diff --git a/cmake/Modules/Packages/GPU.cmake b/cmake/Modules/Packages/GPU.cmake index cf321eee9a..8ac1decc86 100644 --- a/cmake/Modules/Packages/GPU.cmake +++ b/cmake/Modules/Packages/GPU.cmake @@ -60,9 +60,9 @@ if(GPU_API STREQUAL "CUDA") option(CUDA_MPS_SUPPORT "Enable tweaks to support CUDA Multi-process service (MPS)" OFF) if(CUDA_MPS_SUPPORT) if(CUDPP_OPT) - message(FATAL_ERROR "Must use -DCUDPP_OPT=OFF with -DGPU_CUDA_MPS_SUPPORT=ON") + message(FATAL_ERROR "Must use -DCUDPP_OPT=OFF with -DCUDA_MPS_SUPPORT=ON") endif() - set(GPU_CUDA_MPS_FLAGS "-DCUDA_PROXY") + set(GPU_CUDA_MPS_FLAGS "-DCUDA_MPS_SUPPORT") endif() set(GPU_ARCH "sm_50" CACHE STRING "LAMMPS GPU CUDA SM primary architecture (e.g. sm_60)") diff --git a/doc/Makefile b/doc/Makefile index a8e2ba5300..ad80017b7e 100644 --- a/doc/Makefile +++ b/doc/Makefile @@ -214,7 +214,7 @@ style_check : $(VENV) package_check : $(VENV) @(\ - . $(VENV)/bin/activate ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \\ + . $(VENV)/bin/activate ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \ python utils/check-packages.py -s ../src -d src ;\ deactivate ;\ ) diff --git a/doc/src/Commands_compute.rst b/doc/src/Commands_compute.rst index aaa899ef66..c2753b2afc 100644 --- a/doc/src/Commands_compute.rst +++ b/doc/src/Commands_compute.rst @@ -104,6 +104,7 @@ KOKKOS, o = OPENMP, t = OPT. * :doc:`pe/tally ` * :doc:`plasticity/atom ` * :doc:`pressure ` + * :doc:`pressure/alchemy ` * :doc:`pressure/uef ` * :doc:`property/atom ` * :doc:`property/chunk ` diff --git a/doc/src/Commands_fix.rst b/doc/src/Commands_fix.rst index d275b33eba..89cf3e880a 100644 --- a/doc/src/Commands_fix.rst +++ b/doc/src/Commands_fix.rst @@ -29,6 +29,7 @@ OPT. * :doc:`adapt/fep ` * :doc:`addforce ` * :doc:`addtorque ` + * :doc:`alchemy ` * :doc:`amoeba/bitorsion ` * :doc:`amoeba/pitorsion ` * :doc:`append/atoms ` @@ -263,6 +264,7 @@ OPT. * :doc:`wall/lj1043 ` * :doc:`wall/lj126 ` * :doc:`wall/lj93 (k) ` + * :doc:`wall/lepton ` * :doc:`wall/morse ` * :doc:`wall/piston ` * :doc:`wall/reflect (k) ` @@ -270,4 +272,5 @@ OPT. * :doc:`wall/region ` * :doc:`wall/region/ees ` * :doc:`wall/srd ` + * :doc:`wall/table ` * :doc:`widom ` diff --git a/doc/src/Tools.rst b/doc/src/Tools.rst index 20e3d2c094..2eae1aabc7 100644 --- a/doc/src/Tools.rst +++ b/doc/src/Tools.rst @@ -320,7 +320,8 @@ eam generate tool ----------------------------- The tools/eam_generate directory contains several one-file C programs -that convert an analytic formula into a tabulated :doc:`embedded atom method (EAM) ` setfl potential file. The potentials they +that convert an analytic formula into a tabulated :doc:`embedded atom +method (EAM) ` setfl potential file. The potentials they produce are in the potentials directory, and can be used with the :doc:`pair_style eam/alloy ` command. diff --git a/doc/src/compute.rst b/doc/src/compute.rst index 72ea31bbb4..3d74b3884e 100644 --- a/doc/src/compute.rst +++ b/doc/src/compute.rst @@ -258,6 +258,7 @@ The individual style names on the :doc:`Commands compute ` pag * :doc:`pe/tally ` - potential energy between two groups of atoms via the tally callback mechanism * :doc:`plasticity/atom ` - Peridynamic plasticity for each atom * :doc:`pressure ` - total pressure and pressure tensor +* :doc:`pressure/alchemy ` - mixed system total pressure and pressure tensor for :doc:`fix alchemy ` runs * :doc:`pressure/uef ` - pressure tensor in the reference frame of an applied flow field * :doc:`property/atom ` - convert atom attributes to per-atom vectors/arrays * :doc:`property/chunk ` - extract various per-chunk attributes diff --git a/doc/src/compute_pressure_alchemy.rst b/doc/src/compute_pressure_alchemy.rst new file mode 100644 index 0000000000..bdf9802e20 --- /dev/null +++ b/doc/src/compute_pressure_alchemy.rst @@ -0,0 +1,80 @@ +.. index:: compute pressure/alchemy + +compute pressure/alchemy command +================================ + +Syntax +"""""" + +.. code-block:: LAMMPS + + compute ID group-ID pressure/alchemy fix-ID + +* ID, group-ID are documented in :doc:`compute ` command +* pressure/alchemy = style name of this compute command +* fix-ID = ID of :doc:`fix alchemy ` command + +Examples +"""""""" + +.. code-block:: LAMMPS + + fix trans all alchemy + compute mixed all pressure/alchemy trans + thermo_modify press mixed + +Description +""""""""""" + +.. versionadded:: TBD + +Define a compute style that makes the "mixed" system pressure available +for a system that uses the :doc:`fix alchemy ` command to +transform one topology to another. This can be used in combination with +either :doc:`thermo_modify press ` or :doc:`fix_modify +press ` to output and access a pressure consistent with the +simulated combined two topology system. + +The actual pressure is determined with :doc:`compute pressure +` commands that are internally used by :doc:`fix +alchemy ` for each topology individually and then combined. +This command just extracts the information from the fix. + +The ``examples/PACKAGES/alchemy`` folder contains an example input for this command. + +---------- + +Output info +""""""""""" + +This compute calculates a global scalar (the pressure) and a global +vector of length 6 (the pressure tensor), which can be accessed by +indices 1--6. These values can be used by any command that uses global +scalar or vector values from a compute as input. See the :doc:`Howto +output ` page for an overview of LAMMPS output options. + +The ordering of values in the symmetric pressure tensor is as follows: +:math:`p_{xx},` :math:`p_{yy},` :math:`p_{zz},` :math:`p_{xy},` +:math:`p_{xz},` :math:`p_{yz}.` + +The scalar and vector values calculated by this compute are "intensive". +The scalar and vector values will be in pressure :doc:`units `. + +Restrictions +"""""""""""" + +This compute is part of the REPLICA package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package +` page for more info. + + +Related commands +"""""""""""""""" + +:doc:`fix alchemy `, :doc:`compute pressure `, +:doc:`thermo_modify `, :doc:`fix_modify ` + +Default +""""""" + +none diff --git a/doc/src/fix.rst b/doc/src/fix.rst index 2dfe97a3ec..7d505fec63 100644 --- a/doc/src/fix.rst +++ b/doc/src/fix.rst @@ -181,6 +181,7 @@ accelerated styles exist. * :doc:`adapt/fep ` - enhanced version of fix adapt * :doc:`addforce ` - add a force to each atom * :doc:`addtorque ` - add a torque to a group of atoms +* :doc:`alchemy ` - perform an "alchemical transformation" between two partitions * :doc:`amoeba/bitorsion ` - torsion/torsion terms in AMOEBA force field * :doc:`amoeba/pitorsion ` - 6-body terms in AMOEBA force field * :doc:`append/atoms ` - append atoms to a running simulation @@ -415,6 +416,7 @@ accelerated styles exist. * :doc:`wall/lj1043 ` - Lennard-Jones 10--4--3 wall * :doc:`wall/lj126 ` - Lennard-Jones 12--6 wall * :doc:`wall/lj93 ` - Lennard-Jones 9--3 wall +* :doc:`wall/lepton ` - Custom Lepton expression wall * :doc:`wall/morse ` - Morse potential wall * :doc:`wall/piston ` - moving reflective piston wall * :doc:`wall/reflect ` - reflecting wall(s) @@ -422,6 +424,7 @@ accelerated styles exist. * :doc:`wall/region ` - use region surface as wall * :doc:`wall/region/ees ` - use region surface as wall for ellipsoidal particles * :doc:`wall/srd ` - slip/no-slip wall for SRD particles +* :doc:`wall/table ` - Tabulated potential wall wall * :doc:`widom ` - Widom insertions of atoms or molecules Restrictions diff --git a/doc/src/fix_alchemy.rst b/doc/src/fix_alchemy.rst new file mode 100644 index 0000000000..90c436139e --- /dev/null +++ b/doc/src/fix_alchemy.rst @@ -0,0 +1,137 @@ +.. index:: fix alchemy + +fix alchemy command +=================== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID alchemy v_name + +* ID, group-ID are documented in :doc:`fix ` command +* alchemy = style name of this fix command +* v_name = variable with name that determines the :math:`\lambda_p` value + +Examples +"""""""" + +.. code-block:: LAMMPS + + fix trans all alchemy v_ramp + +Description +""""""""""" + +.. versionadded:: TBD + +This fix command enables running an "alchemical transformation" MD +simulation between two topologies (i.e. the same number and positions of +atoms, but differences in atom parameters like type, charge, bonds, +angles and so on). For this a :ref:`multi-partition run ` is +required with exactly two partitions. During the MD run, the fix will +will determine a factor, :math:`\lambda_p`, for each partition *p* that +will be taken from an equal style or equivalent :doc:`variable +`. Typically, this variable would be chose to linearly ramp +*down* from 1.0 to 0.0 for the *first* partition (*p=0*) and linearly +ramp *up* from 0.0 to 1.0 for the *second* partition (*p=1*). The +forces used for the propagation of the atoms will be the sum of the +forces of the two systems combined and scaled with their respective +:math:`\lambda_p` factor. This allows to perform transformations that +are not easily possible with :doc:`pair style hybrid/scaled +`, :doc:`fix adapt ` or :doc:`fix adapt/fep +`. + +.. note:: + + Since the definition of the variable to provide the :math:`\lambda_p` is + independent in the two partitions, no check is made that the two values + remain between 0.0 and 1.0 and that they add up to 1.0. So care needs to + be taken when defining those variables that this is the case. + +Due to the specifics of the implementation, the initial geometry and +dimensions of the system must be exactly the same and the fix will +synchronize them during the run. It is thus not possible to initialize +the two partitions by reading different data files or creating different +systems from scratch, but rather they have to be started from the same +system and then the desired modifications need to be applied to the +system of the second partition. The commands :doc:`pair style +hybrid/scaled `, :doc:`fix adapt ` or :doc:`fix +adapt/fep ` could be used for simulations where the +requirements for fix alchemy are not given. + +The commands below demonstrate how the setup for the second partition +can be done for the example of transforming a pure copper system into a +copper/aluminum bronze. + +.. code-block:: LAMMPS + + variable name world pure alloy + + create_box 2 box + create_atoms 1 box + pair_style eam/alloy + pair_coeff * * AlCu.eam.alloy Cu Al + + # replace 5% of copper with aluminum on the second partition only + variable name world pure alloy + if "${name} == alloy" then & + "set type 1 type/fraction 2 0.05 6745234" + + # define ramp variable to combine the two different partitions + if "${name} == pure" then & + "variable ramp equal ramp(1.0,0.0)" & + else & + "variable ramp equal ramp(0.0,1.0)" + + fix 2 all alchemy v_ramp + + +The ``examples/PACKAGES/alchemy`` folder contains complete example +inputs for this command. + +---------- + +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +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 stores a global scalar (the current value of :math:`\lambda_p`) +and a global vector of length 3 which contains the potential energy of +the first partition, the second partition and the combined value, +respectively. The global scalar is unitless and "intensive", the vector +is in :doc:`energy units ` and "extensive". These values can be +used by any command that uses a global value from a fix as input. See +the :doc:`Howto output ` doc page for an overview of +LAMMPS output options. + +This fix is not invoked during :doc:`energy minimization `. + +Restrictions +"""""""""""" + +This fix is part of the REPLICA package. It is only enabled if LAMMPS +was built with that package. See the :doc:`Build package +` page for more info. + +There may be only one instance of this fix in use at any time. + +This fix requires to perform a :ref:`multi-partition run ` +with *exactly* two partitions. + +This fix is *not* compatible with :doc:`load balancing `. + +Related commands +"""""""""""""""" + +:doc:`compute pressure/alchemy ` command, +:doc:`fix adapt ` command, :doc:`fix adapt/fep ` +command, :doc:`pair_style hybrid/scaled ` command. + +Default +""""""" + +none diff --git a/doc/src/fix_wall.rst b/doc/src/fix_wall.rst index 9f20470bbc..7b38b6035c 100644 --- a/doc/src/fix_wall.rst +++ b/doc/src/fix_wall.rst @@ -4,7 +4,9 @@ .. index:: fix wall/lj1043 .. index:: fix wall/colloid .. index:: fix wall/harmonic +.. index:: fix wall/lepton .. index:: fix wall/morse +.. index:: fix wall/table fix wall/lj93 command ===================== @@ -23,20 +25,31 @@ fix wall/colloid command fix wall/harmonic command ========================= +fix wall/lepton command +========================= + fix wall/morse command ====================== +fix wall/table command +========================= + Syntax """""" .. parsed-literal:: - fix ID group-ID style face args ... keyword value ... + fix ID group-ID style [tabstyle] [N] face args ... keyword value ... * ID, group-ID are documented in :doc:`fix ` command -* style = *wall/lj93* or *wall/lj126* or *wall/lj1043* or *wall/colloid* or *wall/harmonic* or *wall/morse* +* style = *wall/lj93* or *wall/lj126* or *wall/lj1043* or *wall/colloid* or *wall/harmonic* or *wall/lepton* or *wall/morse* or *wall/table* +* tabstyle = *linear* or *spline* = method of table interpolation (only applies to *wall/table*) +* N = use N values in *linear* or *spline* interpolation (only applies to *wall/table*) * one or more face/arg pairs may be appended * face = *xlo* or *xhi* or *ylo* or *yhi* or *zlo* or *zhi* + +.. spacer + * args for styles *lj93* or *lj126* or *lj1043* or *colloid* or *harmonic* .. parsed-literal:: @@ -50,7 +63,19 @@ Syntax epsilon can be a variable (see below) sigma = size factor for wall-particle interaction (distance units) sigma can be a variable (see below) - cutoff = distance from wall at which wall-particle interaction is cut off (distance units) + cutoff = distance from wall at which wall-particle interactions are cut off (distance units) + +* args for style *lepton* + + .. parsed-literal:: + + args = coord expression cutoff + coord = position of wall = EDGE or constant or variable + EDGE = current lo or hi edge of simulation box + constant = number like 0.0 or -30.0 (distance units) + variable = :doc:`equal-style variable ` like v_x or v_wiggle + expression = Lepton expression for the potential (energy units) + cutoff = distance from wall at which wall-particle interactions are cut off (distance units) * args for style *morse* @@ -67,7 +92,20 @@ Syntax alpha can be a variable (see below) r_0 = distance of the potential minimum from the face of region (distance units) r_0 can be a variable (see below) - cutoff = distance from wall at which wall-particle interaction is cut off (distance units) + cutoff = distance from wall at which wall-particle interactions are cut off (distance units) + +* args for style *table* + + .. parsed-literal:: + + args = coord filename keyword cutoff + coord = position of wall = EDGE or constant or variable + EDGE = current lo or hi edge of simulation box + constant = number like 0.0 or -30.0 (distance units) + variable = :doc:`equal-style variable ` like v_x or v_wiggle + filename = file containing tabulated energy and force values + keyword = section identifier to select a specific table in table file + cutoff = distance from wall at which wall-particle interactions are cut off (distance units) * zero or more keyword/value pairs may be appended * keyword = *units* or *fld* or *pbc* @@ -91,9 +129,13 @@ Examples fix wallhi all wall/lj93 xlo -1.0 1.0 1.0 2.5 units box fix wallhi all wall/lj93 xhi EDGE 1.0 1.0 2.5 + fix wallhi all wall/harmonic xhi EDGE 100.0 0.0 4.0 units box fix wallhi all wall/morse xhi EDGE 1.0 1.0 1.0 2.5 units box fix wallhi all wall/lj126 v_wiggle 23.2 1.0 1.0 2.5 fix zwalls all wall/colloid zlo 0.0 1.0 1.0 0.858 zhi 40.0 1.0 1.0 0.858 + fix xwall mobile wall/table spline 200 EDGE -5.0 walltab.dat HARMONIC 4.0 + fix xwalls mobile wall/lepton xlo -5.0 "k*(r-rc)^2;k=100.0" 4.0 xhi 5.0 "k*(r-rc)^2;k=100.0" 4.0 + Description """"""""""" @@ -103,7 +145,7 @@ wall that interacts with the atoms in the group by generating a force on the atom in a direction perpendicular to the wall. The energy of wall-particle interactions depends on the style. -For style *wall/lj93*, the energy E is given by the 9/3 potential: +For style *wall/lj93*, the energy E is given by the 9-3 Lennard-Jones potential: .. math:: @@ -111,7 +153,7 @@ For style *wall/lj93*, the energy E is given by the 9/3 potential: \left(\frac{\sigma}{r}\right)^3 \right] \qquad r < r_c -For style *wall/lj126*, the energy E is given by the 12/6 potential: +For style *wall/lj126*, the energy E is given by the 12-6 Lennard-Jones potential: .. math:: @@ -119,7 +161,7 @@ For style *wall/lj126*, the energy E is given by the 12/6 potential: \left(\frac{\sigma}{r}\right)^6 \right] \qquad r < r_c -For style *wall/lj1043*, the energy E is given by the 10/4/3 potential: +For style *wall/lj1043*, the energy E is given by the 10-4-3 Lennard-Jones potential: .. math:: @@ -138,8 +180,8 @@ of the :doc:`pair_style colloid ` potential: & \left. - \frac{1}{6} \left(\frac{2R(D+R) + D(D+2R) \left[ \ln D - \ln (D+2R) \right]}{D(D+2R)} \right) \right] \qquad r < r_c -For style *wall/harmonic*, the energy E is given by a harmonic spring -potential: +For style *wall/harmonic*, the energy E is given by a repulsive-only harmonic +spring potential: .. math:: @@ -152,6 +194,56 @@ For style *wall/morse*, the energy E is given by a Morse potential: E = D_0 \left[ e^{- 2 \alpha (r - r_0)} - 2 e^{- \alpha (r - r_0)} \right] \qquad r < r_c +For style *wall/lepton*, the energy E is provided as an Lepton +expression string using "r" as the distance variable. The `Lepton +library `_, that the *wall/lepton* +style interfaces with, evaluates this expression string at run time to +compute the wall-particle energy. It also creates an analytical +representation of the first derivative of this expression with respect +to "r" and then uses that to compute the force between the wall and +atoms in the fix group. The Lepton expression must be either enclosed +in quotes or must not contain any whitespace so that LAMMPS recognizes +it as a single keyword. + +Optionally, the expression may use "rc" to refer to the cutoff distance +for the given wall. Further constants in the expression can be defined +in the same string as additional expressions separated by semi-colons. +The expression "k*(r-rc)^2;k=100.0" represents a repulsive-only harmonic +spring as in fix *wall/harmonic* with a force constant *K* (same as +:math:`\epsilon` above) of 100 energy units. More details on the Lepton +expression strings are given below. + +For style *wall/table*, the energy E and forces are determined from +interpolation tables listed in one or more files as a function of +distance. The interpolation tables are used to evaluate energy and +forces between particles and the wall similar to how analytic formulas +are used for the other wall styles. + +The interpolation tables are created as a pre-computation by fitting +cubic splines to the file values and interpolating energy and force +values at each of *N* distances. During a simulation, the tables are +used to interpolate energy and force values as needed for each wall and +particle separated by a distance *R*\ . The interpolation is done in +one of two styles: *linear* or *spline*\ . + +For the *linear* style, the distance *R* is used to find the 2 +surrounding table values from which an energy or force is computed by +linear interpolation. + +For the *spline* style, cubic spline coefficients are computed and +stored for each of the *N* values in the table, one set of splines for +energy, another for force. Note that these splines are different than +the ones used to pre-compute the *N* values. Those splines were fit +to the *Nfile* values in the tabulated file, where often *Nfile* < +*N*\ . The distance *R* is used to find the appropriate set of spline +coefficients which are used to evaluate a cubic polynomial which +computes the energy or force. + +For each wall a filename and a keyword must be provided as in the +examples above. The filename specifies a file containing tabulated +energy and force values. The keyword specifies a section of the file. +The format of this file is described below. + In all cases, *r* is the distance from the particle to the wall at position *coord*, and :math:`r_c` is the *cutoff* distance at which the particle and wall no longer interact. The energy of the wall @@ -180,11 +272,12 @@ box parameters and timestep and elapsed time. Thus it is easy to specify a time-dependent wall position. See examples below. For the *wall/lj93* and *wall/lj126* and *wall/lj1043* styles, -:math:`\epsilon` and :math:`\sigma` are the usual Lennard-Jones parameters, which -determine the strength and size of the particle as it interacts with -the wall. Epsilon has energy units. Note that this :math:`\epsilon` and -:math:`\sigma` may be different than any :math:`\epsilon` or :math:`\sigma` values defined -for a pair style that computes particle-particle interactions. +:math:`\epsilon` and :math:`\sigma` are the usual Lennard-Jones +parameters, which determine the strength and size of the particle as it +interacts with the wall. Epsilon has energy units. Note that this +:math:`\epsilon` and :math:`\sigma` may be different than any +:math:`\epsilon` or :math:`\sigma` values defined for a pair style that +computes particle-particle interactions. The *wall/lj93* interaction is derived by integrating over a 3d half-lattice of Lennard-Jones 12/6 particles. The *wall/lj126* @@ -207,11 +300,11 @@ are the number density of the constituent particles, in the wall and colloid respectively, in units of 1/volume. The *wall/colloid* interaction is derived by integrating over -constituent LJ particles of size :math:`\sigma` within the colloid particle -and a 3d half-lattice of Lennard-Jones 12/6 particles of size :math:`\sigma` -in the wall. As mentioned in the preceding paragraph, the density of -particles in the wall and colloid can be different, as specified by -the :math:`\epsilon` prefactor. +constituent LJ particles of size :math:`\sigma` within the colloid +particle and a 3d half-lattice of Lennard-Jones 12/6 particles of size +:math:`\sigma` in the wall. As mentioned in the preceding paragraph, +the density of particles in the wall and colloid can be different, as +specified by the :math:`\epsilon` prefactor. For the *wall/harmonic* style, :math:`\epsilon` is effectively the spring constant K, and has units (energy/distance\^2). The input parameter @@ -220,20 +313,21 @@ spring is at the *cutoff*\ . This is a repulsive-only spring since the interaction is truncated at the *cutoff* For the *wall/morse* style, the three parameters are in this order: -:math:`D_0` the depth of the potential, :math:`\alpha` the width parameter, and -:math:`r_0` the location of the minimum. :math:`D_0` has energy units, :math:`\alpha` -inverse distance units, and :math:`r_0` distance units. +:math:`D_0` the depth of the potential, :math:`\alpha` the width +parameter, and :math:`r_0` the location of the minimum. :math:`D_0` has +energy units, :math:`\alpha` inverse distance units, and :math:`r_0` +distance units. -For any wall, the :math:`\epsilon` and/or :math:`\sigma` and/or :math:`\alpha` parameter can -be specified -as an :doc:`equal-style variable `, in which case it should be +For any wall that supports them, the :math:`\epsilon` and/or +:math:`\sigma` and/or :math:`\alpha` parameter can be specified as an +:doc:`equal-style variable `, in which case it should be specified as v_name, where name is the variable name. As with a -variable wall position, the variable is evaluated each timestep and -the result becomes the current epsilon or sigma of the wall. -Equal-style variables can specify formulas with various mathematical -functions, and include :doc:`thermo_style ` command -keywords for the simulation box parameters and timestep and elapsed -time. Thus it is easy to specify a time-dependent wall interaction. +variable wall position, the variable is evaluated each timestep and the +result becomes the current epsilon or sigma of the wall. Equal-style +variables can specify formulas with various mathematical functions, and +include :doc:`thermo_style ` command keywords for the +simulation box parameters and timestep and elapsed time. Thus it is +easy to specify a time-dependent wall interaction. .. note:: @@ -266,20 +360,19 @@ define the lattice spacings. The *fld* keyword can be used with a *yes* setting to invoke the wall constraint before pairwise interactions are computed. This allows an implicit FLD model using :doc:`pair_style lubricateU ` -to include the wall force in its calculations. If the setting is -*no*, wall forces are imposed after pairwise interactions, in the -usual manner. +to include the wall force in its calculations. If the setting is *no*, +wall forces are imposed after pairwise interactions, in the usual +manner. -The *pbc* keyword can be used with a *yes* setting to allow walls to -be specified in a periodic dimension. See the -:doc:`boundary ` command for options on simulation box -boundaries. The default for *pbc* is *no*, which means the system -must be non-periodic when using a wall. But you may wish to use a -periodic box. E.g. to allow some particles to interact with the wall -via the fix group-ID, and others to pass through it and wrap around a -periodic box. In this case you should ensure that the wall if -sufficiently far enough away from the box boundary. If you do not, -then particles may interact with both the wall and with periodic +The *pbc* keyword can be used with a *yes* setting to allow walls to be +specified in a periodic dimension. See the :doc:`boundary ` +command for options on simulation box boundaries. The default for *pbc* +is *no*, which means the system must be non-periodic when using a wall. +But you may wish to use a periodic box. E.g. to allow some particles to +interact with the wall via the fix group-ID, and others to pass through +it and wrap around a periodic box. In this case you should ensure that +the wall if sufficiently far enough away from the box boundary. If you +do not, then particles may interact with both the wall and with periodic images on the other side of the box, which is probably not what you want. @@ -328,6 +421,57 @@ perturbation on the particles: ---------- +.. include:: lepton_expression.rst + +---------- + +Table file format +""""""""""""""""" + +Suitable tables for use with fix *wall/table* can be created by the +Python code in the ``tools/tabulate`` folder of the LAMMPS source code +distribution. + +The format of a tabulated file is as follows (without the parenthesized +comments): + +.. parsed-literal:: + + # Tabulated wall potential UNITS: real + + HARMONIC (keyword is the first text on a line) + N 100 FP 200 200 + (blank line) + 1 0.04 1568.16 792.00 (index, distance to wall, energy, force) + 2 0.08 1536.64 784.00 + 3 0.12 1505.44 776.00 + ... + 99 3.96 0.16 8.00 + 100 4.00 0 0 + +A section begins with a non-blank line whose first character is not a +"#"; blank lines or lines starting with "#" can be used as comments +between sections. The first line begins with a keyword which identifies +the section. The line can contain additional text, but the initial text +must match the argument specified in the fix *wall/table* command. The +next line lists (in any order) one or more parameters for the table. +Each parameter is a keyword followed by one or more numeric values. + +The parameter "N" is required and its value is the number of table +entries that follow. Note that this may be different than the *N* +specified in the fix *wall/table* command. Let Ntable = *N* in the fix +command, and Nfile = "N" in the tabulated file. What LAMMPS does is a +preliminary interpolation by creating splines using the Nfile tabulated +values as nodal points. It uses these to interpolate as needed to +generate energy and force values at Ntable different points. The +resulting tables of length Ntable are then used as described above, when +computing energy and force for wall-particle interactions. This means that +if you want the interpolation tables of length Ntable to match exactly +what is in the tabulated file (with effectively no preliminary +interpolation), you should set Ntable = Nfile. + +---------- + Restart, fix_modify, output, run start/stop, minimize info """"""""""""""""""""""""""""""""""""""""""""""""""""""""""" @@ -354,16 +498,15 @@ fix. This allows to set at which level of the :doc:`r-RESPA ` integrator the fix is adding its forces. Default is the outermost level. -This fix computes a global scalar energy and a global vector of -forces, which can be accessed by various :doc:`output commands -`. Note that the scalar energy is the sum of -interactions with all defined walls. If you want the energy on a -per-wall basis, you need to use multiple fix wall commands. The -length of the vector is equal to the number of walls defined by the -fix. Each vector value is the normal force on a specific wall. Note -that an outward force on a wall will be a negative value for *lo* -walls and a positive value for *hi* walls. The scalar and vector -values calculated by this fix are "extensive". +This fix computes a global scalar energy and a global vector of forces, +which can be accessed by various :doc:`output commands `. +Note that the scalar energy is the sum of interactions with all defined +walls. If you want the energy on a per-wall basis, you need to use +multiple fix wall commands. The length of the vector is equal to the +number of walls defined by the fix. Each vector value is the normal +force on a specific wall. Note that an outward force on a wall will be +a negative value for *lo* walls and a positive value for *hi* walls. +The scalar and 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. @@ -386,7 +529,11 @@ invoked by the :doc:`minimize ` command. Restrictions """""""""""" - none + +Fix *wall/lepton* is part of the LEPTON package and only enabled if +LAMMPS was built with this package. See the :doc:`Build package +` page for more info. + Related commands """""""""""""""" diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index d19a72ca02..6c49ad1a62 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -3489,6 +3489,7 @@ sz Sz Tabbernor tabinner +tabstyle Tadmor Tafipolsky tagID diff --git a/examples/PACKAGES/alchemy/AlCu.eam.alloy b/examples/PACKAGES/alchemy/AlCu.eam.alloy new file mode 120000 index 0000000000..c9470b2084 --- /dev/null +++ b/examples/PACKAGES/alchemy/AlCu.eam.alloy @@ -0,0 +1 @@ +../../../potentials/AlCu.eam.alloy \ No newline at end of file diff --git a/examples/PACKAGES/alchemy/h2o.mol b/examples/PACKAGES/alchemy/h2o.mol new file mode 100644 index 0000000000..e5a5e4fe93 --- /dev/null +++ b/examples/PACKAGES/alchemy/h2o.mol @@ -0,0 +1,62 @@ +# Water molecule. SPC/E model. + +3 atoms +2 bonds +1 angles + +Coords + +1 1.12456 0.09298 1.27452 +2 1.53683 0.75606 1.89928 +3 0.49482 0.56390 0.65678 + +Types + +1 1 +2 2 +3 2 + +Charges + +1 -0.8472 +2 0.4236 +3 0.4236 + +Bonds + +1 1 1 2 +2 1 1 3 + +Angles + +1 1 2 1 3 + +Shake Flags + +1 1 +2 1 +3 1 + +Shake Atoms + +1 1 2 3 +2 1 2 3 +3 1 2 3 + +Shake Bond Types + +1 1 1 1 +2 1 1 1 +3 1 1 1 + +Special Bond Counts + +1 2 0 0 +2 1 1 0 +3 1 1 0 + +Special Bonds + +1 2 3 +2 1 3 +3 1 2 diff --git a/examples/PACKAGES/alchemy/in.alloy b/examples/PACKAGES/alchemy/in.alloy new file mode 100644 index 0000000000..8cadcd7f39 --- /dev/null +++ b/examples/PACKAGES/alchemy/in.alloy @@ -0,0 +1,45 @@ +# Example for an alchemical transformation simulation of pure copper into an aluminium bronze + +# set up different names for two partitions +variable name world pure alloy + +# create pure copper system +units metal +lattice fcc 3.75 +region box block 0 6 0 6 0 6 +create_box 2 box + +timestep 0.002 +create_atoms 1 box +displace_atoms all random 0.3 0.3 0.3 57845645 +pair_style eam/alloy +pair_coeff * * AlCu.eam.alloy Cu Al + +# replace 5% of copper with aluminium on the second partition only +if "${name} == alloy" then & + "set type 1 type/fraction 2 0.05 6745234" + +# define ramp variable to combine the two different partitions +if "${name} == pure" then & + "variable ramp equal ramp(1.0,0.0)" & +else & + "variable ramp equal ramp(0.0,1.0)" + +velocity all create 5000.0 6567345 +fix 1 all nvt temp 2500.0 500.0 0.002 +fix 2 all alchemy v_ramp + +compute pressure all pressure/alchemy 2 + +# only need to output a dump file from one partition +#if "${name} == alloy" then & +# "dump 1 all custom 100 ${name}.lammpstrj id type element x y z" & +# "dump_modify 1 element Cu Al" + +thermo_style custom step temp press etotal density pe ke f_2 f_2[3] +thermo_modify colname f_2 lambda colname f_2[3] EPot_mixed +thermo_modify press pressure + +thermo 100 +run 10000 post no + diff --git a/examples/PACKAGES/alchemy/in.twowater b/examples/PACKAGES/alchemy/in.twowater new file mode 100644 index 0000000000..d39b0d9aaa --- /dev/null +++ b/examples/PACKAGES/alchemy/in.twowater @@ -0,0 +1,100 @@ +# Example for an alchemical transformation of two water molecules into a hydronium and hydroxyl ion +# WARNING: This input is intended for demonstrating the method only, +# the force field parameters are mostly made up and NOT suitable for production simulations. + +# set up different names for two partitions +variable name world twowater twoions + +units real +atom_style full +atom_modify map array +region box block -5 5 -5 5 -5 5 +boundary p p p +create_box 2 box bond/types 2 angle/types 2 & + extra/bond/per/atom 3 extra/angle/per/atom 3 extra/special/per/atom 3 + +mass 1 15.9994 +mass 2 1.008 + +pair_style lj/cut/coul/cut 10.0 +pair_coeff 1 1 0.1553 3.166 +pair_coeff 1 2 0.0 1.0 +pair_coeff 2 2 0.0 1.0 + +bond_style harmonic +bond_coeff * 1000.0 1.0 + +angle_style harmonic +angle_coeff * 100.0 109.47 + +molecule water h2o.mol + +# create the two molecules we want to transform ... +create_atoms 0 single -2.0 0.0 0.0 mol water 453624 +create_atoms 0 single 2.0 0.0 0.0 mol water 767353 + +# ... and put them in a group +group transform id 1:6 + +# now fill the rest of the box with more water +create_atoms 0 random 32 34564 NULL mol water 25367 overlap 1.33 + +# change topology and settings for the two states +# we cannot simply create a different topology directly or +# load a different data file because the order and position +# of all atoms must be maintained across both replica + +# we first have to remove all topology data in the transform group +delete_bonds transform bond 1 +delete_bonds transform angle 1 remove + +# then generate different topologies for the two partitions. select by name. +if "${name} == twowater" then & + "create_bonds single/bond 2 1 2" & + "create_bonds single/bond 2 1 3" & + "create_bonds single/bond 2 4 5" & + "create_bonds single/bond 2 4 6" & + "create_bonds single/angle 2 2 1 3" & + "create_bonds single/angle 2 5 4 6" & +else & + "create_bonds single/bond 2 1 2" & + "create_bonds single/bond 2 3 4" & + "create_bonds single/bond 2 4 5" & + "create_bonds single/bond 2 4 6" & + "create_bonds single/angle 2 3 4 5" & + "create_bonds single/angle 2 5 4 6" & + "create_bonds single/angle 2 3 4 6" & + "set atom 1 charge -1.1354" & + "set atom 2 charge 0.1354" & + "set atom 3 charge 0.56775" & + "set atom 4 charge -0.70305" & + "set atom 5*6 charge 0.56775" + +velocity all create 300.0 5463576 +timestep 0.2 + +# define ramp variable to combine the two different partitions +if "${name} == twowater" then & + "variable ramp equal ramp(1.0,0.0)" & +else & + "variable ramp equal ramp(0.0,1.0)" + +# since the trajectory and forces are kept identical through fix alchemy, +# we can do fix npt simulations, but we must use the "mixed" pressure + +fix integrate all npt temp 300 300 1.0 iso 1.0 1.0 10.0 +fix transform all alchemy v_ramp +compute pressure all pressure/alchemy transform +fix_modify integrate press pressure + +# only need to output a dump file from one partition +# if "${name} == twowater" then & +# "dump 1 all atom 100 ${name}.lammpstrj" & +# "dump_modify 1 sort id" + +thermo_style custom step temp press etotal density pe ke f_transform f_transform[3] +thermo_modify colname f_transform lambda colname f_transform[3] EPot_mixed +thermo_modify press pressure + +thermo 100 +run 20000 diff --git a/examples/PACKAGES/alchemy/log.25Feb23.alloy.g++.4 b/examples/PACKAGES/alchemy/log.25Feb23.alloy.g++.4 new file mode 100644 index 0000000000..18375012d0 --- /dev/null +++ b/examples/PACKAGES/alchemy/log.25Feb23.alloy.g++.4 @@ -0,0 +1,13 @@ +LAMMPS (8 Feb 2023) +Running on 2 partitions of processors +Starting alchemical transformation at 0% + Alchemical transformation progress: 10% + Alchemical transformation progress: 20% + Alchemical transformation progress: 30% + Alchemical transformation progress: 40% + Alchemical transformation progress: 50% + Alchemical transformation progress: 60% + Alchemical transformation progress: 70% + Alchemical transformation progress: 80% + Alchemical transformation progress: 90% + Alchemical transformation progress: 100% diff --git a/examples/PACKAGES/alchemy/log.25Feb23.alloy.g++.4.0 b/examples/PACKAGES/alchemy/log.25Feb23.alloy.g++.4.0 new file mode 100644 index 0000000000..c5538c3c3d --- /dev/null +++ b/examples/PACKAGES/alchemy/log.25Feb23.alloy.g++.4.0 @@ -0,0 +1,169 @@ +LAMMPS (8 Feb 2023) +Processor partition = 0 + using 1 OpenMP thread(s) per MPI task +# Example for an alchemical transformation simulation of pure copper into an aluminium bronze + +# set up different names for two partitions +variable name world pure alloy + +# create pure copper system +units metal +lattice fcc 3.75 +Lattice spacing in x,y,z = 3.75 3.75 3.75 +region box block 0 6 0 6 0 6 +create_box 2 box +Created orthogonal box = (0 0 0) to (22.5 22.5 22.5) + 1 by 1 by 2 MPI processor grid + +timestep 0.002 +create_atoms 1 box +Created 864 atoms + using lattice units in orthogonal box = (0 0 0) to (22.5 22.5 22.5) + create_atoms CPU = 0.001 seconds +displace_atoms all random 0.3 0.3 0.3 57845645 +Displacing atoms ... +pair_style eam/alloy +pair_coeff * * AlCu.eam.alloy Cu Al +Reading eam/alloy potential file AlCu.eam.alloy with DATE: 2008-10-01 + +# replace 5% of copper with aluminium on the second partition only +if "${name} == alloy" then "set type 1 type/fraction 2 0.05 6745234" + +# define ramp variable to combine the two different partitions +if "${name} == pure" then "variable ramp equal ramp(1.0,0.0)" else "variable ramp equal ramp(0.0,1.0)" +variable ramp equal ramp(1.0,0.0) + +velocity all create 5000.0 6567345 +fix 1 all nvt temp 2500.0 500.0 0.002 +fix 2 all alchemy v_ramp + +compute pressure all pressure/alchemy 2 + +# only need to output a dump file from one partition +#if "${name} == alloy" then # "dump 1 all custom 100 ${name}.lammpstrj id type element x y z" # "dump_modify 1 element Cu Al" + +thermo_style custom step temp press etotal density pe ke f_2 f_2[3] +thermo_modify colname f_2 lambda colname f_2[3] EPot_mixed +thermo_modify press pressure + +thermo 100 +run 10000 post no +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 8.6825 + ghost atom cutoff = 8.6825 + binsize = 4.34125, bins = 6 6 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair eam/alloy, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.474 | 3.474 | 3.474 Mbytes + Step Temp Press TotEng Density PotEng KinEng lambda EPot_mixed + 0 5000 2135632.8 10911.637 8.0039334 10353.88 557.75753 1 10353.88 + 100 2424.8703 98461.445 -2402.724 8.0039334 -2673.222 270.49793 0.99 -2673.3837 + 200 2404.4922 111478.55 -2381.5114 8.0039334 -2649.7361 268.22473 0.98 -2650.057 + 300 2388.2899 109429.75 -2387.7985 8.0039334 -2654.2158 266.41733 0.97 -2654.7075 + 400 2377.6418 97114.07 -2409.7114 8.0039334 -2674.9409 265.22953 0.96 -2675.755 + 500 2371.5028 98285.746 -2408.3248 8.0039334 -2672.8695 264.54471 0.95 -2673.6895 + 600 2368.0363 101125.13 -2402.9816 8.0039334 -2667.1396 264.15802 0.94 -2668.238 + 700 2364.8386 96916.491 -2410.1795 8.0039334 -2673.9808 263.80131 0.93 -2675.3394 + 800 2361.5815 101050.97 -2404.7579 8.0039334 -2668.1958 263.43797 0.92 -2669.6797 + 900 2355.1085 95290.542 -2416.4508 8.0039334 -2679.1667 262.7159 0.91 -2681.0381 + 1000 2344.579 90348.199 -2430.3553 8.0039334 -2691.8966 261.54132 0.9 -2693.7969 + 1100 2328.7808 87089.44 -2435.1426 8.0039334 -2694.9216 259.779 0.89 -2696.9199 + 1200 2310.0924 89628.642 -2438.4943 8.0039334 -2696.1886 257.69429 0.88 -2698.4983 + 1300 2288.2762 92771.824 -2430.0042 8.0039334 -2685.2648 255.26065 0.87 -2687.6406 + 1400 2258.3028 83029.221 -2451.9432 8.0039334 -2703.8603 251.91707 0.86 -2706.638 + 1500 2226.5131 83386 -2452.9658 8.0039334 -2701.3367 248.37089 0.85 -2704.0915 + 1600 2192.5777 81801.467 -2460.6692 8.0039334 -2705.2546 244.58535 0.84 -2708.3304 + 1700 2158.7421 84933.294 -2456.2782 8.0039334 -2697.0891 240.81093 0.83 -2700.142 + 1800 2123.8912 76700.779 -2474.2534 8.0039334 -2711.1767 236.92327 0.82 -2714.6978 + 1900 2091.3912 82568.985 -2469.6316 8.0039334 -2702.9295 233.29783 0.81 -2706.5643 + 2000 2061.868 79024.983 -2476.3262 8.0039334 -2706.3307 230.00448 0.8 -2710.7 + 2100 2036.179 72408.502 -2493.6936 8.0039334 -2720.8324 227.13884 0.79 -2725.1617 + 2200 2014.0161 81172.694 -2479.0525 8.0039334 -2703.719 224.66652 0.78 -2708.4618 + 2300 1996.2707 78029.129 -2485.3835 8.0039334 -2708.0706 222.687 0.77 -2712.5894 + 2400 1982.6409 79691.571 -2483.2441 8.0039334 -2704.4107 221.16658 0.76 -2709.4434 + 2500 1971.6774 75015.359 -2493.8754 8.0039334 -2713.819 219.94358 0.75 -2719.4159 + 2600 1963.0369 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-2817.532 119.12932 0.27 -2838.9073 + 7400 998.4963 13330.213 -2707.915 8.0039334 -2819.2987 111.38377 0.26 -2840.2979 + 7500 1023.6105 7070.7227 -2712.3293 8.0039334 -2826.5146 114.18529 0.25 -2848.8706 + 7600 970.8256 7694.074 -2717.03 8.0039334 -2825.3271 108.29706 0.24 -2848.0154 + 7700 966.64807 2336.6244 -2727.1914 8.0039334 -2835.0224 107.83105 0.23 -2858.6468 + 7800 961.41051 564.58952 -2731.2826 8.0039334 -2838.5294 107.24679 0.22 -2862.4362 + 7900 880.63112 3569.7496 -2734.8614 8.0039334 -2833.0971 98.235727 0.21 -2857.2329 + 8000 904.4189 -883.03123 -2738.386 8.0039334 -2839.2753 100.88929 0.2 -2864.1778 + 8100 901.36129 -977.71992 -2739.797 8.0039334 -2840.3452 100.54821 0.19 -2864.7239 + 8200 834.53102 2535.4088 -2741.7378 8.0039334 -2834.831 93.093191 0.18 -2859.9007 + 8300 830.12299 -6039.909 -2755.2151 8.0039334 -2847.8166 92.601469 0.17 -2873.9613 + 8400 807.63492 -5386.015 -2755.7433 8.0039334 -2845.8362 90.092891 0.16 -2872.8494 + 8500 792.64609 -6372.4363 -2758.8515 8.0039334 -2847.2724 88.420864 0.15 -2874.8424 + 8600 758.58937 -11610.225 -2770.2002 8.0039334 -2854.822 84.621786 0.14 -2882.1413 + 8700 758.23023 -10178.597 -2769.9169 8.0039334 -2854.4986 84.581724 0.13 -2881.6683 + 8800 743.6008 -12026.268 -2776.0268 8.0039334 -2858.9766 82.949788 0.12 -2886.1335 + 8900 734.90694 -17472.954 -2783.3532 8.0039334 -2865.3332 81.979975 0.11 -2893.7244 + 9000 707.10989 -17006.609 -2785.8037 8.0039334 -2864.6829 78.879173 0.1 -2893.2911 + 9100 695.13334 -20282.325 -2793.2101 8.0039334 -2870.7532 77.543171 0.09 -2899.891 + 9200 642.26078 -20368.748 -2798.1031 8.0039334 -2869.7483 71.645157 0.08 -2899.7706 + 9300 641.79203 -21031.839 -2798.6175 8.0039334 -2870.2104 71.592866 0.07 -2901.0899 + 9400 640.84125 -20243.066 -2799.2216 8.0039334 -2870.7084 71.486807 0.06 -2901.4655 + 9500 609.96498 -23936.746 -2809.3896 8.0039334 -2877.4321 68.042512 0.05 -2908.2797 + 9600 574.1911 -26956.034 -2817.6178 8.0039334 -2881.6696 64.051882 0.04 -2912.6742 + 9700 567.47641 -28321.949 -2818.8602 8.0039334 -2882.163 63.302848 0.03 -2914.4223 + 9800 520.37758 -31000.6 -2828.0252 8.0039334 -2886.0741 58.048903 0.02 -2918.4921 + 9900 506.49368 -32223.744 -2830.1705 8.0039334 -2886.6706 56.500132 0.01 -2920.4741 + 10000 507.13597 -33930.476 -2834.3236 8.0039334 -2890.8954 56.571781 0 -2924.5423 +Loop time of 17.7279 on 2 procs for 10000 steps with 864 atoms + + +Total wall time: 0:00:17 diff --git a/examples/PACKAGES/alchemy/log.25Feb23.alloy.g++.4.1 b/examples/PACKAGES/alchemy/log.25Feb23.alloy.g++.4.1 new file mode 100644 index 0000000000..b71fad8cab --- /dev/null +++ b/examples/PACKAGES/alchemy/log.25Feb23.alloy.g++.4.1 @@ -0,0 +1,172 @@ +LAMMPS (8 Feb 2023) +Processor partition = 1 + using 1 OpenMP thread(s) per MPI task +# Example for an alchemical transformation simulation of pure copper into an aluminium bronze + +# set up different names for two partitions +variable name world pure alloy + +# create pure copper system +units metal +lattice fcc 3.75 +Lattice spacing in x,y,z = 3.75 3.75 3.75 +region box block 0 6 0 6 0 6 +create_box 2 box +Created orthogonal box = (0 0 0) to (22.5 22.5 22.5) + 1 by 1 by 2 MPI processor grid + +timestep 0.002 +create_atoms 1 box +Created 864 atoms + using lattice units in orthogonal box = (0 0 0) to (22.5 22.5 22.5) + create_atoms CPU = 0.000 seconds +displace_atoms all random 0.3 0.3 0.3 57845645 +Displacing atoms ... +pair_style eam/alloy +pair_coeff * * AlCu.eam.alloy Cu Al +Reading eam/alloy potential file AlCu.eam.alloy with DATE: 2008-10-01 + +# replace 5% of copper with aluminium on the second partition only +if "${name} == alloy" then "set type 1 type/fraction 2 0.05 6745234" +set type 1 type/fraction 2 0.05 6745234 +Setting atom values ... + 37 settings made for type/fraction + +# define ramp variable to combine the two different partitions +if "${name} == pure" then "variable ramp equal ramp(1.0,0.0)" else "variable ramp equal ramp(0.0,1.0)" +variable ramp equal ramp(0.0,1.0) + +velocity all create 5000.0 6567345 +fix 1 all nvt temp 2500.0 500.0 0.002 +fix 2 all alchemy v_ramp + +compute pressure all pressure/alchemy 2 + +# only need to output a dump file from