x,y,z,vx,vy,vz,fx,fy,fz = atom attribute (position, velocity, force component)
c_ID = per-atom or local vector calculated by a compute with ID
-c_ID[I] = Ith column of per-atom or local array calculated by a compute with ID
+c_ID[I] = Ith column of per-atom or local array calculated by a compute with ID, I can include wildcard (see below)
f_ID = per-atom or local vector calculated by a fix with ID
-f_ID[I] = Ith column of per-atom or local array calculated by a fix with ID
+f_ID[I] = Ith column of per-atom or local array calculated by a fix with ID, I can include wildcard (see below)
v_name = per-atom vector calculated by an atom-style variable with name
compute 1 all reduce sum c_force
compute 1 all reduce/region subbox sum c_force
compute 2 all reduce min c_press[2] f_ave v_myKE
+compute 2 all reduce min c_press[*] f_ave v_myKE
compute 3 fluid reduce max c_index[1] c_index[2] c_dist replace 1 3 replace 2 3
Note that for values from a compute or fix, the bracketed index I can +be specified using a wildcard asterisk with the index to effectively +specify multiple values. This takes the form “*” or “n” or “n” or +“m*n”. If N = the size of the vector (for mode = scalar) or the +number of columns in the array (for mode = vector), then an asterisk +with no numeric values means all indices from 1 to N. A leading +asterisk means all indices from 1 to n (inclusive). A trailing +asterisk means all indices from n to N (inclusive). A middle asterisk +means all indices from m to n (inclusive).
+Using a wildcard is the same as if the individual columns of the array +had been listed one by one. E.g. these 2 compute reduce commands are +equivalent, since the compute stress/atom +command creates a per-atom array with 6 columns:
+compute myPress all stress/atom NULL
+compute 2 all reduce min myPress[*]
+compute 2 all reduce min myPress[1] myPress[2] myPress[3] &
+ myPress[4] myPress[5] myPress[6]
+The atom attribute values (x,y,z,vx,vy,vz,fx,fy,fz) are self-explanatory. Note that other atom attributes can be used as inputs to this fix by using the compute property/atom command and then specifying @@ -219,7 +240,9 @@ per-atom or local quantities. See the individual is appended, the vector calculated by the compute is used. If a bracketed integer is appended, the Ith column of the array calculated by the compute is used. Users can also write code for their own -compute styles and add them to LAMMPS.
+compute styles and add them to LAMMPS. See the +discussion above for how I can be specified with a wildcard asterisk +to effectively specify multiple values.If a value begins with “f_”, a fix ID must follow which has been previously defined in the input script. Fixes can generate per-atom or local quantities. See the individual fix doc page for @@ -228,7 +251,9 @@ timesteps, which must be compatible with when compute reduce references the values, else an error results. If no bracketed integer is appended, the vector calculated by the fix is used. If a bracketed integer is appended, the Ith column of the array calculated by the fix -is used. Users can also write code for their own fix style and add them to LAMMPS.
+is used. Users can also write code for their own fix style and add them to LAMMPS. See the discussion above for how +I can be specified with a wildcard asterisk to effectively specify +multiple values.If a value begins with “v_”, a variable name must follow which has been previously defined in the input script. It must be an atom-style variable. Atom-style variables can diff --git a/doc/html/dump.html b/doc/html/dump.html index 645ae1814d..fc5f4c89c6 100644 --- a/doc/html/dump.html +++ b/doc/html/dump.html @@ -188,12 +188,12 @@
local args = list of local attributes
- possible attributes = index, c_ID, c_ID[N], f_ID, f_ID[N]
+ possible attributes = index, c_ID, c_ID[I], f_ID, f_ID[I]
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
+ c_ID[I] = Ith column of local array calculated by a compute with ID, I can include wildcard (see below)
f_ID = local vector calculated by a fix with ID
- f_ID[N] = Nth column of local array calculated by a fix with ID
+ f_ID[I] = Ith column of local array calculated by a fix with ID, I can include wildcard (see below)
custom or custom/gz or custom/mpiio args = list of atom attributes @@ -229,9 +229,9 @@ omegax,omegay,omegaz = angular velocity of spherical particle angmomx,angmomy,angmomz = angular momentum of aspherical particle tqx,tqy,tqz = torque on finite-size particles 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 +c_ID[I] = Ith column of per-atom array calculated by a compute with ID, I can include wildcard (see below) 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 +f_ID[I] = Ith column of per-atom array calculated by a fix with ID, I can include wildcard (see below) v_name = per-atom vector calculated by an atom-style variable with name d_name = per-atom floating point vector with name, managed by fix property/atom i_name = per-atom integer vector with name, managed by fix property/atom @@ -246,6 +246,7 @@ i_name = per-atom integer vector with name, managed by fix property/atom dump 2 subgroup atom 50 dump.run.mpiio.bin 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 4b flow custom 100 dump.%.myforce id type c_myF[*] v_ke dump 2 inner cfg 10 dump.snap.*.cfg mass type xs ys zs vx vy vz dump snap all cfg 100 dump.config.*.cfg mass type xs ys zs id type c_Stress[2] dump 1 all xtc 1000 file.xtc @@ -530,6 +531,28 @@ be about 3x smaller than the text version, but will also take longer to write. This option is not available for the dcd and xtc styles.
+Note that in the discussion which follows, for styles which can +reference values from a compute or fix, like the custom, cfg, or +local styles, the bracketed index I can be specified using a +wildcard asterisk with the index to effectively specify multiple +values. This takes the form “*” or “n” or “n” or “m*n”. If N = the +size of the vector (for mode = scalar) or the number of columns in +the array (for mode = vector), then an asterisk with no numeric +values means all indices from 1 to N. A leading asterisk means all +indices from 1 to n (inclusive). A trailing asterisk means all +indices from n to N (inclusive). A middle asterisk means all indices +from m to n (inclusive).
+Using a wildcard is the same as if the individual columns of the array +had been listed one by one. E.g. these 2 dump commands are +equivalent, since the compute stress/atom +command creates a per-atom array with 6 columns:
+++compute myPress all stress/atom NULL +dump 2 all custom 100 tmp.dump id myPress[*] +dump 2 all custom 100 tmp.dump id myPress[1] myPress[2] myPress[3] & + myPress[4] myPress[5] myPress[6] +
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 @@ -540,7 +563,7 @@ 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 +
The c_ID and c_ID[I] 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 @@ -552,19 +575,23 @@ 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 +the compute is printed. If c_ID[I] is used, then I must be in the +range from 1-M, which will print the Ith column of the local array +with M columns calculated by the compute. See the discussion above +for how I can be specified with a wildcard asterisk to effectively +specify multiple values.
+The f_ID and f_ID[I] 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.
-Here is an example of how to dump bond info for a system, -including the distance and energy of each bond:
+the fix is printed. If f_ID[I] is used, then I must be in the +range from 1-M, which will print the Ith column of the local with M +columns calculated by the fix. See the discussion above for how I can +be specified with a wildcard asterisk to effectively specify multiple +values. +Here is an example of how to dump bond info for a system, including +the distance and energy of each bond:
@@ -232,14 +232,32 @@ global quantity. Note that the fix ave/time command. +@@ -171,13 +172,33 @@ component) or can be the result of a fix ave/time command. +compute 1 all property/local batom1 batom2 btype compute 2 all bond/local dist eng dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_1[3] c_2[1] c_2[2] @@ -627,7 +654,7 @@ the ellipsoid atom style defines this quantity.The tqx, tqy, tqz attributes are for finite-size particles that can sustain a rotational torque due to interactions with other particles.
-The c_ID and c_ID[N] attributes allow per-atom vectors or arrays +
The c_ID and c_ID[I] 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 @@ -640,10 +667,12 @@ 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 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] attributes allow vector or array per-atom +by the compute is printed. If c_ID[I] is used, then I must be in +the range from 1-M, which will print the Ith column of the per-atom +array with M columns calculated by the compute. See the discussion +above for how I can be specified with a wildcard asterisk to +effectively specify multiple values.
+The f_ID and f_ID[I] attributes allow vector or array per-atom quantities 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. The fix ave/atom command is one that calculates per-atom @@ -652,9 +681,11 @@ any compute< variable, this allows those time-averaged results to be written to a dump file.
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.
+by the fix is printed. If f_ID[I] is used, then I must be in the +range from 1-M, which will print the Ith column of the per-atom array +with M columns calculated by the fix. See the discussion above for +how I can be specified with a wildcard asterisk to effectively specify +multiple values.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 diff --git a/doc/html/fix_ave_atom.html b/doc/html/fix_ave_atom.html index 713d147446..8b348181c6 100644 --- a/doc/html/fix_ave_atom.html +++ b/doc/html/fix_ave_atom.html @@ -142,9 +142,9 @@ one or more input values can be listed
@@ -153,6 +153,7 @@ one or more input values can be listedx,y,z,vx,vy,vz,fx,fy,fz = atom attribute (position, velocity, force component) c_ID = per-atom vector calculated by a compute with ID -c_ID[I] = Ith column of per-atom array calculated by a compute with ID +c_ID[I] = Ith column of per-atom array calculated by a compute with ID, I can include wildcard (see below) f_ID = per-atom vector calculated by a fix with ID -f_ID[I] = Ith column of per-atom array calculated by a fix with ID +f_ID[I] = Ith column of per-atom array calculated by a fix with ID, I can include wildcard (see below) v_name = per-atom vector calculated by an atom-style variable with nameExamples
fix 1 all ave/atom 1 100 100 vx vy vz fix 1 all ave/atom 10 20 1000 c_my_stress[1] +fix 1 all ave/atom 10 20 1000 c_my_stress[*]Each per-atom value of each input vector is averaged independently.
Computes that produce per-atom vectors or arrays are those which have the word atom in their style name. See the doc pages for individual fixes to determine which ones produce per-atom vectors or arrays. Variables of style atom are the only ones that can be used with this fix since they produce per-atom vectors.
-Each per-atom value of each input vector is averaged independently.
+Note that for values from a compute or fix, the bracketed index I can +be specified using a wildcard asterisk with the index to effectively +specify multiple values. This takes the form “*” or “n” or “n” or +“m*n”. If N = the size of the vector (for mode = scalar) or the +number of columns in the array (for mode = vector), then an asterisk +with no numeric values means all indices from 1 to N. A leading +asterisk means all indices from 1 to n (inclusive). A trailing +asterisk means all indices from n to N (inclusive). A middle asterisk +means all indices from m to n (inclusive).
+Using a wildcard is the same as if the individual columns of the array +had been listed one by one. E.g. these 2 fix ave/atom commands are +equivalent, since the compute stress/atom +command creates a per-atom array with 6 columns:
++compute my_stress all stress/atom NULL +fix 1 all ave/atom 10 20 1000 c_my_stress[*] +fix 1 all ave/atom 10 20 1000 c_my_stress[1] c_my_stress[1] & + c_my_stress[3] c_my_stress[4] & + c_my_stress[5] c_my_stress[6] +
The Nevery, Nrepeat, and Nfreq arguments specify on what timesteps the input values will be used in order to contribute to the @@ -212,7 +233,9 @@ previously defined in the input script. If no bracketed term is appended, the per-atom vector calculated by the compute is used. If a bracketed term containing an index I is appended, the Ith column of the per-atom array calculated by the compute is used. Users can also -write code for their own compute styles and add them to LAMMPS.
+write code for their own compute styles and add them to LAMMPS. See the discussion above for how I can +be specified with a wildcard asterisk to effectively specify multiple +values.If a value begins with “f_”, a fix ID must follow which has been previously defined in the input script. If no bracketed term is appended, the per-atom vector calculated by the fix is used. If a @@ -220,7 +243,9 @@ bracketed term containing an index I is appended, the Ith column of the per-atom array calculated by the fix is used. Note that some fixes only produce their values on certain timesteps, which must be compatible with Nevery, else an error will result. Users can also -write code for their own fix styles and add them to LAMMPS.
+write code for their own fix styles and add them to LAMMPS. See the discussion above for how I can +be specified with a wildcard asterisk to effectively specify multiple +values.If a value begins with “v_”, a variable name must follow which has been previously defined in the input script as an atom-style variable Variables of style atom can reference thermodynamic keywords, or invoke other computes, fixes, or variables diff --git a/doc/html/fix_ave_chunk.html b/doc/html/fix_ave_chunk.html index dc2732aafd..69b4b9a5e0 100644 --- a/doc/html/fix_ave_chunk.html +++ b/doc/html/fix_ave_chunk.html @@ -145,9 +145,9 @@ density/number, density/mass = number or mass density temp = temperature c_ID = per-atom vector calculated by a compute with ID -c_ID[I] = Ith column of per-atom array calculated by a compute with ID +c_ID[I] = Ith column of per-atom array calculated by a compute with ID, I can include wildcard (see below) f_ID = per-atom vector calculated by a fix with ID -f_ID[I] = Ith column of per-atom array calculated by a fix with ID +f_ID[I] = Ith column of per-atom array calculated by a fix with ID, I can include wildcard (see below) v_name = per-atom vector calculated by an atom-style variable with name
The per-atom values of each input vector are summed and averaged +independently of the per-atom values in other input vectors.
Computes that produce per-atom quantities are those which have the word atom in their style name. See the doc pages for individual fixes to determine which ones produce per-atom quantities. Variables of style atom are the only 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.
+Note that for values from a compute or fix, the bracketed index I can +be specified using a wildcard asterisk with the index to effectively +specify multiple values. This takes the form “*” or “n” or “n” or +“m*n”. If N = the size of the vector (for mode = scalar) or the +number of columns in the array (for mode = vector), then an asterisk +with no numeric values means all indices from 1 to N. A leading +asterisk means all indices from 1 to n (inclusive). A trailing +asterisk means all indices from n to N (inclusive). A middle asterisk +means all indices from m to n (inclusive).
+Using a wildcard is the same as if the individual elements of the +vector or columns of the array had been listed one by one. E.g. these +2 fix ave/chunk commands are equivalent, since the compute property/atom command creates, in this +case, a per-atom array with 3 columns:
++compute myAng all property/atom 50 angmomx angmomy angmomz +fix 1 all ave/chunk 100 1 100 cc1 c_myAng[*] file tmp.angmom +fix 2 all ave/chunk 100 1 100 cc1 c_myAng[1] c_myAng[2] c_myAng[3] file tmp.angmom ++Note
This fix works by creating an array of size Nchunk by Nvalues @@ -336,7 +354,9 @@ previously defined in the input script. If no bracketed integer is appended, the per-atom vector calculated by the compute is used. If a bracketed integer is appended, the Ith column of the per-atom array calculated by the compute is used. Users can also write code for -their own compute styles and add them to LAMMPS.
+their own compute styles and add them to LAMMPS. +See the discussion above for how I can be specified with a wildcard +asterisk to effectively specify multiple values.If a value begins with “f_”, a fix ID must follow which has been previously defined in the input script. If no bracketed integer is appended, the per-atom vector calculated by the fix is used. If a @@ -344,7 +364,9 @@ bracketed integer is appended, the Ith column of the per-atom array calculated by the fix is used. Note that some fixes only produce their values on certain timesteps, which must be compatible with Nevery, else an error results. Users can also write code for their -own fix styles and add them to LAMMPS.
+own fix styles and add them to LAMMPS. See the +discussion above for how I can be specified with a wildcard asterisk +to effectively specify multiple values.If a value begins with “v_”, a variable name must follow which has been previously defined in the input script. Variables of style atom can reference thermodynamic keywords and various per-atom diff --git a/doc/html/fix_ave_correlate.html b/doc/html/fix_ave_correlate.html index a949f45708..5386d0dd57 100644 --- a/doc/html/fix_ave_correlate.html +++ b/doc/html/fix_ave_correlate.html @@ -141,9 +141,9 @@
value = c_ID, c_ID[N], f_ID, f_ID[N], v_name @@ -186,6 +186,7 @@ type upper ave running title1 "My correlation data"c_ID = global scalar calculated by a compute with ID -c_ID[I] = Ith component of global vector calculated by a compute with ID +c_ID[I] = Ith component of global vector calculated by a compute with ID, I can include wildcard (see below) f_ID = global scalar calculated by a fix with ID -f_ID[I] = Ith component of global vector calculated by a fix with ID +f_ID[I] = Ith component of global vector calculated by a fix with ID, I can include wildcard (see below) v_name = global value calculated by an equal-style variable with name v_name[I] = Ith component of a vector-style variable with namefix 1 all ave/correlate 1 50 10000 c_thermo_press[*]
Description
@@ -208,6 +209,9 @@ you wish to spatial- or time-average or histogram per-atom quantities from a compute, fix, or variable, then see the fix ave/chunk, fix ave/atom, or fix ave/histo commands. If you wish to convert a per-atom quantity into a single global value, see the compute reduce command. +The input values must either be all scalars. What kinds of +correlations between input values are calculated is determined by the +type keyword as discussed below.
Computes that produce global quantities are those which do not have the word atom in their style name. Only a few fixes produce global quantities. See the doc pages for @@ -215,9 +219,26 @@ individual fixes for info on which ones produce such values. Variables of style equal and vector are the only ones that can be used with this fix. Variables of style atom cannot be used, since they produce per-atom values.
-The input values must either be all scalars. What kinds of -correlations between input values are calculated is determined by the -type keyword as discussed below.
+Note that for values from a compute or fix, the bracketed index I can +be specified using a wildcard asterisk with the index to effectively +specify multiple values. This takes the form “*” or “n” or “n” or +“m*n”. If N = the size of the vector (for mode = scalar) or the +number of columns in the array (for mode = vector), then an asterisk +with no numeric values means all indices from 1 to N. A leading +asterisk means all indices from 1 to n (inclusive). A trailing +asterisk means all indices from n to N (inclusive). A middle asterisk +means all indices from m to n (inclusive).
+Using a wildcard is the same as if the individual elements of the +vector had been listed one by one. E.g. these 2 fix ave/correlate +commands are equivalent, since the compute pressure command creates a global vector with 6 +values.
++compute myPress all pressure NULL +fix 1 all ave/correlate 1 50 10000 c_myPress[*] +fix 1 all ave/correlate 1 50 10000 & + c_myPress[1] c_myPress[2] c_myPress[3] & + c_myPress[4] c_myPress[5] c_myPress[6] +
The Nevery, Nrepeat, and Nfreq arguments specify on what timesteps the input values will be used to calculate correlation data. @@ -255,7 +276,9 @@ default, then Nfreq >= (Nrepeat-1)*Nevery is requi previously defined in the input script. If no bracketed term is appended, the global scalar calculated by the compute is used. If a bracketed term is appended, the Ith element of the global vector -calculated by the compute is used.
+calculated by the compute is used. See the discussion above for how I +can be specified with a wildcard asterisk to effectively specify +multiple values.Note that there is a compute reduce command which can sum per-atom quantities into a global scalar or vector which can thus be accessed by fix ave/correlate. Or it can be a compute @@ -267,7 +290,9 @@ write code for their own compute styles and add them to LAMMPS.
diff --git a/doc/html/fix_ave_histo.html b/doc/html/fix_ave_histo.html index 48a236b5b0..4935a91c00 100644 --- a/doc/html/fix_ave_histo.html +++ b/doc/html/fix_ave_histo.html @@ -147,9 +147,9 @@@@ -187,6 +187,7 @@x,y,z,vx,vy,vz,fx,fy,fz = atom attribute (position, velocity, force component) c_ID = scalar or vector calculated by a compute with ID -c_ID[I] = Ith component of vector or Ith column of array calculated by a compute with ID +c_ID[I] = Ith component of vector or Ith column of array calculated by a compute with ID, I can include wildcard (see below) f_ID = scalar or vector calculated by a fix with ID -f_ID[I] = Ith component of vector or Ith column of array calculated by a fix with ID +f_ID[I] = Ith component of vector or Ith column of array calculated by a fix with ID, I can include wildcard (see below) v_name = value(s) calculated by an equal-style or vector-style or atom-style variable with name v_name[I] = value calculated by a vector-style variable with nameExamples
@@ -194,9 +195,9 @@fix 1 all ave/histo 100 5 1000 0.5 1.5 50 c_myTemp file temp.histo ave running fix 1 all ave/histo 100 5 1000 -5 5 100 c_thermo_press[2] c_thermo_press[3] title1 "My output values" +fix 1 all ave/histo 100 5 1000 -5 5 100 c_thermo_press[*] fix 1 all ave/histo 1 100 1000 -2.0 2.0 18 vx vy vz mode vector ave running beyond extra fix 1 all ave/histo/weight 1 1 1 10 100 2000 c_XRD[1] c_XRD[2]Description
-Use one or more values as inputs every few timesteps, histogram them, -and average the histogram over longer timescales. The resulting -histogram can be used by other output commands, and can also be written to a +
Use one or more values as inputs every few timesteps to create a +single histogram. The histogram can then be averaged over longer +timescales. The resulting histogram can be used by other output commands, and can also be written to a file. The fix ave/histo/weight command has identical syntax to fix ave/histo, except that exactly two values must be specified. See details below.
@@ -218,18 +219,33 @@ different kinds (e.g. global and per-atom) cannot be mixed. Atom attributes are per-atom vector values. See the doc page for individual “compute” and “fix” commands to see what kinds of quantities they generate. -The input values must either be all scalars or all vectors (or -arrays), depending on the setting of the mode keyword.
Note that the output of this command is a single histogram for all input values combined together, not one histogram per input value. See below for details on the format of the output of this fix.
-If mode = vector, then the input values may either be vectors or -arrays. If a global array is listed, then it is the same as if the -individual columns of the array had been listed one by one. -E.g. these 2 fix ave/histo commands are equivalent, since the compute com/chunk command creates a global array -with 3 columns:
+The input values must either be all scalars or all vectors (or +arrays), depending on the setting of the mode keyword.
+If mode = scalar, then the input values must be scalars, or vectors +with a bracketed term appended, indicating the Ith value of the vector +is used.
+If mode = vector, then the input values must be vectors, or arrays +with a bracketed term appended, indicating the Ith column of the array +is used. All vectors must be the same length, which is the length of +the vector or number of rows in the array.
+Note that for values from a compute or fix, the bracketed index I can +be specified using a wildcard asterisk with the index to effectively +specify multiple values. This takes the form “*” or “n” or “n” or +“m*n”. If N = the size of the vector (for mode = scalar) or the +number of columns in the array (for mode = vector), then an asterisk +with no numeric values means all indices from 1 to N. A leading +asterisk means all indices from 1 to n (inclusive). A trailing +asterisk means all indices from n to N (inclusive). A middle asterisk +means all indices from m to n (inclusive).
+Using a wildcard is the same as if the individual elements of the +vector or columns of the array had been listed one by one. E.g. these +2 fix ave/histo commands are equivalent, since the compute com/chunk command creates a global array with +3 columns:
@@ -268,11 +284,11 @@ no bracketed term is appended, the global scalar calculated by the compute is used. If a bracketed term is appended, the Ith element of the global vector calculated by the compute is used. If mode = vector, then if no bracketed term is appended, the global or per-atom -or local vector calculated by the compute is used. Or if the compute -calculates an array, all of the columns of the array are used as if -they had been specified as individual vectors (see description above). -If a bracketed term is appended, the Ith column of the global or -per-atom or local array calculated by the compute is used. +or local vector calculated by the compute is used. If a bracketed +term is appended, the Ith column of the global or per-atom or local +array calculated by the compute is used. See the discussion above for +how I can be specified with a wildcard asterisk to effectively specify +multiple values.compute myCOM all com/chunk -fix 1 all ave/histo 100 1 100 c_myCOM file tmp1.com mode vector +fix 1 all ave/histo 100 1 100 c_myCOM[*] file tmp1.com mode vector fix 2 all ave/histo 100 1 100 c_myCOM[1] c_myCOM[2] c_myCOM[3] file tmp2.com mode vectorNote that there is a compute reduce command which can sum per-atom quantities into a global scalar or vector which can thus be accessed by fix ave/histo. Or it can be a compute defined @@ -285,11 +301,11 @@ no bracketed term is appended, the global scalar calculated by the fix is used. If a bracketed term is appended, the Ith element of the global vector calculated by the fix is used. If mode = vector, then if no bracketed term is appended, the global or per-atom or local -vector calculated by the fix is used. Or if the fix calculates an -array, all of the columns of the array are used as if they had been -specified as individual vectors (see description above). If a -bracketed term is appended, the Ith column of the global or per-atom -or local array calculated by the fix is used.
