(6) Text with spaces can be enclosed in double quotes so it will be treated as a single argument. See the dump modify or fix print commands for examples. A '#' or '$' -character that in text between double quotes will not be treated as a -comment or substituted for as a variable. +character that is in text between double quotes will not be treated as +a comment or substituted for as a variable.
These are fix styles contributed by users, which can be used if diff --git a/doc/Section_commands.txt b/doc/Section_commands.txt index 128cd551b4..d664460efc 100644 --- a/doc/Section_commands.txt +++ b/doc/Section_commands.txt @@ -110,8 +110,8 @@ line are arguments. (6) Text with spaces can be enclosed in double quotes so it will be treated as a single argument. See the "dump modify"_dump_modify.html or "fix print"_fix_print.html commands for examples. A '#' or '$' -character that in text between double quotes will not be treated as a -comment or substituted for as a variable. +character that is in text between double quotes will not be treated as +a comment or substituted for as a variable. :line @@ -380,6 +380,8 @@ of each style or click on the style itself for a full description: "ave/atom"_fix_ave_atom.html, "ave/spatial"_fix_ave_spatial.html, "ave/time"_fix_ave_time.html, +"bond/break"_fix_bond_break.html, +"bond/create"_fix_bond_create.html, "bond/swap"_fix_bond_swap.html, "com"_fix_com.html, "coord/original"_fix_coord_original.html, diff --git a/doc/Section_errors.html b/doc/Section_errors.html index 259f066071..f024e6f1a9 100644 --- a/doc/Section_errors.html +++ b/doc/Section_errors.html @@ -42,8 +42,8 @@ See the discussion of the loop option in the
Similarly, the create_atoms command generates a lattice of atoms. For the same physical system, the ordering and -numbering of atoms (atom ID or tag) may be different depending on the -number of processors. +numbering of atoms by atom ID may be different depending on the number +of processors.
Some commands use random number generators which may be setup to produce different random number streams on each processor and hence diff --git a/doc/Section_errors.txt b/doc/Section_errors.txt index fcdda91ff8..3908a23645 100644 --- a/doc/Section_errors.txt +++ b/doc/Section_errors.txt @@ -39,8 +39,8 @@ See the discussion of the {loop} option in the Similarly, the "create_atoms"_create_atoms.html command generates a lattice of atoms. For the same physical system, the ordering and -numbering of atoms (atom ID or tag) may be different depending on the -number of processors. +numbering of atoms by atom ID may be different depending on the number +of processors. Some commands use random number generators which may be setup to produce different random number streams on each processor and hence diff --git a/doc/angle_hybrid.html b/doc/angle_hybrid.html index 8f43f633cf..97e9163539 100644 --- a/doc/angle_hybrid.html +++ b/doc/angle_hybrid.html @@ -48,9 +48,8 @@ assigned to other hybrid styles, use the style name (e.g. "harmonic") appropriate to that style. The BondBond and BondAngle coeffs for that angle type will then be ignored.
-An angle style of none can be specified as an argument to -angle_style hybrid and the corresponding angle_coeff commands, if you -desire to turn off certain angle types. +
An angle style of none can be specified as the 2nd argument to the +angle_coeff command, if you desire to turn off certain angle types.
Restrictions:
diff --git a/doc/angle_hybrid.txt b/doc/angle_hybrid.txt index 17883b25df..7e6a2f27e6 100644 --- a/doc/angle_hybrid.txt +++ b/doc/angle_hybrid.txt @@ -45,9 +45,8 @@ assigned to other hybrid styles, use the style name (e.g. "harmonic") appropriate to that style. The BondBond and BondAngle coeffs for that angle type will then be ignored. -An angle style of {none} can be specified as an argument to -angle_style hybrid and the corresponding angle_coeff commands, if you -desire to turn off certain angle types. +An angle style of {none} can be specified as the 2nd argument to the +angle_coeff command, if you desire to turn off certain angle types. [Restrictions:] diff --git a/doc/bond_hybrid.html b/doc/bond_hybrid.html index aeef272796..bdf750b8f5 100644 --- a/doc/bond_hybrid.html +++ b/doc/bond_hybrid.html @@ -41,9 +41,8 @@ coefficients 80.0, 1.2 for K, r0. All other bond types (2-N) would be computed with a fene potential with coefficients 30.0, 1.5, 1.0, 1.0 for K, R0, epsilon, sigma. -A bond style of none can be specified as an argument to bond_style -hybrid and the corresponding bond_coeff commands, if you desire to -turn off certain bond types. +
A bond style of none can be specified as the 2nd argument to the +bond_coeff command, if you desire to turn off certain bond types.
Restrictions:
diff --git a/doc/bond_hybrid.txt b/doc/bond_hybrid.txt index 50e6ab1356..9fb42206f2 100644 --- a/doc/bond_hybrid.txt +++ b/doc/bond_hybrid.txt @@ -38,9 +38,8 @@ coefficients 80.0, 1.2 for K, r0. All other bond types (2-N) would be computed with a {fene} potential with coefficients 30.0, 1.5, 1.0, 1.0 for K, R0, epsilon, sigma. -A bond style of {none} can be specified as an argument to bond_style -hybrid and the corresponding bond_coeff commands, if you desire to -turn off certain bond types. +A bond style of {none} can be specified as the 2nd argument to the +bond_coeff command, if you desire to turn off certain bond types. [Restrictions:] diff --git a/doc/dihedral_hybrid.html b/doc/dihedral_hybrid.html index 50e67db17c..63ce89a220 100644 --- a/doc/dihedral_hybrid.html +++ b/doc/dihedral_hybrid.html @@ -50,9 +50,9 @@ to other hybrid styles, use the style name (e.g. "harmonic") appropriate to that style. The MiddleBondTorsion, etc coeffs for that dihedral type will then be ignored. -A dihedral style of none can be specified as an argument to -dihedral_style hybrid and the corresponding dihedral_coeff commands, -if you desire to turn off certain dihedral types. +
A dihedral style of none can be specified as the 2nd argument to the +dihedral_coeff command, if you desire to turn off certain dihedral +types.
Restrictions:
diff --git a/doc/dihedral_hybrid.txt b/doc/dihedral_hybrid.txt index a8baa24d4a..f92fc490d6 100644 --- a/doc/dihedral_hybrid.txt +++ b/doc/dihedral_hybrid.txt @@ -47,9 +47,9 @@ to other hybrid styles, use the style name (e.g. "harmonic") appropriate to that style. The MiddleBondTorsion, etc coeffs for that dihedral type will then be ignored. -A dihedral style of {none} can be specified as an argument to -dihedral_style hybrid and the corresponding dihedral_coeff commands, -if you desire to turn off certain dihedral types. +A dihedral style of {none} can be specified as the 2nd argument to the +dihedral_coeff command, if you desire to turn off certain dihedral +types. [Restrictions:] diff --git a/doc/dump.html b/doc/dump.html index 0e362ba388..001b876a8c 100644 --- a/doc/dump.html +++ b/doc/dump.html @@ -33,7 +33,7 @@ xtc args = none xyz args = none custom args = list of atom attributes - possible attributes = tag, mol, type, + possible attributes = id, mol, type, x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz, vx, vy, vz, fx, fy, fz, q, mux, muy, muz, @@ -41,7 +41,7 @@ angmomx, angmomy, angmomz, quatw, quati, quatj, quatk, tqx, tqy, tqz, c_ID, c_ID[N], f_ID, f_ID[N], v_name - tag = atom ID + id = atom ID mol = molecule ID type = atom type x,y,z = unscaled atom coordinates @@ -69,8 +69,8 @@dump myDump all atom 100 dump.atom dump 2 subgroup atom 50 dump.run.bin -dump 4a all custom 100 dump.myforce.* tag type x y vx fx -dump 4b flow custom 100 dump.%.myforce tag type c_myF[3] v_ke +dump 4a all custom 100 dump.myforce.* id type x y vx fx +dump 4b flow custom 100 dump.%.myforce id type c_myF[3] v_ke dump 1 all xtc 1000 file.xtc
Description: @@ -229,8 +229,8 @@ styles.