one partition +#if "${name} == alloy" then # "dump 1 all custom 100 ${name}.lammpstrj id type element x y z" # "dump_modify 1 element Cu Al" + +thermo_style custom step temp press etotal density pe ke f_2 f_2[3] +thermo_modify colname f_2 lambda colname f_2[3] EPot_mixed +thermo_modify press pressure + +thermo 100 +run 10000 post no +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 8.6825 + ghost atom cutoff = 8.6825 + binsize = 4.34125, bins = 6 6 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair eam/alloy, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.474 | 3.474 | 3.474 Mbytes + Step Temp Press TotEng Density PotEng KinEng lambda EPot_mixed + 0 5000 2135632.8 11134.401 7.8067107 10576.643 557.75753 0 10353.88 + 100 2502.4638 98461.445 -2410.2394 7.8067107 -2689.393 279.1536 0.01 -2673.3837 + 200 2471.2133 111478.55 -2390.1144 7.8067107 -2665.7819 275.66756 0.02 -2650.057 + 300 2442.869 109429.75 -2398.101 7.8067107 -2670.6067 272.50571 0.03 -2654.7075 + 400 2420.4514 97114.07 -2425.2882 7.8067107 -2695.2932 270.005 0.04 -2675.755 + 500 2403.3496 98285.746 -2421.1707 7.8067107 -2689.268 268.09727 0.05 -2673.6895 + 600 2388.6644 101125.13 -2418.9873 7.8067107 -2685.4464 266.45911 0.06 -2668.238 + 700 2372.4091 96916.491 -2428.7444 7.8067107 -2693.3902 264.64581 0.07 -2675.3394 + 800 2356.5786 101050.97 -2423.8648 7.8067107 -2686.7446 262.87989 0.08 -2669.6797 + 900 2337.3256 95290.542 -2439.2282 7.8067107 -2699.9604 260.73219 0.09 -2681.0381 + 1000 2314.6552 90348.199 -2452.6965 7.8067107 -2710.8998 258.20327 0.1 -2693.7969 + 1100 2288.9862 87089.44 -2457.7481 7.8067107 -2713.088 255.33986 0.11 -2696.9199 + 1200 2263.1553 89628.642 -2462.9772 7.8067107 -2715.4356 252.45838 0.12 -2698.4983 + 1300 2238.1696 92771.824 -2453.8691 7.8067107 -2703.5403 249.67118 0.13 -2687.6406 + 1400 2209.3333 83029.221 -2477.2462 7.8067107 -2723.7006 246.45446 0.14 -2706.638 + 1500 2181.9468 83386 -2476.3027 7.8067107 -2719.7022 243.39945 0.15 -2704.0915 + 1600 2156.3929 81801.467 -2483.9294 7.8067107 -2724.4783 240.54887 0.16 -2708.3304 + 1700 2133.221 84933.294 -2477.0832 7.8067107 -2715.0473 237.96401 0.17 -2700.142 + 1800 2110.4496 76700.779 -2495.3147 7.8067107 -2730.7386 235.42383 0.18 -2714.6978 + 1900 2091.8774 82568.985 -2488.7082 7.8067107 -2722.0603 233.35207 0.19 -2706.5643 + 2000 2074.8972 79024.983 -2496.7194 7.8067107 -2728.1773 231.45791 0.2 -2710.7 + 2100 2059.7023 72408.502 -2511.6849 7.8067107 -2741.4478 229.76289 0.21 -2725.1617 + 2200 2046.5649 81172.694 -2496.9796 7.8067107 -2725.277 228.2974 0.22 -2708.4618 + 2300 2033.9024 78029.129 -2500.8329 7.8067107 -2727.7178 226.88488 0.23 -2712.5894 + 2400 2022.0535 79691.571 -2499.8173 7.8067107 -2725.3804 225.56311 0.24 -2709.4434 + 2500 2008.7841 75015.359 -2512.1238 7.8067107 -2736.2067 224.08289 0.25 -2719.4159 + 2600 1995.175 74845.99 -2512.2807 7.8067107 -2734.8455 222.56477 0.26 -2718.1619 + 2700 1979.2542 76756.042 -2512.5095 7.8067107 -2733.2983 220.78879 0.27 -2716.0963 + 2800 1961.2518 70627.84 -2527.3853 7.8067107 -2746.1659 218.78059 0.28 -2730.7999 + 2900 1942.4706 70852.114 -2530.3101 7.8067107 -2746.9956 216.68552 0.29 -2731.5024 + 3000 1922.0973 75867.616 -2518.2668 7.8067107 -2732.6796 214.41284 0.3 -2718.4146 + 3100 1898.9538 68984.855 -2540.7552 7.8067107 -2752.5863 211.83116 0.31 -2738.0966 + 3200 1874.9107 73304.621 -2533.0578 7.8067107 -2742.2069 209.14911 0.32 -2727.1933 + 3300 1848.9824 69447.29 -2538.6006 7.8067107 -2744.8574 206.25677 0.33 -2730.768 + 3400 1821.4108 64973.868 -2552.8877 7.8067107 -2756.0688 203.18111 0.34 -2741.4173 + 3500 1795.4926 64688.566 -2555.5739 7.8067107 -2755.8638 200.2899 0.35 -2740.986 + 3600 1769.4009 56451.766 -2573.338 7.8067107 -2770.7174 197.37934 0.36 -2756.4626 + 3700 1745.5646 68268.147 -2554.1634 7.8067107 -2748.8838 194.72036 0.37 -2735.8618 + 3800 1721.4956 64187.24 -2566.0526 7.8067107 -2758.088 192.03542 0.38 -2742.67 + 3900 1699.517 61697.296 -2573.7098 7.8067107 -2763.2935 189.58368 0.39 -2748.648 + 4000 1680.2819 58960.336 -2579.7058 7.8067107 -2767.1438 187.43798 0.4 -2753.7317 + 4100 1662.2079 49607.708 -2596.9862 7.8067107 -2782.408 185.42179 0.41 -2769.1633 + 4200 1645.509 59615.376 -2582.865 7.8067107 -2766.424 183.55901 0.42 -2753.41 + 4300 1628.9336 57213.496 -2589.5734 7.8067107 -2771.2834 181.71 0.43 -2758.0401 + 4400 1614.2369 57319.854 -2586.3446 7.8067107 -2766.4151 180.07055 0.44 -2754.0451 + 4500 1598.6946 51130.713 -2601.8813 7.8067107 -2780.2181 178.33679 0.45 -2767.0321 + 4600 1583.2816 51209.179 -2603.9706 7.8067107 -2780.5881 176.61745 0.46 -2767.2662 + 4700 1567.3743 51391.73 -2607.2614 7.8067107 -2782.1044 174.84296 0.47 -2768.7565 + 4800 1550.9245 48164.466 -2614.2775 7.8067107 -2787.2854 173.00797 0.48 -2773.7243 + 4900 1532.697 47270.397 -2618.365 7.8067107 -2789.3397 170.97466 0.49 -2777.023 + 5000 1513.7604 46127.507 -2621.8979 7.8067107 -2790.7601 168.86225 0.5 -2777.2298 + 5100 1494.431 45092.69 -2625.438 7.8067107 -2792.144 166.70602 0.51 -2779.7181 + 5200 1472.5263 41485.775 -2633.6681 7.8067107 -2797.9306 164.26252 0.52 -2785.5483 + 5300 1450.7978 39849.775 -2638.7965 7.8067107 -2800.6352 161.83868 0.53 -2788.9493 + 5400 1428.063 39330.898 -2642.8749 7.8067107 -2802.1774 159.30258 0.54 -2790.3996 + 5500 1404.4139 35674.647 -2652.8811 7.8067107 -2809.5456 156.66449 0.55 -2797.922 + 5600 1380.8619 33960.907 -2659.5731 7.8067107 -2813.6103 154.03722 0.56 -2801.8887 + 5700 1357.9957 39122.559 -2650.1374 7.8067107 -2801.6239 151.48646 0.57 -2790.3487 + 5800 1334.8385 34996.372 -2660.8794 7.8067107 -2809.7826 148.90324 0.58 -2798.8306 + 5900 1312.6203 30380.598 -2669.3511 7.8067107 -2815.7758 146.42476 0.59 -2804.9873 + 6000 1290.7337 26910.214 -2681.9175 7.8067107 -2825.9008 143.98328 0.6 -2814.8623 + 6100 1269.6552 34273.343 -2670.9025 7.8067107 -2812.5345 141.63195 0.61 -2801.9949 + 6200 1249.4502 29640.216 -2678.1477 7.8067107 -2817.5258 139.37805 0.62 -2807.555 + 6300 1229.8377 25302.881 -2688.545 7.8067107 -2825.7352 137.19025 0.63 -2815.3412 + 6400 1211.0142 23978.218 -2694.5096 7.8067107 -2829.6 135.09045 0.64 -2820.0498 + 6500 1192.3094 25315.547 -2693.4635 7.8067107 -2826.4674 133.0039 0.65 -2817.3114 + 6600 1174.741 22676.36 -2697.5642 7.8067107 -2828.6083 131.04413 0.66 -2819.6239 + 6700 1117.0829 22497.41 -2705.1682 7.8067107 -2829.7804 124.61228 0.67 -2821.3556 + 6800 1125.4062 18193.925 -2713.8679 7.8067107 -2839.4086 125.54075 0.68 -2830.2267 + 6900 1142.0728 19451.295 -2711.5199 7.8067107 -2838.9199 127.39994 0.69 -2830.1189 + 7000 1148.9469 16757.031 -2713.1595 7.8067107 -2841.3263 128.16676 0.7 -2832.475 + 7100 1044.2332 11734.429 -2733.5965 7.8067107 -2850.0822 116.48578 0.71 -2841.8886 + 7200 1052.3967 15187.579 -2724.5284 7.8067107 -2841.9248 117.39644 0.72 -2834.2885 + 7300 1045.9123 13697.721 -2730.1401 7.8067107 -2846.8132 116.67309 0.73 -2838.9073 + 7400 1082.9806 13330.213 -2726.8679 7.8067107 -2847.676 120.80812 0.74 -2840.2979 + 7500 980.30736 7070.7227 -2746.9678 7.8067107 -2856.3226 109.35476 0.75 -2848.8706 + 7600 982.86602 7694.074 -2745.5399 7.8067107 -2855.1801 109.64018 0.76 -2848.0154 + 7700 958.27863 2336.6244 -2758.806 7.8067107 -2865.7035 106.89742 0.77 -2858.6468 + 7800 991.25495 564.58952 -2758.6032 7.8067107 -2869.1791 110.57598 0.78 -2862.4362 + 7900 901.65217 3569.7496 -2763.0681 7.8067107 -2863.6488 100.58066 0.79 -2857.2329 + 8000 871.00782 -883.03123 -2773.2412 7.8067107 -2870.4035 97.162233 0.8 -2864.1778 + 8100 873.73598 -977.71992 -2772.9758 7.8067107 -2870.4424 97.466563 0.81 -2864.7239 + 8200 859.27838 2535.4088 -2769.5501 7.8067107 -2865.4039 95.853797 0.82 -2859.9007 + 8300 874.88664 -6039.909 -2781.7213 7.8067107 -2879.3163 97.594921 0.83 -2873.9613 + 8400 810.33098 -5386.015 -2787.6011 7.8067107 -2877.9947 90.393641 0.84 -2872.8494 + 8500 812.50682 -6372.4363 -2789.0713 7.8067107 -2879.7077 90.636359 0.85 -2874.8424 + 8600 792.27145 -11610.225 -2798.2095 7.8067107 -2886.5886 88.379073 0.86 -2882.1413 + 8700 737.92522 -10178.597 -2803.4114 7.8067107 -2885.7281 82.316669 0.87 -2881.6683 + 8800 744.31065 -12026.268 -2806.8078 7.8067107 -2889.8367 83.028973 0.88 -2886.1335 + 8900 709.31385 -17472.954 -2818.1084 7.8067107 -2897.2334 79.125027 0.89 -2893.7244 + 9000 704.20763 -17006.609 -2817.9144 7.8067107 -2896.4698 78.555422 0.9 -2893.2911 + 9100 697.72956 -20282.325 -2824.94 7.8067107 -2902.7728 77.832782 0.91 -2899.891 + 9200 696.15397 -20368.748 -2824.7243 7.8067107 -2902.3813 77.657023 0.92 -2899.7706 + 9300 627.98752 -21031.839 -2833.3613 7.8067107 -2903.4142 70.052953 0.93 -2901.0899 + 9400 603.4933 -20243.066 -2836.1082 7.8067107 -2903.4288 67.320586 0.94 -2901.4655 + 9500 599.69375 -23936.746 -2843.0066 7.8067107 -2909.9033 66.89674 0.95 -2908.2797 + 9600 587.42611 -26956.034 -2848.4377 7.8067107 -2913.966 65.528267 0.96 -2912.6742 + 9700 567.47718 -28321.949 -2852.1171 7.8067107 -2915.42 63.302933 0.97 -2914.4223 + 9800 524.81105 -31000.6 -2860.6103 7.8067107 -2919.1537 58.543462 0.98 -2918.4921 + 9900 507.60008 -32223.744 -2864.192 7.8067107 -2920.8155 56.623552 0.99 -2920.4741 + 10000 521.28866 -33930.476 -2866.3918 7.8067107 -2924.5423 58.150534 1 -2924.5423 +Loop time of 17.7277 on 2 procs for 10000 steps with 864 atoms + + +Total wall time: 0:00:17 diff --git a/examples/PACKAGES/alchemy/log.25Feb23.twowater.g++.4 b/examples/PACKAGES/alchemy/log.25Feb23.twowater.g++.4 new file mode 100644 index 0000000000..18375012d0 --- /dev/null +++ b/examples/PACKAGES/alchemy/log.25Feb23.twowater.g++.4 @@ -0,0 +1,13 @@ +LAMMPS (8 Feb 2023) +Running on 2 partitions of processors +Starting alchemical transformation at 0% + Alchemical transformation progress: 10% + Alchemical transformation progress: 20% + Alchemical transformation progress: 30% + Alchemical transformation progress: 40% + Alchemical transformation progress: 50% + Alchemical transformation progress: 60% + Alchemical transformation progress: 70% + Alchemical transformation progress: 80% + Alchemical transformation progress: 90% + Alchemical transformation progress: 100% diff --git a/examples/PACKAGES/alchemy/log.25Feb23.twowater.g++.4.0 b/examples/PACKAGES/alchemy/log.25Feb23.twowater.g++.4.0 new file mode 100644 index 0000000000..49e6c6536d --- /dev/null +++ b/examples/PACKAGES/alchemy/log.25Feb23.twowater.g++.4.0 @@ -0,0 +1,412 @@ +LAMMPS (8 Feb 2023) +Processor partition = 0 + using 1 OpenMP thread(s) per MPI task +# Example for an alchemical transformation of two water molecules into a hydronium and hydroxyl ion +# WARNING: This input is intended for demonstrating the method only, +# the force field parameters are mostly made up and NOT suitable for production simulations. + +# set up different names for two partitions +variable name world twowater twoions + +units real +atom_style full +atom_modify map array +region box block -5 5 -5 5 -5 5 +boundary p p p +create_box 2 box bond/types 2 angle/types 2 extra/bond/per/atom 3 extra/angle/per/atom 3 extra/special/per/atom 3 +Created orthogonal box = (-5 -5 -5) to (5 5 5) + 1 by 1 by 2 MPI processor grid + +mass 1 15.9994 +mass 2 1.008 + +pair_style lj/cut/coul/cut 10.0 +pair_coeff 1 1 0.1553 3.166 +pair_coeff 1 2 0.0 1.0 +pair_coeff 2 2 0.0 1.0 + +bond_style harmonic +bond_coeff * 1000.0 1.0 + +angle_style harmonic +angle_coeff * 100.0 109.47 + +molecule water h2o.mol +Read molecule template water: + 1 molecules + 0 fragments + 3 atoms with max type 2 + 2 bonds with max type 1 + 1 angles with max type 1 + 0 dihedrals with max type 0 + 0 impropers with max type 0 + +# create the two molecules we want to transform ... +create_atoms 0 single -2.0 0.0 0.0 mol water 453624 +Created 3 atoms + using lattice units in orthogonal box = (-5 -5 -5) to (5 5 5) + create_atoms CPU = 0.003 seconds +create_atoms 0 single 2.0 0.0 0.0 mol water 767353 +Created 3 atoms + using lattice units in orthogonal box = (-5 -5 -5) to (5 5 5) + create_atoms CPU = 0.000 seconds + +# ... and put them in a group +group transform id 1:6 +6 atoms in group transform + +# now fill the rest of the box with more water +create_atoms 0 random 32 34564 NULL mol water 25367 overlap 1.33 +Created 96 atoms + using lattice units in orthogonal box = (-5 -5 -5) to (5 5 5) + create_atoms CPU = 0.000 seconds + +# change topology and settings for the two states +# we cannot simply create a different topology directly or +# load a different data file because the order and position +# of all atoms must be maintained across both replica + +# we first have to remove all topology data in the transform group +delete_bonds transform bond 1 +System init for delete_bonds ... +Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 12 + ghost atom cutoff = 12 + binsize = 6, bins = 2 2 2 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut/coul/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Deleting bonds ... + 68 total bonds, 64 turned on, 4 turned off + 34 total angles, 34 turned on, 0 turned off + 0 total dihedrals, 0 turned on, 0 turned off + 0 total impropers, 0 turned on, 0 turned off +delete_bonds transform angle 1 remove +System init for delete_bonds ... +Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule +Deleting bonds ... + 64 total bonds, 64 turned on, 0 turned off + 32 total angles, 32 turned on, 0 turned off + 0 total dihedrals, 0 turned on, 0 turned off + 0 total impropers, 0 turned on, 0 turned off + +# then generate different topologies for the two partitions. select by name. +if "${name} == twowater" then "create_bonds single/bond 2 1 2" "create_bonds single/bond 2 1 3" "create_bonds single/bond 2 4 5" "create_bonds single/bond 2 4 6" "create_bonds single/angle 2 2 1 3" "create_bonds single/angle 2 5 4 6" else "create_bonds single/bond 2 1 2" "create_bonds single/bond 2 3 4" "create_bonds single/bond 2 4 5" "create_bonds single/bond 2 4 6" "create_bonds single/angle 2 3 4 5" "create_bonds single/angle 2 5 4 6" "create_bonds single/angle 2 3 4 6" "set atom 1 charge -1.1354" "set atom 2 charge 0.1354" "set atom 3 charge 0.56775" "set atom 4 charge -0.70305" "set atom 5*6 charge 0.56775" +create_bonds single/bond 2 1 2 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 7 = max # of special neighbors + special bonds CPU = 0.000 seconds +create_bonds single/bond 2 1 3 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 7 = max # of special neighbors + special bonds CPU = 0.000 seconds +create_bonds single/bond 2 4 5 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 7 = max # of special neighbors + special bonds CPU = 0.000 seconds +create_bonds single/bond 2 4 6 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 7 = max # of special neighbors + special bonds CPU = 0.000 seconds +create_bonds single/angle 2 2 1 3 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 7 = max # of special neighbors + special bonds CPU = 0.000 seconds +create_bonds single/angle 2 5 4 6 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 7 = max # of special neighbors + special bonds CPU = 0.000 seconds + +velocity all create 300.0 5463576 +timestep 0.2 + +# define ramp variable to combine the two different partitions +if "${name} == twowater" then "variable ramp equal ramp(1.0,0.0)" else "variable ramp equal ramp(0.0,1.0)" +variable ramp equal ramp(1.0,0.0) + +# since the trajectory and forces are kept identical through fix alchemy, +# we can do fix npt simulations, but we must use the "mixed" pressure + +fix integrate all npt temp 300 300 1.0 iso 1.0 1.0 10.0 +fix transform all alchemy v_ramp +compute pressure all pressure/alchemy transform +fix_modify integrate press pressure + +# only need to output a dump file from one partition +# if "${name} == twowater" then # "dump 1 all atom 100 ${name}.lammpstrj" # "dump_modify 1 sort id" + +thermo_style custom step temp press etotal density pe ke f_transform f_transform[3] +thermo_modify colname f_transform lambda colname f_transform[3] EPot_mixed +thermo_modify press pressure + +thermo 100 +run 20000 +Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule +Per MPI rank memory allocation (min/avg/max) = 7.535 | 7.535 | 7.535 Mbytes + Step Temp Press TotEng Density PotEng KinEng lambda EPot_mixed + 0 300 184631.17 -802.19609 1.0171193 -892.51464 90.318545 1 -892.51464 + 100 293.4335 -513.97927 189.09028 0.3029684 100.74865 88.341623 0.995 207.29243 + 200 320.81838 1513.3 111.09325 0.64509407 14.507087 96.586165 0.99 46.402434 + 300 261.53825 -3808.6942 -538.67351 0.88817871 -617.41269 78.739179 0.985 -614.76481 + 400 308.32444 1375.0327 -804.08042 0.97694485 -896.90513 92.824715 0.98 -897.24386 + 500 292.60623 -12843.384 -1141.5985 1.0140814 -1229.691 88.092563 0.975 -1221.948 + 600 326.16112 91608.645 2882.4855 1.0263567 2784.2908 98.194659 0.97 2786.0743 + 700 317.22811 -60420.408 -1517.0601 0.9919143 -1612.5654 95.505272 0.965 -1616.7677 + 800 309.94673 -56793.931 -1549.4612 1.0024958 -1642.7743 93.313126 0.96 -1640.8606 + 900 272.80718 -5076.2282 -1266.6775 1.0141078 -1348.8093 82.131824 0.955 -1357.1812 + 1000 346.52557 -16919.192 -1406.675 1.0170322 -1511.0006 104.32562 0.95 -1514.1398 + 1100 300.62984 -51826.972 -2469.2821 1.0063592 -2559.7903 90.508164 0.945 -2565.9668 + 1200 293.72767 45222.698 2039.1938 1.0272336 1950.7636 88.430186 0.94 1951.1683 + 1300 289.4971 94600.203 2184.5096 1.0298091 2097.3531 87.156524 0.935 2088.1011 + 1400 328.98666 35468.53 1816.723 1.0198467 1717.6777 99.045321 0.93 1716.9268 + 1500 392.9407 41220.21 1820.7312 1.0194044 1702.4317 118.29944 0.925 1690.6416 + 1600 284.90093 -37995.141 -2439.9256 1.0068497 -2525.6984 85.772791 0.92 -2529.5874 + 1700 267.67454 25275.255 1612.5912 1.0313556 1532.0046 80.586582 0.915 1520.9695 + 1800 247.16495 -68222.994 -2699.1903 1.0018048 -2773.6022 74.41193 0.91 -2788.9545 + 1900 328.41849 -51979.665 -2339.7432 1.0154952 -2438.6175 98.874268 0.905 -2461.3422 + 2000 313.8715 21726.003 1473.9594 1.018831 1379.4647 94.494725 0.9 1363.0739 + 2100 296.07341 66130.11 1379.1597 1.0224882 1290.0233 89.136398 0.895 1272.1884 + 2200 282.67889 51746.464 2376.377 1.0362683 2291.2732 85.103821 0.89 2276.1488 + 2300 281.04207 -71937.759 -2791.0867 1.0111968 -2875.6977 84.611035 0.885 -2892.2526 + 2400 321.00806 -51658.758 -2507.6376 1.0168161 -2604.2809 96.643269 0.88 -2622.9732 + 2500 288.95906 49645.753 2361.024 1.0355648 2274.0295 86.99454 0.875 2275.0348 + 2600 303.0064 -48470.216 -1973.9561 1.000439 -2065.1798 91.223657 0.87 -2082.5895 + 2700 361.7083 54973.584 1929.0772 1.0223169 1820.1806 108.89656 0.865 1817.1972 + 2800 289.27827 33564.017 1783.5154 1.0257088 1696.4248 87.090642 0.86 1682.9162 + 2900 283.94365 -47190.274 -2286.9529 1.0059224 -2372.4375 85.484591 0.855 -2395.9575 + 3000 337.10996 61988.686 2289.363 1.0258 2187.8721 101.49094 0.85 2168.1085 + 3100 305.28249 -50123.109 -1913.7375 1.0143567 -2005.6464 91.9089 0.845 -2040.3453 + 3200 270.19471 -18114.265 -1961.3048 1.0132413 -2042.6502 81.345309 0.84 -2076.9595 + 3300 263.39996 -109301.89 -2351.6647 0.99956867 -2430.9643 79.299671 0.835 -2471.0269 + 3400 249.01722 -37585.949 -2423.3849 1.0080932 -2498.3544 74.969576 0.83 -2537.734 + 3500 267.88868 65528.865 2164.3882 1.0390872 2083.7372 80.651054 0.825 2061.6421 + 3600 351.46458 -67583.574 -2861.4561 1.0059621 -2967.2687 105.81256 0.82 -3004.5028 + 3700 332.82565 -61204.843 -2275.2765 1.0053485 -2375.4776 100.20109 0.815 -2415.4435 + 3800 298.0279 61123.085 1951.1943 1.020672 1861.4695 89.724819 0.81 1831.9734 + 3900 317.04715 43210.045 1848.3875 1.0287838 1752.9367 95.450792 0.805 1721.1961 + 4000 261.75174 -111920.72 -3274.707 0.99457106 -3353.5105 78.803455 0.8 -3394.3528 + 4100 338.34245 89763.083 2115.4809 1.0318272 2013.6189 101.86199 0.795 1973.419 + 4200 288.52623 19989.792 1758.0617 1.0204119 1671.1975 86.86423 0.79 1633.1439 + 4300 322.05593 -33791.403 -2107.1643 1.0155065 -2204.1231 96.958741 0.785 -2246.4353 + 4400 280.59054 -27839.599 -1534.3265 1.0123506 -1618.8016 84.475096 0.78 -1672.1425 + 4500 296.08336 75206.112 2789.7494 1.0329133 2700.61 89.139393 0.775 2670.4908 + 4600 288.02094 -67445.101 -2983.5242 0.99579107 -3070.2363 86.712106 0.77 -3132.6352 + 4700 332.21641 -83964.647 -2746.0748 1.0053915 -2846.0925 100.01768 0.765 -2916.6652 + 4800 305.52557 -93111.682 -2354.6562 0.99824941 -2446.6383 91.982082 0.76 -2514.039 + 4900 272.82262 -53664.198 -2790.1342 0.99527907 -2872.2707 82.136472 0.755 -2947.2062 + 5000 288.96388 39846.089 1975.7895 1.0371205 1888.7935 86.99599 0.75 1833.3716 + 5100 293.25543 -71819.425 -2916.8817 0.99452016 -3005.1697 88.288011 0.745 -3069.7618 + 5200 296.16486 -64484.821 -2416.0381 1.0153125 -2505.2021 89.163931 0.74 -2589.6878 + 5300 342.07246 60255.985 1749.8984 1.0306374 1646.9134 102.98496 0.735 1608.5673 + 5400 295.53315 61421.189 1620.6432 1.0334762 1531.6695 88.973746 0.73 1492.0969 + 5500 285.1755 24845.113 1144.9009 1.0335035 1059.0454 85.855455 0.725 1014.0263 + 5600 276.79246 66244.072 1523.3405 1.0251134 1440.0089 83.331641 0.72 1390.9078 + 5700 288.43485 14629.129 1208.7278 1.02997 1121.8911 86.836719 0.715 1074.3779 + 5800 276.64233 59262.97 914.26981 1.0332305 830.98336 83.286443 0.71 763.27415 + 5900 358.25384 -111203.23 -3370.7104 1.006331 -3478.567 107.85655 0.705 -3561.6283 + 6000 327.82233 -62936.335 -1881.2426 1.0106476 -1979.9373 98.694786 0.7 -2062.107 + 6100 309.86553 -59110.381 -2698.4147 1.0076375 -2791.7034 93.28868 0.695 -2870.9566 + 6200 294.95752 -58011.845 -1819.201 1.0161986 -1908.0014 88.800448 0.69 -1971.2586 + 6300 307.27252 59016.127 1186.0709 1.0225343 1093.5629 92.508022 0.685 1032.9616 + 6400 292.21611 -118857.83 -2992.9227 1.0031304 -3080.8978 87.975114 0.68 -3175.9068 + 6500 332.21108 97132.547 2290.2726 1.0349752 2190.2565 100.01607 0.675 2121.4674 + 6600 321.93985 -50017.836 -2484.5919 1.0076385 -2581.5157 96.923796 0.67 -2673.6819 + 6700 299.07231 -98136.241 -3013.1584 1.0106261 -3103.1976 90.039252 0.665 -3194.0694 + 6800 285.33731 28487.407 455.68104 1.017186 369.77687 85.904169 0.66 294.02418 + 6900 296.41387 50054.533 2028.1018 1.0445934 1938.8629 89.238897 0.655 1851.1397 + 7000 318.34109 -71579.897 -3114.0324 1.007304 -3209.8728 95.840345 0.65 -3305.5715 + 7100 317.2192 12370.315 1139.7687 1.0177238 1044.2661 95.502589 0.645 961.68146 + 7200 289.91091 43944.333 1213.4685 1.0302599 1126.1874 87.281105 0.64 1039.3329 + 7300 324.81227 42859.173 1288.5297 1.0300698 1190.7411 97.788572 0.635 1083.5764 + 7400 305.72634 76516.72 2404.9462 1.0580673 2312.9036 92.042527 0.63 2218.3674 + 7500 283.77479 -87225.247 -3401.4354 0.9936609 -3486.8692 85.433754 0.625 -3581.9003 + 7600 318.72048 16084.995 1848.3396 1.0296163 1752.385 95.954566 0.62 1653.5125 + 7700 307.36895 74007.024 1754.8928 1.0363553 1662.3558 92.537054 0.615 1572.8568 + 7800 297.44704 28693.429 1261.5958 1.0206402 1172.0459 89.549946 0.61 1093.5903 + 7900 288.47173 -94644.76 -2455.4369 1.0095244 -2542.2847 86.847823 0.605 -2648.2974 + 8000 280.5001 63255.987 1584.7287 1.020587 1500.2808 84.44787 0.6 1418.7144 + 8100 320.23351 68383.584 2300.142 1.0419027 2203.7319 