Various fixes can contribute to the total potential energy of the system. See the doc pages for individual fixes for diff --git a/doc/compute_pe.txt b/doc/compute_pe.txt index 8d5d005c23..ea601cff23 100644 --- a/doc/compute_pe.txt +++ b/doc/compute_pe.txt @@ -41,8 +41,7 @@ The Kspace contribution requires 1 extra FFT each timestep the per-atom energy is calculated, if using the PPPM solver via the "kspace_style pppm"_kspace_style.html command. Thus it can increase the cost of the PPPM calculation if it is needed on a large fraction -of the simulation timesteps. Thie "document"_PDF/kspace.pdf describes -how the long-range per-atom energy calculation is performed. +of the simulation timesteps. Various fixes can contribute to the total potential energy of the system. See the doc pages for "individual fixes"_fix.html for diff --git a/doc/compute_pe_atom.html b/doc/compute_pe_atom.html index 42704cf368..7138369832 100644 --- a/doc/compute_pe_atom.html +++ b/doc/compute_pe_atom.html @@ -55,7 +55,8 @@ these terms is included in the pair energy, not the dihedral energy. (Heyes) for the Ewald method and a related method for PPPM, as specified by the kspace_style pppm command. For PPPM, the calcluation requires 1 extra FFT each timestep that -per-atom stress is calculated. +per-atom energy is calculated. Thie document +describes how the long-range per-atom energy calculation is performed.
As an example of per-atom potential energy compared to total potential energy, these lines in an input script should yield the same result diff --git a/doc/compute_pe_atom.txt b/doc/compute_pe_atom.txt index 3d0a6f6697..631e7ed600 100644 --- a/doc/compute_pe_atom.txt +++ b/doc/compute_pe_atom.txt @@ -52,7 +52,8 @@ The KSpace contribution is calculated using the method in "(Heyes)"_#Heyes for the Ewald method and a related method for PPPM, as specified by the "kspace_style pppm"_kspace_style.html command. For PPPM, the calcluation requires 1 extra FFT each timestep that -per-atom stress is calculated. +per-atom energy is calculated. Thie "document"_PDF/kspace.pdf +describes how the long-range per-atom energy calculation is performed. As an example of per-atom potential energy compared to total potential energy, these lines in an input script should yield the same result diff --git a/doc/dump_modify.html b/doc/dump_modify.html index 1e6a307780..cfe26eeea8 100644 --- a/doc/dump_modify.html +++ b/doc/dump_modify.html @@ -358,14 +358,14 @@ In this case, the variable is evaluated at the beginning of a run to determine the next timestep at which a dump snapshot will be written out. On that timestep, the variable will be evaluated again to determine the next timestep, etc. Thus the variable should return -timestep values. See the stagger() and logfreq() math functions for -equal-style variables, as examples of useful functions -to use in this context. Other similar math functions could easily be -added as options for equal-style variables. When -using the variable option with the every keyword, you also need to -use the first option if you want an initial snapshot written to the -dump file. The every keyword cannot be used with the dump dcd -style. +timestep values. See the stagger() and logfreq() and stride() math +functions for equal-style variables, as examples of +useful functions to use in this context. Other similar math functions +could easily be added as options for equal-style +variables. When using the variable option with the +every keyword, you also need to use the first option if you want +an initial snapshot written to the dump file. The every keyword +cannot be used with the dump dcd style.
For example, the following commands will write snapshots at timesteps 0,10,20,30,100,200,300,1000,2000,etc: diff --git a/doc/thermo_modify.html b/doc/thermo_modify.html index 53505611d1..90842ab0fa 100644 --- a/doc/thermo_modify.html +++ b/doc/thermo_modify.html @@ -153,11 +153,12 @@ the beginning of a run to determine the next timestep at which a dump snapshot will be written out. On that timestep, the variable will be evaluated again to determine the next timestep, etc. Thus the variable should return timestep values. See the stagger() and -logfreq() math functions for equal-style variables, as -examples of useful functions to use in this context. Other similar -math functions could easily be added as options for equal-style -variables. In addition, thermodynamic output will -always occur on the first and last timestep of each run. +logfreq() and stride() math functions for equal-style +variables, as examples of useful functions to use in +this context. Other similar math functions could easily be added as +options for equal-style variables. In addition, +thermodynamic output will always occur on the first and last timestep +of each run.
For example, the following commands will output thermodynamic info at timesteps 0,10,20,30,100,200,300,1000,2000,etc: