atom args = none - bond args = none cfg args = same as custom args, see below dcd args = none xtc args = none - xyz args = none - custom args = list of atom attributes + xyz args = none ++
local args = list of local attributes + possible attributes = index, c_ID, c_ID[N], f_ID, f_ID[N] + index = enumeration of local values + c_ID = local vector calculated by a compute with ID + c_ID[N] = Nth column of local array calculated by a compute with ID + f_ID = local vector calculated by a fix with ID + f_ID[N] = Nth column of local array calculated by a fix with ID ++
custom args = list of atom attributes
possible attributes = id, mol, type, mass,
x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz,
vx, vy, vz, fx, fy, fz,
@@ -60,9 +68,9 @@
angmomx,angmomy,angmomz = angular momentum of extended particle
quatw,quati,quatj,quatk = quaternion components for aspherical particles
tqx,tqy,tqz = torque on extended particles
- c_ID = per-atom vector value calculated by a compute with ID
+ c_ID = per-atom vector calculated by a compute with ID
c_ID[N] = Nth column of per-atom array calculated by a compute with ID
- f_ID = per-atom vector value calculated by a fix with ID
+ f_ID = per-atom vector calculated by a fix with ID
f_ID[N] = Nth column of per-atom array calculated by a fix with ID
v_name = per-atom vector calculated by an atom-style variable with name
@@ -98,7 +106,7 @@ box.
dump files (typically one line per atom) may be written in an
indeterminate order. This is because data for a single snapshot is
collected from multiple processors. This is always the case for the
-atom, bond, and custom styles. It is also the case for the
+atom, local, and custom styles. It is also the case for the
xyz style if the dump group is not all. It is not the case for
the dcd and xtc styles which always write atoms in sorted order.
So does the xyz style if the dump group is all. The cfg style
@@ -112,7 +120,7 @@ file and in what format. Settings made via the
dump_modify command can also alter the format of
individual values and the file itself.
-The atom, bond, and custom styles create files in a simple text +
The atom, local, and custom styles create files in a simple text format that is self-explanatory when viewing a dump file. Many of the LAMMPS post-processing tools, including Pizza.py, work with @@ -139,16 +147,6 @@ boundaries. The format can be changed to unscaled coords via the dump_modify settings. Image flags can also be added for each atom via dump_modify.
-For style bond, the bond topology between atoms is written, in the -same format specified in data files read in by the -read_data command. Both atoms in the bond must be in -the dump group for the bond to be written. Any bonds that have been -broken (see the bond_style command) by setting their -bond type to 0 are not written. Bonds that have been turned off (see -the fix shake or delete_bonds -commands) by setting their bond type negative are written into the -file. -
Style custom allows you to specify a list of atom attributes to be written to the dump file for each atom. Possible attributes are listed above and will appear in the order specified. You cannot @@ -156,8 +154,20 @@ specify a quantity that is not defined for a particular simulation - such as q for atom style bond, since that atom style doesn't assign charges. Dumps occur at the very end of a timestep, so atom attributes will include effects due to fixes that are applied during -the timestep. An explanation of the dump custom quantities is given -below. +the timestep. An explanation of the possible dump custom attributes +is given below. +
+For style local, local output generated by computes +and fixes is used to gnerate lines of output that is +written to the dump file. This local data is typically calculated by +each processor based on the atoms it owns, but there may be zero or +more entities per atom, e.g. a list of bond distances. An explanation +of the possible dump local attributes is given below. Note that by +using input from the compute +property/local command with dump local, +it is possible to generate information on bonds, angles, etc that can +be cut and pasted directly into a data file read by the +read_data command.
Style cfg has the same command syntax as style custom and writes extended CFG format files, as used by the @@ -264,11 +274,54 @@ styles.