This section explains the atom quantities that can be specified as part of the custom style.
-The tag, mol, type, x, y, z, vx, vy, vz, fx, fy, -fz, q keywords are self-explanatory. Tag is the atom ID. Mol +
The id, mol, type, x, y, z, vx, vy, vz, fx, fy, +fz, q keywords are self-explanatory. Id is the atom ID. Mol is the molecule ID, included in the data file for molecular systems. The x, y, z keywords write atom coordinates "unscaled", in the appropriate distance units (Angstroms, sigma, etc). Use diff --git a/doc/dump.txt b/doc/dump.txt index b700d71fec..348df6b427 100644 --- a/doc/dump.txt +++ b/doc/dump.txt @@ -24,7 +24,7 @@ args = list of arguments for a particular style :l {xtc} args = none {xyz} args = none {custom} args = list of atom attributes - possible attributes = tag, mol, type, + possible attributes = id, mol, type, x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz, vx, vy, vz, fx, fy, fz, q, mux, muy, muz, @@ -32,7 +32,7 @@ args = list of arguments for a particular style :l angmomx, angmomy, angmomz, quatw, quati, quatj, quatk, tqx, tqy, tqz, c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_name - tag = atom ID + id = atom ID mol = molecule ID type = atom type x,y,z = unscaled atom coordinates @@ -59,8 +59,8 @@ args = list of arguments for a particular style :l dump myDump all atom 100 dump.atom dump 2 subgroup atom 50 dump.run.bin -dump 4a all custom 100 dump.myforce.* tag type x y vx fx -dump 4b flow custom 100 dump.%.myforce tag type c_myF\[3\] v_ke +dump 4a all custom 100 dump.myforce.* id type x y vx fx +dump 4b flow custom 100 dump.%.myforce id type c_myF\[3\] v_ke dump 1 all xtc 1000 file.xtc :pre [Description:] @@ -219,8 +219,8 @@ styles. This section explains the atom quantities that can be specified as part of the {custom} style. -The {tag}, {mol}, {type}, {x}, {y}, {z}, {vx}, {vy}, {vz}, {fx}, {fy}, -{fz}, {q} keywords are self-explanatory. {Tag} is the atom ID. {Mol} +The {id}, {mol}, {type}, {x}, {y}, {z}, {vx}, {vy}, {vz}, {fx}, {fy}, +{fz}, {q} keywords are self-explanatory. {Id} is the atom ID. {Mol} is the molecule ID, included in the data file for molecular systems. The {x}, {y}, {z} keywords write atom coordinates "unscaled", in the appropriate distance "units"_units.html (Angstroms, sigma, etc). Use diff --git a/doc/fix.html b/doc/fix.html index 41e46c1ab7..abb6410e7f 100644 --- a/doc/fix.html +++ b/doc/fix.html @@ -108,6 +108,8 @@ list of fix styles available in LAMMPS:
IMPORTANT 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 wall/reflect 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. -
Restart, fix_modify, output, run start/stop, minimize info:
-An improper style of none can be specified as an argument to -improper_style hybrid and the corresponding improper_coeff commands, -if you desire to turn off certain improper types. +
An improper style of none can be specified as the 2nd argument to +the improper_coeff command, if you desire to turn off certain improper +types.
Restrictions:
diff --git a/doc/improper_hybrid.txt b/doc/improper_hybrid.txt index 9c5e074fa3..6a17b82ee4 100644 --- a/doc/improper_hybrid.txt +++ b/doc/improper_hybrid.txt @@ -46,9 +46,9 @@ to other hybrid styles, use the style name (e.g. "harmonic") appropriate to that style. The AngleAngle coeffs for that improper type will then be ignored. -An improper style of {none} can be specified as an argument to -improper_style hybrid and the corresponding improper_coeff commands, -if you desire to turn off certain improper types. +An improper style of {none} can be specified as the 2nd argument to +the improper_coeff command, if you desire to turn off certain improper +types. [Restrictions:] diff --git a/doc/pair_gran.html b/doc/pair_gran.html index 1682dcd117..0adbe7cb05 100644 --- a/doc/pair_gran.html +++ b/doc/pair_gran.html @@ -74,9 +74,19 @@ The tangential force between 2 particles grows according to a tangential spring and dash-pot model until Ft/Fn = xmu and is then held at Ft = Fn*xmu until the particles lose contact. -For granular styles there are no individual atom type coefficients -that can be set via the pair_coeff command. All -global settings are made via the pair_style command. +
For granular styles there are no additional coefficients to set for +each pair of atom types via the pair_coeff command. +All settings are global and are made via the pair_style command. +However you must still use the pair_coeff for all +pairs of granular atom types. For example the command +
+pair_coeff * * ++
should be used if all atoms in the simulation interact via a granular +potential. If a granular potential is used as part of pair_style +hybrid, then specific atom types can be used in the +pair_coeff command to determine which atoms interact via a granular +potential.
See the citation below for more discussion of granular potentials.
diff --git a/doc/pair_gran.txt b/doc/pair_gran.txt index 513ca7ee87..c5d2f4bfb1 100644 --- a/doc/pair_gran.txt +++ b/doc/pair_gran.txt @@ -66,9 +66,19 @@ The tangential force between 2 particles grows according to a tangential spring and dash-pot model until Ft/Fn = xmu and is then held at Ft = Fn*xmu until the particles lose contact. -For granular styles there are no individual atom type coefficients -that can be set via the "pair_coeff"_pair_coeff.html command. All -global settings are made via the pair_style command. +For granular styles there are no additional coefficients to set for +each pair of atom types via the "pair_coeff"_pair_coeff.html command. +All settings are global and are made via the pair_style command. +However you must still use the "pair_coeff"_pair_coeff.html for all +pairs of granular atom types. For example the command + +pair_coeff * * :pre + +should be used if all atoms in the simulation interact via a granular +potential. If a granular potential is used as part of "pair_style +hybrid"_pair_hybrid.html, then specific atom types can be used in the +pair_coeff command to determine which atoms interact via a granular +potential. See the citation below for more discussion of granular potentials. diff --git a/doc/read_data.html b/doc/read_data.html index e484763c11..612f0df44b 100644 --- a/doc/read_data.html +++ b/doc/read_data.html @@ -78,6 +78,7 @@ is different than the default.If the xy xz yz line does not appear, then LAMMPS will set up an +
If the xy xz yz line does not appear, LAMMPS will set up an axis-aligned (orthogonal) simulation box. If the line does appear, LAMMPS creates a non-orthogonal simulation domain shaped as a parallelepiped with triclinic symmetry. See the region @@ -139,6 +140,11 @@ specified box size to layout the 3d grid of processors. A huge parallel simulation to lose atoms if LAMMPS shrink-wraps the box around the atoms.