96.410082 0.595 2111.2616 + 8200 354.86765 50012.316 1350.3752 1.0292074 1243.5381 106.8371 0.59 1149.0631 + 8300 278.8859 24200.145 772.82478 1.0232468 688.86288 83.961894 0.585 569.83331 + 8400 295.95754 -12010.401 1078.6687 1.0200526 989.56716 89.101514 0.58 872.63254 + 8500 289.57525 -64114.236 -3017.5291 1.0062613 -3104.7091 87.18005 0.575 -3227.8592 + 8600 329.23192 15948.893 1427.4791 1.0271511 1328.3599 99.119161 0.57 1211.3868 + 8700 327.45998 39407.811 1697.908 1.0343756 1599.3223 98.585695 0.565 1480.9482 + 8800 296.99753 18017.036 871.11717 1.0178295 781.70256 89.414616 0.56 657.09357 + 8900 289.10016 79527.35 2536.8041 1.0462904 2449.7671 87.037018 0.555 2338.4742 + 9000 260.53308 -51430.717 -2680.1664 1.0040128 -2758.603 78.436561 0.55 -2894.7913 + 9100 314.17867 40043.249 2043.6144 1.0361707 1949.0272 94.5872 0.545 1836.5399 + 9200 362.21236 -55153.163 -2232.4614 1.0102652 -2341.5097 109.04831 0.54 -2497.8765 + 9300 266.62049 -72193.959 -2980.9254 1.0063615 -3061.1946 80.269248 0.535 -3225.2604 + 9400 259.59316 7674.9295 1378.2484 1.0326879 1300.0948 78.153588 0.53 1171.7119 + 9500 278.72962 -33127.835 -2581.8908 1.0163553 -2665.8057 83.914845 0.525 -2805.1711 + 9600 299.09039 24570.664 1839.3275 1.025317 1749.2828 90.044695 0.52 1631.8392 + 9700 336.65655 37767.059 1415.9074 1.0245842 1314.5529 101.35443 0.515 1218.4022 + 9800 279.68112 -55007.939 -2548.4947 1.0129837 -2632.696 84.201305 0.51 -2775.6909 + 9900 300.55694 14964.424 1332.287 1.0176315 1241.8008 90.486218 0.505 1127.7276 + 10000 276.77193 -75638.817 -3100.7483 1.0019055 -3184.0738 83.325459 0.5 -3341.663 + 10100 316.26926 61548.301 2406.8933 1.0427988 2311.6767 95.216598 0.495 2206.7159 + 10200 297.28171 56814.839 2073.2348 1.0270036 1983.7347 89.500171 0.49 1859.0176 + 10300 276.84774 83572.576 1920.2202 1.0322243 1836.8719 83.348283 0.485 1704.2233 + 10400 263.28687 -16549.994 1144.9186 1.0177296 1065.6529 79.265623 0.48 940.36339 + 10500 332.79252 47379.311 1538.8168 1.0223403 1438.6257 100.19112 0.475 1301.3762 + 10600 329.01105 39299.248 1330.9914 1.0230094 1231.9387 99.052663 0.47 1077.5639 + 10700 339.21335 -4217.0313 981.9193 1.0235915 879.79511 102.12419 0.465 741.87272 + 10800 297.11192 -80013.424 -3682.9794 1.0009566 -3772.4285 89.449054 0.46 -3958.8283 + 10900 299.63096 47783.864 1833.1832 1.0435283 1742.9757 90.207441 0.455 1620.9328 + 11000 363.58243 67370.65 1769.9236 1.0450565 1660.4628 109.46079 0.45 1543.803 + 11100 306.04664 50246.004 1323.7676 1.0341876 1231.6287 92.138957 0.445 1063.5345 + 11200 255.68488 43750.967 2205.2392 1.0530607 2128.2623 76.976955 0.44 1986.9636 + 11300 271.71957 -40289.299 -3083.4093 1.0168497 -3165.2137 81.804388 0.435 -3344.1558 + 11400 291.74007 -115249.24 -3319.2153 1.0067921 -3407.0471 87.831795 0.43 -3569.0256 + 11500 270.22077 28235.119 596.78348 1.0195886 515.43032 81.353155 0.425 373.78255 + 11600 297.08506 29790.701 1031.3514 1.0317561 941.91046 89.440969 0.42 803.92835 + 11700 295.33119 -101140.58 -3068.1166 1.0107252 -3157.0295 88.912943 0.415 -3348.5652 + 11800 308.77287 -120312.75 -3553.1266 0.99681611 -3646.0863 92.95972 0.41 -3835.4663 + 11900 293.86337 82287.969 1847.0953 1.0331446 1758.6242 88.47104 0.405 1625.4846 + 12000 279.9866 27919.689 2249.3175 1.0384909 2165.0242 84.293273 0.4 2028.6311 + 12100 292.19439 47035.018 1220.3593 1.0210948 1132.3908 87.968573 0.395 976.68113 + 12200 317.78325 46886.483 2039.3721 1.0310567 1943.6997 95.672401 0.39 1763.6359 + 12300 357.44038 51492.35 1898.3396 1.0414835 1790.7279 107.61165 0.385 1638.1905 + 12400 288.16042 -50528.478 -2837.5599 1.0130798 -2924.314 86.7541 0.38 -3115.1383 + 12500 300.37356 -114034.29 -3091.586 1.0130272 -3182.017 90.431009 0.375 -3364.511 + 12600 265.4402 73960.28 1297.3012 1.0343798 1217.3873 79.913907 0.37 1094.544 + 12700 287.07994 22722.337 1711.9055 1.0268893 1625.4767 86.428809 0.365 1490.443 + 12800 315.39745 46072.191 926.21362 1.0205906 831.25949 94.954129 0.36 662.83753 + 12900 307.48549 -120472.73 -3181.5418 1.005689 -3274.1139 92.57214 0.355 -3469.7834 + 13000 291.00577 -59154.878 -2652.0402 1.012821 -2739.6509 87.610727 0.35 -2966.2448 + 13100 318.37718 86703.775 2087.145 1.036209 1991.2938 95.851211 0.345 1819.7078 + 13200 280.41509 -107033.79 -2683.9682 1.0135499 -2768.3905 84.422277 0.34 -2953.8355 + 13300 275.01919 112086.85 2632.1169 1.0437945 2549.3192 82.797775 0.335 2394.6707 + 13400 299.46547 -111959.62 -3475.4354 0.98732074 -3565.593 90.157617 0.33 -3792.6798 + 13500 275.65631 17625.49 1762.6531 1.0255473 1679.6636 82.989588 0.325 1521.2745 + 13600 302.63525 122466.63 2853.8095 1.0438137 2762.6976 91.111917 0.32 2611.7188 + 13700 302.21323 -94399.663 -3003.7573 1.0068914 -3094.7422 90.984863 0.315 -3328.4539 + 13800 305.70483 30039.825 1792.3286 1.0225478 1700.2926 92.036052 0.31 1502.8476 + 13900 273.15564 -27822.597 -2346.6702 1.0131002 -2428.9069 82.236732 0.305 -2683.7804 + 14000 257.14635 -1821.0012 1378.2522 1.0172653 1300.8352 77.416947 0.3 1067.8821 + 14100 323.74174 -76139.363 -2747.4152 1.0139806 -2844.8814 97.466276 0.295 -3052.598 + 14200 274.99913 54440.943 983.27131 1.0186356 900.47957 82.791736 0.29 767.64274 + 14300 291.8774 1281.7286 1258.7881 1.0214356 1170.915 87.873139 0.285 1042.8585 + 14400 308.97245 -47961.551 -2680.7892 1.0155221 -2773.809 93.019806 0.28 -3007.3204 + 14500 311.05309 86026.739 2115.2413 1.0311818 2021.5951 93.646208 0.275 1830.5463 + 14600 269.27432 -12972.747 971.48792 1.0172239 890.41971 81.068214 0.27 711.81484 + 14700 262.20739 -77722.459 -3215.6796 1.0029421 -3294.6202 78.940634 0.265 -3537.1929 + 14800 300.33592 -107332.8 -2798.6664 1.0126785 -2889.086 90.419677 0.26 -3125.8439 + 14900 307.0173 -73204.94 -2652.7275 1.016875 -2745.1587 92.431185 0.255 -3016.0143 + 15000 334.08711 64440.709 1615.3385 1.0369481 1514.7576 100.58087 0.25 1323.9179 + 15100 293.46703 35179.395 2020.1996 1.0331703 1931.8479 88.351717 0.245 1768.9681 + 15200 307.80546 54006.291 1111.7619 1.0246134 1019.0935 92.668471 0.24 822.22754 + 15300 336.59792 33832.907 1282.8271 1.0242407 1181.4903 101.33678 0.235 956.25285 + 15400 285.46526 -99629.94 -2336.7535 1.0041261 -2422.6962 85.942688 0.23 -2730.1887 + 15500 269.15938 122546.45 3012.0792 1.0318941 2931.0456 81.033612 0.225 2695.4331 + 15600 294.50818 -104733.19 -1914.0242 1.0017241 -2002.6894 88.665166 0.22 -2281.5773 + 15700 321.05125 -40438.501 -1721.9536 1.0125007 -1818.6099 96.656271 0.215 -2084.0893 + 15800 303.22185 -42224.408 -2145.481 1.0090867 -2236.7695 91.288521 0.21 -2506.3355 + 15900 281.65025 78652.063 2791.9418 1.0460521 2707.1477 84.794136 0.205 2500.7128 + 16000 286.5056 63174.412 1725.0409 1.0185277 1638.785 86.255897 0.2 1442.2427 + 16100 271.74574 -75051.584 -2101.5778 1.0091727 -2183.3901 81.812265 0.195 -2447.1967 + 16200 266.40007 -64120.09 -2223.3693 1.0064388 -2303.5722 80.202888 0.19 -2525.4243 + 16300 330.67137 46204.124 1837.3168 1.0271037 1737.7643 99.552523 0.185 1529.8186 + 16400 310.94573 18510.676 1531.823 1.0188695 1438.2091 93.613887 0.18 1195.3041 + 16500 270.29191 79005.409 1989.9392 1.0354088 1908.5646 81.374574 0.175 1678.7342 + 16600 334.24108 17143.221 1644.1483 1.0230561 1543.521 100.62723 0.17 1379.3215 + 16700 292.28721 -78618.031 -2768.3997 0.99940789 -2856.3962 87.996518 0.165 -3087.379 + 16800 346.09157 -69398.937 -2647.1375 1.0153026 -2751.3325 104.19496 0.16 -3011.3476 + 16900 284.37042 39314.526 2287.7061 1.0343186 2202.093 85.613074 0.155 2045.8316 + 17000 281.69389 86032.163 1817.9125 1.0237583 1733.1052 84.807275 0.15 1528.8391 + 17100 297.2629 55128.393 2617.4156 1.0419182 2527.9211 89.494508 0.145 2369.0347 + 17200 328.81472 47063.86 1880.9768 1.0364627 1781.9832 98.993555 0.14 1526.7115 + 17300 313.41363 -46685.063 -2310.803 1.008117 -2405.1599 94.356878 0.135 -2685.8034 + 17400 288.17114 68721.523 2771.6788 1.0429105 2684.9215 86.757326 0.13 2490.5845 + 17500 260.01702 -23324.539 -1436.6738 1.0100415 -1514.955 78.281195 0.125 -1812.4813 + 17600 297.6633 72795.463 2635.741 1.0362827 2546.126 89.615054 0.12 2336.0152 + 17700 301.02937 93833.118 2690.518 1.0276466 2599.8896 90.628448 0.115 2364.8751 + 17800 238.92837 -78317.212 -2175.2589 1.0084077 -2247.1911 71.932208 0.11 -2579.4429 + 17900 299.27724 -65278.891 -2589.1173 1.0034773 -2679.2182 90.10095 0.105 -2987.498 + 18000 315.15753 -72437.481 -2338.6068 1.0136139 -2433.4887 94.881898 0.1 -2718.125 + 18100 268.39411 -42194.209 -2285.3824 1.0108104 -2366.1856 80.803219 0.095 -2656.3853 + 18200 284.91941 40905.162 2045.1299 1.0266185 1959.3515 85.778354 0.09 1723.6803 + 18300 329.41629 -56526.814 -2104.8386 1.0137784 -2204.0133 99.174667 0.085 -2540.6829 + 18400 293.16732 -22085.551 -1652.5444 1.0163557 -1740.8059 88.261484 0.08 -2052.7864 + 18500 276.28141 29367.359 2314.5497 1.0270087 2231.3719 83.177784 0.075 1971.9405 + 18600 331.18031 94669.124 2466.3928 1.0225403 2366.6871 99.705745 0.07 2081.8675 + 18700 265.4491 49872.536 2571.9864 1.0255308 2492.0698 79.916587 0.065 2260.4261 + 18800 314.51042 60758.629 2560.3258 1.0300818 2465.6387 94.687078 0.06 2219.6547 + 18900 317.70309 66345.835 1768.2041 1.0248229 1672.5558 95.648268 0.055 1410.3087 + 19000 291.39831 -96336.931 -2448.6251 1.0100498 -2536.354 87.728905 0.05 -2805.9396 + 19100 303.37353 -21421.495 -2012.0929 0.99771284 -2103.4271 91.334186 0.045 -2436.2173 + 19200 293.92948 36383.881 2042.0163 1.0251299 1953.5254 88.490944 0.04 1633.579 + 19300 287.24409 -46691.027 -2399.698 1.0112067 -2486.1762 86.478228 0.035 -2811.3506 + 19400 333.42205 21152.63 1524.8699 1.0189912 1424.4893 100.38065 0.03 1118.2463 + 19500 309.17989 60445.761 2298.6966 1.0338543 2205.6144 93.082259 0.025 1928.6181 + 19600 255.92246 -32795.547 -1724.7933 1.0157044 -1801.8418 77.04848 0.02 -2213.9484 + 19700 342.62332 33538.746 2439.138 1.0225905 2335.9872 103.1508 0.015 2081.9185 + 19800 295.68946 81474.342 2308.3249 1.0240743 2219.3041 89.020804 0.01 1910.5545 + 19900 306.4947 43488.052 2330.4958 1.0222707 2238.222 92.27385 0.005 1957.4368 + 20000 313.31679 -25133.284 -1161.6979 1.0163289 -1256.0256 94.327722 0 -1649.7551 +Loop time of 8.92653 on 2 procs for 20000 steps with 102 atoms + +Performance: 38.716 ns/day, 0.620 hours/ns, 2240.513 timesteps/s, 228.532 katom-step/s +96.3% CPU use with 2 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 4.7448 | 5.9908 | 7.2367 | 50.9 | 67.11 +Bond | 0.036126 | 0.03641 | 0.036695 | 0.1 | 0.41 +Neigh | 0.082247 | 0.082294 | 0.082342 | 0.0 | 0.92 +Comm | 0.68467 | 1.9303 | 3.1759 | 89.7 | 21.62 +Output | 0.0023377 | 0.0052347 | 0.0081317 | 4.0 | 0.06 +Modify | 0.8194 | 0.82122 | 0.82303 | 0.2 | 9.20 +Other | | 0.06029 | | | 0.68 + +Nlocal: 51 ave 51 max 51 min +Histogram: 2 0 0 0 0 0 0 0 0 0 +Nghost: 3317 ave 3317 max 3317 min +Histogram: 2 0 0 0 0 0 0 0 0 0 +Neighs: 18320 ave 21941 max 14699 min +Histogram: 1 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 36640 +Ave neighs/atom = 359.21569 +Ave special neighs/atom = 2 +Neighbor list builds = 181 +Dangerous builds = 0 +Total wall time: 0:00:08 diff --git a/examples/PACKAGES/alchemy/log.25Feb23.twowater.g++.4.1 b/examples/PACKAGES/alchemy/log.25Feb23.twowater.g++.4.1 new file mode 100644 index 0000000000..a76489ebb3 --- /dev/null +++ b/examples/PACKAGES/alchemy/log.25Feb23.twowater.g++.4.1 @@ -0,0 +1,437 @@ +LAMMPS (8 Feb 2023) +Processor partition = 1 + using 1 OpenMP thread(s) per MPI task +# Example for an alchemical transformation of two water molecules into a hydronium and hydroxyl ion +# WARNING: This input is intended for demonstrating the method only, +# the force field parameters are mostly made up and NOT suitable for production simulations. + +# set up different names for two partitions +variable name world twowater twoions + +units real +atom_style full +atom_modify map array +region box block -5 5 -5 5 -5 5 +boundary p p p +create_box 2 box bond/types 2 angle/types 2 extra/bond/per/atom 3 extra/angle/per/atom 3 extra/special/per/atom 3 +Created orthogonal box = (-5 -5 -5) to (5 5 5) + 1 by 1 by 2 MPI processor grid + +mass 1 15.9994 +mass 2 1.008 + +pair_style lj/cut/coul/cut 10.0 +pair_coeff 1 1 0.1553 3.166 +pair_coeff 1 2 0.0 1.0 +pair_coeff 2 2 0.0 1.0 + +bond_style harmonic +bond_coeff * 1000.0 1.0 + +angle_style harmonic +angle_coeff * 100.0 109.47 + +molecule water h2o.mol +Read molecule template water: + 1 molecules + 0 fragments + 3 atoms with max type 2 + 2 bonds with max type 1 + 1 angles with max type 1 + 0 dihedrals with max type 0 + 0 impropers with max type 0 + +# create the two molecules we want to transform ... +create_atoms 0 single -2.0 0.0 0.0 mol water 453624 +Created 3 atoms + using lattice units in orthogonal box = (-5 -5 -5) to (5 5 5) + create_atoms CPU = 0.003 seconds +create_atoms 0 single 2.0 0.0 0.0 mol water 767353 +Created 3 atoms + using lattice units in orthogonal box = (-5 -5 -5) to (5 5 5) + create_atoms CPU = 0.000 seconds + +# ... and put them in a group +group transform id 1:6 +6 atoms in group transform + +# now fill the rest of the box with more water +create_atoms 0 random 32 34564 NULL mol water 25367 overlap 1.33 +Created 96 atoms + using lattice units in orthogonal box = (-5 -5 -5) to (5 5 5) + create_atoms CPU = 0.001 seconds + +# change topology and settings for the two states +# we cannot simply create a different topology directly or +# load a different data file because the order and position +# of all atoms must be maintained across both replica + +# we first have to remove all topology data in the transform group +delete_bonds transform bond 1 +System init for delete_bonds ... +Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 12 + ghost atom cutoff = 12 + binsize = 6, bins = 2 2 2 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut/coul/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Deleting bonds ... + 68 total bonds, 64 turned on, 4 turned off + 34 total angles, 34 turned on, 0 turned off + 0 total dihedrals, 0 turned on, 0 turned off + 0 total impropers, 0 turned on, 0 turned off +delete_bonds transform angle 1 remove +System init for delete_bonds ... +Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule +Deleting bonds ... + 64 total bonds, 64 turned on, 0 turned off + 32 total angles, 32 turned on, 0 turned off + 0 total dihedrals, 0 turned on, 0 turned off + 0 total impropers, 0 turned on, 0 turned off + +# then generate different topologies for the two partitions. select by name. +if "${name} == twowater" then "create_bonds single/bond 2 1 2" "create_bonds single/bond 2 1 3" "create_bonds single/bond 2 4 5" "create_bonds single/bond 2 4 6" "create_bonds single/angle 2 2 1 3" "create_bonds single/angle 2 5 4 6" else "create_bonds single/bond 2 1 2" "create_bonds single/bond 2 3 4" "create_bonds single/bond 2 4 5" "create_bonds single/bond 2 4 6" "create_bonds single/angle 2 3 4 5" "create_bonds single/angle 2 5 4 6" "create_bonds single/angle 2 3 4 6" "set atom 1 charge -1.1354" "set atom 2 charge 0.1354" "set atom 3 charge 0.56775" "set atom 4 charge -0.70305" "set atom 5*6 charge 0.56775" +create_bonds single/bond 2 1 2 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 7 = max # of special neighbors + special bonds CPU = 0.002 seconds +create_bonds single/bond 2 3 4 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 7 = max # of special neighbors + special bonds CPU = 0.000 seconds +create_bonds single/bond 2 4 5 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 7 = max # of special neighbors + special bonds CPU = 0.000 seconds +create_bonds single/bond 2 4 6 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 3 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 2 = max # of 1-4 neighbors + 7 = max # of special neighbors + special bonds CPU = 0.000 seconds +create_bonds single/angle 2 3 4 5 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 3 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 2 = max # of 1-4 neighbors + 7 = max # of special neighbors + special bonds CPU = 0.000 seconds +create_bonds single/angle 2 5 4 6 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 3 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 2 = max # of 1-4 neighbors + 7 = max # of special neighbors + special bonds CPU = 0.000 seconds +create_bonds single/angle 2 3 4 6 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 3 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 2 = max # of 1-4 neighbors + 7 = max # of special neighbors + special bonds CPU = 0.000 seconds +set atom 1 charge -1.1354 +Setting atom values ... + 1 settings made for charge +set atom 2 charge 0.1354 +Setting atom values ... + 1 settings made for charge +set atom 3 charge 0.56775 +Setting atom values ... + 1 settings made for charge +set atom 4 charge -0.70305 +Setting atom values ... + 1 settings made for charge +set atom 5*6 charge 0.56775 +Setting atom values ... + 2 settings made for charge + +velocity all create 300.0 5463576 +timestep 0.2 + +# define ramp variable to combine the two different partitions +if "${name} == twowater" then "variable ramp equal ramp(1.0,0.0)" else "variable ramp equal ramp(0.0,1.0)" +variable ramp equal ramp(0.0,1.0) + +# since the trajectory and forces are kept identical through fix alchemy, +# we can do fix npt simulations, but we must use the "mixed" pressure + +fix integrate all npt temp 300 300 1.0 iso 1.0 1.0 10.0 +fix transform all alchemy v_ramp +compute pressure all pressure/alchemy transform +fix_modify integrate press pressure + +# only need to output a dump file from one partition +# if "${name} == twowater" then # "dump 1 all atom 100 ${name}.lammpstrj" # "dump_modify 1 sort id" + +thermo_style custom step temp press etotal density pe ke f_transform f_transform[3] +thermo_modify colname f_transform lambda colname f_transform[3] EPot_mixed +thermo_modify press pressure + +thermo 100 +run 20000 +Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule +WARNING: Bond/angle/dihedral extent > half of periodic box length (src/domain.cpp:936) +Per MPI rank memory allocation (min/avg/max) = 7.535 | 7.535 | 7.535 Mbytes + Step Temp Press TotEng Density PotEng KinEng lambda EPot_mixed + 0 300 184631.17 10769.267 1.0171193 10678.948 90.318545 0 -892.51464 + 100 293.4335 -513.97927 21497.846 0.3029684 21409.505 88.341623 0.005 207.29243 + 200 320.81838 1513.3 3300.6279 0.64509407 3204.0418 96.586165 0.01 46.402434 + 300 261.53825 -3808.6942 -362.14861 0.88817871 -440.88779 78.739179 0.015 -614.76481 + 400 308.32444 1375.0327 -821.01681 0.97694485 -913.84152 92.824715 0.02 -897.24386 + 500 292.60623 -12843.384 -831.87625 1.0140814 -919.96881 88.092563 0.025 -1221.948 + 600 326.16112 91608.645 2941.9339 1.0263567 2843.7393 98.194659 0.03 2786.0743 + 700 317.22811 -60420.408 -1637.1259 0.9919143 -1732.6311 95.505272 0.035 -1616.7677 + 800 309.94673 -56793.931 -1501.6195 1.0024958 -1594.9326 93.313126 0.04 -1640.8606 + 900 272.80718 -5076.2282 -1452.719 1.0141078 -1534.8508 82.131824 0.045 -1357.1812 + 1000 346.52557 -16919.192 -1469.4601 1.0170322 -1573.7857 104.32562 0.05 -1514.1398 + 1100 300.62984 -51826.972 -2581.5818 1.0063592 -2672.09 90.508164 0.055 -2565.9668 + 1200 293.72767 45222.698 2045.9381 1.0272336 1957.5079 88.430186 0.06 1951.1683 + 1300 289.4971 94600.203 2042.1709 1.0298091 1955.0144 87.156524 0.065 2088.1011 + 1400 328.98666 35468.53 1805.9965 1.0198467 1706.9512 99.045321 0.07 1716.9268 + 1500 392.9407 41220.21 1663.5291 1.0194044 1545.2297 118.29944 0.075 1690.6416 + 1600 284.90093 -37995.141 -2488.5372 1.0068497 -2574.31 85.772791 0.08 -2529.5874 + 1700 267.67454 25275.255 1482.7666 1.0313556 1402.18 80.586582 0.085 1520.9695 + 1800 247.16495 -68222.994 -2869.7712 1.0018048 -2944.1832 74.41193 0.09 -2788.9545 + 1900 328.41849 -51979.665 -2578.9515 1.0154952 -2677.8258 98.874268 0.095 -2461.3422 + 2000 313.8715 21726.003 1310.0519 1.018831 1215.5571 94.494725 0.1 1363.0739 + 2100 296.07341 66130.11 1209.3035 1.0224882 1120.1671 89.136398 0.105 1272.1884 + 2200 282.67889 51746.464 2238.8823 1.0362683 2153.7785 85.103821 0.11 2276.1488 + 2300 281.04207 -71937.759 -2935.0422 1.0111968 -3019.6532 84.611035 0.115 -2892.2526 + 2400 321.00806 -51658.758 -2663.4071 1.0168161 -2760.0503 96.643269 0.12 -2622.9732 + 2500 288.95906 49645.753 2369.0667 1.0355648 2282.0722 86.99454 0.125 2275.0348 + 2600 303.0064 -48470.216 -2107.8769 1.000439 -2199.1005 91.223657 0.13 -2082.5895 + 2700 361.7083 54973.584 1906.9779 1.0223169 1798.0813 108.89656 0.135 1817.1972 + 2800 289.27827 33564.017 1687.0255 1.0257088 1599.9349 87.090642 0.14 1682.9162 + 2900 283.94365 -47190.274 -2449.1599 1.0059224 -2534.6445 85.484591 0.145 -2395.9575 + 3000 337.10996 61988.686 2157.6059 1.0258 2056.115 101.49094 0.15 2168.1085 + 3100 305.28249 -50123.109 -2137.6015 1.0143567 -2229.5104 91.9089 0.155 -2040.3453 + 3200 270.19471 -18114.265 -2175.7381 1.0132413 -2257.0834 81.345309 0.16 -2076.9595 + 3300 263.39996 -109301.89 -2594.4684 0.99956867 -2673.7681 79.299671 0.165 -2471.0269 + 3400 249.01722 -37585.949 -2655.0291 1.0080932 -2729.9987 74.969576 0.17 -2537.734 + 3500 267.88868 65528.865 2038.1308 1.0390872 1957.4797 80.651054 0.175 2061.6421 + 3600 351.46458 -67583.574 -3068.3126 1.0059621 -3174.1251 105.81256 0.18 -3004.5028 + 3700 332.82565 -61204.843 -2491.3087 1.0053485 -2591.5097 100.20109 0.185 -2415.4435 + 3800 298.0279 61123.085 1795.9521 1.020672 1706.2273 89.724819 0.19 1831.9734 + 3900 317.04715 43210.045 1685.6151 1.0287838 1590.1643 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90.157617 0.67 -3792.6798 + 13500 275.65631 17625.49 1528.0027 1.0255473 1445.0131 82.989588 0.675 1521.2745 + 13600 302.63525 122466.63 2631.7819 1.0438137 2540.67 91.111917 0.68 2611.7188 + 13700 302.21323 -94399.663 -3344.9423 1.0068914 -3435.9271 90.984863 0.685 -3328.4539 + 13800 305.70483 30039.825 1506.1765 1.0225478 1414.1404 92.036052 0.69 1502.8476 + 13900 273.15564 -27822.597 -2713.3946 1.0131002 -2795.6313 82.236732 0.695 -2683.7804 + 14000 257.14635 -1821.0012 1045.462 1.0172653 968.04508 77.416947 0.7 1067.8821 + 14100 323.74174 -76139.363 -3042.0486 1.0139806 -3139.5149 97.466276 0.705 -3052.598 + 14200 274.99913 54440.943 796.17718 1.0186356 713.38545 82.791736 0.71 767.64274 + 14300 291.8774 1281.7286 1079.6881 1.0214356 991.81498 87.873139 0.715 1042.8585 + 14400 308.97245 -47961.551 -3005.1106 1.0155221 -3098.1304 93.019806 0.72 -3007.3204 + 14500 311.05309 86026.739 1851.7257 1.0311818 1758.0795 93.646208 0.725 1830.5463 + 14600 269.27432 -12972.747 726.82371 1.0172239 645.7555 81.068214 0.73 711.81484 + 14700 262.20739 -77722.459 -3545.7104 1.0029421 -3624.651 78.940634 0.735 -3537.1929 + 14800 300.33592 -107332.8 -3118.6094 1.0126785 -3209.0291 90.419677 0.74 -3125.8439 + 14900 307.0173 -73204.94 -3016.2921 1.016875 -3108.7233 92.431185 0.745 -3016.0143 + 15000 334.08711 64440.709 1360.8856 1.0369481 1260.3047 100.58087 0.75 1323.9179 + 15100 293.46703 35179.395 1804.4648 1.0331703 1716.1131 88.351717 0.755 1768.9681 + 15200 307.80546 54006.291 852.72781 1.0246134 760.05934 