This section explains the atom quantities that can be specified as +
This section explains the local attributes that can be specified as +part of the local style. +
+The index attribute can be used to generate an index number from 1 +to N for each line written into the dump file, where N is the total +number of local datums from all processors, or lines of output that +will appear in the snapshot. Note that because data from different +processors depend on what atoms they currently own, and atoms migrate +between processor, there is no guarantee that the same index will be +used for the same info (e.g. a particular bond) in successive +snapshots. +
+The c_ID and c_ID[N] attributes allow local vectors or arrays +calculated by a compute to be output. The ID in the +attribute should be replaced by the actual ID of the compute that has +been defined previously in the input script. See the +compute command for details. There are computes for +calculating local information such as indices, types, and energies for +bonds and angles. +
+Note that computes which calculate global or per-atom quantities, as +opposed to local quantities, cannot be output in a dump local command. +Instead, global quantities can be output by the thermo_style +custom command, and per-atom quantities can be +output by the dump custom command. +
+If c_ID is used as a attribute, then the local vector calculated by +the compute is printed. If c_ID[N] is used, then N must be in the +range from 1-M, which will print the Nth column of the M-length local +array calculated by the compute. +
+The f_ID and f_ID[N] attributes allow local vectors or arrays +calculated by a fix to be output. The ID in the attribute +should be replaced by the actual ID of the fix that has been defined +previously in the input script. +
+If f_ID is used as a attribute, then the local vector calculated by +the fix is printed. If f_ID[N] is used, then N must be in the +range from 1-M, which will print the Nth column of the M-length local +array calculated by the fix. +
+This section explains the atom attributes that can be specified as part of the custom and cfg styles.
The id, mol, type, mass, vx, vy, vz, fx, fy, -fz, q keywords are self-explanatory. +fz, q attributes are self-explanatory.
Id is the atom ID. Mol is the molecule ID, included in the data file for molecular systems. Type is the atom type. Mass is the @@ -276,7 +329,7 @@ atom mass. Vx, vy, vz, fx, fy, fz, an of atom velocity and force and atomic charge.
There are several options for outputting atom coordinates. The x, -y, z keywords write atom coordinates "unscaled", in the +y, z attributes write atom coordinates "unscaled", in the appropriate distance units (Angstroms, sigma, etc). Use xs, ys, zs if you want the coordinates "scaled" to the box size, so that each value is 0.0 to 1.0. If the simluation box is triclinic @@ -288,57 +341,58 @@ the coordinate would be if it had not been wrapped back into the periodic box. Note that using xu, yu, zu means that the coordinate values may be far outside the box bounds printed with the snapshot. The image flags can be printed directly using the ix, -iy, iz keywords. The dump_modify command +iy, iz attributes. The dump_modify command describes in more detail what is meant by scaled vs unscaled coordinates and the image flags.
-The mux, muy, muz keywords are specific to dipolar systems +
The mux, muy, muz attributes are specific to dipolar systems defined with an atom style of dipole. They give the orientation of the atom's point dipole moment.
-The radius keyword is specific to extended spherical particles +
The radius attribute is specific to extended spherical particles that have a finite size, such as granular particles defined with an atom style of granular.
-The omegax, omegay, and omegaz keywords are specific to extended +
The omegax, omegay, and omegaz attributes are specific to extended spherical or aspherical particles that have an angular velocity. Only certain atom styles, such as granular or dipole define this quantity.
-The angmomx, angmomy, and angmomz keywords are specific to +
The angmomx, angmomy, and angmomz attributes are specific to extended aspherical particles that have an angular momentum. Only the ellipsoid atom style defines this quantity.
-The quatw, quati, quatj, quatk keywords are for aspherical +
The quatw, quati, quatj, quatk attributes are for aspherical particles defined with an atom style of ellipsoid. They are the components of the quaternion that defines the orientation of the particle.
-The tqx, tqy, tqz keywords are for extended spherical or +
The tqx, tqy, tqz attributes are for extended spherical or aspherical particles that can sustain a rotational torque due to interactions with other particles.
-The c_ID and c_ID[N] keywords allow scalar or vector per-atom -quantities calculated by a compute to be output. The -ID in the keyword should be replaced by the actual ID of the compute -that has been defined previously in the input script. See the -compute command for details. There are per-atom -computes for calculating the energy, stress, centro-symmetry -parameter, and coordination number of individual atoms. +
The c_ID and c_ID[N] attributes allow per-atom vectors or arrays +calculated by a compute to be output. The ID in the +attribute should be replaced by the actual ID of the compute that has +been defined previously in the input script. See the +compute command for details. There are computes for +calculating the per-atom energy, stress, centro-symmetry parameter, +and coordination number of individual atoms.