+The "extra bond per atom" setting should be used if new bonds will be +added to the system when a simulation runs, e.g. by using the fix +bond/create command. This will pre-allocate +space in LAMMPS data structures for storing the new bonds. +
These are the section keywords for the body of the file. diff --git a/doc/read_data.txt b/doc/read_data.txt index e793f02dd9..85197862c3 100644 --- a/doc/read_data.txt +++ b/doc/read_data.txt @@ -73,6 +73,7 @@ is different than the default. {angle types} = # of angle types in system {dihedral types} = # of dihedral types in system {improper types} = # of improper types in system +{extra bond per atom} = leave space for this many new bonds per atom {xlo xhi} = simulation box boundaries in x dimension {ylo yhi} = simulation box boundaries in y dimension {zlo zhi} = simulation box boundaries in z dimension @@ -82,7 +83,7 @@ The initial simulation box size is determined by the lo/hi settings. In any dimension, the system may be periodic or non-periodic; see the "boundary"_boundary.html command. -If the {xy xz yz} line does not appear, then LAMMPS will set up an +If the {xy xz yz} line does not appear, LAMMPS will set up an axis-aligned (orthogonal) simulation box. If the line does appear, LAMMPS creates a non-orthogonal simulation domain shaped as a parallelepiped with triclinic symmetry. See the "region @@ -134,6 +135,11 @@ specified box size to layout the 3d grid of processors. A huge parallel simulation to lose atoms if LAMMPS shrink-wraps the box around the atoms. +The "extra bond per atom" setting should be used if new bonds will be +added to the system when a simulation runs, e.g. by using the "fix +bond/create"_fix_bond_create.html command. This will pre-allocate +space in LAMMPS data structures for storing the new bonds. + :line These are the section keywords for the body of the file. diff --git a/doc/replicate.html b/doc/replicate.html index 07f47e92cc..de49ff26ad 100644 --- a/doc/replicate.html +++ b/doc/replicate.html @@ -30,15 +30,14 @@ dimension. A replication factor of 1 in a dimension leaves the simulation domain unchanged.
All properties of the atoms are replicated, including their -velocities, which may or may not be desirable. New atom IDs (tags) -are assigned to new atoms, as are molecule IDs. Bonds and other -topology interactions are created between pairs of new atoms as well -as between old and new atoms. This is done by using the image flag -for each atom to "unwrap" it out of the periodic box before -replicating it. This means that molecular bonds you specify in the -original data file that span the periodic box should be between two -atoms with image flags that differ by 1. This will allow them to be -unwrapped appropriately. +velocities, which may or may not be desirable. New atom IDs are +assigned to new atoms, as are molecule IDs. Bonds and other topology +interactions are created between pairs of new atoms as well as between +old and new atoms. This is done by using the image flag for each atom +to "unwrap" it out of the periodic box before replicating it. This +means that molecular bonds you specify in the original data file that +span the periodic box should be between two atoms with image flags +that differ by 1. This will allow them to be unwrapped appropriately.
Restrictions:
diff --git a/doc/replicate.txt b/doc/replicate.txt index f0091c0d6a..68619cc22a 100644 --- a/doc/replicate.txt +++ b/doc/replicate.txt @@ -27,15 +27,14 @@ dimension. A replication factor of 1 in a dimension leaves the simulation domain unchanged. All properties of the atoms are replicated, including their -velocities, which may or may not be desirable. New atom IDs (tags) -are assigned to new atoms, as are molecule IDs. Bonds and other -topology interactions are created between pairs of new atoms as well -as between old and new atoms. This is done by using the image flag -for each atom to "unwrap" it out of the periodic box before -replicating it. This means that molecular bonds you specify in the -original data file that span the periodic box should be between two -atoms with image flags that differ by 1. This will allow them to be -unwrapped appropriately. +velocities, which may or may not be desirable. New atom IDs are +assigned to new atoms, as are molecule IDs. Bonds and other topology +interactions are created between pairs of new atoms as well as between +old and new atoms. This is done by using the image flag for each atom +to "unwrap" it out of the periodic box before replicating it. This +means that molecular bonds you specify in the original data file that +span the periodic box