hydrodynamic forces. These latter fixes should
only be used if the force coupling constant has been set by the user
(instead of using the default value); if the default force coupling
@@ -210,7 +209,7 @@ used.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
Warning The atoms affected by this fix should not normally be
-time integrated by other fixes (e.g. fix nve, fix nvt), since that will change their positions and
+ Note The atoms affected by this fix should not normally be time
+integrated by other fixes (e.g. fix nve, fix nvt), since that will change their positions and
velocities twice. Warning As atoms move due to this fix, they will pass thru
-periodic boundaries and be remapped to the other side of the
-simulation box, just as they would during normal time integration
-(e.g. via the fix nve command). It is up to you to
-decide whether periodic boundaries are appropriate with the kind of
-atom motion you are prescribing with this fix. Note As atoms move due to this fix, they will pass thru periodic
+boundaries and be remapped to the other side of the simulation box,
+just as they would during normal time integration (e.g. via the fix nve command). It is up to you to decide whether
+periodic boundaries are appropriate with the kind of atom motion you
+are prescribing with this fix. Warning As dicsussed below, atoms are moved relative to their
-initial position at the time the fix is specified. These initial
-coordinates are stored by the fix in “unwrapped” form, by using the
-image flags associated with each atom. See the dump custom command for a discussion of “unwrapped” coordinates.
-See the Atoms section of the read_data command for a
-discussion of image flags and how they are set for each atom. You can
-reset the image flags (e.g. to 0) before invoking this fix by using
-the set image command. Note As dicsussed below, atoms are moved relative to their initial
+position at the time the fix is specified. These initial coordinates
+are stored by the fix in “unwrapped” form, by using the image flags
+associated with each atom. See the dump custom command
+for a discussion of “unwrapped” coordinates. See the Atoms section of
+the read_data command for a discussion of image flags
+and how they are set for each atom. You can reset the image flags
+(e.g. to 0) before invoking this fix by using the set image
+command. The linear style moves atoms at a constant velocity, so that their
@@ -349,7 +349,7 @@ position and velocity of atoms on the outermost rRESPA level.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
The equations of motion used are those of Shinoda et al in
-(Shinoda), which combine the hydrostatic equations of
-Martyna, Tobias and Klein in (Martyna) with the strain
+(Shinoda), which combine the hydrostatic equations of
+Martyna, Tobias and Klein in (Martyna) with the strain
energy proposed by Parrinello and Rahman in
-(Parrinello). The time integration schemes closely
+(Parrinello). The time integration schemes closely
follow the time-reversible measure-preserving Verlet and rRESPA
-integrators derived by Tuckerman et al in (Tuckerman). The thermostat parameters for fix styles nvt and npt is specified
using the temp keyword. Other thermostat-related keywords are
@@ -253,14 +253,14 @@ the temperature in a timespan of (roughly) 10 time units (e.g. tau or
fmsec or psec - see the units command). The atoms in the
fix group are the only ones whose velocities and positions are updated
by the velocity/position update portion of the integration. Warning A Nose-Hoover thermostat will not work well for
-arbitrary values of Tdamp. If Tdamp is too small, the temperature
-can fluctuate wildly; if it is too large, the temperature will take a
-very long time to equilibrate. A good choice for many models is a
-Tdamp of around 100 timesteps. Note that this is NOT the same as
-100 time units for most units settings. Note A Nose-Hoover thermostat will not work well for arbitrary values
+of Tdamp. If Tdamp is too small, the temperature can fluctuate
+wildly; if it is too large, the temperature will take a very long time
+to equilibrate. A good choice for many models is a Tdamp of around
+100 timesteps. Note that this is NOT the same as 100 time units for
+most units settings. The barostat parameters for fix styles npt and nph is specified
@@ -296,14 +296,14 @@ simulation box must be triclinic, even if its initial tilt factors are
relaxed. For example, a value of 10.0 means to relax the pressure in
a timespan of (roughly) 10 time units (e.g. tau or fmsec or psec - see
the units command). Warning A Nose-Hoover barostat will not work well for
-arbitrary values of Pdamp. If Pdamp is too small, the pressure
-and volume can fluctuate wildly; if it is too large, the pressure will
-take a very long time to equilibrate. A good choice for many models
-is a Pdamp of around 1000 timesteps. Note that this is NOT the same
-as 1000 time units for most units settings. Note A Nose-Hoover barostat will not work well for arbitrary values
+of Pdamp. If Pdamp is too small, the pressure and volume can
+fluctuate wildly; if it is too large, the pressure will take a very
+long time to equilibrate. A good choice for many models is a Pdamp
+of around 1000 timesteps. Note that this is NOT the same as 1000 time
+units for most units settings. Regardless of what atoms are in the fix group (the only atoms which
are time integrated), a global pressure or stress tensor is computed
@@ -394,7 +394,7 @@ freedom. A value of 0 corresponds to no thermostatting of the
barostat variables. The mtk keyword controls whether or not the correction terms due to
Martyna, Tuckerman, and Klein are included in the equations of motion
-(Martyna). Specifying no reproduces the original
+(Martyna). Specifying no reproduces the original
Hoover barostat, whose volume probability distribution function
differs from the true NPT and NPH ensembles by a factor of 1/V. Hence
using yes is more correct, but in many cases the difference is
@@ -403,7 +403,7 @@ negligible. The keyword nreset controls how often the reference dimensions used
to define the strain energy are reset. If this keyword is not used,
@@ -445,15 +445,15 @@ far. In all cases, the particle trajectories are unaffected by the
chosen value, except for a time-dependent constant translation of
positions. Warning Using a barostat coupled to tilt dimensions xy,
-xz, yz can sometimes result in arbitrarily large values of the
-tilt dimensions, i.e. a dramatically deformed simulation box. LAMMPS
-allows the tilt factors to grow a small amount beyond the normal limit
-of half the box length (0.6 times the box length), and then performs a
-box “flip” to an equivalent periodic cell. See the discussion of the
-flip keyword above, to allow this bound to be exceeded, if desired. Note Using a barostat coupled to tilt dimensions xy, xz, yz can
+sometimes result in arbitrarily large values of the tilt dimensions,
+i.e. a dramatically deformed simulation box. LAMMPS allows the tilt
+factors to grow a small amount beyond the normal limit of half the box
+length (0.6 times the box length), and then performs a box “flip” to
+an equivalent periodic cell. See the discussion of the flip keyword
+above, to allow this bound to be exceeded, if desired. The flip operation is described in more detail in the doc page for
fix deform. Both the barostat dynamics and the atom
@@ -476,15 +476,15 @@ factor are not enforced, since flipping the box in that dimension does
not change the atom positions due to non-periodicity. In this mode,
if you tilt the system to extreme angles, the simulation will simply
become inefficient due to the highly skewed simulation box. Warning Unlike the fix temp/berendsen command which performs
-thermostatting but NO time integration, these fixes perform
-thermostatting/barostatting AND time integration. Thus you should not
-use any other time integration fix, such as fix nve on
-atoms to which this fix is applied. Likewise, fix nvt and fix npt
-should not normally be used on atoms that also have their temperature
-controlled by another fix - e.g. by fix langevin or fix temp/rescale commands. Note Unlike the fix temp/berendsen command
+which performs thermostatting but NO time integration, these fixes
+perform thermostatting/barostatting AND time integration. Thus you
+should not use any other time integration fix, such as fix nve on atoms to which this fix is applied. Likewise,
+fix nvt and fix npt should not normally be used on atoms that also
+have their temperature controlled by another fix - e.g. by fix langevin or fix temp/rescale
+commands. See this howto section of the manual for
a discussion of different ways to compute temperature and perform
@@ -584,18 +584,17 @@ If you do this, note that the kinetic energy derived from the compute
temperature should be consistent with the virial term computed using
all atoms for the pressure. LAMMPS will warn you if you choose to
compute temperature on a subset of atoms. Warning If both the temp and press keywords are used in a
-single thermo_modify command (or in two separate commands), then the
-order in which the keywords are specified is important. Note that a
-pressure compute defines its own temperature
-compute as an argument when it is specified. The temp keyword will
-override this (for the pressure compute being used by fix npt), but
-only if the temp keyword comes after the press keyword. If the
-temp keyword comes before the press keyword, then the new pressure
-compute specified by the press keyword will be unaffected by the
-temp setting. Note If both the temp and press keywords are used in a single
+thermo_modify command (or in two separate commands), then the order in
+which the keywords are specified is important. Note that a pressure compute defines its own temperature compute as
+an argument when it is specified. The temp keyword will override
+this (for the pressure compute being used by fix npt), but only if the
+temp keyword comes after the press keyword. If the temp keyword
+comes before the press keyword, then the new pressure compute
+specified by the press keyword will be unaffected by the temp
+setting. The fix_modify energy option is supported by these
fixes to add the energy change induced by Nose/Hoover thermostatting
@@ -698,7 +697,7 @@ Martyna, J Phys A: Math Gen, 39, 5629 (2006).
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
Warning there are two different pressures that can be reported
-for eFF when defining the pair_style (see Note there are two different pressures that can be reported for eFF
+when defining the pair_style (see Warning currently, there is no available option for the user
-to set or create temperature distributions that include the radial
-electronic degrees of freedom with the velocity
-command, so the the user must allow for these degrees of freedom to
-equilibrate (i.e. equi-partitioning of energy) through time
-integration. Note currently, there is no available option for the user to set or
+create temperature distributions that include the radial electronic
+degrees of freedom with the velocity command, so the
+the user must allow for these degrees of freedom to equilibrate
+(i.e. equi-partitioning of energy) through time integration. This fix is part of the USER-EFF package. It is only enabled if
LAMMPS was built with that package. See the Making LAMMPS section for more info. Other restriction discussed on the doc page for the fix nvt, npt, and nph commands also apply. Warning The temperature for systems (regions or groups) with
-only electrons and no nuclei is 0.0 (i.e. not defined) in the current
+ Note The temperature for systems (regions or groups) with only
+electrons and no nuclei is 0.0 (i.e. not defined) in the current
temperature calculations, a practical example would be a uniform
electron gas or a very hot plasma, where electrons remain delocalized
from the nuclei. This is because, even though electron virials are
@@ -275,7 +274,7 @@ Martyna, J Phys A: Math Gen, 39, 5629 (2006).