-Note that computes which calculate global scalar and vector -quantities, as opposed to per-atom quantities, cannot be output in a -dump. Instead, these quantities can be output by the thermo_style -custom command. +
Note that computes which calculate global or local quantities, as +opposed to per-atom quantities, cannot be output in a dump custom +command. Instead, global quantities can be output by the +thermo_style custom command, and local quantities +can be output by the dump local command.
-If c_ID is used as a keyword, then the scalar per-atom quantity -calculated by the compute is printed. If c_ID[N] is used, then N -must be in the range from 1-M, which will print the Nth column of -the M-length per-atom array calculated by the compute. +
If c_ID is used as a attribute, then the per-atom vector calculated +by the compute is printed. If c_ID[N] is used, then N must be in +the range from 1-M, which will print the Nth column of the M-length +per-atom array calculated by the compute.
-The f_ID and f_ID[N] keywords allow scalar or vector per-atom +
The f_ID and f_ID[N] attributes allow vector or array per-atom quantities calculated by a fix to be output. The ID in the -keyword should be replaced by the actual ID of the fix that has been +attribute should be replaced by the actual ID of the fix that has been defined previously in the input script. The fix ave/atom command is one that calculates per-atom quantities. Since it can time-average per-atom quantities produced by @@ -346,20 +400,21 @@ any compute, fix, or atom- variable, this allows those time-averaged results to be written to a dump file.
-If f_ID is used as a keyword, then the scalar per-atom quantity -calculated by the fix is printed. If f_ID[N] is used, then N must -be in the range from 1-M, which will print the Nth column of the -M-length per-atom array calculated by the fix. +
If f_ID is used as a attribute, then the per-atom vector calculated +by the fix is printed. If f_ID[N] is used, then N must be in the +range from 1-M, which will print the Nth column of the M-length +per-atom array calculated by the fix.
-The v_name keyword allows per-atom quantities calculated by a -variable to be output. The name in the keyword should -be replaced by the actual name of the variable that has been defined -previously in the input script. Only an atom-style variable can be -referenced, since it is the only style that generates per-atom values. -Variables of style atom can reference individual atom attributes, -per-atom atom attributes, thermodynamic keywords, or invoke other -computes, fixes, or variables when they are evaluated, so this is a -very general means of creating quantities to output to a dump file. +
The v_name attribute allows per-atom vectors calculated by a +variable to be output. The name in the attribute +should be replaced by the actual name of the variable that has been +defined previously in the input script. Only an atom-style variable +can be referenced, since it is the only style that generates per-atom +values. Variables of style atom can reference individual atom +attributes, per-atom atom attributes, thermodynamic keywords, or +invoke other computes, fixes, or variables when they are evaluated, so +this is a very general means of creating quantities to output to a +dump file.
See this section of the manual for information on how to add new compute and fix styles to LAMMPS to calculate @@ -373,10 +428,6 @@ per-atom quantities which could then be output into dump files. -DLAMMPS_GZIP option - see the Making LAMMPS section of the documentation.
-The bond style is part of the "molecular" package. It is only -enabled if LAMMPS was built with that package. See the Making -LAMMPS section for more info. -
The xtc style is part of the "xtc" package. It is only enabled if LAMMPS was built with that package. See the Making LAMMPS section for more info. This is because diff --git a/doc/dump.txt b/doc/dump.txt index f8a1cd173f..25b121b7a7 100644 --- a/doc/dump.txt +++ b/doc/dump.txt @@ -14,16 +14,24 @@ dump ID group-ID style N file args :pre ID = user-assigned name for the dump :ulb,l group-ID = ID of the group of atoms to be dumped :l -style = {atom} or {bond} or {cfg} or {dcd} or {xtc} or {xyz} or {custom} :l +style = {atom} or {cfg} or {dcd} or {xtc} or {xyz} or {local} or {custom} :l N = dump every this many timesteps :l file = name of file to write dump info to :l args = list of arguments for a particular style :l {atom} args = none - {bond} args = none {cfg} args = same as {custom} args, see below {dcd} args = none {xtc} args = none - {xyz} args = none + {xyz} args = none :pre + + {local} args = list of local attributes + possible attributes = index, c_ID, c_ID\[N\], f_ID, f_ID\[N\] + index = enumeration of local values + c_ID = local vector calculated by a compute with ID + c_ID\[N\] = Nth column of local array calculated by a compute with ID + f_ID = local vector calculated by a fix with ID + f_ID\[N\] = Nth column of local array calculated by a fix with ID :pre + {custom} args = list of atom attributes possible attributes = id, mol, type, mass, x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz, @@ -51,9 +59,9 @@ args = list of arguments for a particular style :l angmomx,angmomy,angmomz = angular momentum of extended particle quatw,quati,quatj,quatk = quaternion components for aspherical particles tqx,tqy,tqz = torque on extended particles - c_ID = per-atom vector value calculated by a compute with ID + c_ID = per-atom vector calculated by a compute with ID c_ID\[N\] = Nth column of per-atom array calculated by a compute with ID - f_ID = per-atom vector value calculated by a fix with ID + f_ID = per-atom vector calculated by a fix with ID f_ID\[N\] = Nth column of per-atom array calculated by a fix with ID v_name = per-atom vector calculated by an atom-style variable with name :pre :ule @@ -88,7 +96,7 @@ When LAMMPS is running in parallel, the atom information written to dump files (typically one line per atom) may be written in an indeterminate order. This is because data for a single snapshot is collected from multiple processors. This is always the case for the -{atom}, {bond}, and {custom} styles. It is also the case for the +{atom}, {local}, and {custom} styles. It is also the case for the {xyz} style if the dump group is not {all}. It is not the case for the {dcd} and {xtc} styles which always write atoms in sorted order. So does the {xyz} style if the dump group is {all}. The {cfg} style @@ -102,7 +110,7 @@ file and in what format. Settings made via the "dump_modify"_dump_modify.html command can also alter the format of individual values and the file itself. -The {atom}, {bond}, and {custom} styles create files in a simple text +The {atom}, {local}, and {custom} styles create files in a simple text format that is self-explanatory when viewing a dump file. Many of the LAMMPS "post-processing tools"_Section_tools.html, including "Pizza.py"_http://www.cs.sandia.gov/~sjplimp/pizza.html, work with @@ -129,16 +137,6 @@ boundaries. The format can be changed to unscaled coords via the "dump_modify"_dump_modify.html settings. Image flags can also be added for each atom via dump_modify. -For style {bond}, the bond topology between atoms is written, in the -same format specified in data files read in by the -"read_data"_read_data.html command. Both atoms in the bond must be in -the dump group for the bond to be written. Any bonds that have been -broken (see the "bond_style"_bond_style.html command) by setting their -bond type to 0 are not written. Bonds that have been turned off (see -the "fix shake"_fix_shake.html or "delete_bonds"_delete_bonds.html -commands) by setting their bond type negative are written into the -file. - Style {custom} allows you to specify a list of atom attributes to be written to the dump file for each atom. Possible attributes are listed above and will appear in the order specified. You cannot @@ -146,8 +144,20 @@ specify a quantity that is not defined for a particular simulation - such as {q} for atom style {bond}, since that atom style doesn't assign charges. Dumps occur at the very end of a timestep, so atom attributes will include effects due to fixes that are applied during -the timestep. An explanation of the dump custom quantities is given -below. +the timestep. An explanation of the possible dump custom attributes +is given below. + +For style {local}, local output generated by "computes"_compute.html +and "fixes"_fix.html is used to gnerate lines of output that is +written to the dump file. This local data is typically calculated by +each processor based on the atoms it owns, but there may be zero or +more entities per atom, e.g. a list of bond distances. An explanation +of the possible dump local attributes is given below. Note that by +using input from the "compute +property/local"_compute_property_local.html command with dump local, +it is possible to generate information on bonds, angles, etc that can +be cut and pasted directly into a data file read by the +"read_data"_read_data.html command. Style {cfg} has the same command syntax as style {custom} and writes extended CFG format files, as used by the @@ -254,11 +264,54 @@ styles. :line -This section explains the atom quantities that can be specified as +This section explains the local attributes that can be specified as +part of the {local} style. + +The {index} attribute can be used to generate an index number from 1 +to N for each line written into the dump file, where N is the total +number of local datums from all processors, or lines of output that +will appear in the snapshot. Note that because data from different +processors