+vector calculated by the fix is used. If a bracketed term is +appended, the Ith column of the global or per-atom or local array +calculated by the fix is used. See the discussion above for how I can +be specified with a wildcard asterisk to effectively specify multiple +values.Note that some fixes only produce their values on certain timesteps, which must be compatible with Nevery, else an error will result. Users can also write code for their own fix styles and add them to LAMMPS.
diff --git a/doc/html/fix_ave_time.html b/doc/html/fix_ave_time.html index 8dd384e812..6c6744c5e6 100644 --- a/doc/html/fix_ave_time.html +++ b/doc/html/fix_ave_time.html @@ -140,10 +140,10 @@one or more input values can be listed value = c_ID, c_ID[N], f_ID, f_ID[N], v_name -c_ID = global scalar, vector, or array calculated by a compute with ID -c_ID[I] = Ith component of global vector or Ith column of global array calculated by a compute with ID -f_ID = global scalar, vector, or array calculated by a fix with ID -f_ID[I] = Ith component of global vector or Ith column of global array calculated by a fix with ID +@@ -255,6 +256,28 @@ if your input script specifies a thermo_style command, you should use the thermo_modify command after it.@@ -182,6 +182,7 @@c_ID = global scalar or vector calculated by a compute with ID +c_ID[I] = Ith component of global vector or Ith column of global array calculated by a compute with ID, I can include wildcard (see below) +f_ID = global scalar or vector calculated by a fix with ID +f_ID[I] = Ith component of global vector or Ith column of global array calculated by a fix with ID, I can include wildcard (see below) v_name = value(s) calculated by an equal-style or vector-style variable with name v_name[I] = value calculated by a vector-style variable with name@@ -213,20 +214,33 @@ individual fixes for info on which ones produce such values. Variables of style equal and vector are the only ones that can be used with this fix. Variables of style atom cannot be used, since they produce per-atom values. -fix 1 all ave/time 100 5 1000 c_myTemp c_thermo_temp file temp.profile fix 1 all ave/time 100 5 1000 c_thermo_press[2] ave window 20 & title1 "My output values" +fix 1 all ave/time 100 5 1000 c_thermo_press[*] fix 1 all ave/time 1 100 1000 f_indent f_indent[1] file temp.indent off 1The input values must either be all scalars or all vectors (or -arrays), depending on the setting of the mode keyword. In both -cases, the averaging is performed independently on each input value. -I.e. each input scalar is averaged independently and each element of -each input vector (or array) is averaged independently.
-If mode = vector, then the input values may either be vectors or -arrays and all must be the same “length”, which is the length of the -vector or number of rows in the array. If a global array is listed, -then it is the same as if the individual columns of the array had been -listed one by one. E.g. these 2 fix ave/time commands are equivalent, -since the compute rdf command creates, in this -case, a global array with 3 columns, each of length 50:
+The input values must either be all scalars or all vectors depending +on the setting of the mode keyword. In both cases, the averaging is +performed independently on each input value. I.e. each input scalar +is averaged independently or each element of each input vector is +averaged independently.
+If mode = scalar, then the input values must be scalars, or vectors +with a bracketed term appended, indicating the Ith value of the vector +is used.
+If mode = vector, then the input values must be vectors, or arrays +with a bracketed term appended, indicating the Ith column of the array +is used. All vectors must be the same length, which is the length of +the vector or number of rows in the array.
+Note that for values from a compute or fix, the bracketed index I can +be specified using a wildcard asterisk with the index to effectively +specify multiple values. This takes the form “*” or “n” or “n” or +“m*n”. If N = the size of the vector (for mode = scalar) or the +number of columns in the array (for mode = vector), then an asterisk +with no numeric values means all indices from 1 to N. A leading +asterisk means all indices from 1 to n (inclusive). A trailing +asterisk means all indices from n to N (inclusive). A middle asterisk +means all indices from m to n (inclusive).
+Using a wildcard is the same as if the individual elements of the +vector or columns of the array had been listed one by one. E.g. these +2 fix ave/time commands are equivalent, since the compute rdf command creates, in this case, a global array +with 3 columns, each of length 50:
@@ -253,11 +267,10 @@ no bracketed term is appended, the global scalar calculated by the compute is used. If a bracketed term is appended, the Ith element of the global vector calculated by the compute is used. If mode = vector, then if no bracketed term is appended, the global vector -calculated by the compute is used. Or if the compute calculates an -array, all of the columns of the global array are used as if they had -been specified as individual vectors (see description above). If a -bracketed term is appended, the Ith column of the global array -calculated by the compute is used. +calculated by the compute is used. If a bracketed term is appended, +the Ith column of the global array calculated by the compute is used. +See the discussion above for how I can be specified with a wildcard +asterisk to effectively specify multiple values.compute myRDF all rdf 50 1 2 -fix 1 all ave/time 100 1 100 c_myRDF file tmp1.rdf mode vector +fix 1 all ave/time 100 1 100 c_myRDF[*] file tmp1.rdf mode vector fix 2 all ave/time 100 1 100 c_myRDF[1] c_myRDF[2] c_myRDF[3] file tmp2.rdf mode vectorNote that there is a compute reduce command which can sum per-atom quantities into a global scalar or vector which can thus be accessed by fix ave/time. Or it can be a compute defined @@ -270,10 +283,10 @@ no bracketed term is appended, the global scalar calculated by the fix is used. If a bracketed term is appended, the Ith element of the global vector calculated by the fix is used. If mode = vector, then if no bracketed term is appended, the global vector calculated by the -fix is used. Or if the fix calculates an array, all of the columns of -the global array are used as if they had been specified as individual -vectors (see description above). If a bracketed term is appended, the -Ith column of the global array calculated by the fix is used.
+fix is used. If a bracketed term is appended, the Ith column of the +global array calculated by the fix is used. See the discussion above +for how I can be specified with a wildcard asterisk to effectively +specify multiple values.Note that some fixes only produce their values on certain timesteps, which must be compatible with Nevery, else an error will result. Users can also write code for their own fix styles and add them to LAMMPS.
diff --git a/doc/html/searchindex.js b/doc/html/searchindex.js index da2bc97189..6e3c503661 100644 --- a/doc/html/searchindex.js +++ b/doc/html/searchindex.js @@ -1 +1 @@ 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7,40,63,96,163],comand:61,combiant:106,combin:[2,3,18,32,56,58,59,63,68,71,81,82,103,105,106,110,113,114,115,129,130,149,155,156,158,159,161],come:[0,2,13,62,68,77,78,139,155,156,158,159,163],comit:163,comm:[0,3,30,92,109,139],comm_modifi:[2,97,103,109,113,118],comm_styl:[19,60],comm_world:3,command:[0,1],comment:[3,46,65,74,79,92,93,111,112,114,115,121,134,141,142,143,148,149,155,156,157,158,159,163],commit:163,commmand:2,common:[0,1,2,3,4,30,62,71,81,82,118,120,155,156,158],commonli:[2,9,37,38,58,89,119,124,149,156,158],commun:[1,2,3,4,19,58,60,62,67,68,79,110],comp:[75,92,113,139,146,153,157],compar:[1,2,4,41,44,57,91,92,134,148],comparison:0,compart:90,compass:[6,20,47,57,82,102],compat:[3,19,50,60,63,80,137,139],compens:[2,113],compil:[4,58,137],complain:3,complement:134,complementari:[105,122],complet:[2,3,19,60,71,92,114],complex:[2,3,9,36,38,42,45,67,81,92,113,137],complic:[2,40],compon:[2,29,30,33,34,35,36,37,38,39,40,42,43,58,61,62,63,67,68,69,71,75,81,91,92,109,113,118,131,132,148,149],componenet:2,componennt:40,composit:[2,67,111],compound:[104,113,114,159],compress:[2,58,69,72],compris:[81,115,146],compton:[41,44],comput:[0,1],computation:[2,79,97],compute_modifi:[61,62,68,69],compute_sa:41,compute_xrd:44,concav:81,concentr:[65,74,111,115,142],concept:2,conceptu:[2,62,92,105,134],concern:[2,30,32,66],concis:3,concurr:4,conden:[79,156,158],condens:[2,79,94,107,111,122,159],condit:[2,39,41,43,44,58,59,67,69,70,72,75,76,79,110,113,119],conducit:2,conduct:0,confer:[4,137],configur:[1,2,4,58,62,71,91,92,94,97,112,134,137,155,156,158,159,163],conflict:[139,163],conform:[2,61,62,73,88,92,113],confus:159,conjuct:109,conjug:113,conjunct:[2,32,45,67,92,98,99,105,109,113,120,122,139,144,147],connect:[2,32,61,75,90,92,106,118,154,158],conner:94,connor:94,consecut:[3,45,105,122,126],consequ:[1,2,79,121],conserv:[13,61,66,67,68,74,75,92,108,109,110,118,128,148],consid:[2,29,32,40,60,61,79,113,146,148,154],consider:2,consist:[2,3,39,40,45,51,66,68,69,72,73,74,90,92,94,97,103,105,113,117,131,132,134,137,139,141,142,146,148],consistent_fe_initi:59,constant:0,constantli:63,constitu:[2,80,81,103,146],constrain:[2,63,66,75,76,91,113],constraint:[19,39,43,60,63,75,76,80,91,132],construct:[2,28,29,30,36,38,41,42,44,62,68,73,74,81,108,137,139,154,155],constructor:3,consult:4,consum:1,contact:[0,106,112,114,117,118,146],contain:[0,1,2,3,19,32,35,41,42,44,45,46,57,58,59,60,65,67,70,72,74,79,81,92,93,94,97,104,105,108,111,112,113,115,134,137,141,142,143,145,149,155,156,157,158,159,163],context:[2,4,161],contibut:29,contin:4,continu:[0,2,19,60,61,62,63,66,68,69,72,77,78,79,81,97,109,124,127,146,157],continuum:[2,59,79],contour_integr:59,contract:[62,68],contrain:75,contrast:[1,2,161],contrib:79,contribut:[2,29,32,33,34,35,39,42,43,62,67,75,91,92,109,111,113,131,132,137,139,148,163],control:[2,3,4,11,13,19,32,35,42,48,58,59,60,62,68,69,74,79,113,117,137,155,158],control_typ:59,convect:35,conveni:[2,13,149,163],convent:[13,50,55,57,73,111,113],converg:[2,19,58,60,61,62,69,72,73,75,91,92,104,105,122,148],convers:[42,58,105,106,107,113,122,126,130,144],convert:[2,5,6,8,12,16,17,18,35,45,47,58,82,83,87,88,92,93,111,137,156,158,162],convex:81,cool:63,coord:[2,3,36,38,40,70,80,92],coordb:148,coordbb:148,coordiat:91,coordin:[1,2,3,19,32,33,34,40,42,45,58,60,61,62,63,68,70,75,76,78,79,91,92,93,94,96,112,148],coords:148,copi:[0,3,58,79,92,163],copper:162,coprocessor:[1,4],core:[0,1],coreshel:2,coreshell:[2,99,105,107],cornel:[2,46],corner:[2,58,81,163],corpor:4,corr:104,correct:[2,3,32,46,58,63,68,72,80,81,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,111,112,113,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163],correction_max_iter:59,correctli:[3,68,75,81,92,107,132,137,163],correl:[2,35,36,42,66,71],correpond:65,correspond:[1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,29,32,39,40,41,42,44,46,47,48,49,50,51,52,53,54,55,56,58,62,63,65,67,68,69,70,71,74,75,80,81,82,83,84,86,87,88,89,92,93,94,95,98,99,100,101,102,103,104,105,108,109,111,112,113,114,115,116,117,118,119,120,122,123,124,125,126,127,128,129,130,131,134,135,137,139,140,142,143,144,145,146,147,148,149,150,155,156,157,158,159,160,161,162],correspondingli:[131,132],cosin:2,cosineshift:11,cost:[1,2,3,19,41,43,44,58,60,68,74,79,105,122,126,137,139,155],costheta0:[155,156,158,159],costheta:145,costli:[3,4],coul:[2,4,18,21,22,32,46,91],could:[2,3,19,32,34,39,58,60,72,79,80,81,91,94,116,120],coulomb:[2,43,91,98,99,100,101,102,104,105,106,107,108,113,118,119,122,126,130,133,139,144,147,148,158,159,161],coulommb:2,count:[1,2,3,19,35,46,60,68,75,81,91,92,116,120,139],counterbal:63,counterbalanc:13,counterclockwis:46,coupl:0,couple:[2,3],cours:[4,66,73,80,131,150],cov:148,coval:[2,13,113,134,148],cover:[2,59,67,113],cpp:[1,2,3,32,75],cpu:[1,4],cpuinfo:4,cr2:44,cr3:44,creat:[0,1,2,3,19,35,39,41,45,58,59,60,61,62,65,68,69,70,71,73,79,92,94,97,104,111,112,130,139,140,141,142,145,148,155,156,157,158,159,163],create_atom:[2,19,35],create_box:[2,19,35,45,62,68,154],create_elementset:59,create_faceset:59,create_nodeset:59,createatom:0,creation:45,criteria:[58,61,91],criterion:[19,45,60,61,91,92,104,113,118,148],critic:[2,24,25,79,91],cross:[4,33,40,58,92,101,109,111,119,120,122,124,126,145,147,156,158,162],crossov:1,crozier:0,crucial:72,crystal:[2,4,29,30,38,70,78],crystallin:[2,157],crystallogr:[41,44],crystallographi:[41,44],cs1:44,cs_chunk:2,csanyi:[42,149],cscl:134,csequ:2,csh:[3,4],cshrc:3,csic:[112,155,156,158,159],csinfo:2,csisi:[112,155,156,158,159],cst:111,cstherm:2,csvr:2,ctcm:[93,111],ctype:3,cu1:44,cu2:44,cu3au:134,cube:[2,81],cubes:[19,60],cubic:[38,67,70,111],cuda:1,cuh:97,cummul:[2,61,120],cumul:[2,68,69,92],current:[0,1,2,3,4,19,30,32,43,58,59,60,61,62,63,68,73,74,75,76,79,80,90,91,92,97,104,108,111,113,114,118,121,131,132,134,135,136,139,145,150,156,158,163],curv:[2,45],curvatur:[117,146,162],custom:[0,2,3,33,34,35,43,58,61,62,68,69,72,91,94,116,120],cut:[1,2,4,19],cuthi:70,cutinn:[131,132],cutlo:70,cutmax:145,cutoff1:[102,108,122,126,130,133,144,147],cutoff2:[98,99,100,102,107,108,122,126,130,133,144,147],cutoff:[2,4,21,22,28,29,30,32,36,38,42,61,65,70,72,80,81,91,93,94,95,96,97,98,99,100,101,102,103,105,106,107,108,109,110,111,112,113,114,115,116,117,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162],cutoffa:112,cutoffc:112,cuu3:111,cval:44,cvff:4,cwiggl:80,cyan:58,cycl:[68,69],cyclic:46,cylind:[58,81,90],cylinder_d:90,cylindr:2,cyrot:97,d3q15:67,d3q19:67,d_e:79,daan:78,damp:[2,68,69,72,91,92,98,99,101,105,108,113,118,122,130,144,147],dampflag:118,danger:109,darden:108,darken:58,dash:118,dat:[2,35,59],data2xmovi:0,data:1,databas:0,date:[0,2],datum:2,davenport:133,davi:80,david:[156,158],daw:[111,145],dcd:[2,58,71],deactiv:130,debug:[2,3,41,44,45,71,139],decai:[36,105,162],decid:[2,4,163],decod:58,decompos:[32,149],decomposit:[59,71],decoupl:2,decreas:[4,61,63],dedic:4,defect:[2,29,137],defin:[2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,64,65,67,68,69,70,71,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,94,95,96,98,99,100,101,102,103,105,106,108,109,110,112,113,115,116,117,118,119,120,122,123,124,125,126,127,128,129,130,131,132,133,137,138,139,140,141,142,143,144,145,146,147,149,150,151,152,153,154,155,156,157,158,159,160,161,162],definit:[2,42,64,69,80,97,103,110,113,145,149],deform:[2,43,62,68,131,132],deg2theta:44,degre:[2,5,6,8,12,13,16,17,18,36,38,39,44,45,46,47,49,50,55,56,58,61,68,69,71,73,75,78,82,83,87,88,89,91,108,111,120],delai:2,delet:[28,61,68,139,154,163],delete_atom:45,delete_bond:[20,21,22,23,24,25,26,27,28],delete_el:59,delimit:74,dellago:[2,63],deloc:[113,148],delr:134,delta_1:97,delta_3:97,delta_7:97,delta_ij:[134,145],delta_pi:97,delta_r:145,delta_sigma:97,deltah_f:65,demo:3,demonstr:[72,134],dendrim:120,dendtrit:90,denniston:67,denot:[41,63,105,119],dens:[61,74,113],densiti:[2,19,42,45,59,60,67,79,80,93,94,97,111,134,135,136,141,142,145,146,148,151,152,153],dent:90,depart:0,departur:72,depend:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,21,22,23,24,25,26,27,28,29,36,39,40,42,45,46,47,48,49,50,51,52,53,54,55,57,58,60,62,65,67,68,69,70,74,75,77,79,80,81,82,83,84,86,87,88,89,91,93,94,95,96,97,98,99,100,101,102,103,104,105,106,108,109,111,112,113,114,115,116,117,118,119,120,122,123,124,125,126,127,128,129,130,131,134,135,137,138,140,141,142,143,144,145,146,147,148,149,150,155,156,157,158,159,160,161,162],dependend:2,deposit:[68,75],depth:[26,58,79,115,117,146],der:[32,103,104,130,161],deriv:[2,32,42,62,63,68,69,70,77,78,79,80,81,94,97,103,108,113,114,119,124,128,129,134,137,161],derjagin:161,derlet:70,descib:58,describ:[0,1,2,3,4,19,29,30,41,42,43,44,45,51,54,60,61,62,65,66,67,68,69,70,71,72,74,77,78,80,91,92,94,96,98,99,101,102,103,104,105,108,111,113,114,115,117,118,119,122,123,124,125,126,127,128,129,130,131,132,133,134,137,138,141,142,145,146,147,148,149,150,154,155,156,157,158,159,160,161,162,163],descript:[2,3],descriptor:42,design:[0,2,3,41,44,59,61,68,70,79,95,96,101,105,107,113,130,131,132,135,136,145],desir:[2,3,4,35,39,43,45,62,66,68,75,91,92,109,111,120,131,132,155,156,158],desktop:[2,58],destabil:97,destre:88,destroi:3,detail:[1,2,3,4,19,34,35,39,40,42,43,45,57,58,59,60,61,62,63,66,67,68,69,72,75,78,79,90,91,93,94,96,97,100,101,102,103,104,105,108,109,113,114,117,118,119,120,122,123,124,125,126,127,128,129,130,131,132,133,134,138,139,141,142,146,148,149,150,160,161,163],detect:[36,92,104,120,121],determin:[1,2,4,26,32,39,40,41,43,44,45,58,60,62,65,68,70,71,72,73,74,80,81,94,100,104,108,111,115,116,118,126,134,137,139,142,146,148,154,161],devan:147,devanathan:158,develop:[0,2,3,4,69,72,94,97,113,136,137,148,159],deviat:[69,70,116],devic:1,devin:104,devis:136,dfactor:58,dft:137,dhug:72,dhugoniot:72,dia:134,diag:74,diagnost:[4,61,74],diagon:[2,40,42,43,62,68],diagonalstyl:149,diagram:[19,41,44,57,60,71],diallo:120,diam:58,diamet:[2,45,58,103,117,118,124,146,161],diamond:[113,134],dick:2,did:[91,109,111,118,139,156,158],dielectr:[101,105,106,107,122,126,130,144],diff:[2,4],differ:[1,2,3,4,19,28,29,32,36,42,45,57,58,60,61,62,63,66,67,68,70,71,72,75,76,77,78,79,80,81,82,92,93,94,97,100,101,103,104,109,110,111,113,115,117,118,119,122,123,125,126,133,134,135,136,138,139,140,141,142,143,145,146,147,148,149,150,155,156,158,159,161],differenti:[1,2,13,74,105,145,157],difficult:[62,71,120],difficulti:[36,38,75],diffract:[41,44],diffraction:[41,44],diffus:0,diffuse:2,digit:137,dihedr:[0,4,28,36,38,39,42,43,45,46,47,48,49,50,51,52,53,54,55,56,57,61,73,83,84,85,87,91,94,97,101],dihedral_coeff:[46,47,48,49,50,51,52,53,54,55,56,57],dihedral_cosine_shift_exp:11,dihedral_styl:[0,2,43],dihydrid:113,dij:75,dilat:[62,68,69],dim:[45,134],dimens:[1,2,19,35,40,43,45,58,60,62,67,68,69,72,80,92,139],dimension:[36,39,41,42,44,79,92,145],dimensionless:[37,42,79,149,161],dimer:[2,134],dimstr:[19,60],dintel_offload_noaffinity:4,dipol:0,dipolar:13,dipole:108,dir:[1,3,70,72,145],dirac:42,direc:145,direct:[2,4,13,29,38,41,42,44,45,46,58,67,69,70,72,77,78,79,80,81,91,92,109,110,118,132],directli:[2,3,32,40,42,58,67,74,81,93,94,98,99,100,105,108,111,113,122,126,139,144,147,154],directori:[0,1,2,3,4,77,78,92,93,94,97,104,105,111,112,114,130,134,135,136,137,143,145,148,149,155,156,157,158,159],disabl:[4,79,121],disadvantag:[2,60],disallow:68,discard:[19,60,81],discontinu:[91,128],discourag:134,discret:[2,58,67],discuss:[0,1],disk:[2,36],disloc:[29,137],disord:[29,137],disp:0,dispar:146,disperion:[108,126],dispers:[2,100,108,126,131,139,159],displac:[2,37,62,68,70,118],displai:[3,57,58],disregard:137,dissip:[2,31,64,66,77,78,109,110,118,131,132],dist:[2,35,71,73,154],distanc:[2,5,6,20,21,22,23,24,25,26,27,28,30,33,34,36,37,38,40,41,42,45,47,58,61,62,63,67,68,69,70,72,73,75,76,78,79,80,81,82],distinct:[2,146],distinguish:[2,42,113],distort:93,distrbut:93,distribut:[0,2,3,19,32,42,57,60,66,67,68,93,97,105,111,112,114,134,135,136,139,143,145,146,155,156,157,158,159],distro:145,ditto:162,div:4,diverg:[78,94],divid:[2,4,19,35,39,43,57,60,70,91,92,114,148,159],divis:[2,56,67,97,130],dl_poly:2,dlammps_ffmpeg:58,dlammps_gzip:58,dlammps_jpeg:58,dlammps_memalign:4,dlammps_png:58,dlm:68,dlmp_intel_offload:4,dlopen:2,dlvo:[103,161],dm_lb:67,doc:[0,1,2,3,32,34,37,39,40,43,45,57,58,68,81,90,91,92,93,94,96,104,105,111,112,114,120,134,135,136,139,143,145,149,155,156,158,159,163],docuement:146,doe:[0,1,2,3,19,28,29,32,35,41,44,45,46,57,58,59,60,61,62,63,65,66,67,68,79,80,81,83,84,85,87,88,92,93,94,95,96,97,100,101,102,103,104,105,106,108,109,111,112,113,115,116,117,118,119,121,124,125,127,128,129,131,132,134,135,136,137,139,141,142,145,146,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163],doesn:[45,94,104,112,155,156,157,158,159],dof:39,doi:[2,70],domain:[2,19,41,44,58,60,62,67,68,71,79,80,92,139],domin:[1,113],don:[0,4,81,134,148,163],done:[1,2,19,45,56,58,59,60,61,62,65,68,71,75,77,78,91,92,94,100,111,126,132,133,134,139,141,142,154,163],donor:120,dot:43,doti:[97,145],doubl:[1,2,3,4,32,46,81,97,114,119,137],dover:59,down:[2,3,62,113,139,148],download:3,downsid:2,dpd:2,dpdtheta:[31,110],dpdtheta_i:[64,65],dr_ewald:41,drag:[2,35,68,69,76],dragforc:67,drai:[58,72],drain:91,dramat:[61,62,68,139,148],drautz:97,draw:58,drawn:[58,66],drayleigh:72,dreid:2,dreiding:0,drfourth:37,drho:[93,111,141,142],drift:[2,37,63,66],drive:[3,62,68,70,92],driven:[2,51],driver:2,drop:109,drsquar:37,drude:0,dt_collis:67,dt_lb:67,dt_md:67,dtqm:72,dudarev:44,due:[1,2,4,28,29,33,34,37,41,42,43,44,45,58,61,62,66,67,68,69,70,73,77,78,79,80,81,91,92,106,109,110,111,116,117,131,132,139,145,146,147,154,156,158,161,162],duffi:79,dullweb:68,dumbbel:90,dummi:[13,157],dump:[0,1],dump_modifi:[2,58],dunbrack:[2,5,46,101],duplic:[19,60,70],durat:[57,79,118],dure:[2,4,19,32,40,46,59,60,61,62,63,65,66,67,68,69,70,71,72,73,75,76,77,78,79,80,81,91,92,109,130,137,139,140,141,142],dvlo:161,dvx:2,dx_lb:67,dy3:44,dyanam:2,dynam:[0,2,3,4,19,31,37,45,58,59,60,61,64,66,68,69,71,72,73,77,78,79,91,92,109,110,113,131,132,139,153],dynamo:[93,111,134],dyre:127,e28637:13,e_1:97,e_2:97,e_a:74,e_b:114,e_ee:113,e_hbond:120,e_i:[2,97,114],e_j:[2,97],e_k:97,e_ke:113,e_kl:2,e_lj:[94,108],e_n:97,e_ne:113,e_nn:113,e_pr:113,e_rebo:94,e_torsion:94,