diff --git a/doc/src/compute_angle_local.rst b/doc/src/compute_angle_local.rst index d4491c6945..5bd1692355 100644 --- a/doc/src/compute_angle_local.rst +++ b/doc/src/compute_angle_local.rst @@ -53,15 +53,17 @@ The value *eng* is the interaction energy for the angle. The value *v_name* can be used together with the *set* keyword to compute a user-specified function of the angle theta. The *name* -specified for the *v_name* value is the name of an :doc:`equal-style variable ` which should evaluate a formula based on a +specified for the *v_name* value is the name of an :doc:`equal-style +variable ` which should evaluate a formula based on a variable which will store the angle theta. This other variable must -be an :doc:`internal-style variable ` defined in the input -script; its initial numeric value can be anything. It must be an -internal-style variable, because this command resets its value -directly. The *set* keyword is used to identify the name of this -other variable associated with theta. +be an :doc:`internal-style variable ` specified by the *set* +keyword. It is an internal-style variable, because this command +resets its value directly. The internal-style variable does not need +to be defined in the input script (though it can be); if it is not +defined, then the *set* option creates an :doc:`internal-style +variable ` with the specified name. -Note that the value of theta for each angle which stored in the +Note that the value of theta for each angle which is stored in the internal variable is in radians, not degrees. As an example, these commands can be added to the bench/in.rhodo @@ -70,7 +72,6 @@ system and output the statistics in various ways: .. code-block:: LAMMPS - variable t internal 0.0 variable cos equal cos(v_t) variable cossq equal cos(v_t)*cos(v_t) diff --git a/doc/src/compute_bond_local.rst b/doc/src/compute_bond_local.rst index e070d507b1..27bf14d407 100644 --- a/doc/src/compute_bond_local.rst +++ b/doc/src/compute_bond_local.rst @@ -118,13 +118,15 @@ moving apart. The value *v_name* can be used together with the *set* keyword to compute a user-specified function of the bond distance. The *name* -specified for the *v_name* value is the name of an :doc:`equal-style variable ` which should evaluate a formula based on a -variable which will store the bond distance. This other variable must -be an :doc:`internal-style variable ` defined in the input -script; its initial numeric value can be anything. It must be an -internal-style variable, because this command resets its value -directly. The *set* keyword is used to identify the name of this -other variable associated with theta. +specified for the *v_name* value is the name of an :doc:`equal-style +variable ` which should evaluate a formula based on a +variable which stores the bond distance. This other variable must be +the :doc:`internal-style variable ` specified by the *set* +keyword. It is an internal-style variable, because this command +resets its value directly. The internal-style variable does not need +to be defined in the input script (though it can be); if it is not +defined, then the *set* option creates an :doc:`internal-style +variable ` with the specified name. As an example, these commands can be added to the bench/in.rhodo script to compute the length\ :math:`^2` of every bond in the system and @@ -132,7 +134,6 @@ output the statistics in various ways: .. code-block:: LAMMPS - variable d internal 0.0 variable dsq equal v_d*v_d compute 1 all property/local batom1 batom2 btype diff --git a/doc/src/compute_dihedral_local.rst b/doc/src/compute_dihedral_local.rst index d809cd39ce..77f467721d 100644 --- a/doc/src/compute_dihedral_local.rst +++ b/doc/src/compute_dihedral_local.rst @@ -45,30 +45,31 @@ interactions. The number of datums generated, aggregated across all processors, equals the number of dihedral angles in the system, modified by the group parameter as explained below. -The value *phi* (:math:`\phi`) is the dihedral angle, as defined in the diagram -on the :doc:`dihedral_style ` doc page. +The value *phi* (:math:`\phi`) is the dihedral angle, as defined in +the diagram on the :doc:`dihedral_style ` doc page. -The value *v_name* can be used together with the *set* keyword to compute a -user-specified function of the dihedral angle :math:`\phi`. The *name* -specified for the *v_name* value is the name of an -:doc:`equal-style variable ` which should evaluate a formula based on -a variable which will store the angle :math:`\phi`. This other variable must -be an :doc:`internal-style variable ` defined in the input -script; its initial numeric value can be anything. It must be an -internal-style variable, because this command resets its value -directly. The *set* keyword is used to identify the name of this -other variable associated with :math:`\phi`. +The value *v_name* can be used together with the *set* keyword to +compute a user-specified function of the dihedral angle :math:`\phi`. +The *name* specified for the *v_name* value is the name of an +:doc:`equal-style variable ` which should evaluate a formula +based on a variable which will store the angle :math:`\phi`. This +other variable must be an :doc:`internal-style variable ` +specified by the *set* keyword. It is an internal-style variable, +because this command resets its value directly. The internal-style +variable does not need to be defined in the input script (though it +can be); if it is not defined, then the *set* option creates an +:doc:`internal-style variable ` with the specified name. -Note that the value of :math:`\phi` for each angle which stored in the internal -variable is in radians, not degrees. +Note that the value of :math:`\phi` for each angle which stored in the +internal variable is in radians, not degrees. As an example, these commands can be added to the bench/in.rhodo -script to compute the :math:`\cos\phi` and :math:`\cos^2\phi` of every dihedral -angle in the system and output the statistics in various ways: +script to compute the :math:`\cos\phi` and :math:`\cos^2\phi` of every +dihedral angle in the system and output the statistics in various +ways: .. code-block:: LAMMPS - variable p internal 0.0 variable cos equal cos(v_p) variable cossq equal cos(v_p)*cos(v_p) @@ -100,10 +101,10 @@ no consistent ordering of the entries within the local vector or array from one timestep to the next. The only consistency that is guaranteed is that the ordering on a particular timestep will be the same for local vectors or arrays generated by other compute commands. -For example, dihedral output from the -:doc:`compute property/local ` command can be combined -with data from this command and output by the :doc:`dump local ` -command in a consistent way. +For example, dihedral output from the :doc:`compute property/local +` command can be combined with data from this +command and output by the :doc:`dump local ` command in a +consistent way. Here is an example of how to do this: diff --git a/doc/src/create_atoms.rst b/doc/src/create_atoms.rst index 6d3604215c..8601f02a01 100644 --- a/doc/src/create_atoms.rst +++ b/doc/src/create_atoms.rst @@ -416,24 +416,23 @@ atom, based on its coordinates. They apply to all styles except *single*. The *name* specified for the *var* keyword is the name of an :doc:`equal-style variable ` that should evaluate to a zero or non-zero value based on one or two or three variables that -will store the *x*, *y*, or *z* coordinates of an atom (one variable per -coordinate). If used, these other variables must be -:doc:`internal-style variables ` defined in the input -script; their initial numeric value can be anything. They must be -internal-style variables, because this command resets their values -directly. The *set* keyword is used to identify the names of these -other variables, one variable for the *x*-coordinate of a created atom, -one for *y*, and one for *z*. +will store the *x*, *y*, or *z* coordinates of an atom (one variable +per coordinate). If used, these other variables must be specified by +the *set* keyword. They are internal-style variable, because this +command resets their values