92.668471 0.76 822.22754 + 15300 336.59792 33832.907 988.39905 1.0242407 887.06227 101.33678 0.765 956.25285 + 15400 285.46526 -99629.94 -2736.0944 1.0041261 -2822.0371 85.942688 0.77 -2730.1887 + 15500 269.15938 122546.45 2708.063 1.0318941 2627.0294 81.033612 0.775 2695.4331 + 15600 294.50818 -104733.19 -2271.5729 1.0017241 -2360.238 88.665166 0.78 -2281.5773 + 15700 321.05125 -40438.501 -2060.144 1.0125007 -2156.8002 96.656271 0.785 -2084.0893 + 15800 303.22185 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+ 17000 281.69389 86032.163 1577.5995 1.0237583 1492.7922 84.807275 0.85 1528.8391 + 17100 297.2629 55128.393 2431.5835 1.0419182 2342.089 89.494508 0.855 2369.0347 + 17200 328.81472 47063.86 1584.1492 1.0364627 1485.1556 98.993555 0.86 1526.7115 + 17300 313.41363 -46685.063 -2635.2463 1.008117 -2729.6032 94.356878 0.865 -2685.8034 + 17400 288.17114 68721.523 2548.303 1.0429105 2461.5456 86.757326 0.87 2490.5845 + 17500 260.01702 -23324.539 -1776.7039 1.0100415 -1854.9851 78.281195 0.875 -1812.4813 + 17600 297.6633 72795.463 2396.9788 1.0362827 2307.3638 89.615054 0.88 2336.0152 + 17700 301.02937 93833.118 2424.9649 1.0276466 2334.3364 90.628448 0.885 2364.8751 + 17800 238.92837 -78317.212 -2548.5755 1.0084077 -2620.5077 71.932208 0.89 -2579.4429 + 17900 299.27724 -65278.891 -2933.564 1.0034773 -3023.6649 90.10095 0.895 -2987.498 + 18000 315.15753 -72437.481 -2654.8693 1.0136139 -2749.7512 94.881898 0.9 -2718.125 + 18100 268.39411 -42194.209 -2606.045 1.0108104 -2686.8482 80.803219 0.905 -2656.3853 + 18200 284.91941 40905.162 1786.1505 1.0266185 1700.3722 85.778354 0.91 1723.6803 + 18300 329.41629 -56526.814 -2472.7835 1.0137784 -2571.9582 99.174667 0.915 -2540.6829 + 18400 293.16732 -22085.551 -1991.6537 1.0163557 -2079.9152 88.261484 0.92 -2052.7864 + 18500 276.28141 29367.359 2034.0833 1.0270087 1950.9056 83.177784 0.925 1971.9405 + 18600 331.18031 94669.124 2160.1352 1.0225403 2060.4295 99.705745 0.93 2081.8675 + 18700 265.4491 49872.536 2324.2391 1.0255308 2244.3225 79.916587 0.935 2260.4261 + 18800 314.51042 60758.629 2298.6407 1.0300818 2203.9536 94.687078 0.94 2219.6547 + 18900 317.70309 66345.835 1490.6939 1.0248229 1395.0457 95.648268 0.945 1410.3087 + 19000 291.39831 -96336.931 -2732.3994 1.0100498 -2820.1283 87.728905 0.95 -2805.9396 + 19100 303.37353 -21421.495 -2360.5644 0.99771284 -2451.8986 91.334186 0.955 -2436.2173 + 19200 293.92948 36383.881 1708.7388 1.0251299 1620.2479 88.490944 0.96 1633.579 + 19300 287.24409 -46691.027 -2736.6663 1.0112067 -2823.1445 86.478228 0.965 -2811.3506 + 19400 333.42205 21152.63 1209.1556 1.0189912 1108.7749 100.38065 0.97 1118.2463 + 19500 309.17989 60445.761 2014.5979 1.0338543 1921.5157 93.082259 0.975 1928.6181 + 19600 255.92246 -32795.547 -2145.3103 1.0157044 -2222.3587 77.04848 0.98 -2213.9484 + 19700 342.62332 33538.746 2181.2002 1.0225905 2078.0494 103.1508 0.985 2081.9185 + 19800 295.68946 81474.342 1996.4567 1.0240743 1907.4359 89.020804 0.99 1910.5545 + 19900 306.4947 43488.052 2048.2997 1.0222707 1956.0258 92.27385 0.995 1957.4368 + 20000 313.31679 -25133.284 -1555.4274 1.0163289 -1649.7551 94.327722 1 -1649.7551 +Loop time of 8.92592 on 2 procs for 20000 steps with 102 atoms + +Performance: 38.719 ns/day, 0.620 hours/ns, 2240.664 timesteps/s, 228.548 katom-step/s +96.2% CPU use with 2 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 4.7753 | 6.0676 | 7.3599 | 52.5 | 67.98 +Bond | 0.036352 | 0.036909 | 0.037466 | 0.3 | 0.41 +Neigh | 0.085317 | 0.085383 | 0.085449 | 0.0 | 0.96 +Comm | 0.72794 | 2.022 | 3.3161 | 91.0 | 22.65 +Output | 0.0023255 | 0.005156 | 0.0079865 | 3.9 | 0.06 +Modify | 0.64567 | 0.64689 | 0.64812 | 0.2 | 7.25 +Other | | 0.06196 | | | 0.69 + +Nlocal: 51 ave 51 max 51 min +Histogram: 2 0 0 0 0 0 0 0 0 0 +Nghost: 3317 ave 3317 max 3317 min +Histogram: 2 0 0 0 0 0 0 0 0 0 +Neighs: 18319.5 ave 21940 max 14699 min +Histogram: 1 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 36639 +Ave neighs/atom = 359.20588 +Ave special neighs/atom = 2.0196078 +Neighbor list builds = 181 +Dangerous builds = 0 +Total wall time: 0:00:08 diff --git a/examples/PACKAGES/reaction/create_atoms_polystyrene/in.grow_styrene b/examples/PACKAGES/reaction/create_atoms_polystyrene/in.grow_styrene index b17b321fe5..7860db4e55 100644 --- a/examples/PACKAGES/reaction/create_atoms_polystyrene/in.grow_styrene +++ b/examples/PACKAGES/reaction/create_atoms_polystyrene/in.grow_styrene @@ -16,6 +16,9 @@ dihedral_style class2 improper_style class2 +special_bonds lj/coul 0 0 1 +pair_modify tail yes mix sixthpower + variable T equal 530 read_data trimer.data & diff --git a/examples/PACKAGES/reaction/nylon,6-6_melt/in.large_nylon_melt b/examples/PACKAGES/reaction/nylon,6-6_melt/in.large_nylon_melt index 6fbf46f844..9678a714d6 100644 --- a/examples/PACKAGES/reaction/nylon,6-6_melt/in.large_nylon_melt +++ b/examples/PACKAGES/reaction/nylon,6-6_melt/in.large_nylon_melt @@ -18,6 +18,9 @@ dihedral_style class2 improper_style class2 +special_bonds lj/coul 0 0 1 +pair_modify tail yes mix sixthpower + read_data large_nylon_melt.data.gz & extra/bond/per/atom 5 & extra/angle/per/atom 15 & diff --git a/examples/PACKAGES/reaction/tiny_epoxy/in.tiny_epoxy.stabilized b/examples/PACKAGES/reaction/tiny_epoxy/in.tiny_epoxy.stabilized index 1309eff3a3..57b03b630f 100644 --- a/examples/PACKAGES/reaction/tiny_epoxy/in.tiny_epoxy.stabilized +++ b/examples/PACKAGES/reaction/tiny_epoxy/in.tiny_epoxy.stabilized @@ -17,6 +17,9 @@ dihedral_style class2 improper_style class2 +special_bonds lj/coul 0 0 1 +pair_modify tail yes mix sixthpower + read_data tiny_epoxy.data velocity all create 300.0 4928459 dist gaussian diff --git a/examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.stabilized b/examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.stabilized index 81a12b4ccb..95b39033db 100644 --- a/examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.stabilized +++ b/examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.stabilized @@ -19,6 +19,9 @@ dihedral_style class2 improper_style class2 +special_bonds lj/coul 0 0 1 +pair_modify tail yes mix sixthpower + read_data tiny_nylon.data & extra/bond/per/atom 5 & extra/angle/per/atom 15 & diff --git a/examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.stabilized_variable_probability b/examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.stabilized_variable_probability index 515d4cb2f8..88b5a95a41 100644 --- a/examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.stabilized_variable_probability +++ b/examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.stabilized_variable_probability @@ -19,6 +19,9 @@ dihedral_style class2 improper_style class2 +special_bonds lj/coul 0 0 1 +pair_modify tail yes mix sixthpower + read_data tiny_nylon.data & extra/bond/per/atom 5 & extra/angle/per/atom 15 & diff --git a/examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.unstabilized b/examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.unstabilized index 4891e9ebff..a569e28d43 100644 --- a/examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.unstabilized +++ b/examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.unstabilized @@ -19,6 +19,9 @@ dihedral_style class2 improper_style class2 +special_bonds lj/coul 0 0 1 +pair_modify tail yes mix sixthpower + read_data tiny_nylon.data & extra/bond/per/atom 5 & extra/angle/per/atom 15 & diff --git a/examples/PACKAGES/reaction/tiny_polystyrene/in.tiny_polystyrene.stabilized b/examples/PACKAGES/reaction/tiny_polystyrene/in.tiny_polystyrene.stabilized index ab9c012905..4ecc481719 100644 --- a/examples/PACKAGES/reaction/tiny_polystyrene/in.tiny_polystyrene.stabilized +++ b/examples/PACKAGES/reaction/tiny_polystyrene/in.tiny_polystyrene.stabilized @@ -19,6 +19,9 @@ dihedral_style class2 improper_style class2 +special_bonds lj/coul 0 0 1 +pair_modify tail yes mix sixthpower + variable T equal 530 read_data tiny_polystyrene.data & diff --git a/examples/wall/in.wall.lepton b/examples/wall/in.wall.lepton new file mode 100644 index 0000000000..76d8e71f01 --- /dev/null +++ b/examples/wall/in.wall.lepton @@ -0,0 +1,110 @@ +units real +atom_style bond +boundary f p p +region box block -5.000000000000001 5.000000000000001 -5 5 -5 5 +create_box 1 box bond/types 1 extra/bond/per/atom 1 extra/special/per/atom 1 + +pair_style zero 5.0 +pair_coeff * * +mass * 1.0 +bond_style zero +bond_coeff * 1.0 + +create_atoms 1 single -4.0 0.0 0.0 +create_atoms 1 single 4.0 0.0 0.0 +create_atoms 1 single -5.0 0.0 0.0 +create_atoms 1 single 5.0 0.0 0.0 +create_bonds single/bond 1 3 1 +create_bonds single/bond 1 4 2 + +group move id 1:2 +write_restart walltest.restart + +variable name string wall-harmonic +include wall.inc + +fix 1 move wall/harmonic xlo -5.0 100 0.0 4.0 xhi 5.0 100 1.0 4.0 +fix_modify 1 energy yes +run 5 post no + +variable name string lepton-harmonic +include wall.inc + +fix 1 move wall/lepton xlo -5.0 "k*(r-rc)^2;k=100.0" 4.0 xhi 5.0 "k*(r-rc)^2;k=100.0" 4.0 +fix_modify 1 energy yes +run 5 post no + +variable name string bond-harmonic +include wall.inc + +bond_style harmonic +bond_coeff 1 100 4.0 +run 5 post no + +variable name string pair-harmonic +include wall.inc + +pair_style harmonic/cut +pair_coeff 1 1 100 4.0 +run 5 post no + +variable eps index 0.02 +variable sig index 2.0 +variable name string wall-lj126 +include wall.inc + +fix 1 move wall/lj126 xlo -5.0 ${eps} ${sig} 4.0 xhi 5.0 ${eps} ${sig} 4.0 +fix_modify 1 energy yes +run 5 post no + +variable name string lepton-lj126 +include wall.inc + +fix 1 move wall/lepton xlo -5.0 "4.0*epsilon*((sigma/r)^12 - (sigma/r)^6);epsilon=v_eps;sigma=v_sig" 4.0 & + xhi 5.0 "4.0*epsilon*((sigma/r)^12 - (sigma/r)^6);epsilon=v_eps;sigma=v_sig" 4.0 +fix_modify 1 energy yes +run 5 post no + +variable name string pair-lj126 +include wall.inc + +pair_style lj/cut 4.0 +pair_coeff 1 1 ${eps} ${sig} +pair_modify shift yes +run 5 post no + +variable d0 index 20.0 +variable al index 2.0 +variable r0 index 1.2 + +variable name string wall-morse +include wall.inc + +fix 1 move wall/morse xlo -5.0 ${d0} ${al} ${r0} 4.0 xhi 5.0 ${d0} ${al} ${r0} 4.0 +fix_modify 1 energy yes +run 5 post no + +variable name string lepton-morse +include wall.inc + +fix 1 move wall/lepton xlo -5.0 "d0*(-1.0 + (1.0 - ralpha) * (1.0 - ralpha));ralpha=exp(-alpha*(r-r0));d0=v_d0;alpha=v_al;r0=v_r0" 4.0 & + xhi 5.0 "d0*(-1.0 + (1.0 - ralpha) * (1.0 - ralpha));ralpha=exp(-alpha*(r-r0));d0=v_d0;alpha=v_al;r0=v_r0" 4.0 +fix_modify 1 energy yes +run 5 post no + +variable name string bond-morse +include wall.inc + +bond_style morse +bond_coeff 1 ${d0} ${al} ${r0} +run 5 post no + +variable name string pair-morse +include wall.inc + +pair_style morse 4.0 +pair_coeff 1 1 ${d0} ${al} ${r0} +pair_modify shift yes +run 5 post no + +shell rm -f walltest.restart diff --git a/examples/wall/in.wall.table b/examples/wall/in.wall.table new file mode 100644 index 0000000000..f5b8232ef8 --- /dev/null +++ b/examples/wall/in.wall.table @@ -0,0 +1,129 @@ +units real +atom_style bond +boundary f p p +region box block -5.000000000000001 5.000000000000001 -5 5 -5 5 +create_box 1 box bond/types 1 extra/bond/per/atom 1 extra/special/per/atom 1 + +pair_style zero 5.0 +pair_coeff * * +mass * 1.0 +bond_style zero +bond_coeff * 1.0 + +create_atoms 1 single -4.0 0.0 0.0 +create_atoms 1 single 4.0 0.0 0.0 +create_atoms 1 single -5.0 0.0 0.0 +create_atoms 1 single 5.0 0.0 0.0 +create_bonds single/bond 1 3 1 +create_bonds single/bond 1 4 2 + +group move id 1:2 +write_restart walltest.restart + +variable name string wall-harmonic +include wall.inc + +fix 1 move wall/harmonic xlo -5.0 100 0.0 4.0 xhi 5.0 100 1.0 4.0 +fix_modify 1 energy yes +run 5 post no + +variable name string table-harmonic +include wall.inc + +fix 1 move wall/table linear 1000 xlo -5.0 walltab.dat HARMONIC 4.0 xhi 5.0 walltab.dat HARMONIC 4.0 +fix_modify 1 energy yes +run 5 post no + +variable name string spline-harmonic +include wall.inc + +fix 1 move wall/table spline 200 xlo -5.0 walltab.dat HARMONIC 4.0 xhi 5.0 walltab.dat HARMONIC 4.0 +fix_modify 1 energy yes +run 5 post no + +variable name string bond-harmonic +include wall.inc + +bond_style harmonic +bond_coeff 1 100 4.0 +run 5 post no + +variable name string pair-harmonic +include wall.inc + +pair_style harmonic/cut +pair_coeff 1 1 100 4.0 +run 5 post no + +variable eps index 0.02 +variable sig index 2.0 +variable name string wall-lj126 +include wall.inc + +fix 1 move wall/lj126 xlo -5.0 ${eps} ${sig} 4.0 xhi 5.0 ${eps} ${sig} 4.0 +fix_modify 1 energy yes +run 5 post no + +variable name string table-lj126 +include wall.inc + +fix 1 move wall/table linear 1000 xlo -5.0 walltab.dat LJ126 4.0 xhi 5.0 walltab.dat LJ126 4.0 +fix_modify 1 energy yes +run 5 post no + +variable name string spline-lj126 +include wall.inc + +fix 1 move wall/table spline 200 xlo -5.0 walltab.dat LJ126 4.0 xhi 5.0 walltab.dat LJ126 4.0 +fix_modify 1 energy yes +run 5 post no + +variable name string pair-lj126 +include wall.inc + +pair_style lj/cut 4.0 +pair_coeff 1 1 ${eps} ${sig} +pair_modify shift yes +run 5 post no + +variable d0 index 20.0 +variable al index 2.0 +variable r0 index 1.2 + +variable name string wall-morse +include wall.inc + +fix 1 move wall/morse xlo -5.0 ${d0} ${al} ${r0} 4.0 xhi 5.0 ${d0} ${al} ${r0} 4.0 +fix_modify 1 energy yes +run 5 post no + +variable name string table-morse +include wall.inc + +fix 1 move wall/table linear 1000 xlo -5.0 walltab.dat MORSE 4.0 xhi 5.0 walltab.dat MORSE 4.0 +fix_modify 1 energy yes +run 5 post no + +variable name string spline-morse +include wall.inc + +fix 1 move wall/table spline 1000 xlo -5.0 walltab.dat MORSE 4.0 xhi 5.0 walltab.dat MORSE 4.0 +fix_modify 1 energy yes +run 5 post no + +variable name string bond-morse +include wall.inc + +bond_style morse +bond_coeff 1 ${d0} ${al} ${r0} +run 5 post no + +variable name string pair-morse +include wall.inc + +pair_style morse 4.0 +pair_coeff 1 1 ${d0} ${al} ${r0} +pair_modify shift yes +run 5 post no + +shell rm -f walltest.restart diff --git a/examples/wall/log.23Feb23.wall.lepton.g++.1 b/examples/wall/log.23Feb23.wall.lepton.g++.1 new file mode 100644 index 0000000000..5d555b2717 --- /dev/null +++ b/examples/wall/log.23Feb23.wall.lepton.g++.1 @@ -0,0 +1,882 @@ +LAMMPS (8 Feb 2023) + using 1 OpenMP thread(s) per MPI task +units real +atom_style bond +boundary f p p +region box block -5.000000000000001 5.000000000000001 -5 5 -5 5 +create_box 1 box bond/types 1 extra/bond/per/atom 1 extra/special/per/atom 1 +Created orthogonal box = (-5 -5 -5) to (5 5 5) + 1 by 1 by 1 MPI processor grid + +pair_style zero 5.0 +pair_coeff * * +mass * 1.0 +bond_style zero +bond_coeff * 1.0 + +create_atoms 1 single -4.0 0.0 0.0 +Created 1 atoms + using lattice units in orthogonal box = (-5 -5 -5) to (5 5 5) + create_atoms CPU = 0.000 seconds +create_atoms 1 single 4.0 0.0 0.0 +Created 1 atoms + using lattice units in orthogonal box = (-5 -5 -5) to (5 5 5) + create_atoms CPU = 0.000 seconds +create_atoms 1 single -5.0 0.0 0.0 +Created 1 atoms + using lattice units in orthogonal box = (-5 -5 -5) to (5 5 5) + create_atoms CPU = 0.000 seconds +create_atoms 1 single 5.0 0.0 0.0 +Created 1 atoms + using lattice units in orthogonal box = (-5 -5 -5) to (5 5 5) + create_atoms CPU = 0.000 seconds +create_bonds single/bond 1 3 1 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 1 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds +create_bonds single/bond 1 4 2 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 1 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + +group move id 1:2 +2 atoms in group move +write_restart walltest.restart +System init for write_restart ... +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7 + ghost atom cutoff = 7 + binsize = 3.5, bins = 3 3 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard + +variable name string wall-harmonic +include wall.inc + +clear + using 1 OpenMP thread(s) per MPI task +read_restart walltest.restart +Reading restart file ... + restart file = 8 Feb 2023, LAMMPS = 8 Feb 2023 + restoring atom style bond from restart + orthogonal box = (-5 -5 -5) to (5 5 5) + 1 by 1 by 1 MPI processor grid + restoring pair style zero from restart + restoring bond style zero from restart + 4 atoms + 2 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 1 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_restart CPU = 0.001 seconds +# log ${name}.log + +compute ea move pe/atom +compute pe move reduce sum c_ea +special_bonds lj/coul 1.0 1.0 1.0 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 1 1 1 + special bond factors coul: 1 1 1 + 1 = max # of 1-2 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + +thermo_style custom step temp press ke pe etotal c_pe +thermo 1 +thermo_modify format float %14.10g + +fix 0 move nve +# dump 1 all custom 1 ${name}.dump id x fx +# dump_modify 1 format float %20.15g + +fix 1 move wall/harmonic xlo -5.0 100 0.0 4.0 xhi 5.0 100 1.0 4.0 +fix_modify 1 energy yes +run 5 post no +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7 + ghost atom cutoff = 7 + binsize = 3.5, bins = 3 3 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.429 | 4.429 | 4.429 Mbytes + Step Temp Press KinEng PotEng TotEng c_pe + 0 0 0 0 1800 1800 0 + 1 16146.37291 6600.295604 144.3878119 1652.527054 1796.914866 0 + 2 59294.04011 24238.149 530.232812 1258.437705 1788.670517 0 + 3 115302.7492 47133.32419 1031.086781 746.8819904 1777.968771 0 + 4 165817.4572 67782.66799 1482.811029 285.5057515 1768.31678 0 + 5 194283.6024 79419.02582 1737.367544 25.51012833 1762.877672 0 +Loop time of 7.6828e-05 on 1 procs for 5 steps with 4 atoms + + +variable name string lepton-harmonic +include wall.inc + +clear + using 1 OpenMP thread(s) per MPI task +read_restart walltest.restart +Reading restart file ... + restart file = 8 Feb 2023, LAMMPS = 8 Feb 2023 + restoring atom style bond from restart + orthogonal box = (-5 -5 -5) to (5 5 5) + 1 by 1 by 1 MPI processor grid + restoring pair style zero from restart + restoring bond style zero from restart + 4 atoms + 2 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 1 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_restart CPU = 0.000 seconds +# log ${name}.log + +compute ea move pe/atom +compute pe move reduce sum c_ea +special_bonds lj/coul 1.0 1.0 1.0 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 1 1 1 + special bond factors coul: 1 1 1 + 1 = max # of 1-2 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + +thermo_style custom step temp press ke pe etotal c_pe +thermo 1 +thermo_modify format float %14.10g + +fix 0 move nve +# dump 1 all custom 1 ${name}.dump id x fx +# dump_modify 1 format float %20.15g + +fix 1 move wall/lepton xlo -5.0 "k*(r-rc)^2;k=100.0" 4.0 xhi 5.0 "k*(r-rc)^2;k=100.0" 4.0 +fix_modify 1 energy yes +run 5 post no +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7 + ghost atom cutoff = 7 + binsize = 3.5, bins = 3 3 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.429 | 4.429 | 4.429 Mbytes + Step Temp Press KinEng PotEng TotEng c_pe + 0 0 0 0 1800 1800 0 + 1 16146.37291 6600.295604 144.3878119 1652.527054 1796.914866 0 + 2 59294.04011 24238.149 530.232812 1258.437705 1788.670517 0 + 3 115302.7492 47133.32419 1031.086781 746.8819904 1777.968771 0 + 4 165817.4572 67782.66799 1482.811029 285.5057515 1768.31678 0 + 5 194283.6024 79419.02582 1737.367544 25.51012833 1762.877672 0 +Loop time of 0.00134915 on 1 procs for 5 steps with 4 atoms + + +variable name string bond-harmonic +include wall.inc + +clear + using 1 OpenMP thread(s) per MPI task +read_restart walltest.restart +Reading restart file ... + restart file = 8 Feb 2023, LAMMPS = 8 Feb 2023 + restoring atom style bond from restart + orthogonal box = (-5 -5 -5) to (5 5 5) + 1 by 1 by 1 MPI processor grid + restoring pair style zero from restart + restoring bond style zero from restart + 4 atoms + 2 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 1 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_restart CPU = 0.000 seconds +# log ${name}.log + +compute ea move pe/atom +compute pe move reduce sum c_ea +special_bonds lj/coul 1.0 1.0 1.0 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 1 1 1 + special bond factors coul: 1 1 1 + 1 = max # of 1-2 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + +thermo_style custom step temp press ke pe etotal c_pe +thermo 1 +thermo_modify format float %14.10g + +fix 0 move nve +# dump 1 all custom 1 ${name}.dump id x fx +# dump_modify 1 format float %20.15g + +bond_style harmonic +bond_coeff 1 100 4.0 +run 5 post no +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7 + ghost atom cutoff = 7 + binsize = 3.5, bins = 3 3 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +WARNING: Communication cutoff 7 is shorter than a bond length based estimate of 8. This may lead to errors. (src/comm.cpp:723) +Per MPI rank memory allocation (min/avg/max) = 4.429 | 4.429 | 4.429 Mbytes + Step Temp Press KinEng PotEng TotEng c_pe + 0 0 27427.366 0 1800 1800 900 + 1 16146.37291 36178.74173 144.3878119 1652.527054 1796.914866 826.263527 + 2 59294.04011 58444.6962 530.232812 1258.437705 1788.670517 629.2188524 + 3 115302.7492 83661.44348 1031.086781 746.8819904 1777.968771 373.4409952 + 4 165817.4572 98424.89283 1482.811029 285.5057515 1768.31678 142.7528758 + 5 194283.6024 91313.53086 1737.367544 25.51012833 1762.877672 12.75506417 +Loop time of 4.6572e-05 on 1 procs for 5 steps with 4 atoms + + +variable name string pair-harmonic +include wall.inc + +clear + using 1 OpenMP thread(s) per MPI task +read_restart walltest.restart +Reading restart file ... + restart file = 8 Feb 2023, LAMMPS = 8 Feb 2023 + restoring atom style bond from restart + orthogonal box = (-5 -5 -5) to (5 5 5) + 1 by 1 by 1 MPI processor grid + restoring pair style zero from restart + restoring bond style zero from restart + 4 atoms + 2 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 1 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_restart CPU = 0.000 seconds +# log ${name}.log + +compute ea move pe/atom +compute pe move reduce sum c_ea +special_bonds lj/coul 1.0 1.0 1.0 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 1 1 1 + special bond factors coul: 1 1 1 + 1 = max # of 1-2 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + +thermo_style custom step temp press ke pe etotal c_pe +thermo 1 +thermo_modify format float %14.10g + +fix 0 move nve +# dump 1 all custom 1 ${name}.dump id x fx +# dump_modify 1 format float %20.15g + +pair_style harmonic/cut +pair_coeff 1 1 100 4.0 +run 5 post no +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6 + ghost atom cutoff = 6 + binsize = 3, bins = 4 4 4 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair harmonic/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.43 | 4.43 | 4.43 Mbytes + Step Temp Press KinEng PotEng TotEng c_pe + 0 0 27427.366 0 1800 1800 900 + 1 16146.37291 36178.74173 144.3878119 1652.527054 1796.914866 826.263527 + 2 