e_tot:137,e_vol:137,eaa:82,eaat:47,each:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,32,33,34,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,65,66,67,68,69,70,71,74,75,76,78,79,80,81,82,83,84,85,86,87,88,89,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,158,159,160,161,162],eacn:[19,60],eam:[0,93,105],earli:[19,60],earlier:[92,118,134,139],earth:113,easi:[2,3,32,43,80],easier:[4,58],easili:[3,58,92],eat:47,eaxmpl:2,eba:6,ebb13:47,ebb:6,ebt:47,ec_ii:134,ec_ij:134,ec_jj:134,echo:[3,41,44],ecp:113,edg:[2,19,41,44,58,80,81],edge:80,edit:[4,163],edition:4,edu:[3,111,131],eebt:47,eff:0,effect:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,33,34,37,39,43,46,47,48,49,50,51,52,53,54,55,57,58,59,61,62,63,66,68,69,70,71,72,73,75,78,79,80,81,82,83,84,86,87,88,89,91,92,93,94,95,97,98,99,100,101,102,103,104,105,108,109,111,112,113,114,116,117,118,119,120,122,123,124,125,126,127,128,129,130,131,135,137,139,140,141,142,143,144,146,147,148,150,155,156,157,158,159,160,161,162],effici:[0,1,2,4,39,56,58,62,68,71,75,97,103,105,122,126,137,141,142,146],efficienc:4,efield:[75,91],eggebrecht:[105,148],ehex:2,eigenvalu:71,einstein:[2,78],either:[1,2,3,4,19,29,41,42,43,44,45,58,60,61,62,63,67,68,69,70,74,75,81,91,97,103,111,115,118,131,132,134,137,139,142,145,154,156,158],ejtehadi:[103,117,146],elaps:[80,150],elast:[2,21,22,92,118,157],elastic:0,elba:13,electr:[2,59,114,162],electric:4,electrolyt:161,electron:[2,41,59,79,93,104,108,111,113,114,134,137,145,148,158,159,162],electron_integr:59,electron_temperatur:59,electron_unit:113,electroneg:[2,104,114,148],electroneg_compon:148,electrostat:[2,4,103,108,113,122,130,132,148,161],elem1:[114,134,149],elem2:[114,134,149],elem:148,element1:[93,111,148],element2:[93,111,148],element:[2,33,37,39,42,43,58,59,93,94,97,104,111,112,113,114,134,135,136,137,143,145,148,149,155,156,157,158,159],elementn:[93,111],elementset:59,elif:42,elig:120,elimin:[2,66,75,77,78],elj:108,ellips:2,ellipsoid:[2,45,90,91,117,132,146],els:[58,68,79],elsewher:134,elt:134,emac:0,email:[0,3,114],emb:81,emb_lin_neg:134,embed:[3,13,79,93,111,114,130,134,135,136,145],embt:47,emphas:118,empir:[59,113],empiric:94,emploi:[63,157],empti:121,enabl:[2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,31,32,37,39,40,41,42,44,46,47,48,49,50,51,52,53,54,55,57,61,63,64,65,66,67,68,69,70,71,72,73,74,75,77,78,79,80,81,82,83,84,86,87,88,89,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,134,135,136,137,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162],enclos:[2,134,148],encod:58,encompass:2,encount:38,encourag:[74,76],end:[1,2,3,4,19,47,58,61,63,66,68,73,74,79,92,109,111,117,133,137,146,149,150],endbondtors:47,energet:[61,94],energi:[0,1,2,5,6,7,8,9,10,11,12,13,14,15,16,17,18,20,21,22,23,24,25,26,27,28,31,32,35,39,43,45,46,47,48,49,50,51,52,53,54,55,56,57,59,60,61,62,63,64,65,66,67,68,69,70,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109],energy_compon:148,enforc:[2,58,61,68,75,122],enforce2d:[2,91],eng:[3,104,136],engineer:[59,77,111],enginer:135,enhanc:[59,63],enlarg:58,enough:[45,60,72,80,81,105],enpub:111,ensembl:[2,32,35,68,71,72,109,148],ensight:2,ensur:[2,42,62,66,68,97,130,155,159],enter:[114,137,159],enthalpi:[74,111],entir:[0,2,3,19,31,39,40,41,43,44,45,60,61,63,66,68,69,70,71,74,76,79,108,126,139],entiti:2,entri:[40,41,65,72,97,112,134,141,142,143,149,155,156,157,158,159],entry1:[141,142],enumuer:2,environ:[1,2,3,4,58,70,93,97,104,112,113,145,156],eos:65,epair:[94,116,120],epp:108,epq:108,eps0:161,eps14:130,epsilon0:158,epsilon:[2,18,21,22,27,28,32,46,80,81,91,96,101,102,103,105,106,107,108,115,117,119,120,121,122,123,124,125,126,127,128,129,130,133,138,144,146,147,155,160,161],epsilon_0:162,epsilon_14:101,epsilon_:146,epsilon_d:106,epsilon_i:[117,139,146],epsilon_i_:146,epsilon_i_a:[117,146],epsilon_i_b:[117,146],epsilon_i_c:[117,146],epsilon_ij:139,epsilon_j:[117,139,146],epsilon_j_:146,epsilon_j_a:[117,146],epsilon_j_b:[117,146],epsilon_j_c:[117,146],epsilon_lj:146,eqp:108,eqq:108,equal:[2,3,19,28,32,35,43,45,58,60,62,66,67,69,70,71,72,73,74,77,78,79,80,91,92,94,104,109,110,116,117,120,131,137,138,145,146,148,149,150,159,162],equat:[2,35,38,39,41,44,57,62,63,64,65,67,68,69,70,71,72,74,75,79,80,90,103,108,109,110,113,114,115,118,131,132,134,139,142,146,151,152,153,162],equation:[70,88],equilibr:[2,35,45,61,62,68,72,77,78,104,105],equilibrium:[1,2,6,8,10,11,12,13,16,17,18,20,23,24,25,26,27,47,48,62,66,67,68,69,72,73,75,78,82,83,87,88,104,134,143,148],equilibrium_start:59,equival:[2,13,62,68,73,94,109,113,148,156,158],equlibrium:2,er3:44,eradiu:113,eras:77,erat:132,erc:105,erfc:[105,122,139],erhart:[111,156,158],eros:134,erose_form:134,erot:2,errata:[156,158],erratum:80,error:[0,1,2,3,11,48,58,62,63,65,68,74,79,80,81,91,105,122,139,146,154,156,158],erta:118,especi:[4,45,60,72,73],essenti:[3,11,48,94,105,122,158],essential:69,essex:13,establish:32,estim:[1,2,19,29,35,43,59,60,74,139],esub:134,eta:[2,67,68,72,112,114,117,145,157,159],eta_dot:68,eta_ij:145,eta_ji:114,etap:68,etap_dot:68,etc:[1,2,3,4,28,33,34,35,40,43,45,58,59,66,68,79,81,91,92,111,112,130,132,137,155,156,158,159],etol:[91,92],etot0:72,etot:[2,43,72],eu2:44,eu3:44,euler:[74,91,92],eulerian:59,europhi:67,evalu:[3,32,35,42,45,46,58,59,66,74,80,91,137,139,141,142,145,148],evanseck:[2,5,46,101],evaul:91,even:[2,4,19,29,56,60,62,63,68,79,80,81,91,92,96,113,114,118,139,146,159],evenli:[19,43,60,67],event:[2,68,79],eventu:2,ever:28,everaer:[103,117,146],everi:[0,1,2,3,4,19,35,58,59,60,61,62,63,67,68,69,70,72,74,75,79,92,109,130,148,163],everyth:163,everywher:124,eviri:113,evolut:[63,67,71],evolv:[67,71],ewald:[2,41,43,91,98,99,100,105,108,113,122,126,144,147],ewald_disp:108,exact:[19,60,61,66,79],exactli:[2,19,35,45,60,66,72,109,111,118,131,139,141,142],examin:[2,61,74],exampl:[0,1],exce:[2,4,19,60,62,68,91],exceed:[19,60,68],excel:113,except:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,21,22,23,24,25,26,27,28,33,34,39,43,45,46,47,48,49,50,51,52,53,54,55,57,60,62,68,69,71,75,79,82,83,84,86,87,88,89,92,93,94,95,98,99,100,101,102,103,104,105,107,108,109,111,112,113,114,116,117,118,119,120,122,123,124,125,126,127,128,129,130,131,132,135,140,143,144,146,147,150,155,156,157,158,159,160,161,162],excess:113,exchang:[2,59,63,79,113],excit:113,excite:113,exclud:[2,4,39,40,42,91,118,131,132,139,154],exclus:[1,4,32,46,104,137,139],excurs:68,execut:[1,2,3,58],exempl:148,exemplari:66,exemplifi:113,exert:[2,81],exhaust:59,exhibit:[36,63,68,113],exist:[2,3,29,45,57,58,62,82,83,84,85,87,110,154,163],exit:[3,19,60],expans:[42,56],expect:[1,4,19,60,70,72,134,137,139],expens:[2,70,79],experi:[2,73,92,109,139],experienc:[2,4],explain:[1,2,3,19,30,40,58,60,62,68,70,92,96,111,148,150,163],explan:[2,40,42,70],explic:138,explicit:[2,3,32,74,94,97,101,111,113,121,131,163],explicitli:[2,4,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,39,45,46,47,48,49,50,51,52,53,54,55,66,68,69,72,75,79,82,83,84,86,87,88,89,93,94,95,98,99,100,101,102,103,104,105,106,108,109,111,112,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,135,137,139,140,141,142,143,144,146,147,150,151,152,153,155,156,157,158,159,160,161,162,163],explictli:4,exploit:71,explor:[41,44],expon:[74,111,115,117,120,130,138,147],exponenti:[32,74,115,145,155,159,162],expos:3,exposit:[59,109],express:[2,42,45,62,70,74,79,97,111,113,124,134,148,149],expressiont:97,extend:[0,2],extens:[2,4,21,22,27,32,35,63,68,69,70,73,77,78,79,80,81,117,134,137,146,149],extent:[1,19,21,60,94],exterior:[2,81],extern:[32,58,62,66,67,68,69,79,91,135,136],extra:[2,3,4,19,22,39,41,43,44,45,60,68,72,91,108,118,134,139],extract:[2,3,18,32,92,105,114,134,149],extract_atom:3,extract_comput:3,extract_fix:3,extract_glob:3,extract_vari:3,extrapol:1,extrem:[1,2,58,62,68,78,113,157],extrema:130,extreme:113,extrins:59,f_1:2,f_a:[156,157,158],f_c:157,f_f:158,f_fix_id:72,f_harm:78,f_i:[13,145],f_id:2,f_ij:145,f_int:77,f_j:13,f_jj:35,f_k:145,f_langevin:79,f_max:72,f_r:[156,157,158],f_sigma:97,f_solid:78,f_ss:2,face:[2,80,81,117,134,146],facil:0,facilit:2,fact:[2,4,78,118,148],factor:[1,2,8,12,16,17,18,19,22,23,32,35,41,42,44,46,54,58,60,62,63,67,68,69,71,73,74,75,80,81,87,94,97,98,99,101,105,106,107,109,110,113,118,121,122,134,137,139,141,142,143,144,147,150,155],fail:[3,62,91,92,107],fairli:[3,139,163],faken:30,fall:2,fals:148,famili:159,familiar:[0,3,163],fan:145,far:[2,60,62,68,70,73,80,83,87,92],farrel:[156,158],fashion:[2,19,45,60,68,69,72,78,79,80,92,131],fast:[2,4,72,74,131,132,137],faster:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,21,22,23,24,25,26,27,28,37,39,46,47,48,49,50,51,52,53,54,55,60,68,69,75,77,79,82,83,84,86,87,88,89,93,94,95,97,98,99,100,101,102,103,104,105,108,109,111,112,114,116,117,118,119,120,122,123,124,125,126,127,128,129,130,131,135,140,143,144,146,147,150,155,156,157,158,159,160,161,162],fastest:[1,2,79],fault:29,fava:117,favor:61,fcc:[2,29,30,35,38],fcold:63,fdt:[64,65,74],fdti:32,fe2:44,fe3:44,fe_md_boundari:59,featur:[0,2,3,42,58,61,66,71,81,91,163],fecr:111,feel:[70,81,92,139],fehlberg:74,felling:136,felt:81,fene:[2,4],fennel:[105,122],fep:0,ferguson:[2,46],fermi:[1,158],fermion:113,fernando:133,few:[1,2,3,63,68,75,91,92,94,148],fewer:[1,3,4],feynman:71,ffield:[104,114,148],fflag1:58,fflag2:58,ffmpeg:58,ffplai:58,fft:[1,3,43],fhot:63,ficiti:154,fictiti:[2,71,73,105,122,126,154],field:0,fifth:[2,115,143],figshar:70,figur:[1,4,72,163],fij:108,file0:70,file1:[3,65,70],file2:[3,65],file:[0,1],filenam:[4,19,58,59,60,65,70,74,79,92,93,94,97,105,111,112,114,115,134,135,136,141,142,143,145,148,149,155,156,157,158,159],fill:[45,58,79,97,137,163],filter:59,finchham:[2,107],find:[0,2,3,4,30,32,61,62,65,70,73,91,92,105,122,126,134,141,142,148,163],fine:[4,78,163],finer:[42,45],finger:45,finish:[2,3,19,60],finit:0,finni:111,fire:[91,92],first:[0,1,2,3,4,6,19,21,22,28,29,35,37,38,39,43,44,47,58,60,61,65,66,67,68,70,71,72,75,76,77,78,79,82,91,92,93,94,96,97,98,99,101,104,105,111,113,114,115,118,119,121,122,126,131,132,134,136,137,139,141,142,143,145,148,149,154,155,156,157,158,159,162,163],fischer:[2,5,46,101],fit:[2,73,94,97,134,139,141,142,157,163],five:[30,72,97,135],fix:[0,1],fix_flux:59,fix_heat:63,fix_id:[62,68,69,72],fix_manifoldforc:163,fix_modifi:2,fix_nv:163,fix_rattl:75,fix_shak:75,fixedpoint:[62,68],fixid:[58,59],fji:108,flag:[3,4,33,34,40,41,44,58,61,94,120,121,134,137,154,163],flag_buck:100,flag_coul:[100,108,126],flag_lj:[108,126],flagfld:[131,132],flaghi:[131,132],flaglog:[131,132],flagvf:[131,132],flat:[2,4,79,80],fld:[80,131,132],flexibl:[2,58,113,157],flip:[2,68],fluctuat:[2,32,62,66,67,68,69,70,78,79,88,110],fluid:[2,62],flux:2,flv:58,fly:[19,58,59,75,97,137],fmass:71,fmax:91,fmsec:68,fno:4,fnorm:91,fnve:63,focu:75,foil:[42,70,149],fold:[4,76],follow:[0,1,2,3,4,5,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,35,36,38,42,43,45,46,48,49,50,51,52,53,54,55,56,58,59,60,64,65,66,67,68,69,71,72,73,74,75,77,78,79,83,84,85,86,87,88,89,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163],foo:[3,58,74],foo_species:74,foot:2,forc:[0,1],forcefield:[73,120],forcegroup:67,ford:108,forgiv:68,fork:163,form:[2,28,32,33,34,36,42,43,66,73,74,79,80,81,82,85,88,92,94,97,110,111,113,116,120,121,133,134,136,137,141,142,143,144,145,146,148,149,150,156,157,158,161],formal:[2,35,66,68,71,148],format:[2,19,58,60,65,74,79,92,93,94,97,111,114,115,121,134,136,141,142,147,149,159],formation:65,former:[2,19,60,79,97],formul:[1,2,43,68,73,75,94,97,111,113,117,134],formula:[2,6,28,29,30,32,33,34,35,39,41,43,44,45,47,57,70,76,80,82,84,94,96,97,101,102,103,108,109,111,112,117,118,119,120,121,122,124,125,126,128,129,131,132,134,138,139,140,146,147,150,155,156,157,158,159,160,161],forth:[1,2,3],fortran:[2,3,111,134],forward:[32,92],foster:[97,145],found:[2,30,61,63,67,105,108],four:[2,3,28,42,79,88,92,137],fourier:2,fourth:[2,4,37,73,101,115,143,148],fox:[2,41,46,153],fqq:108,fraction:[1,2,4,19,43,58,61,62,72,74,92,97,115,118,131,132],frame:[42,59,72,117],framer:58,framework:[93,149],frattl:63,free:[2,13,29,32,70,77,78,79,92,113,130,137,140,145,161],freedom:[2,39,61,68,69,71,75,78,91,108],freeli:[0,2,58],freez:2,frenkel:[2,63,78],frequenc:[2,4,71,72,74,109,113,148],frequent:[29,30,36,38,42,63,139],fri:72,friction:[2,72,79,118],from:[0,1],front:72,frontend:58,frozen:[2,39,66,116],fs2:[2,35],ftol:[91,92],fuction:105,fudg:75,fulfil:2,full:[1,2,4,35,58,63,67,70,74,97,111,113,114,117],fuller:91,fulli:[2,70,91,92,105,145,163],fulton:111,fumi:98,funcfl:111,fund:0,funrol:137,further:[2,37,58,67,71,79,91,92,93,96,104,137,148],furthermor:[11,48,63,74,110,113],futur:[0,2,60,66,92,135,136],g_jik:145,g_p:79,ga3:44,gaa:97,gai:117,gain:4,galindo:138,gamma0:13,gamma:[2,13,67,72,109,110,112,117,134,138,151,152,153,155,156,158,159],gamma_:79,gamma_ijk:156,gamma_n:118,gamma_p:79,gamma_t:118,gammaa:138,gammafactor:67,gammar:138,gan:[145,155,156,158,159],gan_sw:145,gan_tersoff:145,gao:[2,5,46,101],gap:[131,132,149],gather:3,gather_atom:3,gathert_atom:3,gauch:51,gauss:106,gaussian:[2,35,37,66,71,73,109,113,116],gave:139,gavhan:4,gaybern:[2,4,91],gcmc:139,gd3:44,gdot:132,ge4:44,gec:[156,158],gen:68,gener:0,gentler:80,gentli:112,geom:2,geometr:[2,40,45,60,68,81,92,96,102,103,105,108,113,115,117,119,122,123,124,125,126,127,128,129,130,131,132,133,138,139,142,146,150,160,161],geometri:[2,9,19,45,60,62,139],gerber:130,germann:[69,124],germano:117,get:[0,1,2,3,4,19,35,40,42,45,58,60,62,81,92,105,159,163],get_natom:3,get_rank:3,get_siz:3,gewald:2,gezelt:[105,122],ghost:[2,4,30,62,68,109,110,113,118,121],gif:58,gifsicl:58,gillan:149,gingold:[151,152],git:163,give:[0,1,2,3,4,28,36,38,45,62,68,70,91,94,97,113,120,134,137,139,146,156,157,158],given:[2,3,4,11,38,42,43,48,57,62,63,66,67,68,69,70,71,72,73,74,75,76,79,80,81,93,94,97,98,99,100,102,103,104,105,106,109,110,111,113,114,115,117,118,120,122,123,124,126,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,162],glosli:137,glotzer:109,glue:3,gnu:0,gnuplot:3,goddard:[2,9,89,113,120],goe:[28,42,45,63,91,108,112,119,124,127,150,162],gold:29,goldman:72,good:[1,2,4,19,30,41,44,60,68,75,92,93,103,111,137,139,159,163],gordan:42,gordon:2,got:163,gould:[2,46],gov:[0,93,111,114],govern:67,gpa:94,gpl:0,gpt:137,gpu:[1,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,39,46,47,48,49,50,51,52,53,54,55,68,69,75,82,83,84,86,87,88,89,93,94],grab:2,grad:2,gradient:[2,62,63,79,92,132,141,142],graft:61,grain:[2,13,18,28,45,51,65,70,74,115,119,137,142,147],gram:111,gran:[2,80,81],grana:90,granular:0,graph:3,graphic:3,graviti:2,grdient:59,great:[72,163],greater:[1,62,66,68,70,96,98,99,100,139],greatli:[41,63],green:[2,35,58,71,97,163],green_kubo:2,grest:[21,22,61,100,118,126],grid:[19,41,44,60,67,79],grigera:2,gromac:91,gromacs:[2,91,119],groot:109,ground:[2,31,64,113],group:[2,3,4,19,29,30,31,32,33,34,35,36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89,92,93,94,95,97,98,99,100,101,102,103,104,105,108,109,111,112,114,116,117,118,119,120,122,123,124,125,126,127,128,129,130,131,134,135,136,137,139,140,143,144,145,146,147,150,154,155,156,157,158,159,160,161,162,163],yourself:[2,62,163],ypo:45,yukawa:103,z_i:[113,158,162],z_j:[158,162],z_meam:134,zannoni:117,zbl:[134,149],zblcut:158,zblcutinn:149,zblcutout:149,zblexpscal:158,zblz:149,zero:[2,3,10,11,19,24,25,29,32,34,36,37,38,39,41,42,43,44,45,46,48,55,57,58,60,62,63,66,67,68,69,71,72,74,75,78,79,80,86,91,92,97,98,99,100,101,103,105,108,109,110,113,117,119,120,122,124,126,127,130,132,133,134,137,139,140,146,147,148,154,159,162],zeta:[67,114],zfactor:58,zhang:118,zhi:[2,80],zhi_bound:2,zhou:[97,114,145,156,158],zhu:153,ziegler:[134,158,162],zimmerman2004:59,zimmerman2010:59,zimmerman:[29,59,97],zlim:148,zlo:[2,80],zlo_bound:2,zmax:67,zmin:67,zn2:44,zone:41,zoom:58,zr4:44,zwall:80,zwall_veloc:67},titles:["LAMMPS Documentation","5. Accelerating LAMMPS performance","6. How-to discussions","11. Python interface to LAMMPS","5.USER-INTEL package","angle_style charmm command","angle_style class2 command","angle_style cosine command","angle_style cosine/delta command","angle_style cosine/periodic command","angle_style cosine/shift command","angle_style cosine/shift/exp command","angle_style cosine/squared command","angle_style dipole command","angle_style fourier command","angle_style fourier/simple command","angle_style harmonic command","angle_style quartic command","angle_style sdk command","balance command","bond_style class2 command","bond_style fene command","bond_style fene/expand command","bond_style harmonic command","bond_style harmonic/shift command","bond_style harmonic/shift/cut command","bond_style morse command","bond_style nonlinear command","bond_style quartic command","compute centro/atom command","compute cna/atom command","compute dpd command","compute fep command","compute gyration command","compute gyration/chunk command","compute heat/flux command","compute hexorder/atom command","compute msd/nongauss command","compute orientorder/atom command","compute pressure command","compute rigid/local command","compute saed command","compute sna/atom command","compute stress/atom command","compute xrd command","create_atoms command","dihedral_style charmm command","dihedral_style class2 command","dihedral_style cosine/shift/exp command","dihedral_style fourier command","dihedral_style harmonic command","dihedral_style helix command","dihedral_style multi/harmonic command","dihedral_style nharmonic command","dihedral_style opls command","dihedral_style quadratic command","dihedral_style spherical command","dihedral_style command","dump image command","fix atc command","fix balance command","fix bond/swap command","fix box/relax command","fix ehex command","fix eos/cv command","fix eos/table/rx command","fix gld command","fix lb/fluid command","fix nvt command","fix nphug command","fix orient/fcc command","fix pimd command","fix qbmsst command","fix restrain command","fix rx command","fix shake command","fix spring/rg command","fix ti/rs command","fix ti/spring command","fix ttm command","fix wall/lj93 command","fix wall/region command","improper_style class2 command","improper_style cossq command","improper_style cvff command","improper_style distance command","improper_style fourier command","improper_style harmonic command","improper_style ring command","improper_style umbrella command","Manifolds (surfacse)","minimize command","neb command","pair_style adp command","pair_style airebo command","pair_style beck command","pair_style body command","pair_style bop command","pair_style born command","pair_style buck command","pair_style buck/long/coul/long command","pair_style lj/charmm/coul/charmm command","pair_style lj/class2 command","pair_style colloid command","pair_style comb command","pair_style coul/cut command","pair_style coul/diel command","pair_style born/coul/long/cs command","pair_style lj/cut/dipole/cut command","pair_style dpd command","pair_style dpd/fdt command","pair_style eam command","pair_style edip command","pair_style eff/cut command","pair_style eim command","pair_style exp6/rx command","pair_style gauss command","pair_style gayberne command","pair_style gran/hooke command","pair_style lj/gromacs command","pair_style hbond/dreiding/lj command","pair_style list command","pair_style lj/cut command","pair_style lj96/cut command","pair_style lj/cubic command","pair_style lj/expand command","pair_style lj/long/coul/long command","pair_style lj/sf command","pair_style lj/smooth command","pair_style lj/smooth/linear command","pair_style lj/cut/soft command","pair_style lubricate command","pair_style lubricateU command","pair_style lj/mdf command","pair_style meam command","pair_style meam/spline","pair_style meam/sw/spline","pair_style mgpt command","pair_style mie/cut command","pair_modify command","pair_style morse command","pair_style multi/lucy command","pair_style multi/lucy/rx command","pair_style nb3b/harmonic command","pair_style nm/cut command","pair_style polymorphic command","pair_style resquared command","pair_style lj/sdk command","pair_style smtbq command","pair_style snap command","pair_style soft command","pair_style sph/idealgas command","pair_style sph/taitwater command","pair_style sph/taitwater/morris command","pair_style srp command","pair_style sw command","pair_style tersoff command","pair_style tersoff/mod command","pair_style tersoff/zbl command","pair_style vashishta command","pair_style yukawa command","pair_style yukawa/colloid command","pair_style zbl command","LAMMPS GitHub 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:25,bond_interact:60,bond_styl:[0,2],bondangl:6,bondbond13:47,bondbond:6,bonet:115,book:[165,168],bookmark:0,boost:1,border:[4,85],boresch:32,boreschkarplu:32,born:[2,32],boron:118,botero:118,both:[1,2,3,4,11,28,32,45,48,57,58,59,62,63,64,65,67,68,69,73,74,78,81,83,84,85,86,87,88,96,97,99,102,103,104,105,106,107,108,113,114,116,117,118,122,123,125,127,129,131,132,133,135,136,137,142,143,144,148,150,151,159,160,161,162,163,167],bottleneck:1,bottom:73,bound:[2,10,11,19,48,58,64,66,74,86,87,96,118],boundari:[2,33,34,35,37,39,41,43,44,45,58,59,60,61,64,68,73,74,76,78,82,85,86,87,124,136,137,142,167],boundary_dynam:60,boundary_faceset:60,boundary_integr:60,bounds:[2,19,58,66],bount:3,box:[0,1],boxcolor:59,boxxlo:3,bptype:158,br1:44,bracket:[2,19,40,58,61,62,63,64,65,66,167],bragg:[41,44],branch:[3,168],branicio2009:163,branicio:[30,163],breakdown:[1,99],brennan:[31,70,115,145,146,158],brenner:99,brick:[19,66],brief:[1,2,74,99,102],briefli:[2,77,109,152,168],brilliantov:123,broadwel:4,broken:[28,29,74,102],brook:2,brown:[4,41,43],brownian:[2,37,136,137],brows:0,browser:59,bryantsev:125,btype:[58,110,127,131,135,158],buc:104,buck:[2,4,32,103],buckingham:[103,104,105,112,138],buckplusattr:152,buffer:59,bufi:59,bug:0,bui:59,build:[0,1,2],built:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,20,21,22,23,24,25,26,27,28,31,32,37,39,41,42,44,46,47,48,49,50,51,52,53,54,55,56,57,58,67,69,70,71,72,73,74,75,76,77,78,80,81,83,84,85,88,89,90,91,92,93,94,95,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166],bulatov:[140,141],bulk:[2,29,73,76,111,139,142,152],bundl:[59,168],button:168,bypass:2,c11:[63,139],c12:63,c13:63,c1n:63,c21:63,c22:63,c23:63,c2n:63,c31:63,c32:63,c33:63,c34:63,c3n:63,c41:63,c42:63,c43:63,c44:63,c_0:[85,99,156,157],c_1:[40,41,44,58,72],c_2:[40,41,44,58],c_3:40,c_cluster:2,c_cstherm:2,c_dist:40,c_doubl:3,c_e:85,c_flux:35,c_forc:40,c_gauss:121,c_hb:125,c_i:71,c_id:[2,32,40,58,61,62,63,64,65,167],c_ij:2,c_ijkl:2,c_index:40,c_k:72,c_my_stress:61,c_myang:62,c_mycentro:62,c_mychunk:[2,34],c_mycom:64,c_mycomput:62,c_myf:58,c_mypress:63,c_myrdf:65,c_mytemp:[63,64,65,167],c_n_k:72,c_p:43,c_peratom:43,c_pi:102,c_press:40,c_prop:2,c_sigma:102,c_size:2,c_stress:58,c_thermo_press:[63,64,65],c_thermo_temp:65,c_xrd:64,ca2:44,cach:4,cacul:81,calcforc:73,calclat:35,calcluat:[37,39,43,110],calcualt:[35,62],calcul:[0,1],caldwel:[2,46],calhoun:77,call:[1,2,3,4,58,77,99,108,165,168],callabl:3,callback:3,caltech:[2,118],calucl:2,calul:[3,29],can:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168],cannot:[1,2,3,4,19,28,40,58,59,61,62,63,64,65,66,67,68,72,74,78,85,86,87,96,97,104,105,107,116,122,124,127,131,133,135,148,150,151,158],canon:[74,77,84,142],cao1:77,cao2:77,cao:77,capabl:[3,4,99,107],capac:[70,85,155],capolungo:[41,44],captur:[2,99,105,118,123,131,139],carbid:110,carbon:[59,94,99,109,139],card:[4,32,125],care:[2,45,56,62,73,74,101],carefulli:[3,28],carlo:[2,67],caro:116,carri:[4,85,123],carrillo:4,cartesian:[2,98],cascad:85,cat:[4,59],cate:73,categori:[0,99],cation:[119,152],caus:[1,2,4,45,58,68,74,76,80,81,86,87,96,97,125,127,133,136,137],caution:1,cautious:99,caveat:99,cbecker:[98,116],cc1:[2,34,62],ccc:[117,159,160,162,163],ccflag:4,ccflags:[4,58],ccm6:116,ccsi:[117,159,160,162,163],ccu:102,cd2:44,cdeam:116,cdll:3,cdof:[2,62],cdte:102,cdte_bop:102,cdtese:102,cdzn:102,cdznte:102,ce3:44,ce4:44,cell:[2,41,44,45,58,68,74,75,78,85,118,142,167],cella:[2,167],cellalpha:[2,167],cellb:[2,167],cellbeta:[2,167],cellc:[2,167],cellgamma:[2,167],center:[2,9,33,34,37,41,45,59,62,64,68,72,74,82,84,86,87,88,101,117,118,122,123,136,137,139,140,141,159,160,161,162,163],centr:69,central:[29,36,38,42,76,81,82,91,142,147,163],centro:2,centroid:77,centrosymmetri:29,certain:[1,2,40,58,59,61,62,63,64,65,67],cfg:[2,58,59],cg_type:151,ch2:81,ch2lmp:[0,2],ch3:81,chain:[0,2,13,28,67,74,75,77,81,84,94,113,114,158],challeng:2,champaign:136,chan:142,chandler:[98,116],chandrasekhar:[2,127],chang:[1,2,3,4,19,22,32,45,58,59,60,66,67,68,73,74,75,76,78,79,80,81,83,84,85,87,96,97,114,118,123,136,137,139,142,152,158,167,168],change_box:2,changeabl:58,chapter:77,charact:[2,19,58,59,66,71,80,118,120,126,145,146,149,152],character:[2,29,38,42,153],characterist:83,charg:[1,2,3,32,41,44,45,58,103,104,109,110,112,113,116,118,119,127,131,135,148,152,162,163,165,166],charmm:0,cheaper:[122,150],check:[2,3,19,35,66,79,81,84,96,97,126,167],checkout:168,chem:[2,5,6,9,20,21,22,32,38,39,43,46,47,54,69,72,73,74,77,78,83,84,86,88,94,95,97,99,103,106,107,109,110,111,113,114,115,118,121,122,124,125,127,131,132,135,139,143,145,146,148,152,158],chemic:[31,41,44,58,60,120,146],chemistri:[78,99,102,118],chen:85,cheng:109,chi:[76,119,122],chiral:94,chmod:3,cho:139,choic:[2,4,19,28,29,32,43,56,62,66,67,73,74,77,97,135],choos:[1,2,13,28,32,40,59,67,68,73,74,75],chose:[160,162],chosen:[2,42,45,51,59,68,72,73,74,75,77,115,118,123,126,129,151,160],chunk:0,chunkid:[34,62],ciccotti:81,cieplak:[2,46],cii:63,cij:63,circular:2,circumv:[36,38],citat:[0,73],cite:152,cl1:44,clarendon:[13,113],clarifi:[160,162],clark:148,classic:[0,2,4,77,78,85,95,118],classifi:163,clean:2,cleanli:167,clear:[2,3],clebsch:42,click:[3,45,57,59,97,168],climb:97,clockwis:46,clone:168,close:[2,3,19,43,58,67,68,73,74,81,87,97,99,102,110,111,139,145,146,162,168],closer:[19,58,66,68,83,97],closest:[76,122,150,158],cloud:152,cluster:[2,4,43,58,69,81],cmax:139,cmd:[3,77],cmdarg:3,cmin:139,cmm:[18,151],cn1:63,cn2:63,cna:29,cnn:63,co2:[44,80,81,120],coars:[13,18,28,51,71,80,120,124,146,151],coarsest:42,code:[0,1],coeff:[6,46,47,56,88,126,154],coeffici:0,coefficienct:114,coefficient0:116,coefficient1:116,coeffieci:[2,100],coeffincientn:116,coexist:118,cohes:[2,119,139],coincid:[87,106,136,137],cold:2,coleman:[41,44],collect:[2,34,45,58,62,108],colliex:44,collis:[73,123,166],colloid:2,color:[19,58,59,66,72,78],column:[2,29,34,36,38,40,42,43,44,58,61,62,63,64,65,78,85,99,121,125,167],colvar:0,com:[2,37,64,69,101,168],comand:67,combiant:111,combin:[2,3,18,32,56,58,59,60,64,69,74,77,87,88,108,110,111,115,118,119,120,134,135,153,159,160,162,163,165],come:[0,2,13,68,74,83,84,159,160,162,163,167,168],comit:168,comm:[0,3,30,97,114],comm_modifi:[2,102,108,114,118,123],comm_styl:[19,66],comm_world:3,command:[0,1],comment:[3,46,58,71,80,85,97,98,116,117,119,120,126,139,145,146,147,152,153,159,160,161,162,163,168],commit:168,commmand:2,common:[0,1,2,3,4,30,68,77,87,88,123,125,159,160,162],commonli:[2,9,37,38,58,59,95,124,129,153,160,162],commun:[1,2,3,4,19,59,66,68,73,74,85,115],comp:[81,97,118,150,157,161],compar:[1,2,4,41,44,57,96,97,139,152],comparison:0,compass:[6,20,47,57,88,107],compat:[3,19,40,50,58,61,62,63,64,65,66,69,86,142],compens:[2,118],compil:[4,58,59,142],complain:3,complement:139,complementari:[110,127],complet:[2,3,19,66,77,97,119],complex:[2,3,9,36,38,42,45,73,87,97,118,142],complic:2,compon:[2,29,30,33,34,35,36,37,38,39,40,42,43,58,59,61,62,63,64,65,67,68,69,73,74,75,77,81,87,96,97,114,118,123,136,137,152,153,167],componenet:2,composit:[2,73,116],compound:[109,118,119,163],compres:62,compress:[2,58,59,62,75,78],compris:[87,120,150],compton:[41,44],comput:[0,1],computation:[2,85,102],compute_modifi:[67,68,74,75,167],compute_sa:41,compute_xrd:44,concav:87,concentr:[71,80,116,120,146],concept:[2,62],conceptu:[2,68,97,110,139],concern:[2,30,32,72],concis:3,concurr:4,conden:[85,160,162],condens:[2,85,99,112,116,127,163],condit:[2,39,41,43,44,58,59,60,73,75,76,78,81,82,85,115,118,124],conducit:2,conduct:0,confer:[4,142],config:58,configur:[1,2,4,58,59,68,77,96,97,99,102,117,139,142,159,160,162,163,167,168],conflict:168,conform:[2,67,68,79,94,97,118],confus:163,conjuct:114,conjug:118,conjunct:[2,32,45,73,97,103,104,110,114,118,125,127,148,151],connect:[2,32,67,81,97,111,123,158,162],conner:99,connor:99,consecut:[3,45,110,127,131],consequ:[1,2,85,126],conserv:[13,67,72,73,74,80,81,97,113,114,115,123,133,152],consid:[2,29,32,58,61,63,66,67,85,118,150,152,158,167],consider:2,consist:[2,3,39,45,51,62,72,74,75,78,79,80,97,99,102,108,110,118,122,136,137,139,142,145,146,150,152],consistent_fe_initi:60,constant:0,constantli:69,constitu:[2,86,87,108,150],constrain:[2,62,69,72,81,82,96,118],constraint:[19,39,43,62,66,69,81,82,86,96,137],construct:[2,28,29,30,36,38,41,42,44,68,74,79,80,87,113,142,158,159],constructor:3,consult:4,consum:1,contact:[0,111,117,119,122,123,150],contain:[0,1,2,3,19,32,35,41,42,44,45,46,57,58,59,60,61,62,63,64,65,66,71,73,76,78,80,85,87,97,98,99,102,109,110,113,116,117,118,120,139,142,145,146,147,149,153,159,160,161,162,163,167,168],content:167,context:[2,4,40,165],contibut:29,contin:4,continu:[0,2,19,62,63,64,65,66,67,68,69,72,74,75,78,83,84,85,87,102,114,129,132,150,161,167],continuum:[2,60,85],contour_integr:60,contract:[68,74],contrain:81,contrast:[1,2,165],contrib:85,contribut:[2,29,32,33,34,35,39,40,42,43,61,62,63,64,65,68,73,81,96,97,114,116,118,136,137,142,152,167,168],control:[2,3,4,11,13,19,32,35,42,48,58,59,60,66,68,74,75,80,85,118,122,142,159,162],control_typ:60,convect:35,conveni:[2,13,58,65,153,168],convent:[13,50,55,57,79,116,118],converg:[2,19,58,59,66,67,68,75,78,79,81,96,97,109,110,127,152],convers:[42,59,63,110,111,112,118,127,131,135,148],convert:[2,5,6,8,12,16,17,18,35,45,47,58,59,63,65,88,89,93,94,97,98,116,142,160,162,166],convex:87,cool:69,cooordin:58,coord1:62,coord2:62,coord3:62,coord:[2,3,36,38,58,64,76,86,97],coordb:152,coordbb:152,coordiat:96,coordin:[1,2,3,19,32,33,34,42,45,58,59,61,62,64,66,67,68,69,74,76,81,82,84,85,96,97,98,99,101,117,152],coordn:62,coords:152,copi:[0,3,59,85,97,168],copper:166,coprocessor:[1,4],core:[0,1],coreshel:2,coreshell:[2,104,110,112],cornel:[2,46],corner:[2,59,87,168],corpor:4,corr:109,correct:[2,3,32,46,59,69,74,78,86,87,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,116,117,118,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168],correction_max_iter:60,correctli:[3,58,74,81,87,97,112,137,142,168],correl:[2,35,36,42,62],correpond:71,correspond:[1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,29,32,39,41,42,44,46,47,48,49,50,51,52,53,54,55,56,58,59,62,64,68,69,71,73,74,75,76,77,80,81,86,87,88,89,90,92,93,94,95,97,98,99,100,103,104,105,106,107,108,109,110,113,114,116,117,118,119,120,121,122,123,124,125,127,128,129,130,131,132,133,134,135,136,139,140,142,144,146,147,148,149,150,151,152,153,154,159,160,161,162,163,164,165,166,167],correspondingli:[136,137],cosin:2,cosineshift:11,cost:[1,2,3,19,41,43,44,59,62,66,74,80,85,110,127,131,142,159],costheta0:[159,160,162,163],costheta:149,costli:[3,4],coul:[2,4,18,21,22,32,46,96],could:[2,3,19,32,34,39,58,59,62,63,66,78,85,86,87,96,99,121,125],coulomb:[2,43,96,103,104,105,106,107,109,110,111,112,113,118,123,124,127,131,135,138,148,151,152,162,163,165,167],coulommb:2,count:[1,2,3,19,35,40,46,62,64,66,74,81,87,96,97,121,125,167],counterbal:69,counterbalanc:13,counterclockwis:46,counterpart:58,coupl:0,couple:[2,3],cours:[4,58,72,79,86,136,154],cov:152,coval:[2,13,118,139,152],cover:[2,60,73,118],cpp:[1,2,3,32,58,81],cpu:[1,4,167],cpuinfo:4,cpuremain:167,cr2:44,cr3:44,crai:58,creat:[0,1,2,3,19,35,39,40,41,45,58,59,60,61,62,63,64,65,66,67,68,71,74,75,76,77,79,85,97,99,102,109,116,117,135,144,145,146,149,152,159,160,161,162,163,167,168],create_atom:[2,19,35],create_box:[2,19,35,45,68,74,158,167],create_elementset:60,create_faceset:60,create_nodeset:60,createatom:0,creation:45,criteria:[59,67,96],criterion:[19,45,66,67,96,97,109,118,123,152],critic:[2,24,25,85,96],cross:[4,33,58,59,61,97,106,114,116,124,125,127,129,131,149,151,160,162,166],crossov:1,crozier:0,crucial:78,crystal:[2,4,29,30,38,76,84,167],crystallin:[2,161],crystallogr:[41,44],crystallograph:167,crystallographi:[41,44],cs1:44,cs_chunk:2,csanyi:[42,153],cscl:139,csequ:2,csh:[3,4],cshrc:3,csic:[117,159,160,162,163],csinfo:2,csisi:[117,159,160,162,163],cst:116,cstherm:2,csvr:2,ctcm:[98,116],ctype:3,cu1:44,cu2:44,cu3au:139,cube:[2,87],cubes:[19,66],cubic:[38,73,76,116],cuda:1,cuh:102,cummul:[2,65,67,125,167],cumul:[2,62,64,74,75,97],current:[0,1,2,3,4,19,30,32,40,43,58,59,60,62,65,66,67,68,69,74,79,80,81,82,85,86,96,97,102,109,113,116,118,119,123,126,136,137,139,140,141,149,154,160,162,167,168],curv:[2,45],curvatur:[122,150,166],custom:[0,2,3,33,34,35,40,43],cut:[1,2,4,19],cuthi:76,cutinn:[136,137],cutlo:76,cutmax:149,cutoff1:[107,113,127,131,135,138,148,151],cutoff2:[103,104,105,107,112,113,127,131,135,138,148,151],cutoff:[2,4,21,22,28,29,30,32,36,38,42,67,71,76,78,86,87,96,98,99,100,101,102,103,104,105,106,107,108,110,111,112,113,114,115,116,117,118,119,120,121,122,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166],cutoffa:117,cutoffc:117,cuu3:116,cval:44,cvff:4,cwiggl:86,cyan:59,cycl:[74,75],cyclic:46,cylind:[59,62,87],cylindr:2,cyrot:102,d3q15:73,d3q19:73,d_e:85,d_name:58,daan:84,damp:[2,74,75,78,96,97,103,104,106,110,113,118,123,127,135,148,151],dampflag:123,danger:[114,167],darden:113,darken:59,dash:123,dat:[2,35,60],data2xmovi:0,data:1,databas:0,date:[0,2],datum:[2,58,63],davenport:138,davi:86,david:[160,162],daw:[116,149],dcd:[2,58,59,77],deactiv:135,debug:[2,3,41,44,45,77],decai:[36,110,166],decid:[2,4,168],decod:59,decompos:[32,153],decomposit:[60,77],decoupl:2,decreas:[4,58,67,69],dedic:4,defect:[2,29,142],defin:[2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,70,71,73,74,75,76,77,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,99,100,101,103,104,105,106,107,108,110,111,113,114,115,117,118,120,121,122,123,124,125,127,128,129,130,131,132,133,134,135,136,137,138,142,143,144,145,146,147,148,149,150,151,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167],definit:[2,42,62,63,64,65,70,75,86,102,108,115,118,149,153],defint:167,deform:[2,43,68,74,136,137],deg2theta:44,degre:[2,5,6,8,12,13,16,17,18,36,38,39,44,45,46,47,49,50,55,56,59,62,67,74,75,77,79,81,84,88,89,93,94,95,96,113,116,125,167],degress:62,delai:[2,167],delet:[28,62,63,64,65,67,74,158,168],delete_atom:45,delete_bond:[20,21,22,23,24,25,26,27,28],delete_el:60,delimit:80,dellago:[2,69],deloc:[118,152],delr:139,delta_1:102,delta_3:102,delta_7:102,delta_ij:[139,149],delta_pi:102,delta_r:149,delta_sigma:102,deltah_f:71,demo:3,demonstr:[78,139],dendrim:125,denniston:73,denot:[41,69,110,124],dens:[67,80,118],densiti:[2,19,42,45,60,62,66,73,85,86,98,99,102,116,139,140,141,145,146,149,150,152,155,156,157,167],depart:0,departur:78,depend:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,21,22,23,24,25,26,27,28,29,36,39,42,45,46,47,48,49,50,51,52,53,54,55,57,58,59,62,64,65,66,68,71,73,74,75,76,80,81,83,85,86,87,88,89,90,92,93,94,95,96,98,99,100,101,102,103,104,105,106,107,108,109,110,111,113,114,116,117,118,119,120,121,122,123,124,125,127,128,129,130,131,132,133,134,135,136,139,140,142,143,144,145,146,147,148,149,150,151,152,153,154,159,160,161,162,163,164,165,166,167],dependend:2,deposit:[74,81],deprect:62,depth:[26,59,85,120,122,150],der:[32,108,109,135,165],deriv:[2,32,42,63,68,69,74,75,76,83,84,85,86,87,99,102,108,113,118,119,124,129,133,134,139,142,165],derjagin:165,derlet:76,descib:59,describ:[0,1,2,3,4,19,29,30,41,42,43,44,45,51,54,58,62,63,64,65,66,67,68,71,72,73,74,75,76,77,78,80,83,84,86,96,97,99,101,103,104,106,107,108,109,110,113,116,118,119,120,122,123,124,127,128,129,130,131,132,133,134,135,136,137,138,139,142,143,145,146,149,150,151,152,153,154,158,159,160,161,162,163,164,165,166,168],descript:[2,3],descriptor:[42,58],design:[0,2,3,41,44,60,67,74,76,85,100,101,106,110,112,118,135,136,137,140,141,149],desir:[2,3,4,35,39,40,43,45,62,65,68,72,74,81,96,97,114,116,125,136,137,159,160,162,167],desktop:[2,59],destabil:102,destre:94,destroi:3,detail:[1,2,3,4,19,34,35,39,40,42,43,45,57,58,59,60,62,63,64,65,66,67,68,69,72,73,74,75,78,81,84,85,96,98,99,101,102,105,106,107,108,109,110,113,114,118,119,122,123,124,125,127,128,129,130,131,132,133,134,135,136,137,138,139,143,145,146,150,152,153,154,164,165,167,168],detect:[36,97,109,125,126],determin:[1,2,4,26,32,39,41,43,44,45,58,59,61,62,63,64,65,66,68,71,74,76,77,78,79,80,86,87,99,105,109,113,116,120,121,123,131,139,142,146,150,152,158,165],devan:151,devanathan:162,develop:[0,2,3,4,75,78,99,102,118,141,142,152,163],deviat:[75,76,121],devic:1,devin:109,devis:141,dfactor:59,dft:142,dhug:78,dhugoniot:78,dia:139,diag:80,diagnost:[4,67,80],diagon:[2,42,43,68,74],diagonalstyl:153,diagram:[19,41,44,57,66,77],diallo:125,diam:59,diamet:[2,45,58,59,108,122,123,129,150,165],diamond:[118,139],dick:2,did:[96,114,116,123,160,162],dielectr:[106,110,111,112,127,131,135,148],diff:[2,4],differ:[1,2,3,4,19,28,29,32,36,42,45,57,58,59,62,64,66,67,68,69,72,73,74,76,77,78,81,82,83,84,85,86,87,88,97,98,99,102,105,106,108,109,114,115,116,118,120,122,123,124,127,128,130,131,138,139,140,141,143,144,145,146,147,149,150,151,152,153,154,159,160,162,163,165,167],differenti:[1,2,13,80,110,149,161],difficult:[68,77,125],difficulti:[36,38,81],diffract:[41,44],diffraction:[41,44],diffus:0,diffuse:2,digit:142,dihedr:[0,4,28,36,38,39,42,43,45,46,47,48,49,50,51,52,53,54,55,56,57,67,79,89,90,91,93,96,99,102,106,167],dihedral_coeff:[46,47,48,49,50,51,52,53,54,55,56,57],dihedral_cosine_shift_exp:11,dihedral_styl:[0,2,43],dihydrid:118,dij:81,dilat:[68,74,75],dim:[45,139],dimens:[1,2,19,35,43,45,58,59,62,66,68,73,74,75,78,86,97,167],dimension:[36,39,41,42,44,62,85,97,149],dimensionless:[37,42,85,153,165],dimer:[2,139],dimstr:[19,66],dintel_offload_noaffinity:4,dipol:0,dipolar:[13,58],dipole:113,dir:[1,3,76,78,149],dirac:42,direc:149,direct:[2,4,13,29,38,41,42,44,45,46,58,59,73,75,76,78,83,84,85,86,87,96,97,114,115,123,137],directli:[2,3,32,42,58,59,73,80,87,98,99,103,104,105,110,113,116,118,127,131,148,151,158,167],directori:[0,1,2,3,4,83,84,97,98,99,102,109,110,116,117,119,135,139,140,141,142,147,149,152,153,159,160,161,162,163],disabl:[4,85,126],disadvantag:[2,66],disallow:[58,74],discard:[19,66,87],discontinu:[96,133],discourag:139,discret:[2,59,73],discuss:[0,1],disk:[2,36],disloc:[29,142],disord:[29,142],disp:0,dispar:150,disperion:[113,131],dispers:[2,105,113,131,136,163],displac:[2,37,68,74,76,123],displai:[3,57,58,59],disregard:142,dissip:[2,31,70,72,83,84,114,115,123,136,137],dist:[2,35,40,58,77,79,158],distanc:[2,5,6,20,21,22,23,24,25,26,27,28,30,33,34,36,37,38,40,41,42,45,47,58,59,62,67,68,69,73,74,75,76,78,79,81,82,84,85,86,87,88],distinct:[2,150],distinguish:[2,42,118],distort:98,distrbut:98,distribut:[0,2,3,19,32,42,57,66,72,73,74,98,102,110,116,117,119,139,140,141,147,149,150,159,160,161,162,163],distro:149,ditto:166,div:4,divd:40,diverg:[84,99],divid:[2,4,19,35,39,40,43,57,62,63,64,66,76,96,97,119,152,163],divis:[2,56,73,102,135,167],dl_poly:2,dlammps_ffmpeg:59,dlammps_gzip:[58,59],dlammps_jpeg:59,dlammps_memalign:4,dlammps_png:59,dlammps_xdr:58,dlm:74,dlmp_intel_offload:4,dlopen:2,dlvo:[108,165],dm_lb:73,doc:[0,1,2,3,32,34,37,39,40,43,45,57,58,59,61,62,63,64,65,74,87,96,97,98,99,101,109,110,116,117,119,125,139,140,141,147,149,153,159,160,162,163,167,168],docuement:150,doe:[0,1,2,3,19,28,29,32,35,40,41,44,45,46,57,58,59,60,62,66,67,68,69,71,72,73,74,85,86,87,89,90,91,93,94,97,98,99,100,101,102,105,106,107,108,109,110,111,113,114,116,117,118,120,121,122,123,124,126,129,130,132,133,134,136,137,139,140,141,142,145,146,149,150,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168],doesn:[45,58,99,109,117,159,160,161,162,163],dof:[39,62],dof_per_atom:62,dof_per_chunk:62,doi:[2,76],domain:[2,19,41,44,59,66,68,73,74,77,85,86,97],domin:[1,118],don:[0,4,87,139,152,168],done:[1,2,19,45,56,58,59,60,62,64,65,66,67,68,71,74,77,81,83,84,96,97,99,105,116,131,137,138,139,145,146,158,167,168],donor:125,dot:43,doti:[102,149],doubl:[1,2,3,4,32,46,87,102,119,124,142],dover:60,down:[2,3,68,118,152],download:3,downsid:2,dpd:2,dpdtheta:[31,115],dpdtheta_i:[70,71],dr_ewald:41,drag:[2,35,74,75,82],dragforc:73,drai:[59,78],drain:96,dramat:[67,68,74,152],drautz:102,draw:59,drawn:[58,59,72],drayleigh:78,dreid:2,dreiding:0,drfourth:37,drho:[98,116,145,146],drift:[2,37,69,72],drive:[3,68,74,76,97],driven:[2,51],driver:2,drop:114,drsquar:37,drude:0,dt_collis:73,dt_lb:73,dt_md:73,dtqm:78,dudarev:44,due:[1,2,4,28,29,33,34,37,41,42,43,44,45,58,59,64,67,68,72,73,74,75,76,79,83,84,85,86,87,96,97,111,114,115,116,121,122,136,137,149,150,151,158,160,162,165,166,167],duffi:85,dullweb:74,dummi:[13,161],dump:[0,1],dump_modifi:[2,58,59],dunbrack:[2,5,46,106],duplic:[19,66,76],durat:[57,62,85,123],dure:[2,4,19,32,46,58,60,61,62,63,64,65,66,67,68,69,71,72,73,74,75,76,77,78,79,81,82,83,84,85,86,87,96,97,114,135,142,144,145,146,167],dvlo:165,dvx:2,dx_lb:73,dy3:44,dyanam:2,dynam:[0,2,3,4,19,31,37,45,58,59,60,66,67,70,72,74,75,77,78,79,83,84,85,96,97,114,115,118,136,137,157],dynamo:[98,116,139],dyre:132,e28637:13,e_1:102,e_2:102,e_a:80,e_b:119,e_ee:118,e_hbond:125,e_i:[2,102,119],e_j:[2,102],e_k:102,e_ke:118,e_kl:2,e_lj:[99,113],e_n:102,e_ne:118,e_nn:118,e_pr:118,e_rebo:99,e_torsion:99,e_tot:142,e_vol:142,eaa:88,eaat:47,each:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,32,33,34,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,71,72,73,74,75,76,77,80,81,82,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,162,163,164,165,166,167],eacn:[19,66],eam:[0,98,110],eangl:167,earli:[19,62,64,65,66],earlier:[97,123,139],earth:118,easi:[2,3,32,43,58,86],easier:[4,58,59],easili:[3,59,97],eat:47,eaxmpl:2,eba:6,ebb13:47,ebb:6,ebond:167,ebt:47,ec_ii:139,ec_ij:139,ec_jj:139,echo:[3,41,44],ecoul:167,ecp:118,edg:[2,19,41,44,58,59,86,87],edge:86,edih:167,edit:[4,168],edition:4,edu:[3,116,136],eebt:47,eff:0,effect:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,33,34,37,39,40,43,46,47,48,49,50,51,52,53,54,55,57,58,59,60,61,62,63,64,65,67,68,69,72,74,75,76,77,78,79,81,84,85,86,87,88,89,90,92,93,94,95,96,97,98,99,100,102,103,104,105,106,107,108,109,110,113,114,116,117,118,119,121,122,123,124,125,127,128,129,130,131,132,133,134,135,136,140,142,144,145,146,147,148,150,151,152,154,159,160,161,162,163,164,165,166,167],effici:[0,1,2,4,39,56,58,59,63,68,74,77,81,102,108,110,127,131,142,145,146,150],efficienc:4,efield:[81,96],eggebrecht:[110,152],ehex:2,eigenvalu:77,eimp:167,einstein:[2,84],either:[1,2,3,4,19,29,41,42,43,44,45,58,59,61,63,64,65,66,67,68,69,73,74,75,76,80,81,87,96,102,108,116,120,123,136,137,139,142,146,149,158,160,162],ejtehadi:[108,122,150],elaplong:167,elaps:[86,154,167],elast:[2,21,22,97,123,161],elastic:0,elba:13,electr:[2,60,119,166],electric:4,electrolyt:165,electron:[2,41,60,85,98,109,113,116,118,119,139,142,149,152,162,163,166],electron_integr:60,electron_temperatur:60,electron_unit:118,electroneg:[2,109,119,152],electroneg_compon:152,electrostat:[2,4,108,113,118,127,135,137,152,165],elem1:[119,139,153],elem2:[119,139,153],elem:152,element1:[98,116,152],element2:[98,116,152],element:[2,33,37,39,40,42,43,58,59,60,62,63,64,65,98,99,102,109,116,117,118,119,139,140,141,142,147,149,152,153,159,160,161,162,163,167],elementn:[98,116],elementset:60,elif:42,elig:125,elimin:[2,72,81,83,84],elj:113,ellips:2,ellipsoid:[2,45,58,96,122,137,150],elong:167,els:[40,59,61,62,63,64,65,74,85],elsewher:[139,167],elt:139,emac:0,email:[0,3,119],emb:87,emb_lin_neg:139,embed:[3,13,85,98,116,119,135,139,140,141,149],embt:47,emol:167,emphas:123,empir:[60,118],empiric:99,emploi:[69,161],empti:126,enabl:[2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,31,32,37,39,41,42,44,46,47,48,49,50,51,52,53,54,55,57,58,67,69,70,71,72,73,74,75,76,77,78,79,80,81,83,84,85,86,87,88,89,90,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,139,140,141,142,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166],enclos:[2,58,139,152],encod:[58,59],encompass:2,encount:[38,64],encourag:[80,82],end:[1,2,3,4,19,47,58,59,63,64,65,67,69,72,74,79,80,85,97,114,116,122,138,142,150,153,154,167],endbondtors:47,energet:[67,99],energi:[0,1,2,5,6,7,8,9,10,11,12,13,14,15,16,17,18,20,21,22,23,24,25,26,27,28,31,32,35,39,43,45,46,47,48,49,50,51,52,53,54,55,56,57,58,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114],energy_compon:152,enforc:[2,58,59,67,74,81,127],enforce2d:[2,96],eng:[3,58,109,141],engineer:[60,83,116],enginer:140,enhanc:[60,69],enlarg:59,enough:[45,66,78,86,87,110],enpub:116,ensembl:[2,32,35,74,77,78,114,152],ensight:2,ensur:[2,42,58,68,72,74,102,135,159,163],enter:[119,142,163],enthalpi:[80,116,167],entir:[0,2,3,19,31,39,41,43,44,45,62,66,67,69,72,74,75,76,77,80,82,85,113,131],entiti:[2,58],entri:[41,64,71,78,102,117,139,145,146,147,153,159,160,161,162,163],entry1:[145,146],enumer:58,enumuer:2,environ:[1,2,3,4,59,76,98,102,109,117,118,149,160],eos:71,epair:[99,121,125,167],epp:113,epq:113,eps0:165,eps14:135,epsilon0:162,epsilon:[2,18,21,22,27,28,32,46,86,87,96,101,106,107,108,110,111,112,113,120,122,124,125,126,127,128,129,130,131,132,133,134,135,138,143,148,150,151,159,164,165],epsilon_0:166,epsilon_14:106,epsilon_:150,epsilon_d:111,epsilon_i:[122,150],epsilon_i_:150,epsilon_i_a:[122,150],epsilon_i_b:[122,150],epsilon_i_c:[122,150],epsilon_j:[122,150],epsilon_j_:150,epsilon_j_a:[122,150],epsilon_j_b:[122,150],epsilon_j_c:[122,150],epsilon_lj:150,eqp:113,eqq:113,equal:[2,3,19,28,32,35,40,43,45,59,63,64,65,66,68,72,73,75,76,77,78,79,80,83,84,85,86,96,97,99,109,114,115,121,122,125,136,142,143,149,150,152,153,154,163,166,167],equat:[2,35,38,39,41,44,57,68,69,70,71,73,74,75,76,77,78,80,81,85,86,108,113,114,115,118,119,120,123,136,137,139,146,150,155,156,157,166],equation:[76,94],equilibr:[2,35,45,63,67,68,74,78,83,84,109,110],equilibrium:[1,2,6,8,10,11,12,13,16,17,18,20,23,24,25,26,27,47,48,68,72,73,74,75,78,79,81,84,88,89,93,94,109,139,147,152],equilibrium_start:60,equival:[2,13,40,58,61,62,63,64,65,68,74,79,99,114,118,152,160,162,167],equlibrium:2,er3:44,eradiu:118,eras:83,erat:137,erc:110,erfc:[110,127],erhart:[116,160,162],eros:139,erose_form:139,erot:2,errata:[160,162],erratum:86,error:[0,1,2,3,11,40,48,58,59,61,62,63,64,65,68,69,71,74,80,85,86,87,96,110,127,150,158,160,162],erta:123,especi:[4,45,66,78,79],essenti:[3,11,48,63,99,110,127,162,167],essential:75,essex:13,establish:32,estim:[1,2,19,29,35,43,60,66,80,167],esub:139,eta:[2,73,74,78,117,119,122,149,161,163],eta_dot:74,eta_ij:149,eta_ji:119,etail:167,etap:74,etap_dot:74,etc:[1,2,3,4,28,33,34,35,43,45,58,59,60,61,62,64,65,72,74,85,87,96,97,116,117,135,137,142,159,160,162,163,167],etol:[96,97],etot0:78,etot:[2,43,78,167],eu2:44,eu3:44,euler:[80,96,97],eulerian:60,europhi:73,evalu:[3,32,35,40,42,45,46,58,59,60,61,62,63,64,65,72,80,86,96,142,145,146,149,152,167],evanseck:[2,5,46,106],evaul:96,evdwl:167,even:[2,4,19,29,56,58,61,62,64,65,66,68,69,74,85,86,87,96,97,101,118,119,123,150,163,167],evenli:[19,43,66,73],event:[2,74,85],eventu:2,ever:28,everaer:[108,122,150],everi:[0,1,2,3,4,19,35,58,59,60,61,62,63,64,65,66,67,68,69,73,74,75,76,78,80,81,85,97,114,135,152,167,168],everyth:168,everywher:129,eviri:118,evolut:[69,73,77],evolv:[73,77],ewald:[2,41,43,96,103,104,105,110,113,118,127,131,148,151],ewald_disp:113,exact:[19,66,67,72,85],exactli:[2,19,35,45,64,66,72,78,114,116,123,136,145,146],examin:[2,67,80],exampl:[0,1],exce:[2,4,19,61,62,64,65,66,68,74,96],exceed:[19,66,74],excel:118,except:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,21,22,23,24,25,26,27,28,33,34,39,40,43,45,46,47,48,49,50,51,52,53,54,55,57,58,62,63,64,66,68,74,75,77,81,85,88,89,90,92,93,94,95,97,98,99,100,103,104,105,106,107,108,109,110,112,113,114,116,117,118,119,121,122,123,124,125,127,128,129,130,131,132,133,134,135,136,137,140,144,147,148,150,151,154,159,160,161,162,163,164,165,166,167],excess:118,exchang:[2,60,69,85,118],excit:118,excite:118,exclud:[2,4,39,42,58,62,96,123,136,137,158],exclus:[1,4,32,46,109,142],excurs:74,execut:[1,2,3,59],exempl:152,exemplari:72,exemplifi:118,exert:[2,87],exhaust:60,exhibit:[36,69,74,118],exist:[2,3,29,45,57,59,68,88,89,90,91,93,115,158,168],exit:[3,19,58,66,167],expans:[42,56,58],expect:[1,4,19,66,76,78,139,142],expens:[2,76,85],experi:[2,79,97,114],experienc:[2,4],expir:167,explain:[1,2,3,19,30,58,59,62,63,65,66,68,74,76,97,101,116,152,154,168],explan:[2,42,58,62,76],explanatori:[40,58,61,62,64],explic:143,explicit:[2,3,32,80,99,102,106,116,118,126,136,168],explicitli:[2,4,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,39,45,46,47,48,49,50,51,52,53,54,55,58,72,74,75,78,81,85,88,89,90,92,93,94,95,98,99,100,103,104,105,106,107,108,109,110,111,113,114,116,117,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,140,142,144,145,146,147,148,150,151,154,155,156,157,159,160,161,162,163,164,165,166,168],explictli:4,exploit:77,explor:[41,44],expon:[80,116,120,122,125,135,143,151],exponenti:[32,80,120,149,159,163,166],expos:3,exposit:[60,114],express:[2,42,45,68,76,80,85,102,116,118,129,139,152,153],expressiont:102,extend:[0,2],extens:[2,4,21,22,27,32,35,40,65,69,74,75,76,79,83,84,85,86,87,122,139,142,150,153,167],extensiv:167,extent:[1,19,21,58,66,99],exterior:[2,87],extern:[32,59,68,72,73,74,75,85,96,140,141],extra:[2,3,4,19,22,39,41,43,44,45,64,66,74,78,96,113,123,139],extract:[2,3,18,32,40,97,110,119,139,153],extract_atom:3,extract_comput:3,extract_fix:3,extract_glob:3,extract_vari:3,extrapol:1,extrem:[1,2,59,68,74,84,118,161],extrema:135,extreme:118,extrins:60,f_1:2,f_a:[160,161,162],f_ave:40,f_c:161,f_f:162,f_fix_id:78,f_harm:84,f_i:[13,149],f_id:[2,40,58,61,62,63,64,65,167],f_ij:149,f_indent:65,f_int:83,f_j:13,f_jj:35,f_k:149,f_langevin:85,f_max:78,f_r:[160,161,162],f_sigma:102,f_solid:84,f_ss:2,face:[2,86,87,122,139,150],facil:0,facilit:2,fact:[2,4,84,123,152],factor:[1,2,8,12,16,17,18,19,22,23,32,35,41,42,44,46,54,58,59,63,66,68,69,73,74,75,77,79,80,81,86,87,93,99,102,103,104,106,110,111,112,114,115,118,123,126,127,139,142,145,146,147,148,151,154,159,167],fail:[3,68,96,97,112],fairli:[3,168],faken:30,fall:[2,64],fals:152,famili:163,familiar:[0,3,168],fan:149,far:[2,58,66,68,74,76,79,86,89,93,97,167],farrel:[160,162],farther:58,fashion:[2,19,45,66,74,75,78,84,85,86,97,136],fast:[2,4,58,78,80,136,137,142,167],faster:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,21,22,23,24,25,26,27,28,37,39,46,47,48,49,50,51,52,53,54,55,58,66,74,75,81,83,85,88,89,90,92,93,94,95,98,99,100,102,103,104,105,106,107,108,109,110,113,114,116,117,119,121,122,123,124,125,127,128,129,130,131,132,133,134,135,136,140,144,147,148,150,151,154,159,160,161,162,163,164,165,166],fastest:[1,2,85],fault:29,fava:122,favor:67,fcc:[2,29,30,35,38],fcold:69,fdt:[70,71,80],fdti:32,fe2:44,fe3:44,fe_md_boundari:60,featur:[0,2,3,42,59,67,72,77,87,96,168],fecr:116,feel:[76,87,97],fehlberg:80,felling:141,felt:87,fene:[2,4],fennel:[110,127],fep:0,ferguson:[2,46],fermi:[1,162],fermion:118,fernando:138,few:[1,2,3,61,62,63,64,65,69,74,81,96,97,99,152],fewer:[1,3,4],feynman:77,ffield:[109,119,152],fflag1:59,fflag2:59,ffmpeg:59,ffplai:59,fft:[1,3,43],fhot:69,ficiti:158,fictiti:[2,77,79,110,127,131,158],field:0,fifth:[2,120,147],figshar:76,figur:[1,4,78,168],fij:113,file0:76,file1:[3,71,76],file2:[3,71],file:[0,1],filenam:[4,19,58,59,60,62,63,64,65,66,71,76,80,85,97,98,99,102,110,116,117,119,120,139,140,141,145,146,147,149,152,153,159,160,161,162,163,167],filep:58,fill:[45,59,85,102,142,168],filter:60,finchham:[2,112],find:[0,2,3,4,30,32,40,67,68,71,76,79,96,97,110,127,131,139,145,146,152,168],fine:[4,84,168],finer:[42,45],finger:45,finish:[2,3,19,66],finit:0,finni:116,fire:[96,97],first:[0,1,2,3,4,6,19,21,22,28,29,35,37,38,39,40,43,44,47,58,59,62,63,64,65,66,67,71,72,73,74,76,77,78,81,82,83,84,85,88,96,97,98,99,101,102,103,104,106,109,110,116,118,119,120,123,124,126,127,131,136,137,139,141,142,145,146,147,149,152,153,158,159,160,161,162,163,166,167,168],fischer:[2,5,46,106],fit:[2,79,99,102,139,145,146,161,168],five:[30,78,102,140],fix:[0,1],fix_flux:60,fix_heat:69,fix_id:[68,74,75,78],fix_manifoldforc:168,fix_modifi:2,fix_nv:168,fix_rattl:81,fix_shak:81,fixedpoint:[68,74],fixid:[59,60],fji:113,flag:[3,4,33,34,41,44,58,59,65,67,99,125,126,139,142,158,168],flag_buck:105,flag_coul:[105,113,131],flag_lj:[113,131],flagfld:[136,137],flaghi:[136,137],flaglog:[136,137],flagvf:[136,137],flat:[2,4,85,86],fld:[86,136,137],flexibl:[2,59,62,118,161,167],flip:[2,74],fluctuat:[2,32,68,72,73,74,75,76,84,85,94,115],fluid:[2,40,68],flux:2,flv:59,fly:[19,59,60,81,102,142,167],fmass:77,fmax:[96,167],fmsec:74,fno:4,fnorm:[96,167],fnve:69,focu:81,foil:[42,76,153],fold:[4,82],follow:[0,1,2,3,4,5,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,35,36,38,40,42,43,45,46,48,49,50,51,52,53,54,55,56,58,59,60,61,62,63,64,65,66,70,71,72,73,74,75,77,78,79,80,81,83,84,85,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,168],foo:[3,58,59,80],foo_species:80,foot:2,forc:[0,1],forcefield:[79,125],forcegroup:73,ford:113,forgiv:74,fork:[58,168],form:[2,28,32,33,34,36,40,42,43,58,61,62,63,64,65,72,79,80,85,86,87,88,91,94,97,99,102,115,116,118,121,125,126,138,139,141,142,145,146,147,148,149,150,152,153,154,160,161,162,165,167],formal:[2,35,72,74,77,152],format:[2,19,58,59,62,64,65,66,71,80,85,97,98,99,102,116,119,120,126,139,141,145,146,151,153,163,167],formation:71,former:[2,19,66,85,102],formul:[1,2,43,74,79,81,99,102,116,118,122,139],formula:[2,6,28,29,30,32,33,34,35,39,41,43,44,45,47,57,58,62,63,64,65,76,82,86,88,90,99,101,102,106,107,108,113,114,116,117,122,123,124,125,126,127,129,130,131,133,134,136,137,139,143,144,150,151,154,159,160,161,162,163,164,165,167],forth:[1,2,3],fortran:[2,3,116,139],forward:[32,97],foster:[102,149],found:[2,30,58,67,69,73,110,113],four:[2,3,28,42,85,94,97,142],fourier:2,fourth:[2,4,37,79,106,120,147,152],fox:[2,41,46,157],fqq:113,fraction:[1,2,4,19,43,59,67,68,78,80,97,102,120,123,136,137],frame:[42,60,78,122],framer:59,framework:[98,153],frattl:69,free:[2,13,29,32,76,83,84,85,97,118,135,142,144,149,165],freedom:[2,39,62,67,74,75,77,81,84,96,113,167],freeli:[0,2,59],freez:2,frenkel:[2,69,84],frequenc:[2,4,77,78,80,114,118,152],frequent:[29,30,36,38,42,69],fri:78,friction:[2,78,85,123],from:[0,1],front:78,frontend:59,frozen:[2,39,72,121],fs2:[2,35],ftol:[96,97],fuction:110,fudg:81,fulfil:2,full:[1,2,4,35,59,63,69,73,76,80,102,116,118,119,122],fuller:96,fulli:[2,76,96,97,110,149,168],fulton:116,fumi:103,funcfl:116,fund:0,funrol:142,further:[2,37,59,62,64,65,73,77,85,96,97,98,101,109,142,152],furthermor:[11,48,69,80,115,118],futur:[0,2,66,72,97,140,141],g_jik:149,g_p:85,ga3:44,gaa:102,gai:122,gain:4,galindo:143,gamma0:13,gamma:[2,13,73,78,114,115,117,122,139,143,155,156,157,159,160,162,163,167],gamma_:85,gamma_ijk:160,gamma_n:123,gamma_p:85,gamma_t:123,gammaa:143,gammafactor:73,gammar:143,gan:[149,159,160,162,163],gan_sw:149,gan_tersoff:149,gao:[2,5,46,106],gap:[136,137,153],gather:3,gather_atom:3,gathert_atom:3,gauch:51,gauss:111,gaussian:[2,35,37,72,77,79,114,118,121],gavhan:4,gaybern:[2,4,96],gd3:44,gdot:137,ge4:44,gec:[160,162],gen:74,gener:0,gentler:86,gentli:117,geom:2,geometr:[2,45,58,66,74,87,97,101,107,108,110,113,118,120,122,124,127,128,129,130,131,132,133,134,135,136,137,138,143,146,150,154,164,165,167],geometri:[2,9,19,45,66,68],gerber:135,germann:[75,129],germano:122,get:[0,1,2,3,4,19,35,42,45,58,59,61,66,68,87,97,110,163,168],get_natom:3,get_rank:3,get_siz:3,gewald:2,gezelt:[110,127],ghost:[2,4,30,68,74,114,115,118,123,126],gif:59,gifsicl:59,gillan:153,gingold:[155,156],git:168,give:[0,1,2,3,4,28,36,38,45,58,62,63,64,65,68,74,76,96,99,102,118,125,139,142,150,160,161,162],given:[2,3,4,11,38,42,43,48,57,58,62,68,69,72,73,74,75,76,77,78,79,80,81,82,85,86,87,98,99,102,103,104,105,107,108,109,110,111,114,115,116,118,119,120,122,123,125,127,128,129,131,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,166],glosli:142,glotzer:114,glue:3,gnu:0,gnuplot:3,goddard:[2,9,95,118,125],goe:[28,42,45,69,96,113,117,124,129,132,154,166],gold:29,goldman:78,good:[1,2,4,19,30,41,44,66,74,81,97,98,108,116,142,163,167,168],gordan:42,gordon:2,got:168,gould:[2,46],gov:[0,98,116,119],govern:73,gpa:99,gpl:0,gpt:142,gpu:[1,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,39,46,47,48,49,50,51,52,53,54,55,74,75,81,88,89,90,92,93,94,95,98,99],grab:2,grad:2,gradient:[2,68,69,85,97,137,145,146],graft:67,grain:[2,13,18,28,45,51,71,76,80,120,124,142,146,151],gram:[62,116],gran:[2,86,87],granular:0,graph:3,graphic:3,graviti:2,grdient:60,great:[78,168],greater:[1,68,72,74,76,101,103,104,105],greatli:[41,69],green:[2,35,59,77,102,168],green_kubo:2,grest:[21,22,67,105,123,131],grid:[19,41,44,66,73,85],grigera:2,gromac:96,gromacs:[2,58,96,124],groot:114,ground:[2,31,70,118],group:[2,3,4,19,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,97,152,163,167],group_id:3,grow:[2,74,76,80,123],growth:2,gsmooth_factor:139,guarante:[45,58],guess:[58,168],gui:[3,168],guid:[1,155,156,157],guidelin:1,gullet:139,gulp:2,gunnel:142,gunsteren:135,guo:[2,5,46,51,106],gyrat:2,gzip:[58,59,97],h12:122,h2o:[120,146],had:[2,3,40,58,61,62,63,64,65,67,68,72,74,75,85,114,123,158,167],hafskjold:[2,69],half:[1,2,4,19,59,61,66,74,85,86,87,102,108,118,142],halfwai:[19,59,168],halperin:36,halsei:123,halt:[19,66,69],halv:59,hamak:[86,87,108,150],hamilton:29,hamiltonian:[74,118],han:116,hand:[2,28,29,45,55,59,73,80,110,118],handl:[4,59,118,136,163],happen:[2,63],hara:161,hard:[1,79,152],harden:154,harder:[86,87],hardi:60,hardwar:[1,4,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,39,46,47,48,49,50,51,52,53,54,55,74,75,81,88,89,90,92,93,94,95,98,99,100,103,104,105,106,107,108,109,110,113,114,116,117,119,121,122,123,124,125,127,128,129,130,131,132,133,134,135,136,140,144,147,148,150,151,154,159,160,161,162,163,164,165,166],harmon:[2,4],harmonic_fix_wal:137,harrison:99,hartre:[116,118,142],hassl:79,hat:2,have:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,21,22,23,24,25,26,27,28,29,30,34,35,36,37,38,39,42,43,45,46,47,48,49,50,51,52,53,54,55,58,59,61,62,63,65,66,67,68,72,73,74,75,76,77,78,81,85,86,87,88,89,90,92,93,94,95,96,97,98,99,100,102,103,104,105,106,107,108,109,110,113,114,115,116,117,119,121,122,123,124,125,127,128,129,130,131,132,133,134,135,136,137,139,140,141,142,144,145,146,147,148,149,150,151,152,154,159,160,161,162,163,164,165,166,167,168],hbond:2,hcn:80,hcp:[29,30,139],he1:44,head:[2,6,47,88,99,121,125,168],header:[2,58,59,62,63,64,65,78,85,98,102,116,158],heat:2,heavili:[19,66],heavisid:85,hebenstreit:4,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159,160,161,162,163,164,165,166],infrequ:[2,74,114],infti:[111,136,137],ingtegr:102,inher:96,inherit:2,inhomogen:85,inidividu:96,init:152,init_fil:85,initi:[2,3,19,32,58,59,60,63,66,67,68,71,72,73,74,75,77,78,79,80,83,84,85,86,96,97,99,113,114,142,145,146,152,167],initial:2,initialt:85,inlclud:3,inner2:[106,124],inner:[4,58,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,113,114,116,117,118,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,148,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166],inner_distance_cutoff:125,innner:133,inorgan:[2,163],inp:[153,163],input1:40,input2:40,input:[0,1],insert:[45,153,158],insid:[2,3,45,58,61,69,73,86,87],inside:[73,129],insight:2,instabl:[73,113],instal:[1,2,3,4,58,59,97,105,106,127,131,135,142,168],install:0,instanc:[2,3,121,149],instantan:[2,67,68,72,74,75,78,167],instanti:[2,3,60],instead:[1,2,3,4,19,29,34,40,46,58,62,64,65,66,68,73,104,105,116,126,128,135,139,142,144],instruct:[2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,39,46,47,48,49,50,51,52,53,54,55,59,74,75,81,88,89,90,92,93,94,95,98,99,100,103,104,105,106,107,108,109,110,113,114,116,117,119,121,122,123,124,125,127,128,129,130,131,132,133,134,135,136,140,144,147,148,150,151,154,159,160,161,162,163,164,165,166],instruction:3,insuffici:2,insult:74,insur:[2,3,30,45,58,59,85,86,87,108,122,150,167],integ:[2,3,29,38,40,42,45,46,49,50,53,56,58,59,62,67,72,73,78,80,85,92,114,115,139,153],integral:[77,145,146],intel:1,intel_coprocessor:4,intel_cpu_intelmpi:4,intel_cpu_mpich:4,intel_cpu_openpmi:4,intend:[2,18,72],intens:[1,2,33,34,35,37,39,40,41,44,62,63,64,65,66,67,74,75,85,167],intensiv:167,inter:[58,67,97,102],interact:[1,2,3,13,28,32,36,38,39,42,43,46,51,56,57,58,67,76,77,79,80,85,86,87,89,90,91,93,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,146,148,149,150,151,152,153,154,158,159,160,161,162,163,164,165,166,167],interatom:[45,58,83,84,98,102,116,118,139,142,152,161],intercept:41,interchang:2,interconvert:118,interesect:87,interest:[1,3,44,77,84,117,137],interf:168,interfac:0,interfer:[74,99],interg:2,interi:137,interior:[2,19,87],interlac:139,interleav:[2,45],intermedi:[2,59,76,94,97],intermolecular:99,intern:[0,2,3,4,5,6,8,12,16,17,18,31,32,43,47,59,60,70,71,74,75,80,88,89,93,94,96,115,120,145,146,155,167],internal:59,internal_element_set:60,internal_quadratur:60,internat:[4,41,44,60],interpenetr:139,interpentr:[155,156],interpol:[2,59,60,71,73,76,97,102,145,146,160],interpret:[2,3,56,59,64,123,154],interrupt:78,intersect:[2,41,87],intersert:87,interspers:96,interstiti:142,interv:[2,35,63,74,78,152],intestieti:41,intial:[2,99],intiial:19,intramolecular:13,introduc:[2,36,38,59,69,74,78,94,98,110,118,127,131,135,159],introduct:0,inv:[41,44],invalid:[33,97,136,137],invari:[38,42],invent:81,invers:[2,26,41,44,78,94,95,103,110,127,164,165],invert:[1,2],invis:87,invoc:67,invok:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,21,22,23,24,25,26,27,28,32,33,34,39,40,45,46,47,48,49,50,51,52,53,54,55,58,59,60,61,62,63,64,65,66,67,68,69,72,73,74,75,76,81,82,83,84,85,86,87,88,89,90,92,93,94,95,96,97,98,99,100,103,104,105,106,107,108,109,110,113,114,116,117,119,121,122,123,124,125,127,128,129,130,131,132,133,134,135,136,137,140,144,147,148,150,151,153,154,159,160,161,162,163,164,165,166,167],involv:[2,40,73,96,97,101,122,159,160,162],ion:[2,85,102,111,119,121,139,142,152,162,166],ionic:[2,103,104,111,118,119,148,152],ioniz:[109,118],ipp:0,ir3:44,ir4:44,irregular:[2,19,66,68,74],irrelev:147,irrespect:[136,137],irrevers:80,isbn:165,isenthalp:74,ismail:[105,131],isn:[3,69],iso:[68,74,75],isobar:[74,115],isodem:118,isoenerget:115,isoenthalp:115,isol:123,isomorph:77,isotherm:[74,115],isotrop:[2,36,122,136,137],issu:[1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,30,39,46,47,48,49,50,51,52,53,54,55,59,67,68,69,74,75,77,81,84,88,89,90,92,93,94,95,97,98,99,100,103,104,105,106,107,108,109,110,113,114,116,117,119,121,122,123,124,125,127,128,129,130,131,132,133,134,135,136,140,144,147,148,150,151,154,158,159,160,161,162,163,164,165,166,167],issue:60,item:[2,19,58,66],iter:[2,19,66,68,81,96,97,152,167],iterat:96,ith:[40,58,61,62,63,64,65,167],itself:[2,3,35,58,59,63,85,97,110,119,122,145,146],ityp:45,izumi:161,j0jt:35,j20:63,j_m:42,jackson:143,jacs:[2,46],janssen:76,januari:139,jaramillo:118,jcp:86,jeffer:4,jello:74,jeremi:141,jik:102,jmm:42,job:81,jochim:74,join:[2,29,123],joint:125,jon:29,jone:[1,2,21,22,32,46,60,69,86,87,96,99,101,104,105,106,107,108,113,122,124,125,126,127,128,129,131,132,134,135,138,143,149,150,151],jonsson:[30,97,152],jorgensen:[2,54,110,127,131],journal:[51,60,116,142,155,156],jpeg:59,jpg:[58,59],judici:2,jump:[2,18,75],jun:4,just:[2,3,13,35,43,58,59,62,85,97,99,101,149,168],justo:117,jusufi:[111,121],jut:87,k11:35,k22:35,k33:35,k_2:91,k_4:91,k_s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2,42,43,58,60,66,67,70,76,80,85,92,96,125,139,152,163,167],post:[0,2,35,58,60,78],pot:123,potentail:119,potenti:0,potentiel:135,potin:142,pour:[2,81],power:[3,4,37,42,102],pparam:32,ppm:[58,59],ppn:4,pppm:[0,1],pproni:72,pr3:44,pr4:44,practic:[68,74,163,168],prb:[160,162],prd:[2,97],pre:[2,79,86,102,123,145,146,152,154],prec:[4,152],preced:[2,46,61,62,63,64,65,80,97,102,125,167],preceed:[3,63,86],precis:[1,4,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,39,45,46,47,48,49,50,51,52,53,54,55,58,62,65,68,69,74,75,81,88,89,90,92,93,94,95,96,98,99,100,103,104,105,106,107,108,109,110,113,114,116,117,119,121,122,123,124,125,127,128,129,130,131,132,133,134,135,136,140,142,144,147,148,150,151,152,154,159,160,161,162,163,164,165,166,167],predefin:[55,118