directly. The internal-style variables do +not need to be defined in the input script (though they can be); if +one (or more) is not defined, then the *set* option creates an +:doc:`internal-style variable ` with the specified name. .. figure:: img/sinusoid.jpg :figwidth: 50% :align: right :target: _images/sinusoid.jpg -When an atom is created, its :math:`(x,y,z)` coordinates become the values for -any *set* variable that is defined. The *var* variable is then -evaluated. If the returned value is 0.0, the atom is not created. If -it is non-zero, the atom is created. +When an atom is about to be created, its :math:`(x,y,z)` coordinates +become the values for any *set* variable that is defined. The *var* +variable is then evaluated. If the returned value is 0.0, the atom is +not created. If it is non-zero, the atom is created. As an example, these commands can be used in a 2d simulation, to create a sinusoidal surface. Note that the surface is "rough" due to @@ -456,8 +455,6 @@ converts lattice spacings to distance. region box block 0 $x 0 $y -0.5 0.5 create_box 1 box - variable xx internal 0.0 - variable yy internal 0.0 variable v equal "(0.2*v_y*ylat * cos(v_xx/xlat * 2.0*PI*4.0/v_x) + 0.5*v_y*ylat - v_yy) > 0.0" create_atoms 1 box var v set x xx set y yy write_dump all atom sinusoid.lammpstrj diff --git a/doc/src/fix_controller.rst b/doc/src/fix_controller.rst index fc8186ef29..4e0414ca92 100644 --- a/doc/src/fix_controller.rst +++ b/doc/src/fix_controller.rst @@ -98,52 +98,53 @@ the following dynamic equation: \frac{dc}{dt} = -\alpha (K_p e + K_i \int_0^t e \, dt + K_d \frac{de}{dt} ) -where *c* is the continuous time analog of the control variable, -*e* =\ *pvar*\ -\ *setpoint* is the error in the process variable, and -:math:`\alpha`, :math:`K_p`, :math:`K_i` , and :math:`K_d` are constants -set by the corresponding -keywords described above. The discretized version of this equation is: +where *c* is the continuous time analog of the control variable, *e* +=\ *pvar*\ -\ *setpoint* is the error in the process variable, and +:math:`\alpha`, :math:`K_p`, :math:`K_i` , and :math:`K_d` are +constants set by the corresponding keywords described above. The +discretized version of this equation is: .. math:: c_n = c_{n-1} -\alpha \left( K_p \tau e_n + K_i \tau^2 \sum_{i=1}^n e_i + K_d (e_n - e_{n-1}) \right) -where :math:`\tau = \mathtt{Nevery} \cdot \mathtt{timestep}` is the time -interval between updates, -and the subscripted variables indicate the values of *c* and *e* at -successive updates. +where :math:`\tau = \mathtt{Nevery} \cdot \mathtt{timestep}` is the +time interval between updates, and the subscripted variables indicate +the values of *c* and *e* at successive updates. From the first equation, it is clear that if the three gain values :math:`K_p`, :math:`K_i`, :math:`K_d` are dimensionless constants, -then :math:`\alpha` must have -units of [unit *cvar*\ ]/[unit *pvar*\ ]/[unit time] e.g. [ eV/K/ps -]. The advantage of this unit scheme is that the value of the -constants should be invariant under a change of either the MD timestep -size or the value of *Nevery*\ . Similarly, if the LAMMPS :doc:`unit style ` is changed, it should only be necessary to change -the value of :math:`\alpha` to reflect this, while leaving :math:`K_p`, -:math:`K_i`, and :math:`K_d` unaltered. +then :math:`\alpha` must have units of [unit *cvar*\ ]/[unit *pvar*\ +]/[unit time] e.g. [ eV/K/ps ]. The advantage of this unit scheme is +that the value of the constants should be invariant under a change of +either the MD timestep size or the value of *Nevery*\ . Similarly, if +the LAMMPS :doc:`unit style ` is changed, it should only be +necessary to change the value of :math:`\alpha` to reflect this, while +leaving :math:`K_p`, :math:`K_i`, and :math:`K_d` unaltered. When choosing the values of the four constants, it is best to first pick a value and sign for :math:`\alpha` that is consistent with the -magnitudes and signs of *pvar* and *cvar*\ . The magnitude of :math:`K_p` -should then be tested over a large positive range keeping :math:`K_i = K_d =0`. -A good value for :math:`K_p` will produce a fast response in *pvar*, -without overshooting the *setpoint*\ . For many applications, proportional -feedback is sufficient, and so :math:`K_i = K_d =0` can be used. In cases -where there is a substantial lag time in the response of *pvar* to a change -in *cvar*, this can be counteracted by increasing :math:`K_d`. In situations +magnitudes and signs of *pvar* and *cvar*\ . The magnitude of +:math:`K_p` should then be tested over a large positive range keeping +:math:`K_i = K_d =0`. A good value for :math:`K_p` will produce a +fast response in *pvar*, without overshooting the *setpoint*\ . For +many applications, proportional feedback is sufficient, and so +:math:`K_i = K_d =0` can be used. In cases where there is a +substantial lag time in the response of *pvar* to a change in *cvar*, +this can be counteracted by increasing :math:`K_d`. In situations where *pvar* plateaus without reaching *setpoint*, this can be -counteracted by increasing :math:`K_i`. In the language of Charles Dickens, -:math:`K_p` represents the error of the present, :math:`K_i` the error of -the past, and :math:`K_d` the error yet to come. +counteracted by increasing :math:`K_i`. In the language of Charles +Dickens, :math:`K_p` represents the error of the present, :math:`K_i` +the error of the past, and :math:`K_d` the error yet to come. Because this fix updates *cvar*, but does not initialize its value, -the initial value :math:`c_0` is that assigned by the user in the input script via -the :doc:`internal-style variable ` command. This value is -used (by every other LAMMPS command that uses the variable) until this -fix performs its first update of *cvar* after *Nevery* timesteps. On -the first update, the value of the derivative term is set to zero, -because the value of :math:`e_{n-1}` is not yet defined. +the initial value :math:`c_0` is that assigned by the user in the +input script via the :doc:`internal-style variable ` +command. This value is used (by every other LAMMPS command that uses +the variable) until this fix performs its first update of *cvar* after +*Nevery* timesteps. On the first update, the value of the derivative +term is set to zero, because the value of :math:`e_{n-1}` is not yet +defined. ---------- @@ -154,21 +155,23 @@ must produce a global quantity, not a per-atom or local quantity. If *pvar* begins with "c\_", a compute ID must follow which has been previously defined in the input script and which generates a global -scalar or vector. See the individual :doc:`compute ` doc page -for details. If no bracketed integer is appended, the scalar +scalar or vector. See the individual :doc:`compute ` doc +page for details. If no bracketed integer is appended, the scalar calculated by the compute is used. If a bracketed integer is appended, the Ith value of the vector calculated by the compute is -used. Users can also write code for their own compute styles and :doc:`add them to LAMMPS `. +used. Users can also write code for their own compute styles and +:doc:`add them to LAMMPS `. If *pvar* begins with "f\_", a fix ID must follow which has been previously defined in the input script and which generates a global scalar or vector. See the individual :doc:`fix ` page for details. Note that some fixes only produce their values on certain timesteps, which must be compatible with when fix controller -references the values, or else an error results. If no bracketed integer -is appended, the scalar calculated by the fix is used. If a bracketed -integer is appended, the Ith value of the vector calculated by the fix -is used. Users can also write code for their own fix style and :doc:`add them to LAMMPS `. +references the values, or else an error results. If no bracketed +integer is appended, the scalar calculated by the fix is used. If a +bracketed integer is appended, the Ith value of the vector calculated +by the fix is used. Users can also write code for their own fix style +and :doc:`add them to LAMMPS `. If *pvar* begins with "v\_", a