59294.04011 58444.6962 530.232812 1258.437705 1788.670517 629.2188524 + 3 115302.7492 83661.44348 1031.086781 746.8819904 1777.968771 373.4409952 + 4 165817.4572 98424.89283 1482.811029 285.5057515 1768.31678 142.7528758 + 5 170540.4005 97560.47089 1525.045619 190.8165235 1715.862142 178.0614593 +Loop time of 8.4058e-05 on 1 procs for 5 steps with 4 atoms + + +variable eps index 0.02 +variable sig index 2.0 +variable name string wall-lj126 +include wall.inc + +clear + using 1 OpenMP thread(s) per MPI task +read_restart walltest.restart +Reading restart file ... + restart file = 8 Feb 2023, LAMMPS = 8 Feb 2023 + restoring atom style bond from restart + orthogonal box = (-5 -5 -5) to (5 5 5) + 1 by 1 by 1 MPI processor grid + restoring pair style zero from restart + restoring bond style zero from restart + 4 atoms + 2 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 1 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_restart CPU = 0.000 seconds +# log ${name}.log + +compute ea move pe/atom +compute pe move reduce sum c_ea +special_bonds lj/coul 1.0 1.0 1.0 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 1 1 1 + special bond factors coul: 1 1 1 + 1 = max # of 1-2 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + +thermo_style custom step temp press ke pe etotal c_pe +thermo 1 +thermo_modify format float %14.10g + +fix 0 move nve +# dump 1 all custom 1 ${name}.dump id x fx +# dump_modify 1 format float %20.15g + +fix 1 move wall/lj126 xlo -5.0 ${eps} ${sig} 4.0 xhi 5.0 ${eps} ${sig} 4.0 +fix 1 move wall/lj126 xlo -5.0 0.02 ${sig} 4.0 xhi 5.0 ${eps} ${sig} 4.0 +fix 1 move wall/lj126 xlo -5.0 0.02 2.0 4.0 xhi 5.0 ${eps} ${sig} 4.0 +fix 1 move wall/lj126 xlo -5.0 0.02 2.0 4.0 xhi 5.0 0.02 ${sig} 4.0 +fix 1 move wall/lj126 xlo -5.0 0.02 2.0 4.0 xhi 5.0 0.02 2.0 4.0 +fix_modify 1 energy yes +run 5 post no +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7 + ghost atom cutoff = 7 + binsize = 3.5, bins = 3 3 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.429 | 4.429 | 4.429 Mbytes + Step Temp Press KinEng PotEng TotEng c_pe + 0 0 0 0 645.1224609 645.1224609 0 + 1 178153.8707 72825.53278 1593.128544 0.2259591031 1593.354503 0 + 2 178262.3593 72869.88065 1594.098696 -0.02237405364 1594.076322 0 + 3 178259.9436 72868.89314 1594.077094 -0.003385746252 1594.073708 0 + 4 178259.4975 72868.71081 1594.073105 0 1594.073105 0 + 5 178259.4975 72868.71081 1594.073105 0 1594.073105 0 +WARNING: Bond/angle/dihedral extent > half of periodic box length (src/domain.cpp:936) +Loop time of 4.3942e-05 on 1 procs for 5 steps with 4 atoms + + +variable name string lepton-lj126 +include wall.inc + +clear + using 1 OpenMP thread(s) per MPI task +read_restart walltest.restart +Reading restart file ... + restart file = 8 Feb 2023, LAMMPS = 8 Feb 2023 + restoring atom style bond from restart + orthogonal box = (-5 -5 -5) to (5 5 5) + 1 by 1 by 1 MPI processor grid + restoring pair style zero from restart + restoring bond style zero from restart + 4 atoms + 2 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 1 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_restart CPU = 0.000 seconds +# log ${name}.log + +compute ea move pe/atom +compute pe move reduce sum c_ea +special_bonds lj/coul 1.0 1.0 1.0 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 1 1 1 + special bond factors coul: 1 1 1 + 1 = max # of 1-2 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + +thermo_style custom step temp press ke pe etotal c_pe +thermo 1 +thermo_modify format float %14.10g + +fix 0 move nve +# dump 1 all custom 1 ${name}.dump id x fx +# dump_modify 1 format float %20.15g + +fix 1 move wall/lepton xlo -5.0 "4.0*epsilon*((sigma/r)^12 - (sigma/r)^6);epsilon=v_eps;sigma=v_sig" 4.0 xhi 5.0 "4.0*epsilon*((sigma/r)^12 - (sigma/r)^6);epsilon=v_eps;sigma=v_sig" 4.0 +fix_modify 1 energy yes +run 5 post no +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7 + ghost atom cutoff = 7 + binsize = 3.5, bins = 3 3 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.429 | 4.429 | 4.429 Mbytes + Step Temp Press KinEng PotEng TotEng c_pe + 0 0 0 0 645.1224609 645.1224609 0 + 1 178153.8707 72825.53278 1593.128544 0.2259591031 1593.354503 0 + 2 178262.3593 72869.88065 1594.098696 -0.02237405364 1594.076322 0 + 3 178259.9436 72868.89314 1594.077094 -0.003385746252 1594.073708 0 + 4 178259.4975 72868.71081 1594.073105 0 1594.073105 0 + 5 178259.4975 72868.71081 1594.073105 0 1594.073105 0 +WARNING: Bond/angle/dihedral extent > half of periodic box length (src/domain.cpp:936) +Loop time of 0.00298781 on 1 procs for 5 steps with 4 atoms + + +variable name string pair-lj126 +include wall.inc + +clear + using 1 OpenMP thread(s) per MPI task +read_restart walltest.restart +Reading restart file ... + restart file = 8 Feb 2023, LAMMPS = 8 Feb 2023 + restoring atom style bond from restart + orthogonal box = (-5 -5 -5) to (5 5 5) + 1 by 1 by 1 MPI processor grid + restoring pair style zero from restart + restoring bond style zero from restart + 4 atoms + 2 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 1 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_restart CPU = 0.000 seconds +# log ${name}.log + +compute ea move pe/atom +compute pe move reduce sum c_ea +special_bonds lj/coul 1.0 1.0 1.0 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 1 1 1 + special bond factors coul: 1 1 1 + 1 = max # of 1-2 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + +thermo_style custom step temp press ke pe etotal c_pe +thermo 1 +thermo_modify format float %14.10g + +fix 0 move nve +# dump 1 all custom 1 ${name}.dump id x fx +# dump_modify 1 format float %20.15g + +pair_style lj/cut 4.0 +pair_coeff 1 1 ${eps} ${sig} +pair_coeff 1 1 0.02 ${sig} +pair_coeff 1 1 0.02 2.0 +pair_modify shift yes +run 5 post no +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6 + ghost atom cutoff = 6 + binsize = 3, bins = 4 4 4 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.43 | 4.43 | 4.43 Mbytes + Step Temp Press KinEng PotEng TotEng c_pe + 0 0 178343.7047 0 645.1224609 645.1224609 322.5612305 + 1 178153.8707 72925.96146 1593.128544 0.2259591031 1593.354503 0.1129795516 + 2 178262.3593 72867.28485 1594.098696 -0.02237405364 1594.076322 -0.01118702682 + 3 178260.8147 72867.80305 1594.084884 -0.007499601847 1594.077384 -0.005806728722 + 4 176007.6835 72778.53677 1573.936415 2.772305717 1576.708721 2.772305717 + 5 1.132219912e+27 4.628275436e+26 1.012479748e+25 3.761972158e+12 1.012479748e+25 3.761972158e+12 +WARNING: Bond/angle/dihedral extent > half of periodic box length (src/domain.cpp:936) +Loop time of 4.4455e-05 on 1 procs for 5 steps with 4 atoms + + +variable d0 index 20.0 +variable al index 2.0 +variable r0 index 1.2 + +variable name string wall-morse +include wall.inc + +clear + using 1 OpenMP thread(s) per MPI task +read_restart walltest.restart +Reading restart file ... + restart file = 8 Feb 2023, LAMMPS = 8 Feb 2023 + restoring atom style bond from restart + orthogonal box = (-5 -5 -5) to (5 5 5) + 1 by 1 by 1 MPI processor grid + restoring pair style zero from restart + restoring bond style zero from restart + 4 atoms + 2 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 1 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_restart CPU = 0.000 seconds +# log ${name}.log + +compute ea move pe/atom +compute pe move reduce sum c_ea +special_bonds lj/coul 1.0 1.0 1.0 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 1 1 1 + special bond factors coul: 1 1 1 + 1 = max # of 1-2 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + +thermo_style custom step temp press ke pe etotal c_pe +thermo 1 +thermo_modify format float %14.10g + +fix 0 move nve +# dump 1 all custom 1 ${name}.dump id x fx +# dump_modify 1 format float %20.15g + +fix 1 move wall/morse xlo -5.0 ${d0} ${al} ${r0} 4.0 xhi 5.0 ${d0} ${al} ${r0} 4.0 +fix 1 move wall/morse xlo -5.0 20.0 ${al} ${r0} 4.0 xhi 5.0 ${d0} ${al} ${r0} 4.0 +fix 1 move wall/morse xlo -5.0 20.0 2.0 ${r0} 4.0 xhi 5.0 ${d0} ${al} ${r0} 4.0 +fix 1 move wall/morse xlo -5.0 20.0 2.0 1.2 4.0 xhi 5.0 ${d0} ${al} ${r0} 4.0 +fix 1 move wall/morse xlo -5.0 20.0 2.0 1.2 4.0 xhi 5.0 20.0 ${al} ${r0} 4.0 +fix 1 move wall/morse xlo -5.0 20.0 2.0 1.2 4.0 xhi 5.0 20.0 2.0 ${r0} 4.0 +fix 1 move wall/morse xlo -5.0 20.0 2.0 1.2 4.0 xhi 5.0 20.0 2.0 1.2 4.0 +fix_modify 1 energy yes +run 5 post no +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7 + ghost atom cutoff = 7 + binsize = 3.5, bins = 3 3 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.429 | 4.429 | 4.429 Mbytes + Step Temp Press KinEng PotEng TotEng c_pe + 0 0 0 0 -30.02905654 -30.02905654 0 + 1 146.0893547 59.71823711 1.30639385 -31.40065042 -30.09425657 0 + 2 485.8091411 198.5884977 4.34431431 -34.55987817 -30.21556386 0 + 3 822.0828974 336.0500941 7.351418888 -37.63613582 -30.28471693 0 + 4 1018.806679 416.4666136 9.110607565 -39.39265114 -30.28204357 0 + 5 1050.331347 429.3532307 9.392514704 -39.63687095 -30.24435625 0 +Loop time of 7.6505e-05 on 1 procs for 5 steps with 4 atoms + + +variable name string lepton-morse +include wall.inc + +clear + using 1 OpenMP thread(s) per MPI task +read_restart walltest.restart +Reading restart file ... + restart file = 8 Feb 2023, LAMMPS = 8 Feb 2023 + restoring atom style bond from restart + orthogonal box = (-5 -5 -5) to (5 5 5) + 1 by 1 by 1 MPI processor grid + restoring pair style zero from restart + restoring bond style zero from restart + 4 atoms + 2 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 1 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_restart CPU = 0.000 seconds +# log ${name}.log + +compute ea move pe/atom +compute pe move reduce sum c_ea +special_bonds lj/coul 1.0 1.0 1.0 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 1 1 1 + special bond factors coul: 1 1 1 + 1 = max # of 1-2 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + +thermo_style custom step temp press ke pe etotal c_pe +thermo 1 +thermo_modify format float %14.10g + +fix 0 move nve +# dump 1 all custom 1 ${name}.dump id x fx +# dump_modify 1 format float %20.15g + +fix 1 move wall/lepton xlo -5.0 "d0*(-1.0 + (1.0 - ralpha) * (1.0 - ralpha));ralpha=exp(-alpha*(r-r0));d0=v_d0;alpha=v_al;r0=v_r0" 4.0 xhi 5.0 "d0*(-1.0 + (1.0 - ralpha) * (1.0 - ralpha));ralpha=exp(-alpha*(r-r0));d0=v_d0;alpha=v_al;r0=v_r0" 4.0 +fix_modify 1 energy yes +run 5 post no +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7 + ghost atom cutoff = 7 + binsize = 3.5, bins = 3 3 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.429 | 4.429 | 4.429 Mbytes + Step Temp Press KinEng PotEng TotEng c_pe + 0 0 0 0 -30.02905654 -30.02905654 0 + 1 146.0893547 59.71823711 1.30639385 -31.40065042 -30.09425657 0 + 2 485.8091411 198.5884977 4.34431431 -34.55987817 -30.21556386 0 + 3 822.0828974 336.0500941 7.351418888 -37.63613582 -30.28471693 0 + 4 1018.806679 416.4666136 9.110607565 -39.39265114 -30.28204357 0 + 5 1050.331347 429.3532307 9.392514704 -39.63687095 -30.24435625 0 +Loop time of 0.00266357 on 1 procs for 5 steps with 4 atoms + + +variable name string bond-morse +include wall.inc + +clear + using 1 OpenMP thread(s) per MPI task +read_restart walltest.restart +Reading restart file ... + restart file = 8 Feb 2023, LAMMPS = 8 Feb 2023 + restoring atom style bond from restart + orthogonal box = (-5 -5 -5) to (5 5 5) + 1 by 1 by 1 MPI processor grid + restoring pair style zero from restart + restoring bond style zero from restart + 4 atoms + 2 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 1 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_restart CPU = 0.000 seconds +# log ${name}.log + +compute ea move pe/atom +compute pe move reduce sum c_ea +special_bonds lj/coul 1.0 1.0 1.0 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 1 1 1 + special bond factors coul: 1 1 1 + 1 = max # of 1-2 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + +thermo_style custom step temp press ke pe etotal c_pe +thermo 1 +thermo_modify format float %14.10g + +fix 0 move nve +# dump 1 all custom 1 ${name}.dump id x fx +# dump_modify 1 format float %20.15g + +bond_style morse +bond_coeff 1 ${d0} ${al} ${r0} +bond_coeff 1 20.0 ${al} ${r0} +bond_coeff 1 20.0 2.0 ${r0} +bond_coeff 1 20.0 2.0 1.2 +run 5 post no +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7 + ghost atom cutoff = 7 + binsize = 3.5, bins = 3 3 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.429 | 4.429 | 4.429 Mbytes + Step Temp Press KinEng PotEng TotEng c_pe + 0 0 2683.187147 0 9.675661328 9.675661328 4.837830664 + 1 146.0893547 2514.939772 1.30639385 8.304067455 9.610461305 4.152033728 + 2 485.8091411 2063.804037 4.34431431 5.144839701 9.489154012 2.572419851 + 3 822.0828974 1456.368913 7.351418888 2.06858205 9.420000938 1.034291025 + 4 1018.806679 823.4383177 9.110607565 0.3120667313 9.422674297 0.1560333657 + 5 1050.331347 253.0262957 9.392514704 0.06784692056 9.460361624 0.03392346028 +Loop time of 0.000120428 on 1 procs for 5 steps with 4 atoms + + +variable name string pair-morse +include wall.inc + +clear + using 1 OpenMP thread(s) per MPI task +read_restart walltest.restart +Reading restart file ... + restart file = 8 Feb 2023, LAMMPS = 8 Feb 2023 + restoring atom style bond from restart + orthogonal box = (-5 -5 -5) to (5 5 5) + 1 by 1 by 1 MPI processor grid + restoring pair style zero from restart + restoring bond style zero from restart + 4 atoms + 2 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 1 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_restart CPU = 0.000 seconds +# log ${name}.log + +compute ea move pe/atom +compute pe move reduce sum c_ea +special_bonds lj/coul 1.0 1.0 1.0 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 1 1 1 + special bond factors coul: 1 1 1 + 1 = max # of 1-2 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + +thermo_style custom step temp press ke pe etotal c_pe +thermo 1 +thermo_modify format float %14.10g + +fix 0 move nve +# dump 1 all custom 1 ${name}.dump id x fx +# dump_modify 1 format float %20.15g + +pair_style morse 4.0 +pair_coeff 1 1 ${d0} ${al} ${r0} +pair_coeff 1 1 20.0 ${al} ${r0} +pair_coeff 1 1 20.0 2.0 ${r0} +pair_coeff 1 1 20.0 2.0 1.2 +pair_modify shift yes +run 5 post no +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6 + ghost atom cutoff = 6 + binsize = 3, bins = 4 4 4 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair morse, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.43 | 4.43 | 4.43 Mbytes + Step Temp Press KinEng PotEng TotEng c_pe + 0 0 2683.187147 0 -30.02905654 -30.02905654 -15.01452827 + 1 146.0893547 2514.939772 1.30639385 -31.40065042 -30.09425657 -15.70032521 + 2 485.8091411 2063.804037 4.34431431 -34.55987817 -30.21556386 -17.27993908 + 3 822.0828974 1456.368913 7.351418888 -37.63613582 -30.28471693 -18.81806791 + 4 1018.806679 823.4383177 9.110607565 -39.39265114 -30.28204357 -19.69632557 + 5 1050.331347 253.0262957 9.392514704 -39.63687095 -30.24435625 -19.81843547 +Loop time of 3.6356e-05 on 1 procs for 5 steps with 4 atoms + + +shell rm -f walltest.restart +Total wall time: 0:00:00 diff --git a/examples/wall/log.23Feb23.wall.lepton.g++.4 b/examples/wall/log.23Feb23.wall.lepton.g++.4 new file mode 100644 index 0000000000..7820f2a9ae --- /dev/null +++ b/examples/wall/log.23Feb23.wall.lepton.g++.4 @@ -0,0 +1,882 @@ +LAMMPS (8 Feb 2023) + using 1 OpenMP thread(s) per MPI task +units real +atom_style bond +boundary f p p +region box block -5.000000000000001 5.000000000000001 -5 5 -5 5 +create_box 1 box bond/types 1 extra/bond/per/atom 1 extra/special/per/atom 1 +Created orthogonal box = (-5 -5 -5) to (5 5 5) + 1 by 2 by 2 MPI processor grid + +pair_style zero 5.0 +pair_coeff * * +mass * 1.0 +bond_style zero +bond_coeff * 1.0 + +create_atoms 1 single -4.0 0.0 0.0 +Created 1 atoms + using lattice units in orthogonal box = (-5 -5 -5) to (5 5 5) + create_atoms CPU = 0.000 seconds +create_atoms 1 single 4.0 0.0 0.0 +Created 1 atoms + using lattice units in orthogonal box = (-5 -5 -5) to (5 5 5) + create_atoms CPU = 0.000 seconds +create_atoms 1 single -5.0 0.0 0.0 +Created 1 atoms + using lattice units in orthogonal box = (-5 -5 -5) to (5 5 5) + create_atoms CPU = 0.000 seconds +create_atoms 1 single 5.0 0.0 0.0 +Created 1 atoms + using lattice units in orthogonal box = (-5 -5 -5) to (5 5 5) + create_atoms CPU = 0.000 seconds +create_bonds single/bond 1 3 1 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 1 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds +create_bonds single/bond 1 4 2 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 1 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.001 seconds + +group move id 1:2 +2 atoms in group move +write_restart walltest.restart +System init for write_restart ... +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7 + ghost atom cutoff = 7 + binsize = 3.5, bins = 3 3 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard + +variable name string wall-harmonic +include wall.inc + +clear + using 1 OpenMP thread(s) per MPI task +read_restart walltest.restart +Reading restart file ... + restart file = 8 Feb 2023, LAMMPS = 8 Feb 2023 + restoring atom style bond from restart + orthogonal box = (-5 -5 -5) to (5 5 5) + 1 by 2 by 2 MPI processor grid + restoring pair style zero from restart + restoring bond style zero from restart + 4 atoms + 2 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 1 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_restart CPU = 0.001 seconds +# log ${name}.log + +compute ea move pe/atom +compute pe move reduce sum c_ea +special_bonds lj/coul 1.0 1.0 1.0 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 1 1 1 + special bond factors coul: 1 1 1 + 1 = max # of 1-2 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + +thermo_style custom step temp press ke pe etotal c_pe +thermo 1 +thermo_modify format float %14.10g + +fix 0 move nve +# dump 1 all custom 1 ${name}.dump id x fx +# dump_modify 1 format float %20.15g + +fix 1 move wall/harmonic xlo -5.0 100 0.0 4.0 xhi 5.0 100 1.0 4.0 +fix_modify 1 energy yes +run 5 post no +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7 + ghost atom cutoff = 7 + binsize = 3.5, bins = 3 3 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.32 | 4.379 | 4.559 Mbytes + Step Temp Press KinEng PotEng TotEng c_pe + 0 0 0 0 1800 1800 0 + 1 16146.37291 6600.295604 144.3878119 1652.527054 1796.914866 0 + 2 59294.04011 24238.149 530.232812 1258.437705 1788.670517 0 + 3 115302.7492 47133.32419 1031.086781 746.8819904 1777.968771 0 + 4 165817.4572 67782.66799 1482.811029 285.5057515 1768.31678 0 + 5 194283.6024 79419.02582 1737.367544 25.51012833 1762.877672 0 +Loop time of 0.000266179 on 4 procs for 5 steps with 4 atoms + + +variable name string lepton-harmonic +include wall.inc + +clear + using 1 OpenMP thread(s) per MPI task +read_restart walltest.restart +Reading restart file ... + restart file = 8 Feb 2023, LAMMPS = 8 Feb 2023 + restoring atom style bond from restart + orthogonal box = (-5 -5 -5) to (5 5 5) + 1 by 2 by 2 MPI processor grid + restoring pair style zero from restart + restoring bond style zero from restart + 4 atoms + 2 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 1 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_restart CPU = 0.001 seconds +# log ${name}.log + +compute ea move pe/atom +compute pe move reduce sum c_ea +special_bonds lj/coul 1.0 1.0 1.0 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 1 1 1 + special bond factors coul: 1 1 1 + 1 = max # of 1-2 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + +thermo_style custom step temp press ke pe etotal c_pe +thermo 1 +thermo_modify format float %14.10g + +fix 0 move nve +# dump 1 all custom 1 ${name}.dump id x fx +# dump_modify 1 format float %20.15g + +fix 1 move wall/lepton xlo -5.0 "k*(r-rc)^2;k=100.0" 4.0 xhi 5.0 "k*(r-rc)^2;k=100.0" 4.0 +fix_modify 1 energy yes +run 5 post no +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7 + ghost atom cutoff = 7 + binsize = 3.5, bins = 3 3 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.32 | 4.379 | 4.559 Mbytes + Step Temp Press KinEng PotEng TotEng c_pe + 0 0 0 0 1800 1800 0 + 1 16146.37291 6600.295604 144.3878119 1652.527054 1796.914866 0 + 2 59294.04011 24238.149 530.232812 1258.437705 1788.670517 0 + 3 115302.7492 47133.32419 1031.086781 746.8819904 1777.968771 0 + 4 165817.4572 67782.66799 1482.811029 285.5057515 1768.31678 0 + 5 194283.6024 79419.02582 1737.367544 25.51012833 1762.877672 0 +Loop time of 0.00230794 on 4 procs for 5 steps with 4 atoms + + +variable name string bond-harmonic +include wall.inc + +clear + using 1 OpenMP thread(s) per MPI task +read_restart walltest.restart +Reading restart file ... + restart file = 8 Feb 2023, LAMMPS = 8 Feb 2023 + restoring atom style bond from restart + orthogonal box = (-5 -5 -5) to (5 5 5) + 1 by 2 by 2 MPI processor grid + restoring pair style zero from restart + restoring bond style zero from restart + 4 atoms + 2 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 1 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_restart CPU = 0.001 seconds +# log ${name}.log + +compute ea move pe/atom +compute pe move reduce sum c_ea +special_bonds lj/coul 1.0 1.0 1.0 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 1 1 1 + special bond factors coul: 1 1 1 + 1 = max # of 1-2 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + +thermo_style custom step temp press ke pe etotal c_pe +thermo 1 +thermo_modify format float %14.10g + +fix 0 move nve +# dump 1 all custom 1 ${name}.dump id x fx +# dump_modify 1 format float %20.15g + +bond_style harmonic +bond_coeff 1 100 4.0 +run 5 post no +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7 + ghost atom cutoff = 7 + binsize = 3.5, bins = 3 3 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +WARNING: Communication cutoff 7 is shorter than a bond length based estimate of 8. This may lead to errors. (src/comm.cpp:723) +Per MPI rank memory allocation (min/avg/max) = 4.32 | 4.379 | 4.559 Mbytes + Step Temp Press KinEng PotEng TotEng c_pe + 0 0 27427.366 0 1800 1800 900 + 1 16146.37291 36178.74173 144.3878119 1652.527054 1796.914866 826.263527 + 2 59294.04011 58444.6962 530.232812 1258.437705 1788.670517 629.2188524 + 3 115302.7492 83661.44348 1031.086781 746.8819904 1777.968771 373.4409952 + 4 165817.4572 98424.89283 1482.811029 285.5057515 1768.31678 142.7528758 + 5 194283.6024 91313.53086 1737.367544 25.51012833 1762.877672 12.75506417 +Loop time of 0.000358068 on 4 procs for 5 steps with 4 atoms + + +variable name string pair-harmonic +include wall.inc + +clear + using 1 OpenMP thread(s) per MPI task +read_restart walltest.restart +Reading restart file ... + restart file = 8 Feb 2023, LAMMPS = 8 Feb 2023 + restoring atom style bond from restart + orthogonal box = (-5 -5 -5) to (5 5 5) + 1 by 2 by 2 MPI processor grid + restoring pair style zero from restart + restoring bond style zero from restart + 4 atoms + 2 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 