pair_style hybrid dpd 1.0 1.0 12345 srp 0.8 * min exclude yes pair_coeff 1 1 dpd 60.0 50 1.0 pair_coeff 1 2 none pair_coeff 2 2 srp 40.0 @@ -62,7 +62,9 @@ bond-pairwise potential, such that the force on bond i due to bond
where r and rij are the distance and unit vector between the two -bonds. The mid option computes r and rij from the midpoint +bonds. The bondtype can also be specified as an asterisk (*) and then +this interaction applied to all bonds. +The mid option computes r and rij from the midpoint distance between bonds. The min option computes r and rij from the minimum distance between bonds. The force acting on a bond is mapped onto the two bond atoms according to the lever rule, diff --git a/doc/pair_srp.txt b/doc/pair_srp.txt index 2944979a72..05a89fde61 100644 --- a/doc/pair_srp.txt +++ b/doc/pair_srp.txt @@ -27,7 +27,7 @@ pair_coeff 1 1 dpd 60.0 4.5 1.0 pair_coeff 1 2 none pair_coeff 2 2 srp 100.0 0.8 :pre -pair_style hybrid dpd 1.0 1.0 12345 srp 0.8 1 min exclude yes +pair_style hybrid dpd 1.0 1.0 12345 srp 0.8 * min exclude yes pair_coeff 1 1 dpd 60.0 50 1.0 pair_coeff 1 2 none pair_coeff 2 2 srp 40.0 :pre @@ -53,7 +53,9 @@ bond-pairwise potential, such that the force on bond {i} due to bond :c,image(Eqs/pair_srp1.jpg) where {r} and {rij} are the distance and unit vector between the two -bonds. The {mid} option computes {r} and {rij} from the midpoint +bonds. The bondtype can also be specified as an asterisk (*) and then +this interaction applied to all bonds. +The {mid} option computes {r} and {rij} from the midpoint distance between bonds. The {min} option computes {r} and {rij} from the minimum distance between bonds. The force acting on a bond is mapped onto the two bond atoms according to the lever rule, diff --git a/doc/special_bonds.html b/doc/special_bonds.html index d5d66ff837..58fa493988 100644 --- a/doc/special_bonds.html +++ b/doc/special_bonds.html @@ -195,7 +195,7 @@ topology of the system). If new bonds are created (or molecules added containing atoms with more special neighbors), the size of this list needs to grow. Note that adding a single bond always adds a new 1st neighbor but may also induce *many* new 2nd and 3rd neighbors, -depending on the molecular topology of your syste. Using the extra +depending on the molecular topology of your system. Using the extra keyword leaves empty space in the list for this N additional 1st, 2nd, or 3rd neighbors to be added. If you do not do this, you may get an error when bonds (or molecules) are added. diff --git a/doc/special_bonds.txt b/doc/special_bonds.txt index 3cafe85eef..1c527c8ddd 100644 --- a/doc/special_bonds.txt +++ b/doc/special_bonds.txt @@ -189,7 +189,7 @@ topology of the system). If new bonds are created (or molecules added containing atoms with more special neighbors), the size of this list needs to grow. Note that adding a single bond always adds a new 1st neighbor but may also induce *many* new 2nd and 3rd neighbors, -depending on the molecular topology of your syste. Using the {extra} +depending on the molecular topology of your system. Using the {extra} keyword leaves empty space in the list for this N additional 1st, 2nd, or 3rd neighbors to be added. If you do not do this, you may get an error when bonds (or molecules) are added. diff --git a/doc/variable.html b/doc/variable.html index cf8e5d66ea..9d10201bf3 100644 --- a/doc/variable.html +++ b/doc/variable.html @@ -123,13 +123,13 @@ per-atom values from a file rather than from a formula. Variables can be hooked to Python functions using code you provide, so that the variable gets its value from the evaluation of the Python code.
-IMPORTANT NOTE: As discussed in Section -3.2 of the manual, an input script can -use "immediate" variables, specified as $(formula) with parenthesis, -where the formula has the same syntax as equal-style variables -described on this page. This is a way to evaluate a formula -immediately without using the variable command to define a named -variable. +
IMPORTANT NOTE: As discussed in Section 3.2 +of the manual, an input script can use "immediate" variables, specified +as $(formula) with parenthesis, where the formula has the same syntax +as equal-style variables described on this page. This is a convenient +way to evaluate a formula immediately without using the variable command +to define a named variable and then evaluate that variable. See below +for a more detailed discussion of this feature.