variable name must follow which has been previously defined in the input script. Only equal-style variables @@ -182,19 +185,21 @@ variable. The target value *setpoint* for the process variable must be a numeric value, in whatever units *pvar* is defined for. -The control variable *cvar* must be the name of an :doc:`internal-style variable ` previously defined in the input script. Note -that it is not specified with a "v\_" prefix, just the name of the -variable. It must be an internal-style variable, because this fix -updates its value directly. Note that other commands can use an -equal-style versus internal-style variable interchangeably. +The control variable *cvar* must be the name of an +:doc:`internal-style variable ` previously defined in the +input script. Note that it is not specified with a "v\_" prefix, just +the name of the variable. It must be an internal-style variable, +because this fix updates its value directly. Note that other commands +can use an equal-style versus internal-style variable interchangeably. ---------- Restart, fix_modify, output, run start/stop, minimize info """"""""""""""""""""""""""""""""""""""""""""""""""""""""""" -Currently, no information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options -are relevant to this fix. +Currently, no information about this fix is written to :doc:`binary +restart files `. None of the :doc:`fix_modify ` +options are relevant to this fix. This fix produces a global vector with 3 values which can be accessed by various :doc:`output commands `. The values can be @@ -211,7 +216,8 @@ variable is in. The vector values calculated by this fix are "extensive". No parameter of this fix can be used with the *start/stop* keywords of -the :doc:`run ` command. This fix is not invoked during :doc:`energy minimization `. +the :doc:`run ` command. This fix is not invoked during +:doc:`energy minimization `. Restrictions """""""""""" diff --git a/doc/src/fix_deposit.rst b/doc/src/fix_deposit.rst index 8f88717a00..09cf328fec 100644 --- a/doc/src/fix_deposit.rst +++ b/doc/src/fix_deposit.rst @@ -225,22 +225,25 @@ rotated configuration of the molecule. .. versionadded:: 21Nov2023 -The *var* and *set* keywords can be used together to provide a criterion -for accepting or rejecting the addition of an individual atom, based on its -coordinates. The *name* specified for the *var* keyword is the name of an -:doc:`equal-style variable ` that should evaluate to a zero or -non-zero value based on one or two or three variables that will store the -*x*, *y*, or *z* coordinates of an atom (one variable per coordinate). If -used, these other variables must be :doc:`internal-style variables -` defined in the input script; their initial numeric value can be -anything. They must be internal-style variables, because this command -resets their values directly. The *set* keyword is used to identify the -names of these other variables, one variable for the *x*-coordinate of a -created atom, one for *y*, and one for *z*. When an atom is created, its -:math:`(x,y,z)` coordinates become the values for any *set* variable that -is defined. The *var* variable is then evaluated. If the returned value -is 0.0, the atom is not created. If it is non-zero, the atom is created. -For an example of how to use these keywords, see the +The *var* and *set* keywords can be used together to provide a +criterion for accepting or rejecting the addition of an individual +atom, based on its coordinates. The *name* specified for the *var* +keyword is the name of an :doc:`equal-style variable ` that +should evaluate to a zero or non-zero value based on one or two or +three variables that will store the *x*, *y*, or *z* coordinates of an +atom (one variable per coordinate). If used, these other variables +must be :doc:`internal-style variables ` specified by the +*set* keyword. They must be internal-style variables, because this +command resets their values directly. The internal-style variables do +not need to be defined in the input script (though they can be); if +one (or more) is not defined, then the *set* option creates an +:doc:`internal-style variable ` with the specified name. + +When an atom is about to be created, its :math:`(x,y,z)` coordinates +become the values for any *set* variable that is defined. The *var* +variable is then evaluated. If the returned value is 0.0, the atom is +not created. If it is non-zero, the atom is created. For an example +of how to use the set/var keywords in a similar context, see the :doc:`create_atoms ` command. The *rate* option moves the insertion volume in the z direction (3d) @@ -304,12 +307,13 @@ units of distance or velocity. Restart, fix_modify, output, run start/stop, minimize info """"""""""""""""""""""""""""""""""""""""""""""""""""""""""" -This fix writes the state of the deposition to :doc:`binary restart files `. This includes information about how many -particles have been deposited, the random number generator seed, the -next timestep for deposition, etc. See the -:doc:`read_restart ` command for info on how to re-specify -a fix in an input script that reads a restart file, so that the -operation of the fix continues in an uninterrupted fashion. +This fix writes the state of the deposition to :doc:`binary restart +files `. This includes information about how many particles +have been deposited, the random number generator seed, the next +timestep for deposition, etc. See the :doc:`read_restart +` command for info on how to re-specify a fix in an +input script that reads a restart file, so that the operation of the +fix continues in an uninterrupted fashion. .. note:: diff --git a/doc/src/python.rst b/doc/src/python.rst index 99f32e7c80..38e36147c0 100644 --- a/doc/src/python.rst +++ b/doc/src/python.rst @@ -10,43 +10,45 @@ Syntax python mode keyword args ... -* mode = *source* or name of Python function +* mode = *source* or *name* of Python function if mode is *source*: .. parsed-literal:: keyword = *here* or name of a *Python file* - *here* arg = inline - inline = one or more lines of Python code which defines func - must be a single argument, typically enclosed between triple quotes + *here* arg = one or more lines of Python code + must be a single argument, typically enclosed between triple quotes + the in-lined Python code will be executed immediately *Python file* = name of a file with Python code which will be executed immediately -* if *mode* is the name of a Python function, one or more keywords with/without arguments must be appended +* if *mode* is *name* of a Python function: .. parsed-literal:: + one or more keywords with/without arguments must be appended keyword = *invoke* or *input* or *return* or *format* or *length* or *file* or *here* or *exists* - *invoke* arg = none = invoke the previously defined Python function + *invoke* arg = none = invoke the previously-defined Python function *input* args = N i1 i2 ... iN N = # of inputs to function i1,...,iN = value, SELF, or LAMMPS variable name value = integer number, floating point number, or string - SELF = reference to LAMMPS itself which can be accessed by Python function - variable = v_name, where name = name of LAMMPS variable, e.g. v_abc + SELF = reference to LAMMPS itself which can then be accessed by Python function + variable = v_name, where name = name of a LAMMPS variable, e.g. v_abc + internal variable = iv_name, where name = name of a LAMMPS internal-style variable, e.g. iv_xyz *return* arg = varReturn varReturn = v_name = LAMMPS variable name which the return value of the Python function will be assigned to *format* arg = fstring with M characters M = N if no return value, where N = # of inputs M = N+1 if there is a return value - fstring = each character (i,f,s,p) corresponds in order to an input or return value - 'i' = integer, 'f' = floating point, 's' = string, 'p' = SELF + fstring = each character (i,f,s,p) corresponds (in order) to an input or return value + 'i' = integer, 'f' = floating point, 's' = string, 'p' = SELF *length* arg = Nlen Nlen = max length of string returned from Python function *file* arg = filename - filename = file of Python