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
Warning Unlike the fix temp/berendsen command which performs
-thermostatting but NO time integration, this fix performs
-thermostatting/barostatting AND time integration. Thus you should not
-use any other time integration fix, such as fix nve on
-atoms to which this fix is applied. Likewise, this fix should not be
-used on atoms that have their temperature controlled by another fix
-- e.g. by fix langevin or fix temp/rescale
-commands. Note Unlike the fix temp/berendsen command
+which performs thermostatting but NO time integration, this fix
+performs thermostatting/barostatting AND time integration. Thus you
+should not use any other time integration fix, such as fix nve on atoms to which this fix is applied. Likewise,
+this fix should not be used on atoms that have their temperature
+controlled by another fix - e.g. by fix langevin or fix temp/rescale commands. This fix computes a temperature and pressure at each timestep. To do
@@ -338,7 +336,7 @@ plus the additional ones mentioned above.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
Warning You should not use fix shake in
-conjunction with this fix. That is because fix shake applies
-contraint forces based on the predicted postitions of atoms after the
-next timestep. It has no way of knowing the timestep may change due
-to this fix, which will cause the constraint forces to be invalid. A
-better strategy is to turn off fix shake when performing initial
-dynamics that need this fix, then turn fix shake on when doing normal
-dynamics with a fixed-size timestep. Note You should not use fix shake in conjunction
+with this fix. That is because fix shake applies contraint forces
+based on the predicted postitions of atoms after the next timestep.
+It has no way of knowing the timestep may change due to this fix,
+which will cause the constraint forces to be invalid. A better
+strategy is to turn off fix shake when performing initial dynamics
+that need this fix, then turn fix shake on when doing normal dynamics
+with a fixed-size timestep.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
Warning Fix deform has an option for
-remapping either atom coordinates or velocities to the changing
-simulation box. To use fix nvt/sllod, fix deform should NOT remap
-atom positions, because fix nvt/sllod adjusts the atom positions and
-velocities to create a velocity profile that matches the changing box
-size/shape. Fix deform SHOULD remap atom velocities when atoms cross
-periodic boundaries since that is consistent with maintaining the
-velocity profile created by fix nvt/sllod. LAMMPS will give an
-error if this setting is not consistent. Note Fix deform has an option for remapping either
+atom coordinates or velocities to the changing simulation box. To use
+fix nvt/sllod, fix deform should NOT remap atom positions, because fix
+nvt/sllod adjusts the atom positions and velocities to create a
+velocity profile that matches the changing box size/shape. Fix deform
+SHOULD remap atom velocities when atoms cross periodic boundaries
+since that is consistent with maintaining the velocity profile created
+by fix nvt/sllod. LAMMPS will give an error if this setting is not
+consistent. The SLLOD equations of motion, originally proposed by Hoover and Ladd
(see (Evans and Morriss)), were proven to be equivalent to
@@ -286,7 +286,7 @@ equilibration.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
Warning This fix implements a complete velocity-verlet
-integrator combined with NH massive chain thermostat, so no
-other time integration fix should be used. Note This fix implements a complete velocity-verlet integrator
+combined with NH massive chain thermostat, so no other time
+integration fix should be used. The method keyword determines what style of PIMD is performed. A
value of pimd is standard PIMD. A value of nmpimd is for
@@ -291,7 +291,7 @@ Path Integrals, McGraw-Hill, New York (1965).
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
The rate option moves the insertion volume in the z direction (3d)
or y direction (2d). This enables pouring particles from a
successively higher height over time. Warning If you are monitoring the temperature of a system
-where the particle count is changing due to adding particles, you
-typically should use the compute_modify dynamic yes command for the temperature compute you are
-using. Note If you are monitoring the temperature of a system where the
+particle count is changing due to adding particles, you typically
+should use the compute_modify dynamic yes
+command for the temperature compute you are using.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
Warning Unlike the fix npt or fix nph commands which perform Nose/Hoover barostatting AND
-time integration, this fix does NOT perform time integration. It only
-modifies the box size and atom coordinates to effect barostatting.
-Thus you must use a separate time integration fix, like fix nve or fix nvt to actually update the
-positions and velocities of atoms. This fix can be used in
-conjunction with thermostatting fixes to control the temperature, such
-as fix nvt or fix langevin or fix temp/berendsen. Note Unlike the fix npt or fix nph
+commands which perform Nose/Hoover barostatting AND time integration,
+this fix does NOT perform time integration. It only modifies the box
+size and atom coordinates to effect barostatting. Thus you must use a
+separate time integration fix, like fix nve or fix nvt to actually update the positions and velocities of
+atoms. This fix can be used in conjunction with thermostatting fixes
+to control the temperature, such as fix nvt or fix langevin or fix temp/berendsen. See this howto section of the manual for
a discussion of different ways to compute temperature and perform
@@ -206,13 +206,13 @@ although you have the option to change that dimension via the units command). Warning The relaxation time is actually also a function of the
-bulk modulus of the system (inverse of isothermal compressibility).
-The bulk modulus has units of pressure and is the amount of pressure
-that would need to be applied (isotropically) to reduce the volume of
-the system by a factor of 2 (assuming the bulk modulus was a constant,
+ Note The relaxation time is actually also a function of the bulk
+modulus of the system (inverse of isothermal compressibility). The
+bulk modulus has units of pressure and is the amount of pressure that
+would need to be applied (isotropically) to reduce the volume of the
+system by a factor of 2 (assuming the bulk modulus was a constant,
independent of density, which it’s not). The bulk modulus can be set
via the keyword modulus. The Pdamp parameter is effectively
multiplied by the bulk modulus, so if the pressure is relaxing faster
@@ -329,7 +329,7 @@ Phys, 81, 3684 (1984).
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
Warning If you use this command with the mol or charge
-vectors than you most likely want to set ghost yes, since these
-properties are stored with ghost atoms if you use an
-atom_style that defines them, and many LAMMPS
-operations that use molecule IDs or charge, such as neighbor lists and
-pair styles, will expect ghost atoms to have these valuse. LAMMPS
-will issue a warning it you define those vectors but do not set
-ghost yes. Note If you use this command with the mol or charge vectors than
+you most likely want to set ghost yes, since these properties are
+stored with ghost atoms if you use an atom_style
+that defines them, and many LAMMPS operations that use molecule IDs or
+charge, such as neighbor lists and pair styles, will expect ghost
+atoms to have these valuse. LAMMPS will issue a warning it you define
+those vectors but do not set ghost yes. Warning The properties for ghost atoms are not updated every
-timestep, but only once every few steps when neighbor lists are
-re-built. Thus the ghost keyword is suitable for static properties,
-like molecule IDs, but not for dynamic properties that change every
-step. For the latter, the code you add to LAMMPS to change the
-properties will also need to communicate their new values to/from
-ghost atoms, an operation that can be invoked from within a pair style or fix or compute
-that you write. Note The properties for ghost atoms are not updated every timestep,
+but only once every few steps when neighbor lists are re-built. Thus
+the ghost keyword is suitable for static properties, like molecule
+IDs, but not for dynamic properties that change every step. For the
+latter, the code you add to LAMMPS to change the properties will also
+need to communicate their new values to/from ghost atoms, an operation
+that can be invoked from within a pair style or
+fix or compute that you write. This fix is one of a small number that can be defined in an input
@@ -332,7 +331,7 @@ This fix is not invoked during
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
Perform the charge equilibration (QEq) method as described in (Rappe and Goddard) and formulated in (Nakano) (also known
-as the matrix inversion method) and in (Rick and Stuart) (also
+as the matrix inversion method) and in (Rick and Stuart) (also
known as the extended Lagrangian method) based on the
electronegativity equilization principle. These fixes can be used with any pair style in
@@ -180,20 +180,20 @@ define the QEq fix, perform a zero-timestep run via the unfix command before performing further dynamics. Warning Computing and using charge values different from
-published values defined for a fixed-charge potential like Buckingham
-or CHARMM or AMBER, can have a strong effect on energies and forces,
-and produces a different model than the published versions. Note Computing and using charge values different from published
+values defined for a fixed-charge potential like Buckingham or CHARMM
+or AMBER, can have a strong effect on energies and forces, and
+produces a different model than the published versions. Warning The fix qeq/comb command must
-still be used to perform charge equliibration with the COMB potential. The fix qeq/reax
+ Note The fix qeq/comb command must still be used
+to perform charge equliibration with the COMB potential. The fix qeq/reax
command can be used to perform charge equilibration with the ReaxFF force field, although fix qeq/shielded yields the
-same results as fix qeq/reax if Nevery, cutoff, and tolerance are
-the same. Eventually the fix qeq/reax command will be deprecated. The QEq method minimizes the electrostatic energy of the system (or
equalizes the derivative of energy with respect to charge of all the
@@ -260,19 +260,18 @@ solve partial charges on atoms using different solvers. Styles
the QEq parameters and Nevery, cutoff, and tolerance are the
same. Style qeq/point is typically faster, but qeq/dynamic scales
better on larger sizes. Warning To avoid the evaluation of the derivative of charge
-with respect to position, which is typically ill-defined, the system
-should have a zero net charge. Note To avoid the evaluation of the derivative of charge with respect
+to position, which is typically ill-defined, the system should have a
+zero net charge. Warning Developing QEq parameters (chi, eta, gamma, zeta, and
-qcore) is an “art”. Charges on atoms are not guaranteed to
-equilibrate with arbitrary choices of these parameters. We do not
-develop these QEq paramters. See the examples/qeq directory for some
-examples. Note Developing QEq parameters (chi, eta, gamma, zeta, and qcore) is
+an “art”. Charges on atoms are not guaranteed to equilibrate with
+arbitrary choices of these parameters. We do not develop these QEq
+paramters. See the examples/qeq directory for some examples.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
Warning Unlike the fix nvt command which
-performs Nose/Hoover thermostatting AND time integration, this fix
-does NOT perform time integration. It only modifies forces to a
-colored thermostat. Thus you must use a separate time integration fix,
-like fix nve or fix nph to actually
-update the velocities and positions of atoms (as shown in the
+ Note Unlike the fix nvt command which performs
+Nose/Hoover thermostatting AND time integration, this fix does NOT
+perform time integration. It only modifies forces to a colored
+thermostat. Thus you must use a separate time integration fix, like
+fix nve or fix nph to actually update the
+velocities and positions of atoms (as shown in the
examples). Likewise, this fix should not normally be used with other
fixes or commands that also specify system temperatures , e.g. fix nvt and fix temp/rescale.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
Note that the velocity command can be used to create
velocities with zero aggregate linear and/or angular momentum. Warning This fix performs its operations at the same point in
-the timestep as other time integration fixes, such as fix nve, fix nvt, or fix npt.
+ Note This fix performs its operations at the same point in the
+timestep as other time integration fixes, such as fix nve, fix nvt, or fix npt.
Thus fix recenter should normally be the last such fix specified in
the input script, since the adjustments it makes to atom coordinates
should come after the changes made by time integration. LAMMPS will
warn you if your fixes are not ordered this way. Warning If you use this fix on a small group of atoms (e.g. a
-molecule in solvent) without using the shift keyword to adjust the
-positions of all atoms in the system, then the results can be
-unpredictable. For example, if the molecule is pushed in one
-direction by the solvent, its velocity will increase. But its
-coordinates will be recentered, meaning it is pushed back towards the
-force. Thus over time, the velocity and temperature of the molecule
-could become very large (though it won’t appear to be moving due to
-the recentering). If you are thermostatting the entire system, then
-the solvent would be cooled to compensate. A better solution for this
-simulation scenario is to use the fix spring command
-to tether the molecule in place. Note If you use this fix on a small group of atoms (e.g. a molecule
+in solvent) without using the shift keyword to adjust the positions
+of all atoms in the system, then the results can be unpredictable.
+For example, if the molecule is pushed in one direction by the
+solvent, its velocity will increase. But its coordinates will be
+recentered, meaning it is pushed back towards the force. Thus over
+time, the velocity and temperature of the molecule could become very
+large (though it won’t appear to be moving due to the recentering).
+If you are thermostatting the entire system, then the solvent would be
+cooled to compensate. A better solution for this simulation scenario
+is to use the fix spring command to tether the
+molecule in place.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
Warning Adding a force to atoms implies a change in their
-potential energy as they move due to the applied force field. For
-dynamics via the run command, this energy can be added to
-the system’s potential energy for thermodynamic output (see below).
-For energy minimization via the minimize command, this
-energy must be added to the system’s potential energy to formulate a
+ Note Adding a force to atoms implies a change in their potential
+energy as they move due to the applied force field. For dynamics via
+the run command, this energy can be added to the system’s
+potential energy for thermodynamic output (see below). For energy
+minimization via the minimize command, this energy
+must be added to the system’s potential energy to formulate a
self-consistent minimization problem (see below). In order for a restraint to be effective, the restraint force must
@@ -267,11 +267,11 @@ current dihedral angle phi is equal to phi0. The fix_modify energy option is supported by this
fix to add the potential energy associated with this fix to the
system’s potential energy as part of thermodynamic output. Warning If you want the fictitious potential energy associated
-with the added forces to be included in the total potential energy of
-the system (the quantity being minimized), you MUST enable the
+ Note If you want the fictitious potential energy associated with the
+added forces to be included in the total potential energy of the
+system (the quantity being minimized), you MUST enable the
fix_modify energy option for this fix. This fix computes a global scalar, which can be accessed by various
@@ -300,7 +300,7 @@ the run command.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
There are two main variants of this fix, fix rigid and fix
rigid/small. The NVE/NVT/NPT/NHT versions belong to one of the two
variants, as their style names indicate. Warning Not all of the bodystyle options and keyword/value
-options are available for both the rigid and rigid/small variants.
-See details below. Note Not all of the bodystyle options and keyword/value options are
+available for both the rigid and rigid/small variants. See
+details below. The rigid variant is typically the best choice for a system with a
small number of large rigid bodies, each of which can extend across
@@ -270,56 +270,56 @@ closest to the geometrical center of the body. The fix operates using
local lists of rigid bodies owned by each processor and information is
exchanged and summed via local communication between neighboring
processors when ghost atom info is accumlated. Warning To use rigid/small the ghost atom cutoff must be
-large enough to span the distance between the atom that owns the body
-and every other atom in the body. This distance value is printed out
-when the rigid bodies are defined. If the
-pair_style cutoff plus neighbor skin does not span
-this distance, then you should use the comm_modify cutoff command with a setting epsilon larger than
-the distance. Note To use rigid/small the ghost atom cutoff must be large enough
+to span the distance between the atom that owns the body and every
+other atom in the body. This distance value is printed out when the
+rigid bodies are defined. If the pair_style cutoff
+plus neighbor skin does not span this distance, then you should use
+the comm_modify cutoff command with a setting
+epsilon larger than the distance. Which of the two variants is faster for a particular problem is hard
to predict. The best way to decide is to perform a short test run.
Both variants should give identical numerical answers for short runs.
Long runs should give statistically similar results, but round-off
differences may accumulate to produce divergent trajectories. Warning You should not update the atoms in rigid bodies via
-other time-integration fixes (e.g. fix nve, Note You should not update the atoms in rigid bodies via other
+time-integration fixes (e.g. fix nve, Warning These fixes are overkill if you simply want to hold a
-collection of atoms stationary or have them move with a constant
-velocity. A simpler way to hold atoms stationary is to not include
-those atoms in your time integration fix. E.g. use “fix 1 mobile nve”
-instead of “fix 1 all nve”, where “mobile” is the group of atoms that
-you want to move. You can move atoms with a constant velocity by
-assigning them an initial velocity (via the velocity
-command), setting the force on them to 0.0 (via the fix setforce command), and integrating them as usual
+ Note These fixes are overkill if you simply want to hold a collection
+of atoms stationary or have them move with a constant velocity. A
+simpler way to hold atoms stationary is to not include those atoms in
+your time integration fix. E.g. use “fix 1 mobile nve” instead of
+“fix 1 all nve”, where “mobile” is the group of atoms that you want to
+move. You can move atoms with a constant velocity by assigning them
+an initial velocity (via the velocity command),
+setting the force on them to 0.0 (via the fix setforce command), and integrating them as usual
(e.g. via the fix nve command). Warning The aggregate properties of each rigid body are
-calculated one time at the start of the first simulation run after
-this fix is specified. The properties include the position and
-velocity of the center-of-mass of the body, its moments of inertia,
-and its angular momentum. This is done using the properties of the
-constituent atoms of the body at that point in time (or see the
-infile keyword option). Thereafter, changing properties of
-individual atoms in the body will have no effect on a rigid body’s
-dynamics, unless they effect the pair_style
-interactions that individual particles are part of. For example, you
-might think you could displace the atoms in a body or add a large
-velocity to each atom in a body to make it move in a desired direction
-before a 2nd run is performed, using the set or
+ Note The aggregate properties of each rigid body are calculated one
+time at the start of the first simulation run after this fix is
+specified. The properties include the position and velocity of the
+center-of-mass of the body, its moments of inertia, and its angular
+momentum. This is done using the properties of the constituent atoms
+of the body at that point in time (or see the infile keyword
+option). Thereafter, changing properties of individual atoms in the
+body will have no effect on a rigid body’s dynamics, unless they
+effect the pair_style interactions that individual
+particles are part of. For example, you might think you could
+displace the atoms in a body or add a large velocity to each atom in a
+body to make it move in a desired direction before a 2nd run is
+performed, using the set or
displace_atoms or velocity
command. But these commands will not affect the internal attributes
of the body, and the position and velocity or individual atoms in the
@@ -329,13 +329,12 @@ body will be reset when time integration starts. Each rigid body must have two or more atoms. An atom can belong to at
most one rigid body. Which atoms are in which bodies can be defined
via several options. Warning With fix rigid/small, which requires bodystyle
-molecule, you can define a system that has no rigid bodies
-initially. This is useful when you are using the mol keyword in
-conjunction with another fix that is adding rigid bodies on-the-fly,
-such as fix deposit or fix pour. Note With fix rigid/small, which requires bodystyle molecule, you
+can define a system that has no rigid bodies initially. This is
+useful when you are using the mol keyword in conjunction with
+another fix that is adding rigid bodies on-the-fly, such as fix deposit or fix pour. For bodystyle single the entire fix group of atoms is treated as one
rigid body. This option is only allowed for fix rigid and its
@@ -352,13 +351,13 @@ includes atoms you want to be part of rigid bodies. Warning To compute the initial center-of-mass position and
-other properties of each rigid body, the image flags for each atom in
-the body are used to “unwrap” the atom coordinates. Thus you must
-insure that these image flags are consistent so that the unwrapping
-creates a valid rigid body (one where the atoms are close together),
+ Note To compute the initial center-of-mass position and other
+properties of each rigid body, the image flags for each atom in the
+body are used to “unwrap” the atom coordinates. Thus you must insure
+that these image flags are consistent so that the unwrapping creates a
+valid rigid body (one where the atoms are close together),
particularly if the atoms in a single rigid body straddle a periodic
boundary. This means the input data file or restart file must define
the image flags for each atom consistently or that you have used the
@@ -395,11 +394,11 @@ means all types from m to n (inclusive). Note that you can use the
force or torque keywords as many times as you like. If a
particular rigid body has its component flags set multiple times, the
settings from the final keyword are used. Warning For computational efficiency, you may wish to turn off
-pairwise and bond interactions within each rigid body, as they no
-longer contribute to the motion. The neigh_modify exclude and delete_bonds
+ Note For computational efficiency, you may wish to turn off pairwise
+and bond interactions within each rigid body, as they no longer
+contribute to the motion. The neigh_modify exclude and delete_bonds
commands are used to do this. If the rigid bodies have strongly
overalapping atoms, you may need to turn off these interactions to
avoid numerical problems due to large equal/opposite intra-body forces
@@ -539,14 +538,14 @@ integer. Warning When the langevin keyword is used with fix rigid
-versus fix rigid/small, different dynamics will result for parallel
-runs. This is because of the way random numbers are used in the two
-cases. The dynamics for the two cases should be statistically
-similar, but will not be identical, even for a single timestep. Note When the langevin keyword is used with fix rigid versus fix
+rigid/small, different dynamics will result for parallel runs. This
+is because of the way random numbers are used in the two cases. The
+dynamics for the two cases should be statistically similar, but will
+not be identical, even for a single timestep. The temp and tparam keywords apply a Nose/Hoover thermostat to the
NVT time integration performed by the rigid/nvt style. They cannot
@@ -566,16 +565,16 @@ of thumb, increasing the chain length should lead to smaller
oscillations. The keyword pchain specifies the number of
thermostats in the chain thermostatting the barostat degrees of
freedom. Warning There are alternate ways to thermostat a system of
-rigid bodies. You can use fix langevin to treat
-the individual particles in the rigid bodies as effectively immersed
-in an implicit solvent, e.g. a Brownian dynamics model. For hybrid
-systems with both rigid bodies and solvent particles, you can
-thermostat only the solvent particles that surround one or more rigid
-bodies by appropriate choice of groups in the compute and fix commands
-for temperature and thermostatting. The solvent interactions with the
+ Note There are alternate ways to thermostat a system of rigid bodies.
+You can use fix langevin to treat the individual
+particles in the rigid bodies as effectively immersed in an implicit
+solvent, e.g. a Brownian dynamics model. For hybrid systems with both
+rigid bodies and solvent particles, you can thermostat only the
+solvent particles that surround one or more rigid bodies by
+appropriate choice of groups in the compute and fix commands for
+temperature and thermostatting. The solvent interactions with the
rigid bodies should then effectively thermostat the rigid body
temperature as well without use of the Langevin or Nose/Hoover options
associated with the fix rigid commands. Also note that when using the mol keyword, extra restart information
about all rigid bodies is written out whenever a restart file is
-written out. See the IMPORTANT NOTE in the next section for details. The infile keyword allows a file of rigid body attributes to be read
in from a file, rather then having LAMMPS compute them. There are 5
@@ -651,11 +650,11 @@ it is inside the box as defined. A value of 2 means add 2 box lengths
to get the true value. A value of -1 means subtract 1 box length to
get the true value. LAMMPS updates these flags as the rigid bodies
cross periodic boundaries during the simulation. Warning If you use the infile or mol keywords and write
-restart files during a simulation, then each time a restart file is
-written, the fix also write an auxiliary restart file with the name
+ Note If you use the infile or mol keywords and write restart
+files during a simulation, then each time a restart file is written,
+the fix also write an auxiliary restart file with the name
rfile.rigid, where “rfile” is the name of the restart file,
e.g. tmp.restart.10000 and tmp.restart.10000.rigid. This auxiliary
file is in the same format described above. Thus it can be used in a
@@ -674,8 +673,8 @@ particles in a particular rigid body. Warning Note You may wish to explicitly subtract additional
degrees-of-freedom if you use the force and torque keywords to
eliminate certain motions of one or more rigid bodies. LAMMPS does
@@ -862,7 +861,7 @@ J Chem Phys, 116, 8649 (2002).
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
Warning This command works by using the current forces on
-atoms to caculate an additional constraint force which when added will
-leave the atoms in positions that satisfy the SHAKE constraints
-(e.g. bond length) after the next time integration step. If you
-define fixes (e.g. fix efield) that add additional
-force to the atoms after fix shake operates, then this fix will not
-take them into account and the time integration will typically not
-satisfy the SHAKE constraints. The solution for this is to make sure
-that fix shake is defined in your input script after any other fixes
-which add or change forces (to atoms that fix shake operates on). Note This command works by using the current forces on atoms to
+caculate an additional constraint force which when added will leave
+the atoms in positions that satisfy the SHAKE constraints (e.g. bond
+length) after the next time integration step. If you define fixes
+(e.g. fix efield) that add additional force to the
+atoms after fix shake operates, then this fix will not take them into
+account and the time integration will typically not satisfy the SHAKE
+constraints. The solution for this is to make sure that fix shake is
+defined in your input script after any other fixes which add or change
+forces (to atoms that fix shake operates on). The mol keyword should be used when other commands, such as fix deposit or fix pour, add molecules
@@ -280,16 +280,16 @@ more instructions on how to use the accelerated styles effectively. The velocity constraints lead to a linear system of equations which
can be solved analytically. The implementation of the algorithm in
LAMMPS closely follows (Andersen (1983)). Warning The fix rattle command modifies forces and velocities
-and thus should be defined after all other integration fixes in your
-input script. If you define other fixes that modify velocities or
-forces after fix rattle operates, then fix rattle will not take them
-into account and the overall time integration will typically not
-satisfy the RATTLE constraints. You can check whether the constraints
-work correctly by setting the value of RATTLE_DEBUG in
-src/fix_rattle.cpp to 1 and recompiling LAMMPS. Note The fix rattle command modifies forces and velocities and thus
+should be defined after all other integration fixes in your input
+script. If you define other fixes that modify velocities or forces
+after fix rattle operates, then fix rattle will not take them into
+account and the overall time integration will typically not satisfy
+the RATTLE constraints. You can check whether the constraints work
+correctly by setting the value of RATTLE_DEBUG in src/fix_rattle.cpp
+to 1 and recompiling LAMMPS.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
Warning The center of mass of a group of atoms is calculated
-in “unwrapped” coordinates using atom image flags, which means that
-the group can straddle a periodic boundary. See the dump
-doc page for a discussion of unwrapped coordinates. It also means
-that a spring connecting two groups or a group and the tether point
-can cross a periodic boundary and its length be calculated correctly.
-One exception is for rigid bodies, which should not be used with the
-fix spring command, if the rigid body will cross a periodic boundary.
+ Note The center of mass of a group of atoms is calculated in
+“unwrapped” coordinates using atom image flags, which means that the
+group can straddle a periodic boundary. See the dump doc
+page for a discussion of unwrapped coordinates. It also means that a
+spring connecting two groups or a group and the tether point can cross
+a periodic boundary and its length be calculated correctly. One
+exception is for rigid bodies, which should not be used with the fix
+spring command, if the rigid body will cross a periodic boundary.
This is because image flags for rigid bodies are used in a different
way, as explained on the fix rigid doc page. The forces due to this fix are imposed during an energy minimization,
invoked by the minimize command. Warning If you want the spring energy to be included in the
-total potential energy of the system (the quantity being minimized),
-you MUST enable the fix_modify energy option for
-this fix. Note If you want the spring energy to be included in the total
+potential energy of the system (the quantity being minimized), you
+MUST enable the fix_modify energy option for this
+fix.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
The forces due to this fix are imposed during an energy minimization,
invoked by the minimize command. Warning If you want the per-atom spring energy to be included
-in the total potential energy of the system (the quantity being
-minimized), you MUST enable the fix_modify energy
-option for this fix. Note If you want the per-atom spring energy to be included in the
+total potential energy of the system (the quantity being minimized),
+you MUST enable the fix_modify energy option for
+this fix.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
Warning The fix srd command can be used with simluations the
-size and/or shape of the simulation box changes. This can be due to
-non-periodic boundary conditions or the use of fixes such as the fix deform or fix wall/srd commands
+ Note The fix srd command can be used with simluations the size and/or
+shape of the simulation box changes. This can be due to non-periodic
+boundary conditions or the use of fixes such as the fix deform or fix wall/srd commands
to impose a shear on an SRD fluid or an interaction with an external
wall. If the box size changes then the size of SRD bins must be
recalculated every reneighboring. This is not necessary if only the
@@ -399,14 +399,13 @@ rescaling off during collisions and the per-bin velocity rotation
operation. The collide and rotate values turn it on for
one of the operations and off for the other. Warning This fix is normally used for simulations with a huge
-number of SRD particles relative to the number of big particles,
-e.g. 100 to 1. In this scenario, computations that involve only big
-particles (neighbor list creation, communication, time integration)
-can slow down dramatically due to the large number of background SRD
-particles. Note This fix is normally used for simulations with a huge number of
+SRD particles relative to the number of big particles, e.g. 100 to 1.
+In this scenario, computations that involve only big particles
+(neighbor list creation, communication, time integration) can slow
+down dramatically due to the large number of background SRD particles. Three other input script commands will largely overcome this effect,
speeding up an SRD simulation by a significant amount. These are the
@@ -522,7 +521,7 @@ Chem Phys, 132, 174106 (2010).
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
Warning The order in which various fixes are applied which
-operate at the same point during the timestep, is the same as the
-order they are specified in the input script. Thus normally, if you
-want to store per-atom forces due to force field interactions, before
-constraints are applied, you should list this fix first within that
-set of fixes, i.e. before other fixes that apply constraints.
-However, if you wish to include certain constraints (e.g. fix shake)
-in the stored force, then it could be specified after some fixes and
-before others. Note The order in which various fixes are applied which operate at
+the same point during the timestep, is the same as the order they are
+specified in the input script. Thus normally, if you want to store
+per-atom forces due to force field interactions, before constraints
+are applied, you should list this fix first within that set of fixes,
+i.e. before other fixes that apply constraints. However, if you wish
+to include certain constraints (e.g. fix shake) in the stored force,
+then it could be specified after some fixes and before others.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
If N is not zero, then the attributes will be updated every N
steps. Warning Actually, only atom attributes specified by keywords
-like xu or vy are initially stored immediately at the point in
-your input script when the fix is defined. Attributes specified by a
-compute, fix, or variable are not initially stored until the first run
+ Note Actually, only atom attributes specified by keywords like xu
+or vy are initially stored immediately at the point in your input
+script when the fix is defined. Attributes specified by a compute,
+fix, or variable are not initially stored until the first run
following the fix definition begins. This is because calculating
those attributes may require quantities that are not defined in
between runs.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
Warning Unlike the fix nvt command which
-performs Nose/Hoover thermostatting AND time integration, this fix
-does NOT perform time integration. It only modifies velocities to
-effect thermostatting. Thus you must use a separate time integration
-fix, like fix nve to actually update the positions of
-atoms using the modified velocities. Likewise, this fix should not
-normally be used on atoms that also have their temperature controlled
-by another fix - e.g. by fix nvt or fix langevin commands. Note Unlike the fix nvt command which performs
+Nose/Hoover thermostatting AND time integration, this fix does NOT
+perform time integration. It only modifies velocities to effect
+thermostatting. Thus you must use a separate time integration fix,
+like fix nve to actually update the positions of atoms
+using the modified velocities. Likewise, this fix should not normally
+be used on atoms that also have their temperature controlled by
+another fix - e.g. by fix nvt or fix langevin commands. See this howto section of the manual for
a discussion of different ways to compute temperature and perform
@@ -290,7 +290,7 @@ Phys, 81, 3684 (1984).