In the discussion that follows, the "name" of the variable is the arbitrary string that is the 1st argument in the variable command. @@ -144,10 +144,12 @@ simulation.
IMPORTANT NOTE: When the input script line is encountered that defines a variable of style equal or atom or python that contains a -formula or Python code, the formula is NOT immediately evaluated and -the result stored. See the discussion below about "Immediate -Evaluation of Variables" if you want to do this. This is also true of -the format style variable since it evaluates another variable when +formula or Python code, the formula is NOT immediately evaluated. +It will be evaluated every time when the variable is used instead. +If you simply want to evaluate a formula in place you can use as +so-called. See the section below about "Immediate Evaluation +of Variables" for more details on the topic. This is also true of +a format style variable since it evaluates another variable when it is invoked.
IMPORTANT NOTE: Variables of style equal and atom can be used as @@ -161,14 +163,6 @@ can also use such a python-style variable. This means that when the LAMMPS command evaluates the variable, the Python function will be executed.
-When the input script line is encountered that defines -a variable of style equal or atom or python that contains a -formula or Python code, the formula is NOT immediately evaluated and -the result stored. See the discussion below about "Immediate -Evaluation of Variables" if you want to do this. This is also true of -the format style variable since it evaluates another variable when -it is invoked. -
IMPORTANT NOTE: When a variable command is encountered in the input script and the variable name has already been specified, the command is ignored. This means variables can NOT be re-defined in an input diff --git a/doc/variable.txt b/doc/variable.txt index f79e5cd580..d5a7a10869 100644 --- a/doc/variable.txt +++ b/doc/variable.txt @@ -117,13 +117,13 @@ per-atom values from a file rather than from a formula. Variables can be hooked to Python functions using code you provide, so that the variable gets its value from the evaluation of the Python code. -IMPORTANT NOTE: As discussed in "Section -3.2"_Section_commands.html#cmd_2 of the manual, an input script can -use "immediate" variables, specified as $(formula) with parenthesis, -where the formula has the same syntax as equal-style variables -described on this page. This is a way to evaluate a formula -immediately without using the variable command to define a named -variable. +IMPORTANT NOTE: As discussed in "Section 3.2"_Section_commands.html#cmd_2 +of the manual, an input script can use "immediate" variables, specified +as $(formula) with parenthesis, where the formula has the same syntax +as equal-style variables described on this page. This is a convenient +way to evaluate a formula immediately without using the variable command +to define a named variable and then evaluate that variable. See below +for a more detailed discussion of this feature. In the discussion that follows, the "name" of the variable is the arbitrary string that is the 1st argument in the variable command. @@ -138,10 +138,12 @@ simulation. IMPORTANT NOTE: When the input script line is encountered that defines a variable of style {equal} or {atom} or {python} that contains a -formula or Python code, the formula is NOT immediately evaluated and -the result stored. See the discussion below about "Immediate -Evaluation of Variables" if you want to do this. This is also true of -the {format} style variable since it evaluates another variable when +formula or Python code, the formula is NOT immediately evaluated. +It will be evaluated every time when the variable is [used] instead. +If you simply want to evaluate a formula in place you can use as +so-called. See the section below about "Immediate Evaluation +of Variables" for more details on the topic. This is also true of +a {format} style variable since it evaluates another variable when it is invoked. IMPORTANT NOTE: Variables of style {equal} and {atom} can be used as @@ -155,14 +157,6 @@ can also use such a python-style variable. This means that when the LAMMPS command evaluates the variable, the Python function will be executed. -When the input script line is encountered that defines -a variable of style {equal} or {atom} or {python} that contains a -formula or Python code, the formula is NOT immediately evaluated and -the result stored. See the discussion below about "Immediate -Evaluation of Variables" if you want to do this. This is also true of -the {format} style variable since it evaluates another variable when -it is invoked. - IMPORTANT NOTE: When a variable command is encountered in the input script and the variable name has already been specified, the command is ignored. This means variables can NOT be re-defined in an input