code, which defines func + filename = file of Python code, which defines the Python function *here* arg = inline - inline = one or more lines of Python code which defines func + inline = one or more lines of Python code which defines the Python function must be a single argument, typically enclosed between triple quotes *exists* arg = none = Python code has been loaded by previous python command @@ -87,37 +89,43 @@ Examples Description """"""""""" -The *python* command allows interfacing LAMMPS with an embedded Python -interpreter and enables either executing arbitrary python code in that -interpreter, registering a Python function for future execution (as a -python style variable, from a fix interfaced with python, or for direct -invocation), or invoking such a previously registered function. +The *python* command interfaces LAMMPS with an embedded Python +interpreter and enables executing arbitrary python code in that +interpreter. This can be done immediately, by using *mode* = +*source*. Or execution can be deferred, by registering a Python +function for later execution, by using *mode* = *name* of a Python +function. -Arguments, including LAMMPS variables, can be passed to the function -from the LAMMPS input script and a value returned by the Python function -assigned to a LAMMPS variable. The Python code for the function can be included -directly in the input script or in a separate Python file. The function -can be standard Python code or it can make "callbacks" to LAMMPS through -its library interface to query or set internal values within LAMMPS. -This is a powerful mechanism for performing complex operations in a -LAMMPS input script that are not possible with the simple input script -and variable syntax which LAMMPS defines. Thus your input script can -operate more like a true programming language. +Later execution can be triggered in one of two ways. One is to use +the python command again with its *invoke* keyword. The other is to +trigger the evaluation of a python-style, equal-style, or atom-style +variable. A python-style variable invokes its associated Python +function; its return value becomes the value of the python-style +variable. Equal- and atom-style variables can use a Python function +wrapper in their formulas which encodes the Python function name, and +specifies arguments to pass to the function. + +Note python-style, equal-style, and atom-style variables can be used +in many different ways within LAMMPS. They can be evaulated directly +in an input script, effectively replacing the variable with its value. +Or they can be passed to various commands as arguments, so that the +variable is evaluated multiple times during a simulation run. See the +:doc:`variable ` command doc page for more details on +variable styles which enable Python function evaluation. + +The Python code for the function can be included directly in the input +script or in a separate Python file. The function can be standard +Python code or it can make "callbacks" to LAMMPS through its library +interface to query or set internal values within LAMMPS. This is a +powerful mechanism for performing complex operations in a LAMMPS input +script that are not possible with the simple input script and variable +syntax which LAMMPS defines. Thus your input script can operate more +like a true programming language. Use of this command requires building LAMMPS with the PYTHON package which links to the Python library so that the Python interpreter is embedded in LAMMPS. More details about this process are given below. -There are two ways to invoke a Python function once it has been -registered. One is using the *invoke* keyword. The other is to assign -the function to a :doc:`python-style variable ` defined in -your input script. Whenever the variable is evaluated, it will execute -the Python function to assign a value to the variable. Note that -variables can be evaluated in many different ways within LAMMPS. They -can be substituted with their result directly in an input script, or -they can be passed to various commands as arguments, so that the -variable is evaluated during a simulation run. - A broader overview of how Python can be used with LAMMPS is given in the :doc:`Use Python with LAMMPS ` section of the documentation. There also is an ``examples/python`` directory which @@ -125,25 +133,31 @@ illustrates use of the python command. ---------- -The first argument of the *python* command is either the *source* -keyword or the name of a Python function. This defines the mode -of the python command. +The first argument is the *mode* setting, which is either *source* or +the *name* of a Python function. .. versionchanged:: 22Dec2022 -If the *source* keyword is used, it is followed by either a file name or -the *here* keyword. No other keywords can be used. The *here* keyword -is followed by a string with python commands, either on a single line -enclosed in quotes, or as multiple lines enclosed in triple quotes. -These Python commands will be passed to the python interpreter and -executed immediately without registering a Python function for future -execution. The code will be loaded into and run in the "main" module of -the Python interpreter. This allows running arbitrary Python code at -any time while processing the LAMMPS input file. This can be used to -pre-load Python modules, initialize global variables, define functions -or classes, or perform operations using the python programming language. -The Python code will be executed in parallel on all MPI processes. No -arguments can be passed. +If *source* is used, it is followed by either the *here* keyword or a +file name containing Python code. The *here* keyword is followed by a +string containing python commands, either on a single line enclosed in +quotes, or as multiple lines enclosed in triple quotes. In either +case, the in-line code or file contents are passed to the python +interpreter and executed immediately. The code will be loaded into +and run in the "main" module of the Python interpreter. This allows +running arbitrary Python code at any time while processing the SPARTA +input file. This can be used to pre-load Python modules, initialize +global variables, define functions or classes, or perform operations +using the Python programming language. The Python code will be +executed in parallel on all the MPI processes being used to run +LAMMPS. Note that no arguments can be passed to the executed Python +code. + +If the *mode* setting is the *name* of a Python function, then it will +be registered with SPARTA for future execution (or already be defined, +see the *exists* keyword). One or more keywords must follow the +*mode* function name. One of the keywords must be *invoke*, *file*, +*here*, or *exists*. In all other cases, the first argument is the name of a Python function that will be registered with LAMMPS for future execution. The function @@ -154,40 +168,79 @@ If the *invoke* keyword is used, no other keywords can be used, and a previous *python* command must have registered the Python function referenced by this command. This invokes the Python function with the previously defined arguments and the return value is processed as -explained below. You can invoke the function as many times as you wish -in your input script. +explained below. You can invoke a registered function as many times +as you wish in your input script. + +NOTE: As indicated with a NOTE in python_impl.cpp, I don't think there +is any access to a value returned by invoking a Py function in this way. +If that is correct, I think this should be clarified in the doc page, +with a better explanation of the utility of using the *invoke* keyword. The *input* keyword defines how many arguments *N* the Python function -expects. If it takes no arguments, then the *input* keyword should not -be used. Each argument can be specified directly as a value, e.g. '6' -or '3.14159' or 'abc' (a string of characters). The type of each -argument is specified by the *format* keyword as explained below, so -that Python will know how to interpret the value. If the word SELF is -used