depend on what atoms they currently own, and atoms migrate +between processor, there is no guarantee that the same index will be +used for the same info (e.g. a particular bond) in successive +snapshots. + +The {c_ID} and {c_ID\[N\]} attributes allow local vectors or arrays +calculated by a "compute"_compute.html to be output. The ID in the +attribute should be replaced by the actual ID of the compute that has +been defined previously in the input script. See the +"compute"_compute.html command for details. There are computes for +calculating local information such as indices, types, and energies for +bonds and angles. + +Note that computes which calculate global or per-atom quantities, as +opposed to local quantities, cannot be output in a dump local command. +Instead, global quantities can be output by the "thermo_style +custom"_thermo_style.html command, and per-atom quantities can be +output by the dump custom command. + +If {c_ID} is used as a attribute, then the local vector calculated by +the compute is printed. If {c_ID\[N\]} is used, then N must be in the +range from 1-M, which will print the Nth column of the M-length local +array calculated by the compute. + +The {f_ID} and {f_ID\[N\]} attributes allow local vectors or arrays +calculated by a "fix"_fix.html to be output. The ID in the attribute +should be replaced by the actual ID of the fix that has been defined +previously in the input script. + +If {f_ID} is used as a attribute, then the local vector calculated by +the fix is printed. If {f_ID\[N\]} is used, then N must be in the +range from 1-M, which will print the Nth column of the M-length local +array calculated by the fix. + +:line + +This section explains the atom attributes that can be specified as part of the {custom} and {cfg} styles. The {id}, {mol}, {type}, {mass}, {vx}, {vy}, {vz}, {fx}, {fy}, -{fz}, {q} keywords are self-explanatory. +{fz}, {q} attributes are self-explanatory. {Id} is the atom ID. {Mol} is the molecule ID, included in the data file for molecular systems. {Type} is the atom type. {Mass} is the @@ -266,7 +319,7 @@ atom mass. {Vx}, {vy}, {vz}, {fx}, {fy}, {fz}, and {q} are components of atom velocity and force and atomic charge. There are several options for outputting atom coordinates. The {x}, -{y}, {z} keywords write atom coordinates "unscaled", in the +{y}, {z} attributes write atom coordinates "unscaled", in the appropriate distance "units"_units.html (Angstroms, sigma, etc). Use {xs}, {ys}, {zs} if you want the coordinates "scaled" to the box size, so that each value is 0.0 to 1.0. If the simluation box is triclinic @@ -278,57 +331,58 @@ the coordinate would be if it had not been wrapped back into the periodic box. Note that using {xu}, {yu}, {zu} means that the coordinate values may be far outside the box bounds printed with the snapshot. The image flags can be printed directly using the {ix}, -{iy}, {iz} keywords. The "dump_modify"_dump_modify.html command +{iy}, {iz} attributes. The "dump_modify"_dump_modify.html command describes in more detail what is meant by scaled vs unscaled coordinates and the image flags. -The {mux}, {muy}, {muz} keywords are specific to dipolar systems +The {mux}, {muy}, {muz} attributes are specific to dipolar systems defined with an atom style of {dipole}. They give the orientation of the atom's point dipole moment. -The {radius} keyword is specific to extended spherical particles +The {radius} attribute is specific to extended spherical particles that have a finite size, such as granular particles defined with an atom style of {granular}. -The {omegax}, {omegay}, and {omegaz} keywords are specific to extended +The {omegax}, {omegay}, and {omegaz} attributes are specific to extended spherical or aspherical particles that have an angular velocity. Only certain atom styles, such as {granular} or {dipole} define this quantity. -The {angmomx}, {angmomy}, and {angmomz} keywords are specific to +The {angmomx}, {angmomy}, and {angmomz} attributes are specific to extended aspherical particles that have an angular momentum. Only the {ellipsoid} atom style defines this quantity. -The {quatw}, {quati}, {quatj}, {quatk} keywords are for aspherical +The {quatw}, {quati}, {quatj}, {quatk} attributes are for aspherical particles defined with an atom style of {ellipsoid}. They are the components of the quaternion that defines the orientation of the particle. -The {tqx}, {tqy}, {tqz} keywords are for extended spherical or +The {tqx}, {tqy}, {tqz} attributes are for extended spherical or aspherical particles that can sustain a rotational torque due to interactions with other particles. -The {c_ID} and {c_ID\[N\]} keywords allow scalar or vector per-atom -quantities calculated by a "compute"_compute.html to be output. The -ID in the keyword should be replaced by the actual ID of the compute -that has been defined previously in the input script. See the -"compute"_compute.html command for details. There are per-atom -computes for calculating the energy, stress, centro-symmetry -parameter, and coordination number of individual atoms. +The {c_ID} and {c_ID\[N\]} attributes allow per-atom vectors or arrays +calculated by a "compute"_compute.html to be output. The ID in the +attribute should be replaced by the actual ID of the compute that has +been defined previously in the input script. See the +"compute"_compute.html command for details. There are computes for +calculating the per-atom energy, stress, centro-symmetry parameter, +and coordination number of individual atoms. -Note that computes which calculate global scalar and vector -quantities, as opposed to per-atom quantities, cannot be output in a -dump. Instead, these quantities can be output by the "thermo_style -custom"_thermo_style.html command. +Note that computes which calculate global or local quantities, as +opposed to per-atom quantities, cannot be output in a dump custom +command. Instead, global quantities can be output by the +"thermo_style custom"_thermo_style.html command, and local quantities +can be output by the dump local command. -If {c_ID} is used as a keyword, then the scalar per-atom quantity -calculated by the compute is printed. If {c_ID\[N\]} is used, then N -must be in the range from 1-M, which will print the Nth column of -the M-length per-atom array calculated by the compute. +If {c_ID} is used as a attribute, then the per-atom vector calculated +by the compute is printed. If {c_ID\[N\]} is used, then N must be in +the range from 1-M, which will print the Nth column of the M-length +per-atom array calculated by the compute. -The {f_ID} and {f_ID\[N\]} keywords allow scalar or vector per-atom +The {f_ID} and {f_ID\[N\]} attributes allow vector or array per-atom quantities calculated by a "fix"_fix.html to be output. The ID in the -keyword should be replaced by the actual ID of the fix that has been +attribute should be replaced by the actual ID of the fix that has been defined previously in the input script. The "fix ave/atom"_fix_ave_atom.html command is one that calculates per-atom quantities. Since it can time-average per-atom quantities produced by @@ -336,20 +390,21 @@ any "compute"_compute.html, "fix"_fix.html, or atom-style "variable"_variable.html, this allows those time-averaged results to be written to a dump file. -If {f_ID} is used as a keyword, then the scalar per-atom quantity -calculated by the fix is printed. If {f_ID\[N\]} is used, then N must -be in the range from 1-M, which will print the Nth column of the -M-length per-atom array calculated by the fix. +If {f_ID} is used as a attribute, then the per-atom vector calculated +by the fix is printed. If {f_ID\[N\]} is used, then N must be in the +range from 1-M, which will print the Nth column of the M-length +per-atom array calculated by the fix. -The {v_name} keyword allows per-atom quantities calculated by a -"variable"_variable.html to be output. The name in the keyword should -be replaced by the actual name of the variable that has been defined -previously in the input script. Only an atom-style variable can be -referenced, since it is the only style that generates per-atom values. -Variables of style {atom} can reference individual atom attributes, -per-atom atom attributes, thermodynamic keywords, or invoke other -computes, fixes, or variables when they are evaluated, so this is a -very general means of creating quantities to output to a dump file. +The {v_name} attribute allows per-atom vectors calculated by a +"variable"_variable.html to be output. The name in the attribute +should be replaced by the actual name of the variable that has been +defined previously in the input script. Only an atom-style variable +can be referenced, since it is the only style that generates per-atom +values. Variables of style {atom} can reference individual atom +attributes, per-atom atom attributes, thermodynamic keywords, or +invoke other computes, fixes, or variables when they are evaluated, so +this is a very general means of creating quantities to output to a +dump file. See "this section"_Section_modify.html of the manual for information on how to add new compute and fix styles to LAMMPS to calculate @@ -363,10 +418,6 @@ To write gzipped dump files, you must compile LAMMPS with the -DLAMMPS_GZIP option - see the "Making LAMMPS"_Section_start.html#2_2 section of the documentation. -The {bond} style is part of the "molecular" package. It is only -enabled if LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#2_3 section for more info. - The {xtc} style is part of the "xtc" package. It is only enabled if LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#2_3 section for more info. This is because