should be between two atoms with image flags +that differ by 1. This will allow them to be unwrapped appropriately. [Restrictions:] diff --git a/doc/reset_timestep.html b/doc/reset_timestep.html index 165467758e..31bdc71630 100644 --- a/doc/reset_timestep.html +++ b/doc/reset_timestep.html @@ -45,6 +45,21 @@ write. See the undump command or fix +ave/spatial or fix +wall/lj126, and also fix +indent. The wall and indeter fixes allow for a +velocity or other time-dependent parameter to be specified, which +would be messed up by resetting the timestep. + +Restting the timestep will clear the flags for computes +that may have calculated some quantity from a previous run. This +means that quantity cannot be accessed by a variable in between runs +until a new run is performed. See the variable +command for more details. +
Related commands: none
Default: none diff --git a/doc/reset_timestep.txt b/doc/reset_timestep.txt index c791597311..3da3655276 100644 --- a/doc/reset_timestep.txt +++ b/doc/reset_timestep.txt @@ -42,6 +42,21 @@ write. See the "undump"_undump.html command or "restart if necessary. New specifications for dump and restart files can be given after the reset_timestep command is used. +This command cannot be used when any fixes are defined that keep track +of time or the timestep in order to perform time-dependent operations. +Examples include the "ave" or "wall" fixes such as "fix +ave/spatial"_fix_ave_spatial.html or "fix +wall/lj126"_fix_wall_lj126.html, and also "fix +indent"_fix_indent.html. The wall and indeter fixes allow for a +velocity or other time-dependent parameter to be specified, which +would be messed up by resetting the timestep. + +Restting the timestep will clear the flags for "computes"_compute.html +that may have calculated some quantity from a previous run. This +means that quantity cannot be accessed by a variable in between runs +until a new run is performed. See the "variable"_variable.html +command for more details. + [Related commands:] none [Default:] none diff --git a/doc/run.html b/doc/run.html index 08a3297cfc..c63fe422da 100644 --- a/doc/run.html +++ b/doc/run.html @@ -157,6 +157,14 @@ command (e.g. print "Protein Rg = $r" as in the example above). This means that, if specified, the every option must be the last keyword used.
+IMPORTANT NOTE: For the every option, if the command includes a +variable (e.g. $x or ${abc}), and you want the variable to be +evaluated afresh each time the command is invoked, then you should +enclose that command argument in double quotes, as in the "Protein Rg += $r" example above. If you don't do this, then the variable will be +substituted for only once initially when the run command is parsed, +just as occurs for any other command containing a variable. +
If the pre and post options are set to "no" when used with the every keyword, then the 1st run will do the full setup and the last run will print the full timing summary, but these operations will be diff --git a/doc/run.txt b/doc/run.txt index 5d71dc481f..2e3b15c0e7 100644 --- a/doc/run.txt +++ b/doc/run.txt @@ -150,6 +150,14 @@ command (e.g. print "Protein Rg = $r" as in the example above). This means that, if specified, the {every} option must be the last keyword used. +IMPORTANT NOTE: For the {every} option, if the command includes a +variable (e.g. $x or $\{abc\}), and you want the variable to be +evaluated afresh each time the command is invoked, then you should +enclose that command argument in double quotes, as in the "Protein Rg += $r" example above. If you don't do this, then the variable will be +substituted for only once initially when the run command is parsed, +just as occurs for any other command containing a variable. + If the {pre} and {post} options are set to "no" when used with the {every} keyword, then the 1st run will do the full setup and the last run will print the full timing summary, but these operations will be diff --git a/doc/special_bonds.html b/doc/special_bonds.html index db52902779..73026d8d36 100644 --- a/doc/special_bonds.html +++ b/doc/special_bonds.html @@ -13,105 +13,125 @@
Syntax:
-special_bonds style args +special_bonds keyword values ...-
charmm args = none - amber args = none - dihedral args = c1 c2 c3 c4 c5 c6 - c1,c2,c3 = weights (0.0 to 1.0) on pairwise Lennard-Jones interactions (and Coulomb if c4,c5,c6 are not specified) - c4,c5,c6 = weights (0.0 to 1.0) on pairwise Coulomb interactions (optional) - explicit args = c1 c2 c3 c4 c5 c6 - c1,c2,c3 = weights (0.0 to 1.0) on pairwise Lennard-Jones interactions (and Coulomb if c4,c5,c6 are not specified) - c4,c5,c6 = weights (0.0 to 1.0) on pairwise Coulomb interactions (optional) +