for an argument it has a special meaning. A pointer is passed to -the Python function which it can convert into a reference to LAMMPS +expects. If it takes no arguments, then the *input* keyword should +not be used. Each argument can be specified directly as a value, +e.g. '6' or '3.14159' or 'abc' (a string of characters). The type of +each argument is specified by the *format* keyword as explained below, +so that Python will know how to interpret the value. If the word SELF +is used for an argument it has a special meaning. A pointer is passed +to the Python function which it can convert into a reference to LAMMPS itself using the :doc:`LAMMPS Python module `. This enables the function to call back to LAMMPS through its library -interface as explained below. This allows the Python function to query -or set values internal to LAMMPS which can affect the subsequent -execution of the input script. A LAMMPS variable can also be used as an -argument, specified as v_name, where "name" is the name of the variable. -Any style of LAMMPS variable returning a scalar or a string can be used, -as defined by the :doc:`variable ` command. The *format* -keyword must be used to set the type of data that is passed to Python. +interface as explained below. This allows the Python function to +query or set values internal to LAMMPS which can affect the subsequent +execution of the input script. + +A LAMMPS variable can also be used as an *input* argument, specified +as v_name, where "name" is the name of the variable defined in the +input script. Any style of LAMMPS variable returning a scalar or a +string can be used, as defined by the :doc:`variable ` +command. The style of variable must be consistent with the *format* +keyword specification for the type of data that is passed to Python. Each time the Python function is invoked, the LAMMPS variable is -evaluated and its value is passed to the Python function. +evaluated and its value is passed as an argument to the Python +function. + +A LAMMPS internal-style variable can also be used as an *input* +argument, specified as iv_name, where "name" is the name of the +internal-style variable. The internal-style variable does not have to +be defined in the input script (though it can be); if it is not +defined, this command creates an :doc:`internal-style variable +` with the specified name. + +An internal-style variable must be used when an equal-style or +atom-style variable triggers the invocation of the Python function +defined by this command, by including a Python function wrapper in its +formula, with one or more arguments also included in the formula. + +In brief, the syntax for a Python function wrapper in a variable +formula is py_varname(arg1,arg2,...argN), where "varname" is the name +of a python-style variable associated with a Python function defined +by this command. One or more arguments to the function wrapper can +themselves be formulas which the variable command will evaluate and +pass as arguments to the Python function. This is done by assigning +the numeric result for each argument to an internal-style variable; +this the *input* keyword must specify the arguments as internal-style +variables and their format (see below) as "f" for floating point. +This is because LAMMPS variable formulas are calculated with floating +point arithmetic (any integer values are converted to floating point). + +See the :doc:`variable ` command doc page for full details +on formula syntax including for Python function wrappers. Examples +using Python function wrappers are shown below. The *return* keyword is only needed if the Python function returns a -value. The specified *varReturn* must be of the form v_name, where -"name" is the name of a python-style LAMMPS variable, defined by the +value. The specified *varReturn* is of the form v_name, where "name" +is the name of a python-style LAMMPS variable, defined by the :doc:`variable ` command. The Python function can return a numeric or string value, as specified by the *format* keyword. -As explained on the :doc:`variable ` doc page, the definition -of a python-style variable associates a Python function name with the -variable. This must match the *Python function name* first argument of -the *python* command. For example these two commands would be -consistent: +---------- + +As explained on the :doc:`variable ` doc page, the +definition of a python-style variable associates a Python function +name with the variable. Its specification must match the *mode* +argument of the *python* command for the Python function name. For +example these two commands would be consistent: .. code-block:: LAMMPS @@ -196,43 +249,43 @@ consistent: The two commands can appear in either order in the input script so long as both are specified before the Python function is invoked for -the first time. Afterwards, the variable 'foo' is associated with -the Python function 'myMultiply'. +the first time. The *format* keyword must be used if the *input* or *return* keywords are used. It defines an *fstring* with M characters, where M = sum of number of inputs and outputs. The order of characters corresponds to the N inputs, followed by the return value (if it exists). Each character must be one of the following: "i" for integer, "f" for -floating point, "s" for string, or "p" for SELF. Each character defines -the type of the corresponding input or output value of the Python -function and affects the type conversion that is performed internally as -data is passed back and forth between LAMMPS and Python. Note that it -is permissible to use a :doc:`python-style variable ` in a -LAMMPS command that allows for an equal-style variable as an argument, -but only if the output of the Python function is flagged as a numeric -value ("i" or "f") via the *format* keyword. +floating point, "s" for string, or "p" for SELF. Each character +defines the type of the corresponding input or output value of the +Python function and affects the type conversion that is performed +internally as data is passed back and forth between LAMMPS and Python. +Note that it is permissible to use a :doc:`python-style variable +` in a LAMMPS command that allows for an equal-style +variable as an argument, but only if the output of the Python function +is flagged as a numeric value ("i" or "f") via the *format* keyword. If the *return* keyword is used and the *format* keyword specifies the output as a string, then the default maximum length of that string is 63 characters (64-1 for the string terminator). If you want to return a longer string, the *length* keyword can be specified with its *Nlen* -value set to a larger number (the code allocates space for Nlen+1 to -include the string terminator). If the Python function generates a +value set to a larger number. LAMMPS will then allocate Nlen+1 space +to include the string terminator. If the Python function generates a string longer than the default 63 or the specified *Nlen*, it will be truncated. ---------- -Either the *file*, *here*, or *exists* keyword must be used, but only -one of them. These keywords specify what Python code to load into the -Python interpreter. The *file* keyword gives the name of a file -containing Python code, which should end with a ".py" suffix. The code -will be immediately loaded into and run in the "main" module of the -Python interpreter. The Python code will be executed in parallel on all -MPI processes. Note that Python code which contains a function -definition does not "execute" the function when it is run; it simply -defines the function so that it can be invoked later. +As noted above, either the *invoke*, *file*, *here*, or *exists* +keyword must be used, but only one of them. These keywords specify +what Python code to load into the Python interpreter. The *file* +keyword gives the name of a file containing Python code, which should +end with a ".py" suffix. The code will be immediately loaded into and +run in the "main" module of the Python interpreter. The Python code +will be executed in parallel on all MPI processes. Note that Python +code which contains a function definition does not "execute" the +function when it is run; it simply defines the function so that it can +be invoked later. The *here* keyword does the same thing, except that the Python code follows as a single argument to the *here* keyword. This can be done @@ -243,15 +296,18 @@ proper indentation, blank lines, and comments, as desired. See the how triple quotes can be used as part of input script syntax. The *exists* keyword takes no argument. It means that Python code -containing the required Python function with the given name has already -been executed, for example by a *python source* command or in the same -file that was used previously with the *file* keyword. +containing the required Python function with the given name has +already been executed, for example by a *python source* command or in +the same file that was used previously with the *file* keyword. This +allows use of a single file of Python code which contains multiple +functions, any of which can be used in the same (or different) input +scripts (see below). -Note that the Python code that is loaded and run must contain a function -with the specified function name. To operate properly when later -invoked, the function code must match the *input* and *return* and -*format* keywords specified by the python command. Otherwise Python -will generate an error. +Note that the Python code that is loaded and run by the *file* or +*here* keyword must contain a function with the specified function +name. To operate properly when later invoked, the function code must +match the *input* and *return* and *format* keywords specified by the +python command. Otherwise Python will generate an error. ---------- @@ -308,13 +364,13 @@ previous value is simply returned, without re-computing it. The "global" statement inside the Python function allows it to overwrite the global variables from within the local context of the function. -Note that if you load Python code multiple times (via multiple python -commands), you can overwrite previously loaded variables and functions -if you are not careful. E.g. if the code above were loaded twice, the -global variables would be re-initialized, which might not be what you -want. Likewise, if a function with the same name exists in two chunks -of Python code you load, the function loaded second will override the -function loaded first. +Also note that if you load Python code multiple times (via multiple +python commands), you can overwrite previously loaded variables and +functions if you are not careful. E.g. if the code above were loaded +twice, the global variables would be re-initialized, which might not +be what you want. Likewise, if a function with the same name exists +in two chunks of Python code you load, the function loaded second will +override the function loaded first. It's important to realize that if you are running LAMMPS in parallel, each MPI task will load the Python interpreter and execute a local @@ -325,15 +381,16 @@ This implies three important things. First, if you put a print or other statement creating output to the screen in your Python function, you will see P copies of the output, when running on P processors. If the prints occur at (nearly) the same -time, the P copies of the output may be mixed together. When loading -the LAMMPS Python module into the embedded Python interpreter, it is -possible to pass the pointer to the current LAMMPS class instance and -via the Python interface to the LAMMPS library interface, it is possible -to determine the MPI rank of the current process and thus adapt the -Python code so that output will only appear on MPI rank 0. The -following LAMMPS input demonstrates how this could be done. The text -'Hello, LAMMPS!' should be printed only once, even when running LAMMPS -in parallel. +time, the P copies of the output may be mixed together. + +It is possible to avoid this issue, by passing the pointer to the +current LAMMPS class instance to the Python function via the {input} +SELF argument described above. The Python function can then use the +Python interface to the LAMMPS library interface, and determine the +MPI rank of the current process. The Python code can then ensure +output will only appear on MPI rank 0. The following LAMMPS input +demonstrates how this could be done. The text 'Hello, LAMPS!' should +be printed only once, even when running LAMMPS in parallel. .. code-block:: LAMMPS @@ -348,13 +405,13 @@ in parallel. python python_hello invoke -If your Python code loads Python modules that are not pre-loaded by the -Python library, then it will load the module from disk. This may be a -bottleneck if 1000s of processors try to load a module at the same time. -On some large supercomputers, loading of modules from disk by Python may -be disabled. In this case you would need to pre-build a Python library -that has the required modules pre-loaded and link LAMMPS with that -library. +Second, if your Python code loads Python modules that are not +pre-loaded by the Python library, then it will load the module from +disk. This may be a bottleneck if 1000s of processors try to load a +module at the same time. On some large supercomputers, loading of +modules from disk by Python may be disabled. In this case you would +need to pre-build a Python library that has the required modules +pre-loaded and link LAMMPS with that library. Third, if your Python code calls back to LAMMPS (discussed in the next section) and causes LAMMPS to perform an MPI operation requires @@ -365,10 +422,10 @@ LAMMPS. Otherwise the code may hang. ---------- -Your Python function can "call back" to LAMMPS through its -library interface, if you use the SELF input to pass Python -a pointer to LAMMPS. The mechanism for doing this in your -Python function is as follows: +As mentioned above, a Python function can "call back" to LAMMPS +through its library interface, if the SELF input is used to pass +Python a pointer to LAMMPS. The mechanism for doing this is as +follows: .. code-block:: python @@ -416,7 +473,7 @@ which loads and runs the following function from ``examples/python/funcs.py``: lmp.set_variable("cut",cut) # set a variable in LAMMPS lmp.command("pair_style lj/cut ${cut}") # LAMMPS command - #lmp.command("pair_style lj/cut %d" % cut) # LAMMPS command option + #lmp.command("pair_style lj/cut %d" % cut) # alternate form of LAMMPS command lmp.command("pair_coeff * * 1.0 1.0") # ditto lmp.command("run 10") # ditto @@ -449,9 +506,9 @@ is a useful way for a Python function to return multiple values to LAMMPS, more than the single value that can be passed back via a return statement. This cutoff value in the "cut" variable is then substituted (by LAMMPS) in the pair_style command that is executed -next. Alternatively, the "LAMMPS command option" line could be used -in place of the 2 preceding lines, to have Python insert the value -into the LAMMPS command string. +next. Alternatively, the "alternate form of LAMMPS command" line +could be used in place of the 2 preceding lines, to have Python insert +the value into the LAMMPS command string. .. note:: @@ -463,20 +520,109 @@ into the LAMMPS command string. file() functions, so long as the command would work if it were executed in the LAMMPS input script directly at the same point. -However, a Python function can also be invoked during a run, whenever -an associated LAMMPS variable it is assigned to is evaluated. If the -variable is an input argument to another LAMMPS command (e.g. :doc:`fix setforce `), then the Python function will be invoked -inside the class for that command, in one of its methods that is -invoked in the middle of a timestep. You cannot execute arbitrary -input script commands from the Python function (again, via the -command() or file() functions) at that point in the run and expect it -to work. Other library functions such as those that invoke computes -or other variables may have hidden side effects as well. In these -cases, LAMMPS has no simple way to check that something illogical is -being attempted. -The same applies to Python functions called during a simulation run at -each time step using :doc:`fix python/invoke `. +---------- + +A Python function can also be invoked during a run, whenever +an associated python-style variable it is assigned to is evaluated. + +If the variable is an input argument to another LAMMPS command +(e.g. :doc:`fix setforce `), then the Python function +will be invoked inside the class for that command, possibly in one of +its methods that is invoked in the middle of a timestep. You cannot +execute arbitrary input script commands from the Python function +(again, via the command() or file() functions) at that point in the +run and expect it to work. Other library functions such as those that +invoke computes or other variables may have hidden side effects as +well. In these cases, LAMMPS has no simple way to check that +something illogical is being attempted. + +The same constraints apply to Python functions called during a +simulation run at each time step using the :doc:`fix python/invoke +` command. + +---------- + +A Python function can also be invoked within the formula for an +equal-style or atom-style varaible. This means the Python function +will be invoked whenever the variable is invoked. In the case of an +atom-style varaible, the Python function can be invoked once per atom. + +Here are two simple examples using equal- and atom-style variables to +trigger execution of a Python function: + +.. code-block:: LAMMPS + + variable foo python truncate + python truncate return v_foo input 1 iv_arg format fi here """ +def truncate(x): + return int(x) +""" + variable ptrunc equal py_foo(press) + print "TRUNCATED pressure = ${ptrunc}" + +The Python "truncate" function simply converts a floating-point value +to an integer value. When the LAMMPS print command evaluates the +equal-style "ptrunc" variable, the current thermodynamic pressure is +passed to the Python function. The truncated value is output to the +screen and logfile by the print command. Note that the *input* +keyword for the *python* command, specifies an internal-style variable +named "arg" as iv_arg which is required to invoke the Python function +from a Python function wrapper. + +The last 2 lines can be replaced by these to define atom-style +varaibles which invoke the same Python "truncate" function: + +.. code-block:: LAMMPS + + variable xtrunc atom py_foo(x) + variable ytrunc atom py_foo(y) + variable ztrunc atom py_foo(z) + dump 1 all custom 100 tmp.dump id x y z v_xtrunc v_ytrunc v_ztrunc + +Now when the dump command invokes the 3 atom-style variables, their +arguments x,y,z to the Python function wrapper are the current +per-atom coordinates of each atom. The Python "truncate" function is +thus invoked 3 times for each atom, and the truncated coordinate +values for each atom are written to the dump file. + +Note that when using a Python function wrapper in a variable, +arguments can be passed to the Python function either from the +varaible formula or by *input* keyword to the *python command. For +example, consider these (made up) commands: + +.. code-block:: LAMMPS + + variable foo python mixedargs + python mixedargs return v_foo input 6 7.5 v_myValue iv_arg1 iv_argy iv_argz v_flags & + format fffffsf here """ +def mixedargs(a,b,x,y,z,flags): + ... + return result +""" + variable flags string optionABC + variable myValue equal "2.0*temp*c_pe" + compute pe all pe + compute peatom all pe/atom + variable field atom py_foo(x+3.0,sqrt(y),(z-zlo)*c_peatom) + +They define a Python "mixedargs" function with 6 arguments. Three of +them are internal-style variables, which the variable formula +calculates as numeric values for each atom and passes to the function. +In this example, these arguments are themselves small formulas +containing the x,y,z coordinates of each atom as well as a per-atom +compute (c_peratom) and thermodynamic keyword (zlo). + +The other three arguements (7.5,v_myValue,v_flags) are defined by the +*python* command. The first and last are constant values (7.5 and the +optionABC string). The second argument (myValue) is the result of an +equal-style variable formula which accesses the system temperature and +potential energy. + +The "result" returned by teach invocation of the Python "mixedargs" +function becomes the per-atom value in the atom-style "field" +variable, which could be output to a dump file or used elsewhere in +the input script. ---------- @@ -563,27 +709,30 @@ If you use Python code which calls back to LAMMPS, via the SELF input argument explained above, there is an extra step required when building LAMMPS. LAMMPS must also be built as a shared library and your Python function must be able to load the :doc:`"lammps" Python module -` that wraps the LAMMPS library interface. These are the -same steps required to use Python by itself to wrap LAMMPS. Details on -these steps are explained on the :doc:`Python ` doc page. -Note that it is important that the stand-alone LAMMPS executable and the -LAMMPS shared library be consistent (built from the same source code -files) in order for this to work. If the two have been built at -different times using different source files, problems may occur. +` that wraps the LAMMPS library interface. + +These are the same steps required to use Python by itself to wrap +LAMMPS. Details on these steps are explained on the :doc:`Python +` doc page. Note that it is important that the +stand-alone LAMMPS executable and the LAMMPS shared library be +consistent (built from the same source code files) in order for this +to work. If the two have been built at different times using +different source files, problems may occur. Another limitation of calling back to Python from the LAMMPS module using the *python* command in a LAMMPS input is that both, the Python interpreter and LAMMPS, must be linked to the same Python runtime as a shared library. If the Python interpreter is linked to Python statically (which seems to happen with Conda) then loading the shared -LAMMPS library will create a second python "main" module that hides the -one from the Python interpreter and all previous defined function and -global variables will become invisible. +LAMMPS library will create a second python "main" module that hides +the one from the Python interpreter and all previous defined function +and global variables will become invisible. Related commands """""""""""""""" -:doc:`shell `, :doc:`variable `, :doc:`fix python/invoke ` +:doc:`shell `, :doc:`variable `, :doc:`fix + python/invoke ` Default """"""" diff --git a/doc/src/variable.rst b/doc/src/variable.rst index a51901fbce..08afb64762 100644 --- a/doc/src/variable.rst +++ b/doc/src/variable.rst @@ -397,13 +397,24 @@ using the :doc:`command-line switch -var `. For the *internal* style a numeric value is provided. This value will be assigned to the variable until a LAMMPS command sets it to a new -value. There are currently only two LAMMPS commands that require -*internal* variables as inputs, because they reset them: -:doc:`create_atoms ` and :doc:`fix controller -`. As mentioned above, an internal-style variable can -be used in place of an equal-style variable anywhere else in an input -script, e.g. as an argument to another command that allows for -equal-style variables. +value. + +Note however, that most commands which use internal-style variables do +not require them to be defined in the input script. They create one +or more internal-style variables if they do not already exist. +Examples are these commands: + +* :doc:`create_atoms ` +* :doc:`fix deposit ` +* :doc:`compute bond/local ` +* :doc:`compute angle/local ` +* :doc:`compute dihedral/local ` +* :doc:`python ` command in conjunction with Python function wrappers used in equal- and atom-style variable formulas + +A command which does require an internal-style variable to be defined +in the input script is the :doc:`fix controller ` command doc page for details. -The *variable pyarg1* command defines an internal-style variable. It -MUST have the name pyarg1. If the Python function has *N* arguments, -*N* internal-style variables MUST be defined with names *pyarg1*, -*pyarg2*, ... *pyargN*. Note that multiple Python function wrappers -can use the same