],predict:[1,2],prefactor:[8,9,12,16,17,18,57,63,86,89,93,94,96,108,121,147,150,151,154,165],prefer:[79,99,168],prefix:[3,59,80],preliminari:[71,145,146],prematur:96,preprint:[42,153],prescrib:[2,60,62],presenc:[58,73,136,137,142,165],present:[1,4,59,72,73,87,109,118,126,135,142,150,152],preserv:[68,74,81],press:[2,4,13,32,43,68,74,75,113,139,162,165,167],pressur:[1,2],pressure_with_eviri:118,presum:[30,97],prevent:[2,56,94,96,97,114,155,156,158],previou:[0,2,3,62,64,65,66,96,102,123,125,139,145,146,167],previous:[3,40,45,58,61,62,63,64,65,81,85,86,123,167],price:[2,113],primari:[0,2,85],prime:[124,142,160,162],primit:[2,87],princip:152,principl:[2,3,118,142,159,168],print:[0,1,2,3,4,19,35,40,42,58,59,62,63,64,65,67,68,73,74,75,76,78,80,81,96,97,99,114,121,125,152,167],printfluid:73,prism:2,privileg:3,probab:154,probabl:[56,66,67,74,86,96,145,146],problem:[0,1,2,3,19,35,60,66,68,79,84,87,96,97,110,113,125,168],proc:[1,3,4,58],proce:[19,28,66,97,142,167],procedur:[2,19,66,74,75,83,84,96,97,99],proceed:142,procesor:19,process:1,processor:[1,2,3,4,19,45,58,59,60,62,66,67,68,72,73,74,77,81,85,97,114,152],processsor:[19,66],procp1:58,produc:[1,2,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,21,22,23,24,25,26,27,28,39,40,43,46,47,48,49,50,51,52,53,54,55,58,59,61,62,63,64,65,66,67,72,74,75,78,80,81,85,86,88,89,90,92,93,94,95,96,97,98,99,100,103,104,105,106,107,108,109,110,113,114,116,117,118,119,121,122,123,124,125,127,128,129,130,131,132,133,134,135,136,140,144,147,148,149,150,151,154,159,160,161,162,163,164,165,166,167],product:[2,4,42,80,118,120,146],profil:[2,62,65,69,97],program:[2,3,4,58,59,73,116],progress:[1,19,66,78,96,97,167],project:[2,168],promot:102,prompt:3,proni:72,prop:2,propag:[74,78,118],propens:2,proper:[67,76,139,168],properli:[97,115],properti:0,proport:[2,19,32,66,78,80,123],propos:[2,42,68,74,127,141,161],protein:[4,45,82],proton:[162,166],prouduc:65,prove:[31,70,73],provid:[1,2,3,4,13,29,41,44,45,59,61,62,65,67,68,73,74,78,83,84,97,99,102,109,110,114,117,118,123,125,126,135,136,139,141,142,149,152,153,158,159,160,161,162,163,167,168],pscrozi:0,psec:74,pseudo:118,pseudopotenti:142,psf:2,psi:[119,165],psi_ij:119,pstart:[74,75],pstop:[74,75],pstyle:32,psxevar:4,pt2:44,pt4:44,ptarget:68,pthread:4,ptr:[2,3],pu3:44,pu4:44,pu6:44,publish:[73,110,139,142,160,162],pull:168,puls:85,pump:[136,137],purchas:59,pure:[3,140,141,160,162],purport:3,purpos:[2,41,44,45,58,65,67,68,76,77,79,105,131,142],push:[76,96,123,154,168],put:[2,3,45,58],pxx:[68,74,167],pxy:[2,167],pxz:[2,167],pydir:3,pyi:[68,74,167],pymol:3,pymol_aspher:0,pympi:3,pypar:3,python:[0,2],pythonpath:3,pyz:[2,167],pzz:[68,74,78,167],q_1:152,q_2:152,q_3:152,q_i:[119,135],q_j:135,qdist:[110,127,131,135],qeq:[2,109,110,152],qeqall:152,qeqallparallel:152,qfile:110,qinitmod:152,qoffload:4,qopenmp:4,qoverrid:4,qtb:78,quadrant:4,quadratur:[32,60],quadrupl:98,quadruplet:[57,88,89,90,91,93,94],qualiti:[59,99],quantic:152,quantit:[37,123],quantiti:1,quantum:[2,42,77,78,99,102,118,142,152],quantum_temperatur:78,quartic_spher:60,quartz:78,quasi:77,quaternion:[2,45,122],queri:[3,28],quest:2,question:[76,168],quick:[0,4],quickli:[36,66,96,97,99],quickmin:[96,97],quicktim:59,quit:[73,153,167],quot:139,quotat:152,r10:102,r12:122,r_1:42,r_2:42,r_c:[111,113,121,162],r_cut:[102,138],r_e:119,r_fu:[136,137],r_i:[13,42],r_ii:42,r_ij:[13,102,118,149,166],r_ik:149,r_j:13,r_jik:149,r_m:138,r_me:111,r_mh:121,r_min:112,r_ub:5,ra2:44,rad2theta:44,radial:[42,62,96,118,125,145,146],radian:[5,6,8,12,16,17,18,44,47,55,79,88,89,93,94],radiat:[41,44,85],radii:[42,67,108,116,122,123,136,137,142,165],radit:118,radiu:[2,33,34,41,42,58,59,73,82,86,87,102,108,118,119,123,127,135,136,137,138,139,152,153,162,165],rahman:[2,68,74,78],rai:44,ram:162,raman:4,ramp:[2,72,74,78,86,106,114,124,135,136,138,154,166],ran:[2,3],random:[2,45,59,67,72,73,74,77,78,85,114,115],randomli:45,rang:[1,2,4,38,39,40,42,43,44,51,58,59,60,96,99,100,102,103,104,105,106,107,108,110,111,112,113,114,116,118,120,122,124,125,127,128,129,130,131,132,133,134,135,136,137,138,139,142,143,144,148,149,150,151,152,158,162,164,165,166,167],rank:[2,3],rankin:75,rapid:[2,3],rapidli:[67,74,110,114],rare:2,rasmol:2,rasmussen:122,raster3d:2,rate:[2,4,60,78,80,83,84,120,136,13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135,136,139,140,142,144,147,148,150,151,152,153,154,159,160,161,162,163,164,165,166],respond:[2,118],respons:2,resquar:[2,122],rest:[2,79,102,137,139,167],restart1:77,restart2:77,restart2data:0,restart:[0,1],restor:[45,167],restrain:13,restraint:[79,126],restratin:79,restrict:[1,2],result:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,21,22,23,24,25,26,27,28,32,34,35,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,58,59,61,62,63,64,65,66,67,68,69,72,73,74,75,77,80,81,83,84,85,86,88,89,90,92,93,94,95,97,98,99,100,103,104,105,106,107,108,109,110,113,114,116,117,118,119,121,122,123,124,125,127,128,129,130,131,132,133,134,135,136,137,139,140,142,144,145,146,147,148,150,151,154,159,160,161,162,163,164,165,166],retain:[99,102,142],retriev:[2,140,141],rev:[2,29,36,38,42,43,74,75,83,84,102,108,109,110,113,116,117,118,122,123,129,136,137,138,139,141,145,146,149,150,153,159,160,161,162,163],revers:[2,32,50,67,74,76,83,97,135],review:[42,142,153,168],rewrap:58,rfac0:[42,153],rg0:82,rh3:44,rh4:44,rheolog:2,rhi:[145,146],rho0:[139,156,157],rho0_meam:139,rho:[73,98,103,104,105,116,138,139,140,141,145,146,150,155],rho_0:[156,157],rho_alpha_beta:116,rho_bkgd:139,rho_colloid:86,rho_e:85,rho_i:[140,141],rho_ref_meam:139,rho_wal:86,rhodopsin:[1,4],rhosum:[155,156,157],rhot:69,rhs:80,rick:[109,152],right:[2,3,19,29,45,55,57,66,67,73,76,80,110,168],rightmost:[19,66],rii:[33,34],rij:[36,38,76,114,115,145,146,158],rin:[125,132,133],ring:[2,46,77],rino:[30,163],rirj:123,risi:[42,153],risk:79,rix:[33,34],rk4:80,rkf45:80,rlo:[145,146],rmin0:[42,153],rmin:129,rms:80,rnemd:2,robust:96,rock:139,rockett:149,role:2,ronchetti:38,root:[3,32,33,34,116],rose:139,ross:139,rosski:77,rot:[2,35,77,79],rotat:[2,42,45,58,62,87,96,113,122,150,167],rotation:38,rough:[2,45,59],roughli:[19,59,74,97],round:[1,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,39,46,47,48,49,50,51,52,53,54,55,74,75,81,88,89,90,92,93,94,95,98,99,100,103,104,105,106,107,108,109,110,113,114,116,117,119,121,122,123,124,125,127,128,129,130,131,132,133,134,135,136,140,144,145,146,147,148,150,151,154,159,160,161,162,163,164,165,166],rous:72,rout:[32,125,135],routin:[2,3,4,73,142],roux:2,row:[2,34,44,62,63,64,65,85,118],rozero:139,rrespa:[1,4,74,98,99,100,101,103,104,105,106,107,108,109,110,111,113,114,116,117,118,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,136,137,138,139,140,141,143,144,145,146,148,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166],rsq:[145,146],rsurfac:85,ru3:44,ru4:44,rub:5,rubia:[140,141],rule:[0,2,13,29,45,63,67,74,87,98,100,101,107,108,113,125,130,139,143,154,158,159,160,162,166],run1:2,run2:2,run3:2,run4:2,run5:2,run6:2,run7:2,run8:2,run:[0,1],run_styl:[4,74,96,98,99,100,101,102,103,104,105,106,107,108,109,110,111,113,114,116,117,118,121,122,123,124,125,126,127,128,129,130,131,132,133,134,136,137,138,139,140,141,142,143,144,145,146,148,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166],rung:80,runtim:59,rutherford:85,rutuparna:[160,162],rxn:80,ryckaert:[81,94],rydberg:142,s0st:2,s2050:1,s2629:116,s319:60,s_i:[2,118],s_ij:2,saddl:97,sadigh:[116,140,141],saed_vtk:41,safe:[59,168],safran:165,sagui:113,sai:[1,168],said:96,sakai:161,sall:152,salt:[111,121,139],salter:152,same:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,21,22,23,24,25,26,27,28,32,33,34,35,36,37,38,39,40,42,43,45,46,47,48,49,50,51,52,53,54,55,58,59,60,61,62,63,64,65,66,67,68,69,72,73,74,75,76,77,78,79,81,83,84,85,87,88,89,90,92,93,94,95,97,98,99,100,102,103,104,105,106,107,108,109,110,111,112,113,114,116,117,118,119,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,139,140,143,144,147,148,149,150,151,152,154,158,159,160,161,162,163,164,165,166,167,168],sampl:[1,2,3,35,59,62,63,74,77,82,84,102],sample_frequ:60,sandia:[0,29,119,139],saniti:79,satellit:2,satisfi:[30,41,42,44,68,69,73,75,81,96,123],satur:111,save:[2,59,67,72,80,85,102],sb3:44,sb5:44,sc3:44,scalabl:[0,1,4],scale:[0,1,2,4,35,40,42,46,58,59,60,63,68,73,74,75,77,78,83,84,85,98,99,111,118,120,123,136,137,139,142,167],scalegamma:73,scalexi:[68,74,75],scalexz:[68,74,75],scaleyz:[68,74,75],scatter:[3,41,44],scatter_atom:3,scatter_coord:3,scenario:[2,67,87],schaik:135,schell:161,schemat:67,scheme:[2,72,74,77,81,85],schmid:114,schroding:118,schroeder:38,sci:[30,109,141,149,152],scienc:[60,67,76,83,116,140,152,161],scientif:[42,116],scm:3,scratch:[19,66],screen:[0,1,2,3,4,41,44,59,73,81,97,106,110,127,139,159,162,163,164,165,166,167],screenshot:3,scripe:3,script:[0,1],sea:3,search:[0,36,38,96,97,123],secant:71,second:[1,2,3,4,28,29,35,37,38,39,43,44,56,58,62,63,64,65,67,69,71,72,77,79,81,82,83,84,85,96,97,101,102,103,104,105,109,110,116,118,119,120,123,124,126,129,139,147,152,159,161,162,163,166,167],second_mo:152,secondari:51,section:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,31,32,33,34,35,37,39,41,42,44,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,62,63,64,65,66,67,69,70,71,72,73,74,75,76,77,78,80,81,83,84,85,88,89,90,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Documentation","5. Accelerating LAMMPS performance","6. How-to discussions","11. Python interface to LAMMPS","5.USER-INTEL package","angle_style charmm command","angle_style class2 command","angle_style cosine command","angle_style cosine/delta command","angle_style cosine/periodic command","angle_style cosine/shift command","angle_style cosine/shift/exp command","angle_style cosine/squared command","angle_style dipole command","angle_style fourier command","angle_style fourier/simple command","angle_style harmonic command","angle_style quartic command","angle_style sdk command","balance command","bond_style class2 command","bond_style fene command","bond_style fene/expand command","bond_style harmonic command","bond_style harmonic/shift command","bond_style harmonic/shift/cut command","bond_style morse command","bond_style nonlinear command","bond_style quartic command","compute centro/atom command","compute cna/atom command","compute dpd command","compute fep command","compute gyration command","compute gyration/chunk command","compute heat/flux command","compute hexorder/atom command","compute msd/nongauss command","compute orientorder/atom command","compute pressure command","compute reduce command","compute saed command","compute sna/atom command","compute stress/atom command","compute xrd command","create_atoms command","dihedral_style charmm command","dihedral_style class2 command","dihedral_style cosine/shift/exp command","dihedral_style fourier command","dihedral_style harmonic command","dihedral_style helix command","dihedral_style multi/harmonic command","dihedral_style nharmonic command","dihedral_style opls command","dihedral_style quadratic command","dihedral_style spherical command","dihedral_style command","dump command","dump image command","fix atc command","fix ave/atom command","fix ave/chunk command","fix ave/correlate command","fix ave/histo command","fix ave/time command","fix balance command","fix bond/swap command","fix box/relax command","fix ehex command","fix eos/cv command","fix eos/table/rx command","fix gld 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command","pair_style morse command","pair_style multi/lucy command","pair_style multi/lucy/rx command","pair_style nb3b/harmonic command","pair_style nm/cut command","pair_style polymorphic command","pair_style resquared command","pair_style lj/sdk command","pair_style smtbq command","pair_style snap command","pair_style soft command","pair_style sph/idealgas command","pair_style sph/taitwater command","pair_style sph/taitwater/morris command","pair_style srp command","pair_style sw command","pair_style tersoff command","pair_style tersoff/mod command","pair_style tersoff/zbl command","pair_style vashishta command","pair_style yukawa command","pair_style yukawa/colloid command","pair_style zbl command","thermo_style command","LAMMPS GitHub tutorial"],titleterms:{"default":[29,32,36,37,38,41,42,44,45,57,58,59,60,62,65,68,72,73,74,75,77,78,83,84,86,102,118,136,137,142,158,167],"long":[103,104,105,106,107,110,112,113,127,131,135,148,151],acceler:1,adiabat:2,adp:98,airebo:99,alloi:116,amber:2,angle_styl:[5,6,7,8,9,10,11,12,13,14,15,16,17,18],arrai:2,aspher:2,atc:60,atom:[2,29,30,36,38,42,43,61],balanc:[19,66],barostat:2,bcc:76,beck:100,between:2,bodi:[2,101],bond:67,bond_styl:[20,21,22,23,24,25,26,27,28],bop:102,born:[103,112],box:[2,68],buck:[104,105,112,138],build:3,calcul:2,centro:29,charmm:[2,5,46,106,135],chunk:[2,34,62],class2:[6,20,47,88,107],cna:30,code:2,coeffici:2,colloid:[86,108,165],comb3:109,comb:109,command:[2,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167],comparison:1,compos:2,comput:[2,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44],conduct:2,constant:2,core:2,correl:63,cosin:[7,8,9,10,11,12,48],cossq:89,coul:[103,104,105,106,107,110,111,112,124,127,131,135,148,151],coupl:2,create_atom:45,cubic:129,custom:58,cut:[25,104,107,110,113,118,121,127,128,135,143,148],cvff:90,data:2,deby:[110,127],delta:8,descript:[5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167],diel:111,diffus:2,dihedral_styl:[46,47,48,49,50,51,52,53,54,55,56,57],dipol:[2,13,113],discuss:2,disp:2,distanc:91,document:0,dpd:[31,114,115],dreid:125,dreiding:2,drude:2,dsf:[110,127],dump:[2,58,59],eam:116,edip:117,eff:118,ehex:69,eim:119,elastic:2,energi:115,exampl:[2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167],exp6:120,exp:[11,48],expand:[22,130],extend:3,fcc:76,fdt:115,fene:[21,22],fep:32,field:2,file:2,finit:2,fix:[2,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87],fix_modifi:[60,61,62,63,64,65,66,68,69,73,74,75,76,78,79,81,82,83,84,85,86,87],flow:2,fluid:73,flux:35,forc:2,fourier:[14,15,49,92],from:[2,3],gauss:121,gaybern:122,gener:[1,2],github:168,gld:72,global:2,gpu:[100,103,104,106,107,108,110,113,114,116,121,122,124,127,128,129,130,143,144,150,151,154,159,160,161,162,164,165,166],gran:123,granular:2,gromac:124,gyrat:[33,34],h5md:58,harmon:[16,23,24,25,50,52,86,93,147],hbond:125,heat:35,helix:51,hertz:123,hexord:36,histo:64,histori:123,hook:123,how:2,idealga:155,imag:[58,59],implicit:106,improper_styl:[88,89,90,91,92,93,94,95],indice:0,induc:2,info:[0,60,61,62,63,64,65,66,68,69,73,74,75,76,78,79,81,82,83,84,85,86,87],input:2,install:3,integr:2,intel:[4,5,16,21,23,46,50,54,74,90,93,104,106,122,127,159,160],interfac:[2,3],jul:0,kspace_styl:2,lammps:[0,1,2,3,168],lennard:138,librari:[2,3],linear:[134,144],list:126,lj1043:86,lj126:86,lj93:86,lj96:128,local:2,lubric:136,lubricateu:137,luci:[145,146],mdf:138,meam:[139,140,141],measur:1,mgpt:142,mie:143,minim:[60,61,62,63,64,65,66,68,69,73,74,75,76,78,79,81,82,83,84,85,86,87,96],mod:[85,161],model:2,molfil:58,morri:157,mors:[26,99,125,144],movi:[58,59],mpi:3,msd:37,msm:[103,104,106,110,127],multi:[2,52,145,146],multipl:2,nb3b:147,neb:97,nemd:2,nharmon:53,non:2,nongauss:37,nonlinear:27,nph:74,nphug:75,npt:74,nvt:74,omp:[5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,46,47,48,49,50,51,52,53,54,55,74,75,88,89,90,92,93,94,95,98,99,100,103,104,105,106,107,108,109,110,111,113,114,116,119,121,122,123,124,125,127,128,129,130,131,132,133,134,135,136,140,141,144,147,148,150,151,154,159,160,161,162,163,164,165,166],opl:54,opt:[106,116,127,131,144],optim:1,option:2,orient:76,orientord:38,orthogon:2,other:2,output:[2,60,61,62,63,64,65,66,68,69,73,74,75,76,78,79,81,82,83,84,85,86,87],overview:3,packag:[1,4],pair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\ No newline at end of file diff --git a/doc/html/thermo_style.html b/doc/html/thermo_style.html index 6bbcc98b44..c76cf8115a 100644 --- a/doc/html/thermo_style.html +++ b/doc/html/thermo_style.html @@ -196,10 +196,10 @@ cella,cellb,cellc = periodic cell lattice constants a,b,c cellalpha, cellbeta, cellgamma = periodic cell angles alpha,beta,gamma c_ID = global scalar value calculated by a compute with ID - c_ID[I] = Ith component of global vector calculated by a compute with ID + c_ID[I] = Ith component of global vector calculated by a compute with ID, I can include wildcard (see below) c_ID[I][J] = I,J component of global array calculated by a compute with ID f_ID = global scalar value calculated by a fix with ID - f_ID[I] = Ith component of global vector calculated by a fix with ID + f_ID[I] = Ith component of global vector calculated by a fix with ID, I can include wildcard (see below) f_ID[I][J] = I,J component of global array calculated by a fix with ID v_name = value calculated by an equal-style variable with name v_name[I] = value calculated by a vector-style variable with name @@ -210,6 +210,7 @@thermo_style multi thermo_style custom step temp pe etotal press vol thermo_style custom step temp etotal c_myTemp v_abc +thermo_style custom step temp etotal c_myTemp[*] v_abc
+Note that for values from a compute or fix, the bracketed index I used +to index a vector, as in c_ID[I] or f_ID[I], can be specified +using a wildcard asterisk with the index to effectively specify +multiple values. This takes the form “*” or “n” or “n” or “m*n”. +If N = the size of the vector (for mode = scalar) or the number of +columns in the array (for mode = vector), then an asterisk with no +numeric values means all indices from 1 to N. A leading asterisk +means all indices from 1 to n (inclusive). A trailing asterisk means +all indices from n to N (inclusive). A middle asterisk means all +indices from m to n (inclusive).
+Using a wildcard is the same as if the individual elements of the +vector had been listed one by one. E.g. these 2 thermo_style commands +are equivalent, since the compute temp command +creates a global vector with 6 values.
+++compute myTemp all temp +thermo_style custom step temp etotal c_myTemp[*] +thermo_style custom step temp etotal & + c_myTemp[1] c_myTemp[2] c_myTemp[3] & + c_myTemp[4] c_myTemp[5] c_myTemp[6] +
Several of the thermodynamic quantities require a temperature to be computed: “temp”, “press”, “ke”, “etotal”, “enthalpy”, “pxx”, etc. By default this is done by using a temperature compute which is created @@ -394,9 +417,12 @@ of these quantities in terms of the internal LAMMPS cell dimensions values calculated by a compute to be output. As discussed on the compute doc page, computes can calculate global, per-atom, or local values. Only global values can be referenced by -this command. However, per-atom compute values can be referenced in a -variable and the variable referenced by thermo_style -custom, as discussed below.
+this command. However, per-atom compute values for an individual atom +can be referenced in a variable and the variable +referenced by thermo_style custom, as discussed below. See the +discussion above for how the I in c_ID[I] can be specified with a +wildcard asterisk to effectively specify multiple values from a global +compute vector.The ID in the keyword should be replaced by the actual ID of a compute that has been defined elsewhere in the input script. See the compute command for details. If the compute calculates @@ -413,9 +439,11 @@ the compute group) when output, depending on the fix doc page, fixes can calculate global, per-atom, or local values. Only global values can be referenced by this command. -However, per-atom fix values can be referenced in a -variable and the variable referenced by thermo_style -custom, as discussed below.
+However, per-atom fix values can be referenced for an individual atom +in a variable and the variable referenced by +thermo_style custom, as discussed below. See the discussion above for +how the I in f_ID[I] can be specified with a wildcard asterisk to +effectively specify multiple values from a global fix vector.The ID in the keyword should be replaced by the actual ID of a fix that has been defined elsewhere in the input script. See the fix command for details. If the fix calculates a global @@ -434,11 +462,14 @@ output. The name in the keyword should be replaced by the variable name that has been defined elsewhere in the input script. Only equal-style and vector-style variables can be referenced; the latter requires a bracketed term to specify the Ith element of the vector -calculated by the variable. See the variable command -for details. Variables of style equal and vector define a formula -which can reference per-atom properties or thermodynamic keywords, or -they can invoke other computes, fixes, or variables when evaluated, so -this is a very general means of creating thermodynamic output.
+calculated by the variable. However, an atom-style variable can be +referenced for an individual atom by an equal-style variable and that +variable referenced. See the variable command for +details. Variables of style equal and vector and atom define a +formula which can reference per-atom properties or thermodynamic +keywords, or they can invoke other computes, fixes, or variables when +evaluated, so this is a very general means of creating thermodynamic +output.Note that equal-style and vector-style variables are assumed to produce “intensive” global quantities, which are thus printed as-is, without normalization by thermo_style custom. You can include a diff --git a/doc/src/compute_reduce.txt b/doc/src/compute_reduce.txt index 22a7ec52ed..09ab48b12f 100644 --- a/doc/src/compute_reduce.txt +++ b/doc/src/compute_reduce.txt @@ -23,9 +23,9 @@ one or more inputs can be listed :l input = x, y, z, vx, vy, vz, fx, fy, fz, c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_name :l x,y,z,vx,vy,vz,fx,fy,fz = atom attribute (position, velocity, force component) c_ID = per-atom or local vector calculated by a compute with ID - c_ID\[I\] = Ith column of per-atom or local array calculated by a compute with ID + c_ID\[I\] = Ith column of per-atom or local array calculated by a compute with ID, I can include wildcard (see below) f_ID = per-atom or local vector calculated by a fix with ID - f_ID\[I\] = Ith column of per-atom or local array calculated by a fix with ID + f_ID\[I\] = Ith column of per-atom or local array calculated by a fix with ID, I can include wildcard (see below) v_name = per-atom vector calculated by an atom-style variable with name :pre zero or more keyword/args pairs may be appended :l @@ -40,6 +40,7 @@ keyword = {replace} :l compute 1 all reduce sum c_force compute 1 all reduce/region subbox sum c_force compute 2 all reduce min c_press\[2\] f_ave v_myKE +compute 2 all reduce min c_press\[*\] f_ave v_myKE compute 3 fluid reduce max c_index\[1\] c_index\[2\] c_dist replace 1 3 replace 2 3 :pre [Description:] @@ -80,6 +81,28 @@ component) or can be the result of a "compute"_compute.html or "fix"_fix.html or the evaluation of an atom-style "variable"_variable.html. +Note that for values from a compute or fix, the bracketed index I can +be specified using a wildcard asterisk with the index to effectively +specify multiple values. This takes the form "*" or "*n" or "n*" or +"m*n". If N = the size of the vector (for {mode} = scalar) or the +number of columns in the array (for {mode} = vector), then an asterisk +with no numeric values means all indices from 1 to N. A leading +asterisk means all indices from 1 to n (inclusive). A trailing +asterisk means all indices from n to N (inclusive). A middle asterisk +means all indices from m to n (inclusive). + +Using a wildcard is the same as if the individual columns of the array +had been listed one by one. E.g. these 2 compute reduce commands are +equivalent, since the "compute stress/atom"_compute_stress/atom.html +command creates a per-atom array with 6 columns: + +compute myPress all stress/atom NULL +compute 2 all reduce min myPress\[*\] +compute 2 all reduce min myPress\[1\] myPress\[2\] myPress\[3\] & + myPress\[4\] myPress\[5\] myPress\[6\] :pre + +:line + The atom attribute values (x,y,z,vx,vy,vz,fx,fy,fz) are self-explanatory. Note that other atom attributes can be used as inputs to this fix by using the "compute @@ -93,7 +116,9 @@ per-atom or local quantities. See the individual is appended, the vector calculated by the compute is used. If a bracketed integer is appended, the Ith column of the array calculated by the compute is used. Users can also write code for their own -compute styles and "add them to LAMMPS"_Section_modify.html. +compute styles and "add them to LAMMPS"_Section_modify.html. See the +discussion above for how I can be specified with a wildcard asterisk +to effectively specify multiple values. If a value begins with "f_", a fix ID must follow which has been previously defined in the input script. Fixes can generate per-atom @@ -104,7 +129,9 @@ references the values, else an error results. If no bracketed integer is appended, the vector calculated by the fix is used. If a bracketed integer is appended, the Ith column of the array calculated by the fix is used. Users can also write code for their own fix style and "add -them to LAMMPS"_Section_modify.html. +them to LAMMPS"_Section_modify.html. See the discussion above for how +I can be specified with a wildcard asterisk to effectively specify +multiple values. If a value begins with "v_", a variable name must follow which has been previously defined in the input script. It must be an diff --git a/doc/src/dump.txt b/doc/src/dump.txt index f816ef33e0..2c7ae96101 100644 --- a/doc/src/dump.txt +++ b/doc/src/dump.txt @@ -46,12 +46,12 @@ args = list of arguments for a particular style :l {molfile} args = discussed on "dump molfile"_dump_molfile.html doc page :pre {local} args = list of local attributes - possible attributes = index, c_ID, c_ID\[N\], f_ID, f_ID\[N\] + possible attributes = index, c_ID, c_ID\[I\], f_ID, f_ID\[I\] 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 + c_ID\[I\] = Ith column of local array calculated by a compute with ID, I can include wildcard (see below) 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 + f_ID\[I\] = Ith column of local array calculated by a fix with ID, I can include wildcard (see below) :pre {custom} or {custom/gz} or {custom/mpiio} args = list of atom attributes possible attributes = id, mol, proc, procp1, type, element, mass, @@ -85,9 +85,9 @@ args = list of arguments for a particular style :l angmomx,angmomy,angmomz = angular momentum of aspherical particle tqx,tqy,tqz = torque on finite-size particles 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 + c_ID\[I\] = Ith column of per-atom array calculated by a compute with ID, I can include wildcard (see below) 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 + f_ID\[I\] = Ith column of per-atom array calculated by a fix with ID, I can include wildcard (see below) v_name = per-atom vector calculated by an atom-style variable with name d_name = per-atom floating point vector with name, managed by fix property/atom i_name = per-atom integer vector with name, managed by fix property/atom :pre @@ -102,6 +102,7 @@ dump 2 subgroup atom 50 dump.run.bin dump 2 subgroup atom 50 dump.run.mpiio.bin 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 4b flow custom 100 dump.%.myforce id type c_myF\[*\] v_ke dump 2 inner cfg 10 dump.snap.*.cfg mass type xs ys zs vx vy vz dump snap all cfg 100 dump.config.*.cfg mass type xs ys zs id type c_Stress\[2\] dump 1 all xtc 1000 file.xtc :pre @@ -418,6 +419,30 @@ styles. :line +Note that in the discussion which follows, for styles which can +reference values from a compute or fix, like the {custom}, {cfg}, or +{local} styles, the bracketed index I can be specified using a +wildcard asterisk with the index to effectively specify multiple +values. This takes the form "*" or "*n" or "n*" or "m*n". If N = the +size of the vector (for {mode} = scalar) or the number of columns in +the array (for {mode} = vector), then an asterisk with no numeric +values means all indices from 1 to N. A leading asterisk means all +indices from 1 to n (inclusive). A trailing asterisk means all +indices from n to N (inclusive). A middle asterisk means all indices +from m to n (inclusive). + +Using a wildcard is the same as if the individual columns of the array +had been listed one by one. E.g. these 2 dump commands are +equivalent, since the "compute stress/atom"_compute_stress/atom.html +command creates a per-atom array with 6 columns: + +compute myPress all stress/atom NULL +dump 2 all custom 100 tmp.dump id myPress\[*\] +dump 2 all custom 100 tmp.dump id myPress\[1\] myPress\[2\] myPress\[3\] & + myPress\[4\] myPress\[5\] myPress\[6\] :pre + +:line + This section explains the local attributes that can be specified as part of the {local} style. @@ -430,7 +455,7 @@ 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 +The {c_ID} and {c_ID\[I\]} 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 @@ -445,22 +470,26 @@ 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 compute is printed. If {c_ID\[I\]} is used, then I must be in the +range from 1-M, which will print the Ith column of the local array +with M columns calculated by the compute. See the discussion above +for how I can be specified with a wildcard asterisk to effectively +specify multiple values. -The {f_ID} and {f_ID\[N\]} attributes allow local vectors or arrays +The {f_ID} and {f_ID\[I\]} 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. +the fix is printed. If {f_ID\[I\]} is used, then I must be in the +range from 1-M, which will print the Ith column of the local with M +columns calculated by the fix. See the discussion above for how I can +be specified with a wildcard asterisk to effectively specify multiple +values. -Here is an example of how to dump bond info for a system, -including the distance and energy of each bond: +Here is an example of how to dump bond info for a system, including +the distance and energy of each bond: compute 1 all property/local batom1 batom2 btype compute 2 all bond/local dist eng @@ -536,7 +565,7 @@ The {tqx}, {tqy}, {tqz} attributes are for finite-size particles that can sustain a rotational torque due to interactions with other particles. -The {c_ID} and {c_ID\[N\]} attributes allow per-atom vectors or arrays +The {c_ID} and {c_ID\[I\]} 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 @@ -551,11 +580,13 @@ command. Instead, global quantities can be output by the can be output by the dump local command. 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. +by the compute is printed. If {c_ID\[I\]} is used, then I must be in +the range from 1-M, which will print the Ith column of the per-atom +array with M columns calculated by the compute. See the discussion +above for how I can be specified with a wildcard asterisk to +effectively specify multiple values. -The {f_ID} and {f_ID\[N\]} attributes allow vector or array per-atom +The {f_ID} and {f_ID\[I\]} attributes allow vector or array per-atom quantities 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. The "fix @@ -566,9 +597,11 @@ any "compute"_compute.html, "fix"_fix.html, or atom-style be written to a dump file. 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. +by the fix is printed. If {f_ID\[I\]} is used, then I must be in the +range from 1-M, which will print the Ith column of the per-atom array +with M columns calculated by the fix. See the discussion above for +how I can be specified with a wildcard asterisk to effectively specify +multiple values. The {v_name} attribute allows per-atom vectors calculated by a "variable"_variable.html to be output. The name in the attribute diff --git a/doc/src/fix_ave_atom.txt b/doc/src/fix_ave_atom.txt index 1d5053d37b..ef2b0e914a 100644 --- a/doc/src/fix_ave_atom.txt +++ b/doc/src/fix_ave_atom.txt @@ -21,16 +21,17 @@ one or more input values can be listed :l value = x, y, z, vx, vy, vz, fx, fy, fz, c_ID, c_ID\[i\], f_ID, f_ID\[i\], v_name :l x,y,z,vx,vy,vz,fx,fy,fz = atom attribute (position, velocity, force component) c_ID = per-atom vector calculated by a compute with ID - c_ID\[I\] = Ith column of per-atom array calculated by a compute with ID + c_ID\[I\] = Ith column of per-atom array calculated by a compute with ID, I can include wildcard (see below) f_ID = per-atom vector calculated by a fix with ID - f_ID\[I\] = Ith column of per-atom array calculated by a fix with ID + f_ID\[I\] = Ith column of per-atom array calculated by a fix with ID, I can include wildcard (see below) v_name = per-atom vector calculated by an atom-style variable with name :pre :ule [Examples:] fix 1 all ave/atom 1 100 100 vx vy vz -fix 1 all ave/atom 10 20 1000 c_my_stress\[1\] :pre +fix 1 all ave/atom 10 20 1000 c_my_stress\[1\] +fix 1 all ave/atom 10 20 1000 c_my_stress\[*\] :pre [Description:] @@ -53,6 +54,8 @@ local quantity. If you wish to time-average global quantities from a compute, fix, or variable, then see the "fix ave/time"_fix_ave_time.html command. +Each per-atom value of each input vector is averaged independently. + "Computes"_compute.html that produce per-atom vectors or arrays are those which have the word {atom} in their style name. See the doc pages for individual "fixes"_fix.html to determine which ones produce @@ -60,7 +63,26 @@ per-atom vectors or arrays. "Variables"_variable.html of style {atom} are the only ones that can be used with this fix since they produce per-atom vectors. -Each per-atom value of each input vector is averaged independently. +Note that for values from a compute or fix, the bracketed index I can +be specified using a wildcard asterisk with the index to effectively +specify multiple values. This takes the form "*" or "*n" or "n*" or +"m*n". If N = the size of the vector (for {mode} = scalar) or the +number of columns in the array (for {mode} = vector), then an asterisk +with no numeric values means all indices from 1 to N. A leading +asterisk means all indices from 1 to n (inclusive). A trailing +asterisk means all indices from n to N (inclusive). A middle asterisk +means all indices from m to n (inclusive). + +Using a wildcard is the same as if the individual columns of the array +had been listed one by one. E.g. these 2 fix ave/atom commands are +equivalent, since the "compute stress/atom"_compute_stress/atom.html +command creates a per-atom array with 6 columns: + +compute my_stress all stress/atom NULL +fix 1 all ave/atom 10 20 1000 c_my_stress\[*\] +fix 1 all ave/atom 10 20 1000 c_my_stress\[1\] c_my_stress\[1\] & + c_my_stress\[3\] c_my_stress\[4\] & + c_my_stress\[5\] c_my_stress\[6\] :pre :line @@ -102,7 +124,9 @@ appended, the per-atom vector calculated by the compute is used. If a bracketed term containing an index I is appended, the Ith column of the per-atom array calculated by the compute is used. Users can also write code for their own compute styles and "add them to -LAMMPS"_Section_modify.html. +LAMMPS"_Section_modify.html. See the discussion above for how I can +be specified with a wildcard asterisk to effectively specify multiple +values. If a value begins with "f_", a fix ID must follow which has been previously defined in the input script. If no bracketed term is @@ -112,7 +136,9 @@ the per-atom array calculated by the fix is used. Note that some fixes only produce their values on certain timesteps, which must be compatible with {Nevery}, else an error will result. Users can also write code for their own fix styles and "add them to -LAMMPS"_Section_modify.html. +LAMMPS"_Section_modify.html. See the discussion above for how I can +be specified with a wildcard asterisk to effectively specify multiple +values. If a value begins with "v_", a variable name must follow which has been previously defined in the input script as an "atom-style diff --git a/doc/src/fix_ave_chunk.txt b/doc/src/fix_ave_chunk.txt index 0ebbafd6ca..65cd27c2f2 100644 --- a/doc/src/fix_ave_chunk.txt +++ b/doc/src/fix_ave_chunk.txt @@ -24,9 +24,9 @@ value = vx, vy, vz, fx, fy, fz, density/mass, density/number, temp, c_ID, c_ID\[ density/number, density/mass = number or mass density temp = temperature c_ID = per-atom vector calculated by a compute with ID - c_ID\[I\] = Ith column of per-atom array calculated by a compute with ID + c_ID\[I\] = Ith column of per-atom array calculated by a compute with ID, I can include wildcard (see below) f_ID = per-atom vector calculated by a fix with ID - f_ID\[I\] = Ith column of per-atom array calculated by a fix with ID + f_ID\[I\] = Ith column of per-atom array calculated by a fix with ID, I can include wildcard (see below) v_name = per-atom vector calculated by an atom-style variable with name :pre zero or more keyword/arg pairs may be appended :l @@ -118,6 +118,9 @@ any attribute defined and stored by atoms. If you wish to time-average global quantities from a compute, fix, or variable, then see the "fix ave/time"_fix_ave_time.html command. +The per-atom values of each input vector are summed and averaged +independently of the per-atom values in other input vectors. + "Computes"_compute.html that produce per-atom quantities are those which have the word {atom} in their style name. See the doc pages for individual "fixes"_fix.html to determine which ones produce per-atom @@ -125,8 +128,25 @@ quantities. "Variables"_variable.html of style {atom} are the only 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. +Note that for values from a compute or fix, the bracketed index I can +be specified using a wildcard asterisk with the index to effectively +specify multiple values. This takes the form "*" or "*n" or "n*" or +"m*n". If N = the size of the vector (for {mode} = scalar) or the +number of columns in the array (for {mode} = vector), then an asterisk +with no numeric values means all indices from 1 to N. A leading +asterisk means all indices from 1 to n (inclusive). A trailing +asterisk means all indices from n to N (inclusive). A middle asterisk +means all indices from m to n (inclusive). + +Using a wildcard is the same as if the individual elements of the +vector or columns of the array had been listed one by one. E.g. these +2 fix ave/chunk commands are equivalent, since the "compute +property/atom"_compute_property/atom.html command creates, in this +case, a per-atom array with 3 columns: + +compute myAng all property/atom 50 angmomx angmomy angmomz +fix 1 all ave/chunk 100 1 100 cc1 c_myAng\[*\] file tmp.angmom +fix 2 all ave/chunk 100 1 100 cc1 c_myAng\[1\] c_myAng\[2\] c_myAng\[3\] file tmp.angmom :pre 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 @@ -237,6 +257,8 @@ appended, the per-atom vector calculated by the compute is used. If a bracketed integer is appended, the Ith column of the per-atom array calculated by the compute is used. Users can also write code for their own compute styles and "add them to LAMMPS"_Section_modify.html. +See the discussion above for how I can be specified with a wildcard +asterisk to effectively specify multiple values. If a value begins with "f_", a fix ID must follow which has been previously defined in the input script. If no bracketed integer is @@ -245,7 +267,9 @@ bracketed integer is appended, the Ith column of the per-atom array calculated by the fix is used. Note that some fixes only produce their values on certain timesteps, which must be compatible with {Nevery}, else an error results. Users can also write code for their -own fix styles and "add them to LAMMPS"_Section_modify.html. +own fix styles and "add them to LAMMPS"_Section_modify.html. See the +discussion above for how I can be specified with a wildcard asterisk +to effectively specify multiple values. If a value begins with "v_", a variable name must follow which has been previously defined in the input script. Variables of style diff --git a/doc/src/fix_ave_correlate.txt b/doc/src/fix_ave_correlate.txt index ae785b4fc5..c4df7671aa 100644 --- a/doc/src/fix_ave_correlate.txt +++ b/doc/src/fix_ave_correlate.txt @@ -20,9 +20,9 @@ Nfreq = calculate time window averages every this many timesteps :l one or more input values can be listed :l value = c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_name :l c_ID = global scalar calculated by a compute with ID - c_ID\[I\] = Ith component of global vector calculated by a compute with ID + c_ID\[I\] = Ith component of global vector calculated by a compute with ID, I can include wildcard (see below) f_ID = global scalar calculated by a fix with ID - f_ID\[I\] = Ith component of global vector calculated by a fix with ID + f_ID\[I\] = Ith component of global vector calculated by a fix with ID, I can include wildcard (see below) v_name = global value calculated by an equal-style variable with name v_name\[I\] = Ith component of a vector-style variable with name :pre @@ -59,6 +59,7 @@ fix 1 all ave/correlate 5 100 1000 c_myTemp file temp.correlate fix 1 all ave/correlate 1 50 10000 & c_thermo_press\[1\] c_thermo_press\[2\] c_thermo_press\[3\] & type upper ave running title1 "My correlation data" :pre +fix 1 all ave/correlate 1 50 10000 c_thermo_press\[*\] [Description:] @@ -88,6 +89,10 @@ ave/chunk"_fix_ave_chunk.html, "fix ave/atom"_fix_ave_atom.html, or per-atom quantity into a single global value, see the "compute reduce"_compute_reduce.html command. +The input values must either be all scalars. What kinds of +correlations between input values are calculated is determined by the +{type} keyword as discussed below. + "Computes"_compute.html that produce global quantities are those which do not have the word {atom} in their style name. Only a few "fixes"_fix.html produce global quantities. See the doc pages for @@ -96,9 +101,27 @@ individual fixes for info on which ones produce such values. ones that can be used with this fix. Variables of style {atom} cannot be used, since they produce per-atom values. -The input values must either be all scalars. What kinds of -correlations between input values are calculated is determined by the -{type} keyword as discussed below. +Note that for values from a compute or fix, the bracketed index I can +be specified using a wildcard asterisk with the index to effectively +specify multiple values. This takes the form "*" or "*n" or "n*" or +"m*n". If N = the size of the vector (for {mode} = scalar) or the +number of columns in the array (for {mode} = vector), then an asterisk +with no numeric values means all indices from 1 to N. A leading +asterisk means all indices from 1 to n (inclusive). A trailing +asterisk means all indices from n to N (inclusive). A middle asterisk +means all indices from m to n (inclusive). + +Using a wildcard is the same as if the individual elements of the +vector had been listed one by one. E.g. these 2 fix