amber values = none + charmm values = none + fene values = none + lj/coul values = w1,w2,w3 + w1,w2,w3 = weights (0.0 to 1.0) on pairwise Lennard-Jones and Coulombic interactions + lj values = w1,w2,w3 + w1,w2,w3 = weights (0.0 to 1.0) on pairwise Lennard-Jones interactions + coul values = w1,w2,w3 + w1,w2,w3 = weights (0.0 to 1.0) on pairwise Coulombic interactions + dihedral value = yes or no + extra value = N + N = number of extra 1-2,1-3,1-4 interactions to save space for
Examples:
-special_bonds charmm -special_bonds amber -special_bonds dihedral 0.0 0.0 0.5 -special_bonds explicit 0 1 1 -special_bonds 0 1 1 -special_bonds 0.0 0.0 1.0 0.0 0.0 0.5 +special_bonds amber +special_bonds charmm +special_bonds fene dihedral no +special_bonds lj/coul 0.0 0.0 0.5 dihedral yes +special_bonds lj 0.0 0.0 0.5 coul 0.0 0.0 0.0 dihedral yes +special_bonds lj/coul 0 1 1 extra 2Description:
-Set the weighting coefficients for the pairwise force and energy -contributions from atom pairs that are also bonded to each other -directly or indirectly. For Lennard-Jones and Coulombic pairwise -interactions, the 1st coefficient is the weighting factor on 1-2 atom -pairs, which are those directly bonded to each other. The 2nd -coefficient is the weighting factor on 1-3 atom pairs which are those -separated by 2 bonds (e.g. the 2 H atoms in a water molecule). The -3rd coefficient is the weighting factor on 1-4 atom pairs which are -separated by 3 bonds (e.g. the 1st and 4th atoms in a dihedral -interaction). +
Set weighting coefficients for pairwise energy and force contributions +from atom pairs that are also bonded to each other directly or +indirectly. For Lennard-Jones (LJ) and Coulombic pairwise +interactions, these coefficients come in sets of three. The 1st +coefficient is the weighting factor on 1-2 atom pairs, which are those +directly bonded to each other. The 2nd coefficient is the weighting +factor on 1-3 atom pairs which are those separated by 2 bonds +(e.g. the two H atoms in a water molecule). The 3rd coefficient is +the weighting factor on 1-4 atom pairs which are those separated by 3 +bonds (e.g. the 1st and 4th atoms in a dihedral interaction). Thus if +the 1-2 coefficient is set to 0.0, then the pairwise interaction is +effectively turned off for all pairs of atoms bonded to each other.
-Note that for purposes of computing weighted pairwise interactions, -1-3 and 1-4 interactions are NOT defined from the list of angles or -dihedrals used by the simulation. Rather, they are inferred -topologically by the set of bonds defined when atoms are read in from -a file (read_data or -read_restart). Thus the set of 1-2,1-3,1-4 -interactions is the same whether angle and dihedral potentials are +
IMPORTANT NOTE: For purposes of computing weighted pairwise +interactions, 1-3 and 1-4 interactions are not defined from the list +of angles or dihedrals used by the simulation. Rather, they are +inferred topologically from the set of bonds defined when the +simulation is defined from a data or restart file (see +read_data or read_restart +commands). Thus the set of 1-2,1-3,1-4 interactions that the weights +apply to is the same whether angle and dihedral potentials are computed or not, and remains the same even if bonds are constrained, or turned off, or removed during a simulation.
-The two exceptions to this rule are (a) if the special_bonds -dihedral style is used (see below), or (b) if the +
The two exceptions to this rule are (a) if the dihedral keyword is +set to yes (see below), or (b) if the delete_bonds command is used with the special option that recomputes the 1-2,1-3,1-4 topologies after bonds are deleted; see the delete_bonds command for more details.
-The charmm style sets all 3 coefficients to 0.0 for both LJ and -Coulombic interactions, which is the default for the CHARMM force -field. In pair styles lj/charmm/coul/charmm and -lj/charmm/coul/long the 1-4 coefficients are defined explicitly, and -these pair-wise contributions are computed in the charmm dihedral -style - see the pair_coeff and -dihedral_style commands for more information. -
-The amber style sets the 3 coefficients to 0.0 0.0 0.5 for LJ -interactions and to 0.0 0.0 0.8333 for Coulombic interactions, which -is the default for a particular version of the AMBER force field, +
The amber keyword sets the 3 coefficients to 0.0, 0.0, 0.5 for LJ +interactions and to 0.0, 0.0, 0.8333 for Coulombic interactions, which +is the default for a commonly used version of the AMBER force field, where the last value is really 5/6.