internal-style variables. - The next three commands define atom-style variables *xtrunc*, *ytrunc*, and *ztrunc*. Each of them include the same Python function wrapper in their formula, with a different argument. The atom-style @@ -1242,15 +1247,27 @@ will in turn invoke the Python-coded *truncate()* method. Because *xtrunc* is an atom-style variable, and the argument *x* in the Python function wrapper is a per-atom quantity (the x-coord of each atom), each processor will invoke the *truncate()* method once per atom, for -the atoms it owns. When invoked for the Ith atom, the x-coord of the -Ith atom becomes the value of the *pyarg1* internal-style variable. -The call to the *truncate()* function uses the value of the *pyarg1* -variable as its first (and only) argument. +the atoms it owns. + +When invoked for the Ith atom, the value of the *arg* internal-style +variable, defined by the *python* command, is set to the x-coord of +the Ith atom. The call via python-style variable *foo* to the Python +*truncate()* function passes the value of the *arg* variable as its +first (and only) argument. Likewise, the return value of the Python +function becomes is stored by the python-style variable *foo* and used +in the *xtrunc* atom-style variable formula for the Ith atom. The resulting per-atom vector for *xtrunc* will thus contain the truncated x-coord of every atom in the system. The dump command includes the truncated xyz coords for each atom in its output. +See the :doc:`python ' command for more details on options the +*python* command can specify as well as examples of more complex +Python functions which can be wrapped in this manner. In particular, +the Python function can take a variety of arguments, some generated by +the *python* command, and others by the arguments of the Python +function wrapper. + ---------- Atom Values and Vectors diff --git a/examples/python/in.python.wrap b/examples/python/in.python.wrap index 19ecec8f66..35c080f11b 100644 --- a/examples/python/in.python.wrap +++ b/examples/python/in.python.wrap @@ -25,11 +25,10 @@ neigh_modify delay 0 every 20 check no fix 1 all nve variable foo python truncate -python truncate return v_foo input 1 v_pyarg1 format fi here """ +python truncate return v_foo input 1 iv_arg format fi here """ def truncate(x): return int(x) """ -variable pyarg1 internal 0.0 variable scalar equal py_foo(4.5) print "TRUNCATE ${scalar}" @@ -40,7 +39,6 @@ variable ztrunc atom py_foo(z) # examine dump file to see truncated xyz coords of each atom -#dump 1 all custom 100 tmp.dump id x y z dump 1 all custom 100 tmp.dump id x y z v_xtrunc v_ytrunc v_ztrunc run 100 diff --git a/examples/python/log.1May25.python.wrap.g++.1 b/examples/python/log.1May25.python.wrap.g++.1 index 8038b600f3..a5edfe079e 100644 --- a/examples/python/log.1May25.python.wrap.g++.1 +++ b/examples/python/log.1May25.python.wrap.g++.1 @@ -1,4 +1,4 @@ -LAMMPS (2 Apr 2025 - Development - patch_2Apr2025-125-g7ca493917a-modified) +LAMMPS (2 Apr 2025 - Development - patch_2Apr2025-266-gebfb94a717-modified) # 3d Lennard-Jones melt with equal- and atom-style variables which # use a Python function wrapper in their formulas @@ -35,11 +35,10 @@ neigh_modify delay 0 every 20 check no fix 1 all nve variable foo python truncate -python truncate return v_foo input 1 v_pyarg1 format fi here """ +python truncate return v_foo input 1 iv_arg format fi here """ def truncate(x): return int(x) """ -variable pyarg1 internal 0.0 variable scalar equal py_foo(4.5) print "TRUNCATE ${scalar}" @@ -49,7 +48,8 @@ variable xtrunc atom py_foo(x) variable ytrunc atom py_foo(y) variable ztrunc atom py_foo(z) -#dump 1 all custom 100 tmp.dump id x y z +# examine dump file to see truncated xyz coords of each atom + dump 1 all custom 100 tmp.dump id x y z v_xtrunc v_ytrunc v_ztrunc run 100 @@ -70,20 +70,20 @@ Per MPI rank memory allocation (min/avg/max) = 2.644 | 2.644 | 2.644 Mbytes Step Temp E_pair E_mol TotEng Press 0 1.44 -6.7733681 0 -4.6176881 -5.0221006 100 0.75627408 -5.7580082 0 -4.6258659 0.21870071 -Loop time of 0.0160255 on 1 procs for 100 steps with 500 atoms +Loop time of 0.014627 on 1 procs for 100 steps with 500 atoms -Performance: 2695709.610 tau/day, 6240.069 timesteps/s, 3.120 Matom-step/s +Performance: 2953445.899 tau/day, 6836.680 timesteps/s, 3.418 Matom-step/s 100.0% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.011326 | 0.011326 | 0.011326 | 0.0 | 70.67 -Neigh | 0.002924 | 0.002924 | 0.002924 | 0.0 | 18.25 -Comm | 0.00046255 | 0.00046255 | 0.00046255 | 0.0 | 2.89 -Output | 0.0010398 | 0.0010398 | 0.0010398 | 0.0 | 6.49 -Modify | 0.00020589 | 0.00020589 | 0.00020589 | 0.0 | 1.28 -Other | | 6.725e-05 | | | 0.42 +Pair | 0.010546 | 0.010546 | 0.010546 | 0.0 | 72.10 +Neigh | 0.0027775 | 0.0027775 | 0.0027775 | 0.0 | 18.99 +Comm | 0.00044818 | 0.00044818 | 0.00044818 | 0.0 | 3.06 +Output | 0.00060601 | 0.00060601 | 0.00060601 | 0.0 | 4.14 +Modify | 0.00018516 | 0.00018516 | 0.00018516 | 0.0 | 1.27 +Other | | 6.39e-05 | | | 0.44 Nlocal: 500 ave 500 max 500 min Histogram: 1 0 0 0 0 0 0 0 0 0 diff --git a/examples/python/log.1May25.python.wrap.g++.4 b/examples/python/log.1May25.python.wrap.g++.4 index 3abf6d27fa..ff3e94ddf7 100644 --- a/examples/python/log.1May25.python.wrap.g++.4 +++ b/examples/python/log.1May25.python.wrap.g++.4 @@ -1,4 +1,4 @@ -LAMMPS (2 Apr 2025 - Development - patch_2Apr2025-125-g7ca493917a-modified) +LAMMPS (2 Apr 2025 - Development - patch_2Apr2025-266-gebfb94a717-modified) # 3d Lennard-Jones melt with equal- and atom-style variables which # use a Python function wrapper in their formulas @@ -35,11 +35,10 @@ neigh_modify delay 0 every 20 check no fix 1 all nve variable foo python truncate -python truncate return v_foo input 1 v_pyarg1 format fi here """ +python truncate return v_foo input 1 iv_arg format fi here """ def truncate(x): return int(x) """ -variable pyarg1 internal 0.0 variable scalar equal py_foo(4.5) print "TRUNCATE ${scalar}" @@ -49,7 +48,8 @@ variable xtrunc atom py_foo(x) variable ytrunc atom py_foo(y) variable ztrunc atom py_foo(z) -#dump 1 all custom 100 tmp.dump id x y z +# examine dump file to see truncated xyz coords of each atom + dump 1 all custom 100 tmp.dump id x y z v_xtrunc v_ytrunc v_ztrunc run 100 @@ -70,20 +70,20 @@ Per MPI rank memory allocation (min/avg/max) = 2.609 | 2.609 | 2.609 Mbytes Step Temp E_pair E_mol TotEng Press 0 1.44 -6.7733681 0 -4.6176881 -5.0221006 100 0.75627408 -5.7580082 0 -4.6258659 0.21870071 -Loop time of 0.00641075 on 4 procs for 100 steps with 500 atoms +Loop time of 0.0062374 on 4 procs for 100 steps with 500 atoms -Performance: 6738684.275 tau/day, 15598.806 timesteps/s, 7.799 Matom-step/s -100.0% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 6925957.189 tau/day, 16032.308 timesteps/s, 8.016 Matom-step/s +74.7% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.0028061 | 0.0028831 | 0.0029657 | 0.1 | 44.97 -Neigh | 0.00086635 | 0.00088279 | 0.00089739 | 0.0 | 13.77 -Comm | 0.0020095 | 0.0020768 | 0.0021521 | 0.1 | 32.40 -Output | 0.00041634 | 0.00042457 | 0.00043221 | 0.0 | 6.62 -Modify | 6.2967e-05 | 6.4188e-05 | 6.5205e-05 | 0.0 | 1.00 -Other | | 7.934e-05 | | | 1.24 +Pair | 0.0027648 | 0.0028431 | 0.0029465 | 0.1 | 45.58 +Neigh | 0.00084567 | 0.00086563 | 0.00088168 | 0.0 | 13.88 +Comm | 0.0020822 | 0.0021609 | 0.0022418 | 0.1 | 34.64 +Output | 0.00021567 | 0.00022125 | 0.00022624 | 0.0 | 3.55 +Modify | 6.2567e-05 | 6.4105e-05 | 6.63e-05 | 0.0 | 1.03 +Other | | 8.241e-05 | | | 1.32 Nlocal: 125 ave 126 max 123 min Histogram: 1 0 0 0 0 0 1 0 0 2 diff --git a/src/PYTHON/python_impl.cpp b/src/PYTHON/python_impl.cpp index c3c30fe677..e556dc2f18 100644 --- a/src/PYTHON/python_impl.cpp +++ b/src/PYTHON/python_impl.cpp @@ -415,7 +415,7 @@ void PythonImpl::invoke_function(int ifunc, char *result, double *dvalue) strncpy(result, value.c_str(), Variable::VALUELENGTH - 1); } } else if (otype == DOUBLE) { - if (*dvalue) *dvalue = PyFloat_AsDouble(pValue); + if (dvalue) *dvalue = PyFloat_AsDouble(pValue); else { auto value = fmt::format("{:.15g}", PyFloat_AsDouble(pValue)); strncpy(result, value.c_str(), Variable::VALUELENGTH - 1);