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
Warning Unlike the fix nvt command which
-performs Nose/Hoover thermostatting AND time integration, these fixes
-do NOT perform time integration. They only modify velocities to effect
+ Note Unlike the fix nvt command which performs
+Nose/Hoover thermostatting AND time integration, these fixes do NOT
+perform time integration. They only modify velocities to effect
thermostatting. Thus you must use a separate time integration fix,
like fix nve to actually update the positions of atoms
using the modified velocities. Likewise, these fixes should not
@@ -289,7 +289,7 @@ over time or the atom count becomes very small.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
Warning Unlike the fix nvt command which
-performs Nose/Hoover thermostatting AND time integration, this fix
-does NOT perform time integration. It only modifies velocities to
-effect thermostatting. Thus you must use a separate time integration
-fix, like fix nve to actually update the positions of
-atoms using the modified velocities. Likewise, this fix should not
-normally be used on atoms that also have their temperature controlled
-by another fix - e.g. by fix nvt or fix langevin commands. Note Unlike the fix nvt command which performs
+Nose/Hoover thermostatting AND time integration, this fix does NOT
+perform time integration. It only modifies velocities to effect
+thermostatting. Thus you must use a separate time integration fix,
+like fix nve to actually update the positions of atoms
+using the modified velocities. Likewise, this fix should not normally
+be used on atoms that also have their temperature controlled by
+another fix - e.g. by fix nvt or fix langevin commands. See this howto section of the manual for
a discussion of different ways to compute temperature and perform
@@ -290,7 +290,7 @@ calculated by this fix is “extensive”.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
Warning the com and rot keywords should not be used if an
-external force is acting on the specified fix group, along the
-included directions. This can be either a true external force (e.g.
-through fix wall) or forces due to the interaction
-with atoms not included in the fix group. This is because in such
-cases, translations or rotations of the fix group could be induced by
-these external forces, and removing them will lead to a violation of
+ Note the com and rot keywords should not be used if an external
+force is acting on the specified fix group, along the included
+directions. This can be either a true external force (e.g. through
+fix wall) or forces due to the interaction with atoms
+not included in the fix group. This is because in such cases,
+translations or rotations of the fix group could be induced by these
+external forces, and removing them will lead to a violation of
detailed balance.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
Warning If your system is periodic in the direction of the
-heat flux, then the flux is going in 2 directions. This means the
-effective heat flux in one direction is reduced by a factor of 2. You
-will see this in the equations for thermal conductivity (kappa) in the
-Muller-Plathe paper. LAMMPS is simply tallying kinetic energy which
-does not account for whether or not your system is periodic; you must
-use the value appropriately to yield a kappa for your system. Note If your system is periodic in the direction of the heat flux,
+then the flux is going in 2 directions. This means the effective heat
+flux in one direction is reduced by a factor of 2. You will see this
+in the equations for thermal conductivity (kappa) in the Muller-Plathe
+paper. LAMMPS is simply tallying kinetic energy which does not
+account for whether or not your system is periodic; you must use the
+value appropriately to yield a kappa for your system. Warning After equilibration, if the temperature gradient you
-observe is not linear, then you are likely swapping energy too
-frequently and are not in a regime of linear response. In this case
-you cannot accurately infer a thermal conductivity and should try
-increasing the Nevery parameter. Note After equilibration, if the temperature gradient you observe is
+not linear, then you are likely swapping energy too frequently and are
+not in a regime of linear response. In this case you cannot
+accurately infer a thermal conductivity and should try increasing the
+Nevery parameter.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
Warning It is importante to keep the center of mass fixed
-during the thermodynamic integration, a non-zero total velocity will
-result in divergencies during the integration due to the fact that the
-atoms are ‘attatched’ to its equilibrium positions by the Einstein
+ Note It is importante to keep the center of mass fixed during the
+thermodynamic integration, a non-zero total velocity will result in
+divergencies during the integration due to the fact that the atoms are
+‘attatched’ to its equilibrium positions by the Einstein
crystal. Check the option zero of fix langevin
and velocity. The use of the Nose-Hoover thermostat
( The forces due to this fix are imposed during an energy minimization,
invoked by the minimize command. Warning If you want the per-atom spring energy to be included
-in the total potential energy of the system (the quantity being
-minimized), you MUST enable the fix modify energy
-option for this fix. Note If you want the per-atom spring energy to be included in the
+total potential energy of the system (the quantity being minimized),
+you MUST enable the fix modify energy option for
+this fix. An example script using this command is provided in the
examples/USER/misc/ti directory.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
Warning The current implementations of these fixes create a
-copy of the electron grid that overlays the entire simulation domain,
-for each processor. Values on the grid are summed across all
-processors. Thus you should insure that this grid is not too large,
-else your simulation could incur high memory and communication costs. Note The current implementations of these fixes create a copy of the
+electron grid that overlays the entire simulation domain, for each
+processor. Values on the grid are summed across all processors. Thus
+you should insure that this grid is not too large, else your
+simulation could incur high memory and communication costs. Additional details for fix ttm/mod
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
Warning If your system is periodic in the direction of the
-momentum flux, then the flux is going in 2 directions. This means the
+ Note If your system is periodic in the direction of the momentum
+flux, then the flux is going in 2 directions. This means the
effective momentum flux in one direction is reduced by a factor of 2.
You will see this in the equations for viscosity in the Muller-Plathe
paper. LAMMPS is simply tallying momentum which does not account for
whether or not your system is periodic; you must use the value
appropriately to yield a viscosity for your system. Warning After equilibration, if the velocity profile you
-observe is not linear, then you are likely swapping momentum too
-frequently and are not in a regime of linear response. In this case
-you cannot accurately infer a viscosity and should try increasing
-the Nevery parameter. Note After equilibration, if the velocity profile you observe is not
+linear, then you are likely swapping momentum too frequently and are
+not in a regime of linear response. In this case you cannot
+accurately infer a viscosity and should try increasing the Nevery
+parameter. An alternative method for calculating a viscosity is to run a NEMD
simulation, as described in Section_howto 13 of the manual. NEMD simulations
@@ -284,7 +284,7 @@ solvent particles.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
Warning You should specify gamma in force/velocity units.
-This is not the same as mass/time units, at least for some of the
-LAMMPS units options like “real” or “metal” that are not
+ Note You should specify gamma in force/velocity units. This is not
+the same as mass/time units, at least for some of the LAMMPS
+units options like “real” or “metal” that are not
self-consistent. In a Brownian dynamics context, gamma = Kb T / D, where Kb =
@@ -247,7 +247,7 @@ for details.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
Warning For all of the styles, you must insure that r is
-always > 0 for all particles in the group, or LAMMPS will generate an
-error. This means you cannot start your simulation with particles at
-the wall position coord (r = 0) or with particles on the wrong side
-of the wall (r < 0). For the wall/lj93 and wall/lj126 styles, the
-energy of the wall/particle interaction (and hence the force on the
-particle) blows up as r -> 0. The wall/colloid style is even more
+ Note For all of the styles, you must insure that r is always > 0 for
+all particles in the group, or LAMMPS will generate an error. This
+means you cannot start your simulation with particles at the wall
+position coord (r = 0) or with particles on the wrong side of the
+wall (r < 0). For the wall/lj93 and wall/lj126 styles, the energy
+of the wall/particle interaction (and hence the force on the particle)
+blows up as r -> 0. The wall/colloid style is even more
restrictive, since the energy blows up as D = r-R -> 0. This means
the finite-size particles of radius R must be a distance larger than R
from the wall position coord. The harmonic style is a softer
@@ -375,12 +375,12 @@ The scalar and vector values calculated by this fix are “extensive”.
the run command. The forces due to this fix are imposed during an energy minimization,
invoked by the minimize command. Warning If you want the atom/wall interaction energy to be
-included in the total potential energy of the system (the quantity
-being minimized), you MUST enable the fix_modify
-energy option for this fix. Note If you want the atom/wall interaction energy to be included in
+the total potential energy of the system (the quantity being
+minimized), you MUST enable the fix_modify energy
+option for this fix.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
Warning Note As discussed on the doc page for pair_style granular, versions of LAMMPS before 9Jan09 used a
different equation for Hertzian interactions. This means Hertizian
wall/particle interactions have also changed. They now include a
@@ -285,7 +285,7 @@ LAMMPS was built with that package. See the
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
Warning As discussed on the region command doc
-page, regions in LAMMPS do not get wrapped across periodic boundaries.
-It is up to you to insure that periodic or non-periodic boundaries are
+ Note As discussed on the region command doc page,
+regions in LAMMPS do not get wrapped across periodic boundaries. It
+is up to you to insure that periodic or non-periodic boundaries are
specified appropriately via the boundary command when
using a region as a wall that bounds particle motion. This also means
that if you embed a region in your simulation box and want it to
@@ -183,41 +183,41 @@ repulse particles from its surface (using the “side out” option in t
region command), that its repulsive force will not be
felt across a periodic boundary. Warning For primitive regions with sharp corners and/or edges
-(e.g. a block or cylinder), wall/particle forces are computed
-accurately for both interior and exterior regions. For union and
-intersect regions, additional sharp corners and edges may be present
-due to the intersection of the surfaces of 2 or more primitive
-volumes. These corners and edges can be of two types: concave or
-convex. Concave points/edges are like the corners of a cube as seen
-by particles in the interior of a cube. Wall/particle forces around
-these features are computed correctly. Convex points/edges are like
-the corners of a cube as seen by particles exterior to the cube,
-i.e. the points jut into the volume where particles are present.
-LAMMPS does NOT compute the location of these convex points directly,
-and hence wall/particle forces in the cutoff volume around these
-points suffer from inaccuracies. The basic problem is that the
-outward normal of the surface is not continuous at these points. This
-can cause particles to feel no force (they don’t “see” the wall) when
-in one location, then move a distance epsilon, and suddenly feel a
-large force because they now “see” the wall. In a worst-case
-scenario, this can blow particles out of the simulation box. Thus, as
-a general rule you should not use the fix wall/region command with
-union or interesect regions that have convex points or edges. Note For primitive regions with sharp corners and/or edges (e.g. a
+block or cylinder), wall/particle forces are computed accurately for
+both interior and exterior regions. For union and intersect
+regions, additional sharp corners and edges may be present due to the
+intersection of the surfaces of 2 or more primitive volumes. These
+corners and edges can be of two types: concave or convex. Concave
+points/edges are like the corners of a cube as seen by particles in
+the interior of a cube. Wall/particle forces around these features
+are computed correctly. Convex points/edges are like the corners of a
+cube as seen by particles exterior to the cube, i.e. the points jut
+into the volume where particles are present. LAMMPS does NOT compute
+the location of these convex points directly, and hence wall/particle
+forces in the cutoff volume around these points suffer from
+inaccuracies. The basic problem is that the outward normal of the
+surface is not continuous at these points. This can cause particles
+to feel no force (they don’t “see” the wall) when in one location,
+then move a distance epsilon, and suddenly feel a large force because
+they now “see” the wall. In a worst-case scenario, this can blow
+particles out of the simulation box. Thus, as a general rule you
+should not use the fix wall/region command with union or
+interesect regions that have convex points or edges. Warning Similarly, you should not define union or
-intersert regions for use with this command that share a common
-face, even if the face is smooth. E.g. two regions of style block in
-a union region, where the two blocks have the same face. This is
-because LAMMPS discards points that are part of multiple sub-regions
-when calculating wall/particle interactions, to avoid double-counting
-the interaction. Having two coincident faces could cause the face to
-become invisible to the particles. The solution is to make the two
-faces differ by epsilon in their position. Note Similarly, you should not define union or intersert regions
+for use with this command that share a common face, even if the face
+is smooth. E.g. two regions of style block in a union region, where
+the two blocks have the same face. This is because LAMMPS discards
+points that are part of multiple sub-regions when calculating
+wall/particle interactions, to avoid double-counting the interaction.
+Having two coincident faces could cause the face to become invisible
+to the particles. The solution is to make the two faces differ by
+epsilon in their position. The energy of wall-particle interactions depends on the specified
style. Warning For all of the styles, you must insure that r is
-always > 0 for all particles in the group, or LAMMPS will generate an
-error. This means you cannot start your simulation with particles on
-the region surface (r = 0) or with particles on the wrong side of the
-region surface (r < 0). For the wall/lj93 and wall/lj126 styles,
-the energy of the wall/particle interaction (and hence the force on
-the particle) blows up as r -> 0. The wall/colloid style is even
-more restrictive, since the energy blows up as D = r-R -> 0. This
-means the finite-size particles of radius R must be a distance larger
-than R from the region surface. The harmonic style is a softer
-potential and does not blow up as r -> 0, but you must use a large
-enough epsilon that particles always reamin on the correct side of
-the region surface (r > 0). Note For all of the styles, you must insure that r is always > 0 for
+all particles in the group, or LAMMPS will generate an error. This
+means you cannot start your simulation with particles on the region
+surface (r = 0) or with particles on the wrong side of the region
+surface (r < 0). For the wall/lj93 and wall/lj126 styles, the
+energy of the wall/particle interaction (and hence the force on the
+particle) blows up as r -> 0. The wall/colloid style is even more
+restrictive, since the energy blows up as D = r-R -> 0. This means
+the finite-size particles of radius R must be a distance larger than R
+from the region surface. The harmonic style is a softer potential
+and does not blow up as r -> 0, but you must use a large enough
+epsilon that particles always reamin on the correct side of the
+region surface (r > 0). The forces due to this fix are imposed during an energy minimization,
invoked by the minimize command. Warning If you want the atom/wall interaction energy to be
-included in the total potential energy of the system (the quantity
-being minimized), you MUST enable the fix_modify
-energy option for this fix. Note If you want the atom/wall interaction energy to be included in
+the total potential energy of the system (the quantity being
+minimized), you MUST enable the fix_modify energy
+option for this fix.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
Warning Because the trajectory of the SRD particle is tracked
-as it collides with the wall, you must insure that r = distance of the
+ Note Because the trajectory of the SRD particle is tracked as it
+collides with the wall, you must insure that r = distance of the
particle from the wall, is always > 0 for SRD particles, or LAMMPS
will generate an error. This means you cannot start your simulation
with SRD particles at the wall position coord (r = 0) or with
particles on the wrong side of the wall (r < 0). Warning If you have 2 or more walls that come together at an
-edge or corner (e.g. walls in the x and y dimensions), then be sure to
-set the overlap keyword to yes in the fix srd
-command, since the walls effectively overlap when SRD particles
-collide with them. LAMMPS will issue a warning if you do not do this. Note If you have 2 or more walls that come together at an edge or
+corner (e.g. walls in the x and y dimensions), then be sure to set the
+overlap keyword to yes in the fix srd command,
+since the walls effectively overlap when SRD particles collide with
+them. LAMMPS will issue a warning if you do not do this. Warning The walls of this fix only interact with SRD
-particles, as defined by the fix srd command. If you
-are simulating a mixture containing other kinds of particles, then you
-should typically use another wall command to act on
-the other particles. Since SRD particles will be colliding both with
-the walls and the other particles, it is important to insure that the
-other particle’s finite extent does not overlap an SRD wall. If you
-do not do this, you may generate errors when SRD particles end up
-“inside” another particle or a wall at the beginning of a collision
-step. Note The walls of this fix only interact with SRD particles, as
+defined by the fix srd command. If you are simulating
+a mixture containing other kinds of particles, then you should
+typically use another wall command to act on the other
+particles. Since SRD particles will be colliding both with the walls
+and the other particles, it is important to insure that the other
+particle’s finite extent does not overlap an SRD wall. If you do not
+do this, you may generate errors when SRD particles end up “inside”
+another particle or a wall at the beginning of a collision step. The units keyword determines the meaning of the distance units used
to define a wall position, but only when a numeric constant is used.
@@ -321,7 +320,7 @@ the run command. Thi
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
Warning By default groups are static, meaning the atoms are
-permanently assigned to the group. For example, if the region style
-is used to assign atoms to a group, the atoms will remain in the group
-even if they later move out of the region. As explained below, the
-dynamic style can be used to make a group dynamic so that a periodic
+ Note By default groups are static, meaning the atoms are permanently
+assigned to the group. For example, if the region style is used to
+assign atoms to a group, the atoms will remain in the group even if
+they later move out of the region. As explained below, the dynamic
+style can be used to make a group dynamic so that a periodic
determination is made as to which atoms are in the group. Since many
LAMMPS commands operate on groups of atoms, you should think carefully
about whether making a group dynamic makes sense for your model. Warning The include molecule operation is relatively
-expensive in a parallel sense. This is because it requires
-communication of relevant molecule IDs between all the processors and
-each processor to loop over its atoms once per processor, to compare
-its atoms to the list of molecule IDs from every other processor.
-Hence it scales as N, rather than N/P as most of the group operations
-do, where N is the number of atoms, and P is the number of processors. Note The include molecule operation is relatively expensive in a
+parallel sense. This is because it requires communication of relevant
+molecule IDs between all the processors and each processor to loop
+over its atoms once per processor, to compare its atoms to the list of
+molecule IDs from every other processor. Hence it scales as N, rather
+than N/P as most of the group operations do, where N is the number of
+atoms, and P is the number of processors. The subtract style takes a list of two or more existing group names
as arguments. All atoms that belong to the 1st group, but not to any
@@ -337,15 +337,15 @@ has been performed, and before neighbor lists or forces are computed.
This is the point in the timestep where atom positions have just
changed due to the time integration, so the region criterion should be
accurate, if applied. Warning If the region keyword is used to determine what
-atoms are in the dynamic group, atoms can move outside of the
-simulation box between reneighboring events. Thus if you want to
-include all atoms on the left side of the simulation box, you probably
-want to set the left boundary of the region to be outside the
-simulation box by some reasonable amount (e.g. up to the cutoff of the
-potential), else they may be excluded from the dynamic region. Note If the region keyword is used to determine what atoms are in
+the dynamic group, atoms can move outside of the simulation box
+between reneighboring events. Thus if you want to include all atoms
+on the left side of the simulation box, you probably want to set the
+left boundary of the region to be outside the simulation box by some
+reasonable amount (e.g. up to the cutoff of the potential), else they
+may be excluded from the dynamic region. Here is an example of using a dynamic group to shrink the set of atoms
being integrated by using a spherical region with a variable radius
@@ -363,12 +363,12 @@ group mobile static
run ${nsteps}
Warning All fixes and computes take a group ID as an argument,
-but they do not all allow for use of a dynamic group. If you get an
-error message that this is not allowed, but feel that it should be for
-the fix or compute in question, then please post your reasoning to the
+ Note All fixes and computes take a group ID as an argument, but they
+do not all allow for use of a dynamic group. If you get an error
+message that this is not allowed, but feel that it should be for the
+fix or compute in question, then please post your reasoning to the
LAMMPS mail list and we can change it. The static style removes the setting for a dynamic group, converting
@@ -403,7 +403,7 @@ those currently in the dynamic group.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
Warning Note If a command itself requires a quoted argument (e.g. a
print command), then double and single quotes can be used
and nested in the usual manner, as in the examples above and below.
@@ -312,7 +312,7 @@ non-zero. If the result is zero, the expression result is FALSE.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
Warning Note When both an improper and pair style is defined, the
special_bonds command often needs to be used to
turn off (or weight) the pairwise interaction that would otherwise
@@ -223,7 +223,7 @@ a package.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
If the word “SELF” is used for the filename, then the current input
script is re-opened and read again. Warning The SELF option is not guaranteed to work when the
-current input script is being read through stdin (standard input),
-e.g. Note The SELF option is not guaranteed to work when the current input
+script is being read through stdin (standard input), e.g.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
Warning Currently, not all PPPM styles support the ad
-option. Support for those PPPM variants will be added later. Note Currently, not all PPPM styles support the ad option. Support
+for those PPPM variants will be added later. The kmax/ewald keyword sets the number of kspace vectors in each
dimension for kspace style ewald. The three values must be positive
@@ -436,7 +436,7 @@ Chem Theory Comput, 9, 5412 (2013).