-The dihedral style requires you to set 3 or 6 coefficients (see the -explicit style), but it turns off the 1-4 weighting factor for -individual atom pairs if they are not listed as the first and last +
The charmm keyword sets the 3 coefficients to 0.0, 0.0, 0.0 for both +LJ and Coulombic interactions, which is the default for a commonly +used version of the CHARMM force field. Note that in pair styles +lj/charmm/coul/charmm and lj/charmm/coul/long the 1-4 coefficients +are defined explicitly, and these pairwise contributions are computed +as part of the charmm dihedral style - see the +pair_coeff and dihedral_style +commands for more information. +
+The fene keyword sets the 3 coefficients to 0.0, 1.0, 1.0 for both +LJ and Coulombic interactions, which is consistent with a +coarse-grained polymer model with FENE bonds. +
+The lj/coul, lj, and coul keywords allow the 3 coefficients to +be set explicitly. The lj/coul keyword sets both the LJ and +Coulombic coefficients to the same 3 values. The lj and coul +keywords only set either the LJ or Coulombic coefficients. Use both +of them if you wish to set the LJ coefficients to different values +than the Coulombic coefficients. +
+The dihedral keyword allows the 1-4 weighting factor to be ignored +for individual atom pairs if they are not listed as the first and last atoms in any dihedral defined in the simulation. For example, imagine -you have set the 1-4 weighting factor to 0.5 and you have a linear -molecule with 5 atoms and bonds as follows: 1-2-3-4-5. If your data -file defines 1-2-3-4 as a dihedral, but does not define 2-3-4-5 as a -dihedral, then the pairwise interaction between atoms 1 and 4 will be -weighted by 0.5, but the interaction between atoms 2 and 5 will be -unaffected (full weighting of 1.0). Note that if any of the other -special_bond styles are used, then the 2,5 interaction would also be -weighted by 0.5. The dihedral style is provided because some force -fields follow this rule. +the 1-4 weighting factor is set to 0.5 and you have a linear molecule +with 5 atoms and bonds as follows: 1-2-3-4-5. If your data file +defines 1-2-3-4 as a dihedral, but does not define 2-3-4-5 as a +dihedral, then the pairwise interaction between atoms 1 and 4 will +always be weighted by 0.5, but different force fields use different +rules for weighting the pairwise interaction between atoms 2 and 5. +If the dihedral keyword is specified as yes, then the pairwise +interaction between atoms 2 and 5 will be unaffected (full weighting +of 1.0). If the dihedral keyword is specified as no which is the +default, then the 2,5 interaction will also be weighted by 0.5.
-The explicit style requires you to set 3 or 6 coefficients directly. -If 3 are specified, they are used for both LJ and Coulombic -interactions. If 6 are specified then the first 3 are LJ coefficients -and the second 3 are Coulombic coefficients. Note that the explicit -keyword itself is optional; the special_bonds command can just take 3 -or 6 numeric arguments by themselves. -
-IMPORTANT NOTE: For a lj units system with FENE -bonds a setting of special bonds 0 1 1 should be used. +
The extra keyword is used when additional bonds will be created +during a simulation run, e.g. by the fix +bond/create command. A list of 1-2,1-3,1-4 +neighbors for each atom is calculated and stored by LAMMPS. If new +bonds are created, the list needs to grow. Using the extra keyword +leaves empty space in the list for N additional bonds to be added. If +you do not do this, you may get an error when bonds are added.
Restrictions: none
Related commands:
-Default:
-special_bonds 0.0 0.0 0.0 -+All 3 Lennard-Jones and 3 Coulobmic weighting coefficients = 0.0, +dihedral = no, and extra = 0. +