ave/correlate +commands are equivalent, since the "compute +pressure"_compute_pressure.html command creates a global vector with 6 +values. + +compute myPress all pressure NULL +fix 1 all ave/correlate 1 50 10000 c_myPress\[*\] +fix 1 all ave/correlate 1 50 10000 & + c_myPress\[1\] c_myPress\[2\] c_myPress\[3\] & + c_myPress\[4\] c_myPress\[5\] c_myPress\[6\] :pre :line @@ -141,7 +164,9 @@ If a value begins with "c_", a compute ID must follow which has been previously defined in the input script. If no bracketed term is appended, the global scalar calculated by the compute is used. If a bracketed term is appended, the Ith element of the global vector -calculated by the compute is used. +calculated by the compute is used. See the discussion above for how I +can be specified with a wildcard asterisk to effectively specify +multiple values. Note that there is a "compute reduce"_compute_reduce.html command which can sum per-atom quantities into a global scalar or vector which @@ -151,13 +176,15 @@ output"_thermo_style.html or other fixes such as "fix nvt"_fix_nh.html or "fix temp/rescale"_fix_temp_rescale.html. See the doc pages for these commands which give the IDs of these computes. Users can also write code for their own compute styles and "add them to -LAMMPS"_Section_modify.html. +LAMMPS"_Section_modify.html. If a value begins with "f_", a fix ID must follow which has been previously defined in the input script. If no bracketed term is appended, the global scalar calculated by the fix is used. If a bracketed term is appended, the Ith element of the global vector -calculated by the fix is used. +calculated by the fix is used. See the discussion above for how I can +be specified with a wildcard asterisk to effectively specify multiple +values. Note that some fixes only produce their values on certain timesteps, which must be compatible with {Nevery}, else an error will result. diff --git a/doc/src/fix_ave_histo.txt b/doc/src/fix_ave_histo.txt index 3d287d4fe4..0c8a2f31c7 100644 --- a/doc/src/fix_ave_histo.txt +++ b/doc/src/fix_ave_histo.txt @@ -24,9 +24,9 @@ one or more input values can be listed :l value = x, y, z, vx, vy, vz, fx, fy, fz, c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_name :l x,y,z,vx,vy,vz,fx,fy,fz = atom attribute (position, velocity, force component) c_ID = scalar or vector calculated by a compute with ID - c_ID\[I\] = Ith component of vector or Ith column of array calculated by a compute with ID + c_ID\[I\] = Ith component of vector or Ith column of array calculated by a compute with ID, I can include wildcard (see below) f_ID = scalar or vector calculated by a fix with ID - f_ID\[I\] = Ith component of vector or Ith column of array calculated by a fix with ID + f_ID\[I\] = Ith component of vector or Ith column of array calculated by a fix with ID, I can include wildcard (see below) v_name = value(s) calculated by an equal-style or vector-style or atom-style variable with name v_name\[I\] = value calculated by a vector-style variable with name :pre @@ -60,14 +60,15 @@ keyword = {mode} or {file} or {ave} or {start} or {beyond} or {overwrite} or {ti fix 1 all ave/histo 100 5 1000 0.5 1.5 50 c_myTemp file temp.histo ave running fix 1 all ave/histo 100 5 1000 -5 5 100 c_thermo_press\[2\] c_thermo_press\[3\] title1 "My output values" +fix 1 all ave/histo 100 5 1000 -5 5 100 c_thermo_press\[*\] fix 1 all ave/histo 1 100 1000 -2.0 2.0 18 vx vy vz mode vector ave running beyond extra fix 1 all ave/histo/weight 1 1 1 10 100 2000 c_XRD\[1\] c_XRD\[2\] :pre [Description:] -Use one or more values as inputs every few timesteps, histogram them, -and average the histogram over longer timescales. The resulting -histogram can be used by other "output +Use one or more values as inputs every few timesteps to create a +single histogram. The histogram can then be averaged over longer +timescales. The resulting histogram can be used by other "output commands"_Section_howto.html#howto_15, and can also be written to a file. The fix ave/histo/weight command has identical syntax to fix ave/histo, except that exactly two values must be specified. See @@ -94,22 +95,40 @@ attributes are per-atom vector values. See the doc page for individual "compute" and "fix" commands to see what kinds of quantities they generate. -The input values must either be all scalars or all vectors (or -arrays), depending on the setting of the {mode} keyword. - Note that the output of this command is a single histogram for all input values combined together, not one histogram per input value. See below for details on the format of the output of this fix. -If {mode} = vector, then the input values may either be vectors or -arrays. If a global array is listed, then it is the same as if the -individual columns of the array had been listed one by one. -E.g. these 2 fix ave/histo commands are equivalent, since the "compute -com/chunk"_compute_com_chunk.html command creates a global array -with 3 columns: +The input values must either be all scalars or all vectors (or +arrays), depending on the setting of the {mode} keyword. + +If {mode} = scalar, then the input values must be scalars, or vectors +with a bracketed term appended, indicating the Ith value of the vector +is used. + +If {mode} = vector, then the input values must be vectors, or arrays +with a bracketed term appended, indicating the Ith column of the array +is used. All vectors must be the same length, which is the length of +the vector or number of rows in the array. + +Note that for values from a compute or fix, the bracketed index I can +be specified using a wildcard asterisk with the index to effectively +specify multiple values. This takes the form "*" or "*n" or "n*" or +"m*n". If N = the size of the vector (for {mode} = scalar) or the +number of columns in the array (for {mode} = vector), then an asterisk +with no numeric values means all indices from 1 to N. A leading +asterisk means all indices from 1 to n (inclusive). A trailing +asterisk means all indices from n to N (inclusive). A middle asterisk +means all indices from m to n (inclusive). + +Using a wildcard is the same as if the individual elements of the +vector or columns of the array had been listed one by one. E.g. these +2 fix ave/histo commands are equivalent, since the "compute +com/chunk"_compute_com_chunk.html command creates a global array with +3 columns: compute myCOM all com/chunk -fix 1 all ave/histo 100 1 100 c_myCOM file tmp1.com mode vector +fix 1 all ave/histo 100 1 100 c_myCOM\[*\] file tmp1.com mode vector fix 2 all ave/histo 100 1 100 c_myCOM\[1\] c_myCOM\[2\] c_myCOM\[3\] file tmp2.com mode vector :pre If the fix ave/histo/weight command is used, exactly two values must @@ -154,11 +173,11 @@ no bracketed term is appended, the global scalar calculated by the compute is used. If a bracketed term is appended, the Ith element of the global vector calculated by the compute is used. If {mode} = vector, then if no bracketed term is appended, the global or per-atom -or local vector calculated by the compute is used. Or if the compute -calculates an array, all of the columns of the array are used as if -they had been specified as individual vectors (see description above). -If a bracketed term is appended, the Ith column of the global or -per-atom or local array calculated by the compute is used. +or local vector calculated by the compute is used. If a bracketed +term is appended, the Ith column of the global or per-atom or local +array calculated by the compute is used. See the discussion above for +how I can be specified with a wildcard asterisk to effectively specify +multiple values. Note that there is a "compute reduce"_compute_reduce.html command which can sum per-atom quantities into a global scalar or vector which @@ -176,11 +195,11 @@ no bracketed term is appended, the global scalar calculated by the fix is used. If a bracketed term is appended, the Ith element of the global vector calculated by the fix is used. If {mode} = vector, then if no bracketed term is appended, the global or per-atom or local -vector calculated by the fix is used. Or if the fix calculates an -array, all of the columns of the array are used as if they had been -specified as individual vectors (see description above). If a -bracketed term is appended, the Ith column of the global or per-atom -or local array calculated by the fix is used. +vector calculated by the fix is used. If a bracketed term is +appended, the Ith column of the global or per-atom or local array +calculated by the fix is used. See the discussion above for how I can +be specified with a wildcard asterisk to effectively specify multiple +values. Note that some fixes only produce their values on certain timesteps, which must be compatible with {Nevery}, else an error will result. diff --git a/doc/src/fix_ave_time.txt b/doc/src/fix_ave_time.txt index 7eca1abe6d..56796a9e8c 100644 --- a/doc/src/fix_ave_time.txt +++ b/doc/src/fix_ave_time.txt @@ -19,10 +19,10 @@ Nrepeat = # of times to use input values for calculating averages :l Nfreq = calculate averages every this many timesteps :l one or more input values can be listed :l value = c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_name :l - c_ID = global scalar, vector, or array calculated by a compute with ID - c_ID\[I\] = Ith component of global vector or Ith column of global array calculated by a compute with ID - f_ID = global scalar, vector, or array calculated by a fix with ID - f_ID\[I\] = Ith component of global vector or Ith column of global array calculated by a fix with ID + c_ID = global scalar or vector calculated by a compute with ID + c_ID\[I\] = Ith component of global vector or Ith column of global array calculated by a compute with ID, I can include wildcard (see below) + f_ID = global scalar or vector calculated by a fix with ID + f_ID\[I\] = Ith component of global vector or Ith column of global array calculated by a fix with ID, I can include wildcard (see below) v_name = value(s) calculated by an equal-style or vector-style variable with name v_name\[I\] = value calculated by a vector-style variable with name :pre @@ -57,6 +57,7 @@ keyword = {mode} or {file} or {ave} or {start} or {off} or {overwrite} or {title fix 1 all ave/time 100 5 1000 c_myTemp c_thermo_temp file temp.profile fix 1 all ave/time 100 5 1000 c_thermo_press\[2\] ave window 20 & title1 "My output values" +fix 1 all ave/time 100 5 1000 c_thermo_press\[*\] fix 1 all ave/time 1 100 1000 f_indent f_indent\[1\] file temp.indent off 1 :pre [Description:] @@ -92,22 +93,39 @@ individual fixes for info on which ones produce such values. ones that can be used with this fix. Variables of style {atom} cannot be used, since they produce per-atom values. -The input values must either be all scalars or all vectors (or -arrays), depending on the setting of the {mode} keyword. In both -cases, the averaging is performed independently on each input value. -I.e. each input scalar is averaged independently and each element of -each input vector (or array) is averaged independently. +The input values must either be all scalars or all vectors depending +on the setting of the {mode} keyword. In both cases, the averaging is +performed independently on each input value. I.e. each input scalar +is averaged independently or each element of each input vector is +averaged independently. -If {mode} = vector, then the input values may either be vectors or -arrays and all must be the same "length", which is the length of the -vector or number of rows in the array. If a global array is listed, -then it is the same as if the individual columns of the array had been -listed one by one. E.g. these 2 fix ave/time commands are equivalent, -since the "compute rdf"_compute_rdf.html command creates, in this -case, a global array with 3 columns, each of length 50: +If {mode} = scalar, then the input values must be scalars, or vectors +with a bracketed term appended, indicating the Ith value of the vector +is used. + +If {mode} = vector, then the input values must be vectors, or arrays +with a bracketed term appended, indicating the Ith column of the array +is used. All vectors must be the same length, which is the length of +the vector or number of rows in the array. + +Note that for values from a compute or fix, the bracketed index I can +be specified using a wildcard asterisk with the index to effectively +specify multiple values. This takes the form "*" or "*n" or "n*" or +"m*n". If N = the size of the vector (for {mode} = scalar) or the +number of columns in the array (for {mode} = vector), then an asterisk +with no numeric values means all indices from 1 to N. A leading +asterisk means all indices from 1 to n (inclusive). A trailing +asterisk means all indices from n to N (inclusive). A middle asterisk +means all indices from m to n (inclusive). + +Using a wildcard is the same as if the individual elements of the +vector or columns of the array had been listed one by one. E.g. these +2 fix ave/time commands are equivalent, since the "compute +rdf"_compute_rdf.html command creates, in this case, a global array +with 3 columns, each of length 50: compute myRDF all rdf 50 1 2 -fix 1 all ave/time 100 1 100 c_myRDF file tmp1.rdf mode vector +fix 1 all ave/time 100 1 100 c_myRDF\[*\] file tmp1.rdf mode vector fix 2 all ave/time 100 1 100 c_myRDF\[1\] c_myRDF\[2\] c_myRDF\[3\] file tmp2.rdf mode vector :pre :line @@ -137,11 +155,10 @@ no bracketed term is appended, the global scalar calculated by the compute is used. If a bracketed term is appended, the Ith element of the global vector calculated by the compute is used. If {mode} = vector, then if no bracketed term is appended, the global vector -calculated by the compute is used. Or if the compute calculates an -array, all of the columns of the global array are used as if they had -been specified as individual vectors (see description above). If a -bracketed term is appended, the Ith column of the global array -calculated by the compute is used. +calculated by the compute is used. If a bracketed term is appended, +the Ith column of the global array calculated by the compute is used. +See the discussion above for how I can be specified with a wildcard +asterisk to effectively specify multiple values. Note that there is a "compute reduce"_compute_reduce.html command which can sum per-atom quantities into a global scalar or vector which @@ -159,10 +176,10 @@ no bracketed term is appended, the global scalar calculated by the fix is used. If a bracketed term is appended, the Ith element of the global vector calculated by the fix is used. If {mode} = vector, then if no bracketed term is appended, the global vector calculated by the -fix is used. Or if the fix calculates an array, all of the columns of -the global array are used as if they had been specified as individual -vectors (see description above). If a bracketed term is appended, the -Ith column of the global array calculated by the fix is used. +fix is used. If a bracketed term is appended, the Ith column of the +global array calculated by the fix is used. See the discussion above +for how I can be specified with a wildcard asterisk to effectively +specify multiple values. Note that some fixes only produce their values on certain timesteps, which must be compatible with {Nevery}, else an error will result. diff --git a/doc/src/thermo_style.txt b/doc/src/thermo_style.txt index 597ad3c1be..60d684f9af 100644 --- a/doc/src/thermo_style.txt +++ b/doc/src/thermo_style.txt @@ -74,10 +74,10 @@ args = list of arguments for a particular style :l cella,cellb,cellc = periodic cell lattice constants a,b,c cellalpha, cellbeta, cellgamma = periodic cell angles alpha,beta,gamma c_ID = global scalar value calculated by a compute with ID - c_ID\[I\] = Ith component of global vector calculated by a compute with ID + c_ID\[I\] = Ith component of global vector calculated by a compute with ID, I can include wildcard (see below) c_ID\[I\]\[J\] = I,J component of global array calculated by a compute with ID f_ID = global scalar value calculated by a fix with ID - f_ID\[I\] = Ith component of global vector calculated by a fix with ID + f_ID\[I\] = Ith component of global vector calculated by a fix with ID, I can include wildcard (see below) f_ID\[I\]\[J\] = I,J component of global array calculated by a fix with ID v_name = value calculated by an equal-style variable with name v_name\[I\] = value calculated by a vector-style variable with name :pre @@ -87,7 +87,8 @@ args = list of arguments for a particular style :l thermo_style multi thermo_style custom step temp pe etotal press vol -thermo_style custom step temp etotal c_myTemp v_abc :pre +thermo_style custom step temp etotal c_myTemp v_abc +thermo_style custom step temp etotal c_myTemp\[*\] v_abc :pre [Description:] @@ -137,6 +138,30 @@ the thermo_modify command after it. :line +Note that for values from a compute or fix, the bracketed index I used +to index a vector, as in {c_ID\[I\]} or {f_ID\[I\]}, can be specified +using a wildcard asterisk with the index to effectively specify +multiple values. This takes the form "*" or "*n" or "n*" or "m*n". +If N = the size of the vector (for {mode} = scalar) or the number of +columns in the array (for {mode} = vector), then an asterisk with no +numeric values means all indices from 1 to N. A leading asterisk +means all indices from 1 to n (inclusive). A trailing asterisk means +all indices from n to N (inclusive). A middle asterisk means all +indices from m to n (inclusive). + +Using a wildcard is the same as if the individual elements of the +vector had been listed one by one. E.g. these 2 thermo_style commands +are equivalent, since the "compute temp"_compute_temp.html command +creates a global vector with 6 values. + +compute myTemp all temp +thermo_style custom step temp etotal c_myTemp\[*\] +thermo_style custom step temp etotal & + c_myTemp\[1\] c_myTemp\[2\] c_myTemp\[3\] & + c_myTemp\[4\] c_myTemp\[5\] c_myTemp\[6\] :pre + +:line + Several of the thermodynamic quantities require a temperature to be computed: "temp", "press", "ke", "etotal", "enthalpy", "pxx", etc. By default this is done by using a {temperature} compute which is created @@ -298,9 +323,12 @@ The {c_ID} and {c_ID\[I\]} and {c_ID\[I\]\[J\]} keywords allow global values calculated by a compute to be output. As discussed on the "compute"_compute.html doc page, computes can calculate global, per-atom, or local values. Only global values can be referenced by -this command. However, per-atom compute values can be referenced in a -"variable"_variable.html and the variable referenced by thermo_style -custom, as discussed below. +this command. However, per-atom compute values for an individual atom +can be referenced in a "variable"_variable.html and the variable +referenced by thermo_style custom, as discussed below. See the +discussion above for how the I in {c_ID\[I\]} can be specified with a +wildcard asterisk to effectively specify multiple values from a global +compute vector. The ID in the keyword should be replaced by the actual ID of a compute that has been defined elsewhere in the input script. See the @@ -321,9 +349,11 @@ The {f_ID} and {f_ID\[I\]} and {f_ID\[I\]\[J\]} keywords allow global values calculated by a fix to be output. As discussed on the "fix"_fix.html doc page, fixes can calculate global, per-atom, or local values. Only global values can be referenced by this command. -However, per-atom fix values can be referenced in a -"variable"_variable.html and the variable referenced by thermo_style -custom, as discussed below. +However, per-atom fix values can be referenced for an individual atom +in a "variable"_variable.html and the variable referenced by +thermo_style custom, as discussed below. See the discussion above for +how the I in {f_ID\[I\]} can be specified with a wildcard asterisk to +effectively specify multiple values from a global fix vector. The ID in the keyword should be replaced by the actual ID of a fix that has been defined elsewhere in the input script. See the @@ -345,11 +375,14 @@ output. The name in the keyword should be replaced by the variable name that has been defined elsewhere in the input script. Only equal-style and vector-style variables can be referenced; the latter requires a bracketed term to specify the Ith element of the vector -calculated by the variable. See the "variable"_variable.html command -for details. Variables of style {equal} and {vector} define a formula -which can reference per-atom properties or thermodynamic keywords, or -they can invoke other computes, fixes, or variables when evaluated, so -this is a very general means of creating thermodynamic output. +calculated by the variable. However, an atom-style variable can be +referenced for an individual atom by an equal-style variable and that +variable referenced. See the "variable"_variable.html command for +details. Variables of style {equal} and {vector} and {atom} define a +formula which can reference per-atom properties or thermodynamic +keywords, or they can invoke other computes, fixes, or variables when +evaluated, so this is a very general means of creating thermodynamic +output. Note that equal-style and vector-style variables are assumed to produce "intensive" global quantities, which are thus printed as-is,