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
Warning Using pppm/stagger may not give the same increase in
-the accuracy of energy and pressure as it does in forces, so some
-caution must be used if energy and/or pressure are quantities of
-interest, such as when using a barostat. Note Using pppm/stagger may not give the same increase in the
+accuracy of energy and pressure as it does in forces, so some caution
+must be used if energy and/or pressure are quantities of interest,
+such as when using a barostat. The pppm/disp and pppm/disp/tip4p styles add a mesh-based long-range
@@ -293,17 +293,16 @@ and how to choose them is described in (Isele-Holder2) and the
How-To discussion. Warning All of the PPPM styles can be used with
-single-precision FFTs by using the compiler switch -DFFT_SINGLE for
-the FFT_INC setting in your lo-level Makefile. This setting also
-changes some of the PPPM operations (e.g. mapping charge to mesh and
-interpolating electric fields to particles) to be performed in single
-precision. This option can speed-up long-range calulations,
-particularly in parallel or on GPUs. The use of the -DFFT_SINGLE flag
-is discussed in this section of the
-manual. MSM does not currently support the -DFFT_SINGLE compiler switch. Note All of the PPPM styles can be used with single-precision FFTs by
+using the compiler switch -DFFT_SINGLE for the FFT_INC setting in your
+lo-level Makefile. This setting also changes some of the PPPM
+operations (e.g. mapping charge to mesh and interpolating electric
+fields to particles) to be performed in single precision. This option
+can speed-up long-range calulations, particularly in parallel or on
+GPUs. The use of the -DFFT_SINGLE flag is discussed in this section of the manual. MSM does not
+currently support the -DFFT_SINGLE compiler switch. The msm style invokes a multi-level summation method MSM solver,
@@ -457,7 +456,7 @@ Illinois at Urbana-Champaign, (2006).
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
Warning The preceding paragraph describing lattice directions
-is only valid for orthogonal cubic unit cells (or square in 2d). If
-you are using a hcp or hex lattice or the more general lattice
-style custom with non-orthogonal a1,a2,a3 vectors, then you should
-think of the 3 orient vectors as creating a 3x3 rotation matrix
-which is applied to a1,a2,a3 to rotate the original unit cell to a new
+ Note The preceding paragraph describing lattice directions is only
+valid for orthogonal cubic unit cells (or square in 2d). If you are
+using a hcp or hex lattice or the more general lattice style
+custom with non-orthogonal a1,a2,a3 vectors, then you should think
+of the 3 orient vectors as creating a 3x3 rotation matrix which is
+applied to a1,a2,a3 to rotate the original unit cell to a new
orientation in the simulation box. Warning Though they are called lattice spacings, all the
-commands that have a “units lattice” option, simply use the 3 values
-as scale factors on the distance units defined by the
-units command. Thus if you do not like the lattice
-spacings computed by LAMMPS (e.g. for a non-orthogonal or rotated unit
-cell), you can define the 3 values to be whatever you wish, via the
-spacing option. Note Though they are called lattice spacings, all the commands that
+have a “units lattice” option, simply use the 3 values as scale
+factors on the distance units defined by the units
+command. Thus if you do not like the lattice spacings computed by
+LAMMPS (e.g. for a non-orthogonal or rotated unit cell), you can
+define the 3 values to be whatever you wish, via the spacing option. If the spacing option is not specified, the lattice spacings are
computed by LAMMPS in the following way. A unit cell of the lattice
@@ -323,18 +322,18 @@ dimension are simply the scale factor (described above) multiplied by
the length of a1,a2,a3. Thus a hex style lattice with a scale
factor of 3.0 Angstroms, would have a lattice spacing of 3.0 in x and
3*sqrt(3.0) in y. Warning For non-orthogonal unit cells and/or when a rotation
-is applied via the orient keyword, then the lattice spacings
-computed by LAMMPS are typically less intuitive. In particular, in
-these cases, there is no guarantee that a particular lattice spacing
-is an integer multiple of the periodicity of the lattice in that
-direction. Thus, if you create an orthogonal periodic simulation box
-whose size in a dimension is a multiple of the lattice spacing, and
-then fill it with atoms via the create_atoms
-command, you will NOT necessarily create a periodic system.
-I.e. atoms may overlap incorrectly at the faces of the simulation box. Note For non-orthogonal unit cells and/or when a rotation is applied
+via the orient keyword, then the lattice spacings computed by LAMMPS
+are typically less intuitive. In particular, in these cases, there is
+no guarantee that a particular lattice spacing is an integer multiple
+of the periodicity of the lattice in that direction. Thus, if you
+create an orthogonal periodic simulation box whose size in a dimension
+is a multiple of the lattice spacing, and then fill it with atoms via
+the create_atoms command, you will NOT necessarily
+create a periodic system. I.e. atoms may overlap incorrectly at the
+faces of the simulation box. The spacing option sets the 3 lattice spacings directly. All must
be non-zero (use 1.0 for dz in a 2d simulation). The specified values
@@ -414,7 +413,7 @@ a2 = 0 1 0, and a3 = 0 0 1.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
Either the quickmin and fire styles are useful in the context of
nudged elastic band (NEB) calculations via the neb command. Warning The damped dynamic minimizers use whatever timestep
-you have defined via the timestep command. Often they
-will converge more quickly if you use a timestep about 10x larger than
-you would normally use for dynamics simulations. Note The damped dynamic minimizers use whatever timestep you have
+defined via the timestep command. Often they will
+converge more quickly if you use a timestep about 10x larger than you
+would normally use for dynamics simulations. Warning The quickmin and fire styles do not yet support
-the use of the fix box/relax command or
-minimizations involving the electron radius in eFF
-models. Note The quickmin and fire styles do not yet support the use of
+the fix box/relax command or minimizations
+involving the electron radius in eFF models.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
The minimization styles quickmin and fire perform
damped dynamics using an Euler integration step. Thus they require a
timestep be defined. Warning The damped dynamic minimizers use whatever timestep
-you have defined via the timestep command. Often they
-will converge more quickly if you use a timestep about 10x larger than
-you would normally use for dynamics simulations. Note The damped dynamic minimizers use whatever timestep you have
+defined via the timestep command. Often they will
+converge more quickly if you use a timestep about 10x larger than you
+would normally use for dynamics simulations. In all cases, the objective function being minimized is the total
@@ -274,8 +274,8 @@ reduced. The iterations and force evaluation values are what is checked by the
maxiter and maxeval parameters. Warning Note There are several force fields in LAMMPS which have
discontinuities or other approximations which may prevent you from
performing an energy minimization to high tolerances. For example,
@@ -324,10 +324,10 @@ examples of fixes that can be used include: Warning Some fixes which are invoked during minimization have
-an associated potential energy. For that energy to be included in the
+ Note Some fixes which are invoked during minimization have an
+associated potential energy. For that energy to be included in the
total potential energy of the system (the quantity being minimized),
you MUST enable the fix_modify energy option for
that fix. The doc pages for individual fix commands
@@ -375,7 +375,7 @@ system will not fully relax.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
Warning The molecule command can be used to define molecules
-with bonds, angles, dihedrals, imporopers, or special bond lists of
-neighbors within a molecular topology, so that you can later add the
-molecules to your simulation, via one or more of the commands listed
-above. If such molecules do not already exist when LAMMPS creates the
-simulation box, via the create_box or
+ Note The molecule command can be used to define molecules with bonds,
+angles, dihedrals, imporopers, or special bond lists of neighbors
+within a molecular topology, so that you can later add the molecules
+to your simulation, via one or more of the commands listed above. If
+such molecules do not already exist when LAMMPS creates the simulation
+box, via the create_box or
read_data command, when you later add them you may
overflow the pre-allocated data structures which store molecular
topology information with each atom, and an error will be generated.
@@ -292,15 +292,14 @@ reason to list the special bond info explicitly is for the
thermalized Drude oscillator model which treats
the bonds between nuclear cores and Drude electrons in a different
manner. Warning Whether a section is required depends on how the
-molecule template is used by other LAMMPS commands. For example, to
-add a molecule via the fix deposit command, the
-Coords and Types sections are required. To add a rigid body via the
- Note Whether a section is required depends on how the molecule
+template is used by other LAMMPS commands. For example, to add a
+molecule via the fix deposit command, the Coords
+and Types sections are required. To add a rigid body via the
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
Warning The current NEB implementation in LAMMPS only allows
-there to be one processor per replica. Note The current NEB implementation in LAMMPS only allows there to be
+one processor per replica. Warning As explained below, a NEB calculation perfoms a damped
-dynamics minimization across all the replicas. The mimimizer uses
-whatever timestep you have defined in your input script, via the
+ Note As explained below, a NEB calculation perfoms a damped dynamics
+minimization across all the replicas. The mimimizer uses whatever
+timestep you have defined in your input script, via the
timestep command. Often NEB will converge more
quickly if you use a timestep about 10x larger than you would normally
use for dynamics simulations. Warning Note None of the file-style settings change the initial
configuration of any atom in the first replica. The first replica
must thus be in the correct initial configuration at the time the neb
@@ -356,8 +356,8 @@ MEP, and the configurations of the replicas should be a sequence of
configurations along the MEP. A few other settings in your input script are required or advised to
-perform a NEB calculation. See the IMPORTANT NOTE about the choice of
-timestep at the beginning of this doc page. An atom map must be defined which it is not by default for atom_style atomic problems. The atom_modify map command can be used to do this. The “atom_modify sort 0 0.0” command should be used to turn off atom
sorting.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
Note that the exclude options only affect pairwise interactions; see
the delete_bonds command for information on
turning off bond interactions. Warning Excluding pairwise interactions will not work
-correctly when also using a long-range solver via the
+ Note Excluding pairwise interactions will not work correctly when
+also using a long-range solver via the
kspace_style command. LAMMPS will give a warning
to this effect. This is because the short-range pairwise interaction
needs to subtract off a term from the total energy for pairs whose
@@ -277,18 +277,18 @@ after another as they fill up. The size of each page is set by the
could potentially overflow the list. This threshold is set by the
one value which tells LAMMPS the maximum number of neighbor’s one
atom can have. Warning LAMMPS can crash without an error message if the
-number of neighbors for a single particle is larger than the page
-setting, which means it is much, much larger than the one setting.
-This is because LAMMPS doesn’t error check these limits for every
-pairwise interaction (too costly), but only after all the particle’s
-neighbors have been found. This problem usually means something is
-very wrong with the way you’ve setup your problem (particle spacing,
-cutoff length, neighbor skin distance, etc). If you really expect
-that many neighbors per particle, then boost the one and page
-settings accordingly. Note LAMMPS can crash without an error message if the number of
+neighbors for a single particle is larger than the page setting,
+which means it is much, much larger than the one setting. This is
+because LAMMPS doesn’t error check these limits for every pairwise
+interaction (too costly), but only after all the particle’s neighbors
+have been found. This problem usually means something is very wrong
+with the way you’ve setup your problem (particle spacing, cutoff
+length, neighbor skin distance, etc). If you really expect that many
+neighbors per particle, then boost the one and page settings
+accordingly. The binsize option allows you to specify what size of bins will be
used in neighbor list construction to sort and find neighboring atoms.
@@ -334,7 +334,7 @@ cluster = no, include = all, exclude = none, page = 100000, one =
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
Warning A package command for a particular style can be
-invoked multiple times when a simulation is setup, e.g. by the “-c
-on”, “-k on”, “-sf”, and “-pk” command-line switches, and by using this command in an
-input script. Each time it is used all of the style options are set,
-either to default values or to specified settings. I.e. settings from
-previous invocations do not persist across multiple invocations. Note A package command for a particular style can be invoked multiple
+times when a simulation is setup, e.g. by the “-c on”, “-k on”, “-sf”,
+and “-pk” command-line switches, and by
+using this command in an input script. Each time it is used all of
+the style options are set, either to default values or to specified
+settings. I.e. settings from previous invocations do not persist
+across multiple invocations. See the Section Accelerate section of the
manual for more details about using the various accelerator packages
@@ -442,11 +443,11 @@ if LAMMPS was built with coprocessor support; see the balance
keyword discussion below. If you are running with less MPI tasks/node
than there are CPUs, it can be advantageous to use OpenMP threading on
the CPUs. Warning The omp keyword has nothing to do with coprocessor
-threads on the Xeon Phi; see the tpc and tptask keywords below for
-a discussion of coprocessor threads. Note The omp keyword has nothing to do with coprocessor threads on
+the Xeon Phi; see the tpc and tptask keywords below for a
+discussion of coprocessor threads. The Nthread value for the omp keyword sets the number of OpenMP
threads allocated for each MPI task. Setting Nthread = 0 (the
@@ -459,15 +460,15 @@ environment variable, see the discussion of the Nthreads setting on
this doc page for the “package omp” command. Nthreads is a required
argument for the USER-OMP package. Its meaning is exactly the same
for the USER-INTEL pacakge. Warning If you build LAMMPS with both the USER-INTEL and
-USER-OMP packages, be aware that both packages allow setting of the
-Nthreads value via their package commands, but there is only a
-single global Nthreads value used by OpenMP. Thus if both package
-commands are invoked, you should insure the two values are consistent.
-If they are not, the last one invoked will take precedence, for both
-packages. Also note that if the “-sf hybrid intel omp” command-line switch is used, it invokes a “package
+ Note If you build LAMMPS with both the USER-INTEL and USER-OMP
+packages, be aware that both packages allow setting of the Nthreads
+value via their package commands, but there is only a single global
+Nthreads value used by OpenMP. Thus if both package commands are
+invoked, you should insure the two values are consistent. If they are
+not, the last one invoked will take precedence, for both packages.
+Also note that if the “-sf hybrid intel omp” command-line switch is used, it invokes a “package
intel” command, followed by a “package omp” command, both with a
setting of Nthreads = 0.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
Warning In the example just described, all 30 interactions are
-computed even if the distance between a particular pair of
-sub-particles is greater than the cutoff. Likewise, no interaction
-between two body particles is computed if the two COMs are further
-apart than the cutoff, even if the distance between some pairs of
-their sub-particles is within the cutoff. Thus care should be used in
-defining the cutoff distances for body particles, depending on their
-shape and size. Note In the example just described, all 30 interactions are computed
+even if the distance between a particular pair of sub-particles is
+greater than the cutoff. Likewise, no interaction between two body
+particles is computed if the two COMs are further apart than the
+cutoff, even if the distance between some pairs of their sub-particles
+is within the cutoff. Thus care should be used in defining the cutoff
+distances for body particles, depending on their shape and size. Similar rules apply for a body particle interacting with a point
particle. The distance between the two particles is calculated using
@@ -234,7 +233,7 @@ body/particle interactions requires the use of the
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
Warning Note Note that unlike for other potentials, cutoffs for BOP
potentials are not set in the pair_style or pair_coeff command; they
are specified in the BOP potential files themselves. Likewise, the
@@ -507,7 +507,7 @@ Zimmerman, Phys. Rev. B, 85,115206 (2012).
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
- © Copyright .
+ © Copyright 2013 Sandia Corporation.
Warning For all these pair styles, the terms with A and C are
-always cutoff. The additional Coulombic term can be cutoff or
-long-range (no cutoff) depending on whether the style name includes
-coul/cut or coul/long or coul/msm. If you wish the C/r^6 term to be
-long-range (no cutoff), then see the Description¶
@@ -241,7 +241,7 @@ a package.
-
@@ -268,7 +268,7 @@ as the initial mapping attempted to be.
@@ -656,7 +656,7 @@ mp4).
compute 1 all property/local batom1 batom2
dump 1 all local 100 tmp.bonds index c_1[1] c_1[2]
@@ -484,11 +484,11 @@ as dcd and xtc, require sorting by atom ID to format the outpu
file correctly. If multiple processors are writing the dump file, via
the “%” wildcard in the dump filename, then sorting cannot be
performed.
-
compute chunk/atom
-command. Nvalues is the number of input values specified. Each
-processor loops over its atoms, tallying its values to the appropriate
-chunk. Then the entire array is summed across all processors. This
-means that using a large number of chunks will incur an overhead in
-memory and computational cost (summing across processors), so be
-careful to define a reasonable number of chunks.compute chunk/atom command.
+Nvalues is the number of input values specified. Each processor loops
+over its atoms, tallying its values to the appropriate chunk. Then
+the entire array is summed across all processors. This means that
+using a large number of chunks will incur an overhead in memory and
+computational cost (summing across processors), so be careful to
+define a reasonable number of chunks.
@@ -327,10 +327,10 @@ may be used.
A lattice value means the distance units are in lattice spacings.
The lattice command must have been previously used to
define the lattice spacing.
-
angle_style command, then any new 3-body
@@ -243,13 +243,13 @@ of type angletype, with parameters assigned by the corresponding
angle_coeff command. Likewise, the dtype and
itype keywords will create new dihedrals and impropers of type
dihedraltype and impropertype.
@@ -370,7 +370,7 @@ prob = 1.0.
@@ -402,18 +400,17 @@ in its temperature and pressure calculation, as described above. Note
that as described above, if you assign a pressure compute to this fix
that includes a kinetic energy component it will affect the
minimization, most likely in an undesirable way.
-fix lavgevin (with a bias provided by compute temp/deform), will typically accomplish
+fix lavgevin
+(with a bias provided by compute temp/deform), will typically accomplish
that. If you do not use a thermostat, then there is no driving force
pushing the atoms to flow in a manner consistent with the deforming
box. E.g. for a shearing system the box deformation velocity may vary
@@ -584,14 +584,14 @@ command, that matches the box deformation rate. This also typically
helps the system come to equilibrium more quickly, even if a
thermostat is used.
fix fDIRECT all drude/transform/direct
@@ -280,7 +292,7 @@ to add a fix momentum command:
-
-
-
-
-
-
-
-comm_modify vel yes
-pair eff/cut to understand these settings), one
-(default) that considers electrons do not contribute radial virial
-components (i.e. electrons treated as incompressible ‘rigid’ spheres)
-and one that does. The radial electronic contributions to the virials
-are only tallied if the flexible pressure option is set, and this will
-affect both global and per-atom quantities. In principle, the true
-pressure of a system is somewhere in between the rigid and the
-flexible eFF pressures, but, for most cases, the difference between
-these two pressures will not be significant over long-term averaged
-runs (i.e. even though the energy partitioning changes, the total
-energy remains similar).pair eff/cut to
+understand these settings), one (default) that considers electrons do
+not contribute radial virial components (i.e. electrons treated as
+incompressible ‘rigid’ spheres) and one that does. The radial
+electronic contributions to the virials are only tallied if the
+flexible pressure option is set, and this will affect both global and
+per-atom quantities. In principle, the true pressure of a system is
+somewhere in between the rigid and the flexible eFF pressures, but,
+for most cases, the difference between these two pressures will not be
+significant over long-term averaged runs (i.e. even though the energy
+partitioning changes, the total energy remains similar).
-
@@ -341,7 +341,7 @@ Additional option defaults are diam = one 1.0, dens = 1.0 1.0, vol =
Description¶
fix nvt, fix npt), or you will be integrating
+fix nvt, fix npt), or you will be integrating
their motion more than once each timestep. When performing a hybrid
simulation with some atoms in rigid bodies, and some not, a separate
time integration fix like fix nve or fix nvt should be used for the non-rigid particles.fix viscous doc page for details.
-
@@ -333,7 +333,7 @@ J of Comp Phys, 23, 327-341 (1977).
-fix nvt) is NOT recommended due to its well documented
@@ -226,12 +226,12 @@ fix are “extensive”.
lmp_g++ < in.script
-
@@ -299,15 +299,14 @@ orientation in the simulation box.
inferred from “lattice spacings” in the x,y,z box directions.
E.g. the region command can create a block of size
10x20x20, where 10 means 10 lattice spacings in the x direction.
-
-fix pour command, the Bonds (Angles, etc) sections are
-not required, since the molecule will be treated as a rigid body.
-Some sections are optional. For example, the fix pour
+fix pour command, the Bonds (Angles, etc) sections are not
+required, since the molecule will be treated as a rigid body. Some
+sections are optional. For example, the fix pour
command can be used to add “molecules” which are clusters of
finite-size granular particles. If the Diameters section is not
specified, each particle in the molecule will have a default diameter
@@ -549,7 +548,7 @@ of SHAKE clusters.