1 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_restart CPU = 0.001 seconds +# log ${name}.log + +compute ea move pe/atom +compute pe move reduce sum c_ea +special_bonds lj/coul 1.0 1.0 1.0 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 1 1 1 + special bond factors coul: 1 1 1 + 1 = max # of 1-2 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + +thermo_style custom step temp press ke pe etotal c_pe +thermo 1 +thermo_modify format float %14.10g + +fix 0 move nve +# dump 1 all custom 1 ${name}.dump id x fx +# dump_modify 1 format float %20.15g + +pair_style harmonic/cut +pair_coeff 1 1 100 4.0 +run 5 post no +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6 + ghost atom cutoff = 6 + binsize = 3, bins = 4 4 4 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair harmonic/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.32 | 4.38 | 4.56 Mbytes + Step Temp Press KinEng PotEng TotEng c_pe + 0 0 27427.366 0 1800 1800 900 + 1 16146.37291 36178.74173 144.3878119 1652.527054 1796.914866 826.263527 + 2 59294.04011 58444.6962 530.232812 1258.437705 1788.670517 629.2188524 + 3 115302.7492 83661.44348 1031.086781 746.8819904 1777.968771 373.4409952 + 4 165817.4572 98424.89283 1482.811029 285.5057515 1768.31678 142.7528758 + 5 170540.4005 97560.47089 1525.045619 190.8165235 1715.862142 178.0614593 +Loop time of 0.000341881 on 4 procs for 5 steps with 4 atoms + + +variable eps index 0.02 +variable sig index 2.0 +variable name string wall-lj126 +include wall.inc + +clear + using 1 OpenMP thread(s) per MPI task +read_restart walltest.restart +Reading restart file ... + restart file = 8 Feb 2023, LAMMPS = 8 Feb 2023 + restoring atom style bond from restart + orthogonal box = (-5 -5 -5) to (5 5 5) + 1 by 2 by 2 MPI processor grid + restoring pair style zero from restart + restoring bond style zero from restart + 4 atoms + 2 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 1 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_restart CPU = 0.001 seconds +# log ${name}.log + +compute ea move pe/atom +compute pe move reduce sum c_ea +special_bonds lj/coul 1.0 1.0 1.0 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 1 1 1 + special bond factors coul: 1 1 1 + 1 = max # of 1-2 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + +thermo_style custom step temp press ke pe etotal c_pe +thermo 1 +thermo_modify format float %14.10g + +fix 0 move nve +# dump 1 all custom 1 ${name}.dump id x fx +# dump_modify 1 format float %20.15g + +fix 1 move wall/lj126 xlo -5.0 ${eps} ${sig} 4.0 xhi 5.0 ${eps} ${sig} 4.0 +fix 1 move wall/lj126 xlo -5.0 0.02 ${sig} 4.0 xhi 5.0 ${eps} ${sig} 4.0 +fix 1 move wall/lj126 xlo -5.0 0.02 2.0 4.0 xhi 5.0 ${eps} ${sig} 4.0 +fix 1 move wall/lj126 xlo -5.0 0.02 2.0 4.0 xhi 5.0 0.02 ${sig} 4.0 +fix 1 move wall/lj126 xlo -5.0 0.02 2.0 4.0 xhi 5.0 0.02 2.0 4.0 +fix_modify 1 energy yes +run 5 post no +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7 + ghost atom cutoff = 7 + binsize = 3.5, bins = 3 3 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.32 | 4.379 | 4.559 Mbytes + Step Temp Press KinEng PotEng TotEng c_pe + 0 0 0 0 645.1224609 645.1224609 0 + 1 178153.8707 72825.53278 1593.128544 0.2259591031 1593.354503 0 + 2 178262.3593 72869.88065 1594.098696 -0.02237405364 1594.076322 0 + 3 178259.9436 72868.89314 1594.077094 -0.003385746252 1594.073708 0 + 4 178259.4975 72868.71081 1594.073105 0 1594.073105 0 + 5 178259.4975 72868.71081 1594.073105 0 1594.073105 0 +WARNING: Bond/angle/dihedral extent > half of periodic box length (src/domain.cpp:936) +Loop time of 0.000345376 on 4 procs for 5 steps with 4 atoms + + +variable name string lepton-lj126 +include wall.inc + +clear + using 1 OpenMP thread(s) per MPI task +read_restart walltest.restart +Reading restart file ... + restart file = 8 Feb 2023, LAMMPS = 8 Feb 2023 + restoring atom style bond from restart + orthogonal box = (-5 -5 -5) to (5 5 5) + 1 by 2 by 2 MPI processor grid + restoring pair style zero from restart + restoring bond style zero from restart + 4 atoms + 2 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 1 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_restart CPU = 0.001 seconds +# log ${name}.log + +compute ea move pe/atom +compute pe move reduce sum c_ea +special_bonds lj/coul 1.0 1.0 1.0 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 1 1 1 + special bond factors coul: 1 1 1 + 1 = max # of 1-2 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + +thermo_style custom step temp press ke pe etotal c_pe +thermo 1 +thermo_modify format float %14.10g + +fix 0 move nve +# dump 1 all custom 1 ${name}.dump id x fx +# dump_modify 1 format float %20.15g + +fix 1 move wall/lepton xlo -5.0 "4.0*epsilon*((sigma/r)^12 - (sigma/r)^6);epsilon=v_eps;sigma=v_sig" 4.0 xhi 5.0 "4.0*epsilon*((sigma/r)^12 - (sigma/r)^6);epsilon=v_eps;sigma=v_sig" 4.0 +fix_modify 1 energy yes +run 5 post no +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7 + ghost atom cutoff = 7 + binsize = 3.5, bins = 3 3 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.32 | 4.379 | 4.559 Mbytes + Step Temp Press KinEng PotEng TotEng c_pe + 0 0 0 0 645.1224609 645.1224609 0 + 1 178153.8707 72825.53278 1593.128544 0.2259591031 1593.354503 0 + 2 178262.3593 72869.88065 1594.098696 -0.02237405364 1594.076322 0 + 3 178259.9436 72868.89314 1594.077094 -0.003385746252 1594.073708 0 + 4 178259.4975 72868.71081 1594.073105 0 1594.073105 0 + 5 178259.4975 72868.71081 1594.073105 0 1594.073105 0 +WARNING: Bond/angle/dihedral extent > half of periodic box length (src/domain.cpp:936) +Loop time of 0.00332789 on 4 procs for 5 steps with 4 atoms + + +variable name string pair-lj126 +include wall.inc + +clear + using 1 OpenMP thread(s) per MPI task +read_restart walltest.restart +Reading restart file ... + restart file = 8 Feb 2023, LAMMPS = 8 Feb 2023 + restoring atom style bond from restart + orthogonal box = (-5 -5 -5) to (5 5 5) + 1 by 2 by 2 MPI processor grid + restoring pair style zero from restart + restoring bond style zero from restart + 4 atoms + 2 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 1 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_restart CPU = 0.001 seconds +# log ${name}.log + +compute ea move pe/atom +compute pe move reduce sum c_ea +special_bonds lj/coul 1.0 1.0 1.0 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 1 1 1 + special bond factors coul: 1 1 1 + 1 = max # of 1-2 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + +thermo_style custom step temp press ke pe etotal c_pe +thermo 1 +thermo_modify format float %14.10g + +fix 0 move nve +# dump 1 all custom 1 ${name}.dump id x fx +# dump_modify 1 format float %20.15g + +pair_style lj/cut 4.0 +pair_coeff 1 1 ${eps} ${sig} +pair_coeff 1 1 0.02 ${sig} +pair_coeff 1 1 0.02 2.0 +pair_modify shift yes +run 5 post no +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6 + ghost atom cutoff = 6 + binsize = 3, bins = 4 4 4 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.32 | 4.38 | 4.56 Mbytes + Step Temp Press KinEng PotEng TotEng c_pe + 0 0 178343.7047 0 645.1224609 645.1224609 322.5612305 + 1 178153.8707 72925.96146 1593.128544 0.2259591031 1593.354503 0.1129795516 + 2 178262.3593 72867.28485 1594.098696 -0.02237405364 1594.076322 -0.01118702682 + 3 178260.8147 72867.80305 1594.084884 -0.007499601847 1594.077384 -0.005806728722 + 4 176007.6835 72778.53677 1573.936415 2.772305717 1576.708721 2.772305717 + 5 1.132219912e+27 4.628275436e+26 1.012479748e+25 3.761972158e+12 1.012479748e+25 3.761972158e+12 +WARNING: Bond/angle/dihedral extent > half of periodic box length (src/domain.cpp:936) +Loop time of 0.000404238 on 4 procs for 5 steps with 4 atoms + + +variable d0 index 20.0 +variable al index 2.0 +variable r0 index 1.2 + +variable name string wall-morse +include wall.inc + +clear + using 1 OpenMP thread(s) per MPI task +read_restart walltest.restart +Reading restart file ... + restart file = 8 Feb 2023, LAMMPS = 8 Feb 2023 + restoring atom style bond from restart + orthogonal box = (-5 -5 -5) to (5 5 5) + 1 by 2 by 2 MPI processor grid + restoring pair style zero from restart + restoring bond style zero from restart + 4 atoms + 2 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 1 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_restart CPU = 0.001 seconds +# log ${name}.log + +compute ea move pe/atom +compute pe move reduce sum c_ea +special_bonds lj/coul 1.0 1.0 1.0 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 1 1 1 + special bond factors coul: 1 1 1 + 1 = max # of 1-2 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + +thermo_style custom step temp press ke pe etotal c_pe +thermo 1 +thermo_modify format float %14.10g + +fix 0 move nve +# dump 1 all custom 1 ${name}.dump id x fx +# dump_modify 1 format float %20.15g + +fix 1 move wall/morse xlo -5.0 ${d0} ${al} ${r0} 4.0 xhi 5.0 ${d0} ${al} ${r0} 4.0 +fix 1 move wall/morse xlo -5.0 20.0 ${al} ${r0} 4.0 xhi 5.0 ${d0} ${al} ${r0} 4.0 +fix 1 move wall/morse xlo -5.0 20.0 2.0 ${r0} 4.0 xhi 5.0 ${d0} ${al} ${r0} 4.0 +fix 1 move wall/morse xlo -5.0 20.0 2.0 1.2 4.0 xhi 5.0 ${d0} ${al} ${r0} 4.0 +fix 1 move wall/morse xlo -5.0 20.0 2.0 1.2 4.0 xhi 5.0 20.0 ${al} ${r0} 4.0 +fix 1 move wall/morse xlo -5.0 20.0 2.0 1.2 4.0 xhi 5.0 20.0 2.0 ${r0} 4.0 +fix 1 move wall/morse xlo -5.0 20.0 2.0 1.2 4.0 xhi 5.0 20.0 2.0 1.2 4.0 +fix_modify 1 energy yes +run 5 post no +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7 + ghost atom cutoff = 7 + binsize = 3.5, bins = 3 3 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.32 | 4.379 | 4.559 Mbytes + Step Temp Press KinEng PotEng TotEng c_pe + 0 0 0 0 -30.02905654 -30.02905654 0 + 1 146.0893547 59.71823711 1.30639385 -31.40065042 -30.09425657 0 + 2 485.8091411 198.5884977 4.34431431 -34.55987817 -30.21556386 0 + 3 822.0828974 336.0500941 7.351418888 -37.63613582 -30.28471693 0 + 4 1018.806679 416.4666136 9.110607565 -39.39265114 -30.28204357 0 + 5 1050.331347 429.3532307 9.392514704 -39.63687095 -30.24435625 0 +Loop time of 0.000748817 on 4 procs for 5 steps with 4 atoms + + +variable name string lepton-morse +include wall.inc + +clear + using 1 OpenMP thread(s) per MPI task +read_restart walltest.restart +Reading restart file ... + restart file = 8 Feb 2023, LAMMPS = 8 Feb 2023 + restoring atom style bond from restart + orthogonal box = (-5 -5 -5) to (5 5 5) + 1 by 2 by 2 MPI processor grid + restoring pair style zero from restart + restoring bond style zero from restart + 4 atoms + 2 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 1 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_restart CPU = 0.001 seconds +# log ${name}.log + +compute ea move pe/atom +compute pe move reduce sum c_ea +special_bonds lj/coul 1.0 1.0 1.0 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 1 1 1 + special bond factors coul: 1 1 1 + 1 = max # of 1-2 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + +thermo_style custom step temp press ke pe etotal c_pe +thermo 1 +thermo_modify format float %14.10g + +fix 0 move nve +# dump 1 all custom 1 ${name}.dump id x fx +# dump_modify 1 format float %20.15g + +fix 1 move wall/lepton xlo -5.0 "d0*(-1.0 + (1.0 - ralpha) * (1.0 - ralpha));ralpha=exp(-alpha*(r-r0));d0=v_d0;alpha=v_al;r0=v_r0" 4.0 xhi 5.0 "d0*(-1.0 + (1.0 - ralpha) * (1.0 - ralpha));ralpha=exp(-alpha*(r-r0));d0=v_d0;alpha=v_al;r0=v_r0" 4.0 +fix_modify 1 energy yes +run 5 post no +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7 + ghost atom cutoff = 7 + binsize = 3.5, bins = 3 3 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.32 | 4.379 | 4.559 Mbytes + Step Temp Press KinEng PotEng TotEng c_pe + 0 0 0 0 -30.02905654 -30.02905654 0 + 1 146.0893547 59.71823711 1.30639385 -31.40065042 -30.09425657 0 + 2 485.8091411 198.5884977 4.34431431 -34.55987817 -30.21556386 0 + 3 822.0828974 336.0500941 7.351418888 -37.63613582 -30.28471693 0 + 4 1018.806679 416.4666136 9.110607565 -39.39265114 -30.28204357 0 + 5 1050.331347 429.3532307 9.392514704 -39.63687095 -30.24435625 0 +Loop time of 0.00347272 on 4 procs for 5 steps with 4 atoms + + +variable name string bond-morse +include wall.inc + +clear + using 1 OpenMP thread(s) per MPI task +read_restart walltest.restart +Reading restart file ... + restart file = 8 Feb 2023, LAMMPS = 8 Feb 2023 + restoring atom style bond from restart + orthogonal box = (-5 -5 -5) to (5 5 5) + 1 by 2 by 2 MPI processor grid + restoring pair style zero from restart + restoring bond style zero from restart + 4 atoms + 2 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 1 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.001 seconds + read_restart CPU = 0.001 seconds +# log ${name}.log + +compute ea move pe/atom +compute pe move reduce sum c_ea +special_bonds lj/coul 1.0 1.0 1.0 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 1 1 1 + special bond factors coul: 1 1 1 + 1 = max # of 1-2 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + +thermo_style custom step temp press ke pe etotal c_pe +thermo 1 +thermo_modify format float %14.10g + +fix 0 move nve +# dump 1 all custom 1 ${name}.dump id x fx +# dump_modify 1 format float %20.15g + +bond_style morse +bond_coeff 1 ${d0} ${al} ${r0} +bond_coeff 1 20.0 ${al} ${r0} +bond_coeff 1 20.0 2.0 ${r0} +bond_coeff 1 20.0 2.0 1.2 +run 5 post no +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7 + ghost atom cutoff = 7 + binsize = 3.5, bins = 3 3 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.32 | 4.379 | 4.559 Mbytes + Step Temp Press KinEng PotEng TotEng c_pe + 0 0 2683.187147 0 9.675661328 9.675661328 4.837830664 + 1 146.0893547 2514.939772 1.30639385 8.304067455 9.610461305 4.152033728 + 2 485.8091411 2063.804037 4.34431431 5.144839701 9.489154012 2.572419851 + 3 822.0828974 1456.368913 7.351418888 2.06858205 9.420000938 1.034291025 + 4 1018.806679 823.4383177 9.110607565 0.3120667313 9.422674297 0.1560333657 + 5 1050.331347 253.0262957 9.392514704 0.06784692056 9.460361624 0.03392346028 +Loop time of 0.000859458 on 4 procs for 5 steps with 4 atoms + + +variable name string pair-morse +include wall.inc + +clear + using 1 OpenMP thread(s) per MPI task +read_restart walltest.restart +Reading restart file ... + restart file = 8 Feb 2023, LAMMPS = 8 Feb 2023 + restoring atom style bond from restart + orthogonal box = (-5 -5 -5) to (5 5 5) + 1 by 2 by 2 MPI processor grid + restoring pair style zero from restart + restoring bond style zero from restart + 4 atoms + 2 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 1 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_restart CPU = 0.001 seconds +# log ${name}.log + +compute ea move pe/atom +compute pe move reduce sum c_ea +special_bonds lj/coul 1.0 1.0 1.0 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 1 1 1 + special bond factors coul: 1 1 1 + 1 = max # of 1-2 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + +thermo_style custom step temp press ke pe etotal c_pe +thermo 1 +thermo_modify format float %14.10g + +fix 0 move nve +# dump 1 all custom 1 ${name}.dump id x fx +# dump_modify 1 format float %20.15g + +pair_style morse 4.0 +pair_coeff 1 1 ${d0} ${al} ${r0} +pair_coeff 1 1 20.0 ${al} ${r0} +pair_coeff 1 1 20.0 2.0 ${r0} +pair_coeff 1 1 20.0 2.0 1.2 +pair_modify shift yes +run 5 post no +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6 + ghost atom cutoff = 6 + binsize = 3, bins = 4 4 4 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair morse, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.32 | 4.38 | 4.56 Mbytes + Step Temp Press KinEng PotEng TotEng c_pe + 0 0 2683.187147 0 -30.02905654 -30.02905654 -15.01452827 + 1 146.0893547 2514.939772 1.30639385 -31.40065042 -30.09425657 -15.70032521 + 2 485.8091411 2063.804037 4.34431431 -34.55987817 -30.21556386 -17.27993908 + 3 822.0828974 1456.368913 7.351418888 -37.63613582 -30.28471693 -18.81806791 + 4 1018.806679 823.4383177 9.110607565 -39.39265114 -30.28204357 -19.69632557 + 5 1050.331347 253.0262957 9.392514704 -39.63687095 -30.24435625 -19.81843547 +Loop time of 0.00029769 on 4 procs for 5 steps with 4 atoms + + +shell rm -f walltest.restart +Total wall time: 0:00:00 diff --git a/examples/wall/log.23Feb23.wall.table.g++.1 b/examples/wall/log.23Feb23.wall.table.g++.1 new file mode 100644 index 0000000000..f734be7403 --- /dev/null +++ b/examples/wall/log.23Feb23.wall.table.g++.1 @@ -0,0 +1,1116 @@ +LAMMPS (8 Feb 2023) + using 1 OpenMP thread(s) per MPI task +units real +atom_style bond +boundary f p p +region box block -5.000000000000001 5.000000000000001 -5 5 -5 5 +create_box 1 box bond/types 1 extra/bond/per/atom 1 extra/special/per/atom 1 +Created orthogonal box = (-5 -5 -5) to (5 5 5) + 1 by 1 by 1 MPI processor grid + +pair_style zero 5.0 +pair_coeff * * +mass * 1.0 +bond_style zero +bond_coeff * 1.0 + +create_atoms 1 single -4.0 0.0 0.0 +Created 1 atoms + using lattice units in orthogonal box = (-5 -5 -5) to (5 5 5) + create_atoms CPU = 0.000 seconds +create_atoms 1 single 4.0 0.0 0.0 +Created 1 atoms + using lattice units in orthogonal box = (-5 -5 -5) to (5 5 5) + create_atoms CPU = 0.001 seconds +create_atoms 1 single -5.0 0.0 0.0 +Created 1 atoms + using lattice units in orthogonal box = (-5 -5 -5) to (5 5 5) + create_atoms CPU = 0.000 seconds +create_atoms 1 single 5.0 0.0 0.0 +Created 1 atoms + using lattice units in orthogonal box = (-5 -5 -5) to (5 5 5) + create_atoms CPU = 0.000 seconds +create_bonds single/bond 1 3 1 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 1 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds +create_bonds single/bond 1 4 2 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 1 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + +group move id 1:2 +2 atoms in group move +write_restart walltest.restart +System init for write_restart ... +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7 + ghost atom cutoff = 7 + binsize = 3.5, bins = 3 3 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard + +variable name string wall-harmonic +include wall.inc + +clear + using 1 OpenMP thread(s) per MPI task +read_restart walltest.restart +Reading restart file ... + restart file = 8 Feb 2023, LAMMPS = 8 Feb 2023 + restoring atom style bond from restart + orthogonal box = (-5 -5 -5) to (5 5 5) + 1 by 1 by 1 MPI processor grid + restoring pair style zero from restart + restoring bond style zero from restart + 4 atoms + 2 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 1 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_restart CPU = 0.001 seconds +# log ${name}.log + +compute ea move pe/atom +compute pe move reduce sum c_ea +special_bonds lj/coul 1.0 1.0 1.0 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 1 1 1 + special bond factors coul: 1 1 1 + 1 = max # of 1-2 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + +thermo_style custom step temp press ke pe etotal c_pe +thermo 1 +thermo_modify format float %14.10g + +fix 0 move nve +# dump 1 all custom 1 ${name}.dump id x fx +# dump_modify 1 format float %20.15g + +fix 1 move wall/harmonic xlo -5.0 100 0.0 4.0 xhi 5.0 100 1.0 4.0 +fix_modify 1 energy yes +run 5 post no +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7 + ghost atom cutoff = 7 + binsize = 3.5, bins = 3 3 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.429 | 4.429 | 4.429 Mbytes + Step Temp Press KinEng PotEng TotEng c_pe + 0 0 0 0 1800 1800 0 + 1 16146.37291 6600.295604 144.3878119 1652.527054 1796.914866 0 + 2 59294.04011 24238.149 530.232812 1258.437705 1788.670517 0 + 3 115302.7492 47133.32419 1031.086781 746.8819904 1777.968771 0 + 4 165817.4572 67782.66799 1482.811029 285.5057515 1768.31678 0 + 5 194283.6024 79419.02582 1737.367544 25.51012833 1762.877672 0 +Loop time of 4.6507e-05 on 1 procs for 5 steps with 4 atoms + + +variable name string table-harmonic +include wall.inc + +clear + using 1 OpenMP thread(s) per MPI task +read_restart walltest.restart +Reading restart file ... + restart file = 8 Feb 2023, LAMMPS = 8 Feb 2023 + restoring atom style bond from restart + orthogonal box = (-5 -5 -5) to (5 5 5) + 1 by 1 by 1 MPI processor grid + restoring pair style zero from restart + restoring bond style zero from restart + 4 atoms + 2 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 1 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_restart CPU = 0.000 seconds +# log ${name}.log + +compute ea move pe/atom +compute pe move reduce sum c_ea +special_bonds lj/coul 1.0 1.0 1.0 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 1 1 1 + special bond factors coul: 1 1 1 + 1 = max # of 1-2 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + +thermo_style custom step temp press ke pe etotal c_pe +thermo 1 +thermo_modify format float %14.10g + +fix 0 move nve +# dump 1 all custom 1 ${name}.dump id x fx +# dump_modify 1 format float %20.15g + +fix 1 move wall/table linear 1000 xlo -5.0 walltab.dat HARMONIC 4.0 xhi 5.0 walltab.dat HARMONIC 4.0 +Reading fix wall/table table potential file walltab.dat with DATE: 2023-02-23 +Reading fix wall/table table potential file walltab.dat with DATE: 2023-02-23 +fix_modify 1 energy yes +run 5 post no +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7 + ghost atom cutoff = 7 + binsize = 3.5, bins = 3 3 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.429 | 4.429 | 4.429 Mbytes + Step Temp Press KinEng PotEng TotEng c_pe + 0 0 0 0 1800.000356 1800.000356 0 + 1 16146.37291 6600.295604 144.3878119 1652.527723 1796.915535 0 + 2 59294.04011 24238.149 530.232812 1258.437853 1788.670665 0 + 3 115302.7492 47133.32419 1031.086781 746.8824148 1777.969196 0 + 4 165817.4572 67782.66799 1482.811029 285.5061521 1768.317181 0 + 5 194283.6024 79419.02582 1737.367544 25.51090543 1762.878449 0 +Loop time of 5.7549e-05 on 1 procs for 5 steps with 4 atoms + + +variable name string spline-harmonic +include wall.inc + +clear + using 1 OpenMP thread(s) per MPI task +read_restart walltest.restart +Reading restart file ... + restart file = 8 Feb 2023, LAMMPS = 8 Feb 2023 + restoring atom style bond from restart + orthogonal box = (-5 -5 -5) to (5 5 5) + 1 by 1 by 1 MPI processor grid + restoring pair style zero from restart + restoring bond style zero from restart + 4 atoms + 2 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 1 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_restart CPU = 0.000 seconds +# log ${name}.log + +compute ea move pe/atom +compute pe move reduce sum c_ea +special_bonds lj/coul 1.0 1.0 1.0 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 1 1 1 + special bond factors coul: 1 1 1 + 1 = max # of 1-2 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + +thermo_style custom step temp press ke pe etotal c_pe +thermo 1 +thermo_modify format float %14.10g + +fix 0 move nve +# dump 1 all custom 1 ${name}.dump id x fx +# dump_modify 1 format float %20.15g + +fix 1 move wall/table spline 200 xlo -5.0 walltab.dat HARMONIC 4.0 xhi 5.0 walltab.dat HARMONIC 4.0 +Reading fix wall/table table potential file walltab.dat with DATE: 2023-02-23 +Reading fix wall/table table potential file walltab.dat with DATE: 2023-02-23 +fix_modify 1 energy yes +run 5 post no +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7 + ghost atom cutoff = 7 + binsize = 3.5, bins = 3 3 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.429 | 4.429 | 4.429 Mbytes + Step Temp Press KinEng PotEng TotEng c_pe + 0 0 0 0 1800 1800 0 + 1 16146.37291 6600.295604 144.3878119 1652.527054 1796.914866 0 + 2 59294.04011 24238.149 530.232812 1258.437705 1788.670517 0 + 3 115302.7492 47133.32419 1031.086781 746.8819904 1777.968771 0 + 4 165817.4572 67782.66799 1482.811029 285.5057515 1768.31678 0 + 5 194283.6024 79419.02582 1737.367544 25.51012833 1762.877672 0 +Loop time of 7.285e-05 on 1 procs for 5 steps with 4 atoms + + +variable name string bond-harmonic +include wall.inc + +clear + using 1 OpenMP thread(s) per MPI task +read_restart walltest.restart +Reading restart file ... + restart file = 8 Feb 2023, LAMMPS = 8 Feb 2023 + restoring atom style bond from restart + orthogonal box = (-5 -5 -5) to (5 5 5) + 1 by 1 by 1 MPI processor grid + restoring pair style zero from restart + restoring bond style zero from restart + 4 atoms + 2 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 1 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_restart CPU = 0.000 seconds +# log ${name}.log + +compute ea move pe/atom +compute pe move reduce sum c_ea +special_bonds lj/coul 1.0 1.0 1.0 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 1 1 1 + special bond factors coul: 1 1 1 + 1 = max # of 1-2 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + +thermo_style custom step temp press ke pe etotal c_pe +thermo 1 +thermo_modify format float %14.10g + +fix 0 move nve +# dump 1 all custom 1 ${name}.dump id x fx +# dump_modify 1 format float %20.15g + +bond_style harmonic +bond_coeff 1 100 4.0 +run 5 post no +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7 + ghost atom cutoff = 7 + binsize = 3.5, bins = 3 3 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +WARNING: Communication cutoff 7 is shorter than a bond length based estimate of 8. This may lead to errors. (src/comm.cpp:723) +Per MPI rank memory allocation (min/avg/max) = 4.429 | 4.429 | 4.429 Mbytes + Step Temp Press KinEng PotEng TotEng c_pe + 0 0 27427.366 0 1800 1800 900 + 1 16146.37291 36178.74173 144.3878119 1652.527054 1796.914866 826.263527 + 2 59294.04011 58444.6962 530.232812 1258.437705 1788.670517 629.2188524 + 3 115302.7492 83661.44348 1031.086781 746.8819904 1777.968771 373.4409952 + 4 165817.4572 98424.89283 1482.811029 285.5057515 1768.31678 142.7528758 + 5 194283.6024 91313.53086 1737.367544 25.51012833 1762.877672 12.75506417 +Loop time of 4.5844e-05 on 1 procs for 5 steps with 4 atoms + + +variable name string pair-harmonic +include wall.inc + +clear + using 1 OpenMP thread(s) per MPI task +read_restart walltest.restart +Reading restart file ... + restart file = 8 Feb 2023, LAMMPS = 8 Feb 2023 + restoring atom style bond from restart + orthogonal box = (-5 -5 -5) to (5 5 5) + 1 by 1 by 1 MPI processor grid + restoring pair style zero from restart + restoring bond style zero from restart + 4 atoms + 2 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 1 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_restart CPU = 0.000 seconds +# log ${name}.log + +compute ea move pe/atom +compute pe move reduce sum c_ea +special_bonds lj/coul 1.0 1.0 1.0 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 1 1 1 + special bond factors coul: 1 1 1 + 1 = max # of 1-2 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + +thermo_style custom step temp press ke pe etotal c_pe +thermo 1 +thermo_modify format float %14.10g + +fix 0 move nve +# dump 1 all custom 1 ${name}.dump id x fx +# dump_modify 1 format float %20.15g + +pair_style harmonic/cut +pair_coeff 1 1 100 4.0 +run 5 post no +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6 + ghost atom cutoff = 6 + binsize = 3, bins = 4 4 4 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair harmonic/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.43 | 4.43 | 4.43 Mbytes + Step Temp Press KinEng PotEng TotEng c_pe + 0 0 27427.366 0 1800 1800 900 + 1 16146.37291 36178.74173 144.3878119 1652.527054 1796.914866 826.263527 + 2 59294.04011 58444.6962 530.232812 1258.437705 1788.670517 629.2188524 + 3 115302.7492 83661.44348 1031.086781 746.8819904 1777.968771 373.4409952 + 4 165817.4572 98424.89283 1482.811029 285.5057515 1768.31678 142.7528758 + 5 170540.4005 97560.47089 1525.045619 190.8165235 1715.862142 178.0614593 +Loop time of 4.6409e-05 on 1 procs for 5 steps with 4 atoms + + +variable eps index 0.02 +variable sig index 2.0 +variable name string wall-lj126 +include wall.inc + +clear + using 1 OpenMP thread(s) per MPI task +read_restart walltest.restart +Reading restart file ... + restart file = 8 Feb 2023, LAMMPS = 8 Feb 2023 + restoring atom style bond from restart + orthogonal box = (-5 -5 -5) to (5 5 5) + 1 by 1 by 1 MPI processor grid + restoring pair style zero from restart + restoring bond style zero from restart + 4 atoms + 2 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 1 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_restart CPU = 0.000 seconds +# log ${name}.log + +compute ea move pe/atom +compute pe move reduce sum c_ea +special_bonds lj/coul 1.0 1.0 1.0 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 1 1 1 + special bond factors coul: 1 1 1 + 1 = max # of 1-2 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + +thermo_style custom step temp press ke pe etotal c_pe +thermo 1 +thermo_modify format float %14.10g + +fix 0 move nve +# dump 1 all custom 1 ${name}.dump id x fx +# dump_modify 1 format float %20.15g + +fix 1 move wall/lj126 xlo -5.0 ${eps} ${sig} 4.0 xhi 5.0 ${eps} ${sig} 4.0 +fix 1 move wall/lj126 xlo -5.0 0.02 ${sig} 4.0 xhi 5.0 ${eps} ${sig} 4.0 +fix 1 move wall/lj126 xlo -5.0 0.02 2.0 4.0 xhi 5.0 ${eps} ${sig} 4.0 +fix 1 move wall/lj126 xlo -5.0 0.02 2.0 4.0 xhi 5.0 0.02 ${sig} 4.0 +fix 1 move wall/lj126 xlo -5.0 0.02 2.0 4.0 xhi 5.0 0.02 2.0 4.0 +fix_modify 1 energy yes +run 5 post no +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7 + ghost atom cutoff = 7 + binsize = 3.5, bins = 3 3 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.429 | 4.429 | 4.429 Mbytes + Step Temp Press KinEng PotEng TotEng c_pe + 0 0 0 0 645.1224609 645.1224609 0 + 1 178153.8707 72825.53278 1593.128544 0.2259591031 1593.354503 0 + 2 178262.3593 72869.88065 1594.098696 -0.02237405364 1594.076322 0 + 3 178259.9436 72868.89314 1594.077094 -0.003385746252 1594.073708 0 + 4 178259.4975 72868.71081 1594.073105 0 1594.073105 0 + 5 178259.4975 72868.71081 1594.073105 0 1594.073105 0 +WARNING: Bond/angle/dihedral extent > half of periodic box length (src/domain.cpp:936) +Loop time of 4.3816e-05 on 1 procs for 5 steps with 4 atoms + + +variable name string table-lj126 +include wall.inc + +clear + using 1 OpenMP thread(s) per MPI task +read_restart walltest.restart +Reading restart file ... + restart file = 8 Feb 2023, LAMMPS = 8 Feb 2023 + restoring atom style bond from restart + orthogonal box = (-5 -5 -5) to (5 5 5) + 1 by 1 by 1 MPI processor grid + restoring pair style zero from restart + restoring bond style zero from restart + 4 atoms + 2 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 1 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_restart CPU = 0.000 seconds +# log ${name}.log + +compute ea move pe/atom +compute pe move reduce sum c_ea +special_bonds lj/coul 1.0 1.0 1.0 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 1 1 1 + special bond factors coul: 1 1 1 + 1 = max # of 1-2 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + +thermo_style custom step temp press ke pe etotal c_pe +thermo 1 +thermo_modify format float %14.10g + +fix 0 move nve +# dump 1 all custom 1 ${name}.dump id x fx +# dump_modify 1 format float %20.15g + +fix 1 move wall/table linear 1000 xlo -5.0 walltab.dat LJ126 4.0 xhi 5.0 walltab.dat LJ126 4.0 +Reading fix wall/table table potential file walltab.dat with DATE: 2023-02-23 +WARNING: 1 of 400 force values in table are inconsistent with -dE/dr. +WARNING: Should only be flagged at inflection points (src/fix_wall_table.cpp:244) +Reading fix wall/table table potential file walltab.dat with DATE: 2023-02-23 +WARNING: 1 of 400 force values in table are inconsistent with -dE/dr. +WARNING: Should only be flagged at inflection points (src/fix_wall_table.cpp:244) +fix_modify 1 energy yes +run 5 post no +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7 + ghost atom cutoff = 7 + binsize = 3.5, bins = 3 3 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.429 | 4.429 | 4.429 Mbytes + Step Temp Press KinEng PotEng TotEng c_pe + 0 0 0 0 645.2141852 645.2141852 0 + 1 178212.5398 72849.51549 1593.653189 0.2256644171 1593.878854 0 + 2 178320.9331 72893.82438 1594.622489 -0.02236253394 1594.600126 0 + 3 178318.518 72892.83712 1594.600891 -0.0033818408 1594.597509 0 + 4 178318.0722 72892.6549 1594.596905 0 1594.596905 0 + 5 178318.0722 72892.6549 1594.596905 0 1594.596905 0 +WARNING: Bond/angle/dihedral extent > half of periodic box length (src/domain.cpp:936) +Loop time of 4.2027e-05 on 1 procs for 5 steps with 4 atoms + + +variable name string spline-lj126 +include wall.inc + +clear + using 1 OpenMP thread(s) per MPI task +read_restart walltest.restart +Reading restart file ... + restart file = 8 Feb 2023, LAMMPS = 8 Feb 2023 + restoring atom style bond from restart + orthogonal box = (-5 -5 -5) to (5 5 5) + 1 by 1 by 1 MPI processor grid + restoring pair style zero from restart + restoring bond style zero from restart + 4 atoms + 2 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 1 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_restart CPU = 0.000 seconds +# log ${name}.log + +compute ea move pe/atom +compute pe move reduce sum c_ea +special_bonds lj/coul 1.0 1.0 1.0 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 1 1 1 + special bond factors coul: 1 1 1 + 1 = max # of 1-2 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + +thermo_style custom step temp press ke pe etotal c_pe +thermo 1 +thermo_modify format float %14.10g + +fix 0 move nve +# dump 1 all custom 1 ${name}.dump id x fx +# dump_modify 1 format float %20.15g + +fix 1 move wall/table spline 200 xlo -5.0 walltab.dat LJ126 4.0 xhi 5.0 walltab.dat LJ126 4.0 +Reading fix wall/table table potential file walltab.dat with DATE: 2023-02-23 +WARNING: 1 of 400 force values in table are inconsistent with -dE/dr. +WARNING: Should only be flagged at inflection points (src/fix_wall_table.cpp:244) +Reading fix wall/table table potential file walltab.dat with DATE: 2023-02-23 +WARNING: 1 of 400 force values in table are inconsistent with -dE/dr. +WARNING: Should only be flagged at inflection points (src/fix_wall_table.cpp:244) +fix_modify 1 energy yes +run 5 post no +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7 + ghost atom cutoff = 7 + binsize = 3.5, bins = 3 3 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.429 | 4.429 | 4.429 Mbytes + Step Temp Press KinEng PotEng TotEng c_pe + 0 0 0 0 645.3361317 645.3361317 0 + 1 161871.9611 66169.83266 1447.528705 0.3353251002 1447.86403 0 + 2 162015.342 66228.44376 1448.810879 -0.02581160308 1448.785068 0 + 3 162012.784 66227.39811 1448.788005 -0.004635008226 1448.78337 0 + 4 162012.2554 66227.18201 1448.783278 0 1448.783278 0 + 5 162012.2554 66227.18201 1448.783278 0 1448.783278 0 +WARNING: Bond/angle/dihedral extent > half of periodic box length (src/domain.cpp:936) +Loop time of 7.5223e-05 on 1 procs for 5 steps with 4 atoms + + +variable name string pair-lj126 +include wall.inc + +clear + using 1 OpenMP thread(s) per MPI task +read_restart walltest.restart +Reading restart file ... + restart file = 8 Feb 2023, LAMMPS = 8 Feb 2023 + restoring atom style bond from restart + orthogonal box = (-5 -5 -5) to (5 5 5) + 1 by 1 by 1 MPI processor grid + restoring pair style zero from restart + restoring bond style zero from restart + 4 atoms + 2 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 1 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_restart CPU = 0.000 seconds +# log ${name}.log + +compute ea move pe/atom +compute pe move reduce sum c_ea +special_bonds lj/coul 1.0 1.0 1.0 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 1 1 1 + special bond factors coul: 1 1 1 + 1 = max # of 1-2 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + +thermo_style custom step temp press ke pe etotal c_pe +thermo 1 +thermo_modify format float %14.10g + +fix 0 move nve +# dump 1 all custom 1 ${name}.dump id x fx +# dump_modify 1 format float %20.15g + +pair_style lj/cut 4.0 +pair_coeff 1 1 ${eps} ${sig} +pair_coeff 1 1 0.02 ${sig} +pair_coeff 1 1 0.02 2.0 +pair_modify shift yes +run 5 post no +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6 + ghost atom cutoff = 6 + binsize = 3, bins = 4 4 4 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.43 | 4.43 | 4.43 Mbytes + Step Temp Press KinEng PotEng TotEng c_pe + 0 0 178343.7047 0 645.1224609 645.1224609 322.5612305 + 1 178153.8707 72925.96146 1593.128544 0.2259591031 1593.354503 0.1129795516 + 2 178262.3593 72867.28485 1594.098696 -0.02237405364 1594.076322 -0.01118702682 + 3 178260.8147 72867.80305 1594.084884 -0.007499601847 1594.077384 -0.005806728722 + 4 176007.6835 72778.53677 1573.936415 2.772305717 1576.708721 2.772305717 + 5 1.132219912e+27 4.628275436e+26 1.012479748e+25 3.761972158e+12 1.012479748e+25 3.761972158e+12 +WARNING: Bond/angle/dihedral extent > half of periodic box length (src/domain.cpp:936) +Loop time of 8.0904e-05 on 1 procs for 5 steps with 4 atoms + + +variable d0 index 20.0 +variable al index 2.0 +variable r0 index 1.2 + +variable name string wall-morse +include wall.inc + +clear + using 1 OpenMP thread(s) per MPI task +read_restart walltest.restart +Reading restart file ... + restart file = 8 Feb 2023, LAMMPS = 8 Feb 2023 + restoring atom style bond from restart + orthogonal box = (-5 -5 -5) to (5 5 5) + 1 by 1 by 1 MPI processor grid + restoring pair style zero from restart + restoring bond style zero from restart + 4 atoms + 2 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 1 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_restart CPU = 0.000 seconds +# log ${name}.log + +compute ea move pe/atom +compute pe move reduce sum c_ea +special_bonds lj/coul 1.0 1.0 1.0 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 1 1 1 + special bond factors coul: 1 1 1 + 1 = max # of 1-2 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + +thermo_style custom step temp press ke pe etotal c_pe +thermo 1 +thermo_modify format float %14.10g + +fix 0 move nve +# dump 1 all custom 1 ${name}.dump id x fx +# dump_modify 1 format float %20.15g + +fix 1 move wall/morse xlo -5.0 ${d0} ${al} ${r0} 4.0 xhi 5.0 ${d0} ${al} ${r0} 4.0 +fix 1 move wall/morse xlo -5.0 20.0 ${al} ${r0} 4.0 xhi 5.0 ${d0} ${al} ${r0} 4.0 +fix 1 move wall/morse xlo -5.0 20.0 2.0 ${r0} 4.0 xhi 5.0 ${d0} ${al} ${r0} 4.0 +fix 1 move wall/morse xlo -5.0 20.0 2.0 1.2 4.0 xhi 5.0 ${d0} ${al} ${r0} 4.0 +fix 1 move wall/morse xlo -5.0 20.0 2.0 1.2 4.0 xhi 5.0 20.0 ${al} ${r0} 4.0 +fix 1 move wall/morse xlo -5.0 20.0 2.0 1.2 4.0 xhi 5.0 20.0 2.0 ${r0} 4.0 +fix 1 move wall/morse xlo -5.0 20.0 2.0 1.2 4.0 xhi 5.0 20.0 2.0 1.2 4.0 +fix_modify 1 energy yes +run 5 post no +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7 + ghost atom cutoff = 7 + binsize = 3.5, bins = 3 3 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.429 | 4.429 | 4.429 Mbytes + Step Temp Press KinEng PotEng TotEng c_pe + 0 0 0 0 -30.02905654 -30.02905654 0 + 1 146.0893547 59.71823711 1.30639385 -31.40065042 -30.09425657 0 + 2 485.8091411 198.5884977 4.34431431 -34.55987817 -30.21556386 0 + 3 822.0828974 336.0500941 7.351418888 -37.63613582 -30.28471693 0 + 4 1018.806679 416.4666136 9.110607565 -39.39265114 -30.28204357 0 + 5 1050.331347 429.3532307 9.392514704 -39.63687095 -30.24435625 0 +Loop time of 7.721e-05 on 1 procs for 5 steps with 4 atoms + + +variable name string table-morse +include wall.inc + +clear + using 1 OpenMP thread(s) per MPI task +read_restart walltest.restart +Reading restart file ... + restart file = 8 Feb 2023, LAMMPS = 8 Feb 2023 + restoring atom style bond from restart + orthogonal box = (-5 -5 -5) to (5 5 5) + 1 by 1 by 1 MPI processor grid + restoring pair style zero from restart + restoring bond style zero from restart + 4 atoms + 2 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 1 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_restart CPU = 0.000 seconds +# log ${name}.log + +compute ea move pe/atom +compute pe move reduce sum c_ea +special_bonds lj/coul 1.0 1.0 1.0 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 1 1 1 + special bond factors coul: 1 1 1 + 1 = max # of 1-2 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + +thermo_style custom step temp press ke pe etotal c_pe +thermo 1 +thermo_modify format float %14.10g + +fix 0 move nve +# dump 1 all custom 1 ${name}.dump id x fx +# dump_modify 1 format float %20.15g + +fix 1 move wall/table linear 1000 xlo -5.0 walltab.dat MORSE 4.0 xhi 5.0 walltab.dat MORSE 4.0 +Reading fix wall/table table potential file walltab.dat with DATE: 2023-02-23 +Reading fix wall/table table potential file walltab.dat with DATE: 2023-02-23 +fix_modify 1 energy yes +run 5 post no +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7 + ghost atom cutoff = 7 + binsize = 3.5, bins = 3 3 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.429 | 4.429 | 4.429 Mbytes + Step Temp Press KinEng PotEng TotEng c_pe + 0 0 0 0 -30.0282104 -30.0282104 0 + 1 146.0967469 59.72125889 1.306459954 -31.40033773 -30.09387777 0 + 2 485.8417772 198.6018386 4.344606156 -34.55851819 -30.21391203 0 + 3 822.1558136 336.0799007 7.352070936 -37.63533573 -30.28326479 0 + 4 1018.904947 416.5067832 9.111486314 -39.39200056 -30.28051425 0 + 5 1050.436268 429.3961205 9.393452958 -39.63643565 -30.24298269 0 +Loop time of 5.4273e-05 on 1 procs for 5 steps with 4 atoms + + +variable name string spline-morse +include wall.inc + +clear + using 1 OpenMP thread(s) per MPI task +read_restart walltest.restart +Reading restart file ... + restart file = 8 Feb 2023, LAMMPS = 8 Feb 2023 + restoring atom style bond from restart + orthogonal box = (-5 -5 -5) to (5 5 5) + 1 by 1 by 1 MPI processor grid + restoring pair style zero from restart + restoring bond style zero from restart + 4 atoms + 2 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 1 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_restart CPU = 0.000 seconds +# log ${name}.log + +compute ea move pe/atom +compute pe move reduce sum c_ea +special_bonds lj/coul 1.0 1.0 1.0 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 1 1 1 + special bond factors coul: 1 1 1 + 1 = max # of 1-2 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + +thermo_style custom step temp press ke pe etotal c_pe +thermo 1 +thermo_modify format float %14.10g + +fix 0 move nve +# dump 1 all custom 1 ${name}.dump id x fx +# dump_modify 1 format float %20.15g + +fix 1 move wall/table spline 1000 xlo -5.0 walltab.dat MORSE 4.0 xhi 5.0 walltab.dat MORSE 4.0 +Reading fix wall/table table potential file walltab.dat with DATE: 2023-02-23 +Reading fix wall/table table potential file walltab.dat with DATE: 2023-02-23 +fix_modify 1 energy yes +run 5 post no +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7 + ghost atom cutoff = 7 + binsize = 3.5, bins = 3 3 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.429 | 4.429 | 4.429 Mbytes + Step Temp Press KinEng PotEng TotEng c_pe + 0 0 0 0 -30.02905657 -30.02905657 0 + 1 146.0893531 59.71823647 1.306393836 -31.40065068 -30.09425684 0 + 2 485.809133 198.5884944 4.344314238 -34.55987846 -30.21556422 0 + 3 822.0828818 336.0500877 7.351418748 -37.63613601 -30.28471726 0 + 4 1018.80666 416.4666056 9.110607389 -39.39265128 -30.28204389 0 + 5 1050.331328 429.353223 9.392514534 -39.63687099 -30.24435645 0 +Loop time of 3.4052e-05 on 1 procs for 5 steps with 4 atoms + + +variable name string bond-morse +include wall.inc + +clear + using 1 OpenMP thread(s) per MPI task +read_restart walltest.restart +Reading restart file ... + restart file = 8 Feb 2023, LAMMPS = 8 Feb 2023 + restoring atom style bond from restart + orthogonal box = (-5 -5 -5) to (5 5 5) + 1 by 1 by 1 MPI processor grid + restoring pair style zero from restart + restoring bond style zero from restart + 4 atoms + 2 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 1 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_restart CPU = 0.000 seconds +# log ${name}.log + +compute ea move pe/atom +compute pe move reduce sum c_ea +special_bonds lj/coul 1.0 1.0 1.0 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 1 1 1 + special bond factors coul: 1 1 1 + 1 = max # of 1-2 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + +thermo_style custom step temp press ke pe etotal c_pe +thermo 1 +thermo_modify format float %14.10g + +fix 0 move nve +# dump 1 all custom 1 ${name}.dump id x fx +# dump_modify 1 format float %20.15g + +bond_style morse +bond_coeff 1 ${d0} ${al} ${r0} +bond_coeff 1 20.0 ${al} ${r0} +bond_coeff 1 20.0 2.0 ${r0} +bond_coeff 1 20.0 2.0 1.2 +run 5 post no +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7 + ghost atom cutoff = 7 + binsize = 3.5, bins = 3 3 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.429 | 4.429 | 4.429 Mbytes + Step Temp Press KinEng PotEng TotEng c_pe + 0 0 2683.187147 0 9.675661328 9.675661328 4.837830664 + 1 146.0893547 2514.939772 1.30639385 8.304067455 9.610461305 4.152033728 + 2 485.8091411 2063.804037 4.34431431 5.144839701 9.489154012 2.572419851 + 3 822.0828974 1456.368913 7.351418888 2.06858205 9.420000938 1.034291025 + 4 1018.806679 823.4383177 9.110607565 0.3120667313 9.422674297 0.1560333657 + 5 1050.331347 253.0262957 9.392514704 0.06784692056 9.460361624 0.03392346028 +Loop time of 7.2553e-05 on 1 procs for 5 steps with 4 atoms + + +variable name string pair-morse +include wall.inc + +clear + using 1 OpenMP thread(s) per MPI task +read_restart walltest.restart +Reading restart file ... + restart file = 8 Feb 2023, LAMMPS = 8 Feb 2023 + restoring atom style bond from restart + orthogonal box = (-5 -5 -5) to (5 5 5) + 1 by 1 by 1 MPI processor grid + restoring pair style zero from restart + restoring bond style zero from restart + 4 atoms + 2 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 1 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_restart CPU = 0.000 seconds +# log ${name}.log + +compute ea move pe/atom +compute pe move reduce sum c_ea +special_bonds lj/coul 1.0 1.0 1.0 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 1 1 1 + special bond factors coul: 1 1 1 + 1 = max # of 1-2 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + +thermo_style custom step temp press ke pe etotal c_pe +thermo 1 +thermo_modify format float %14.10g + +fix 0 move nve +# dump 1 all custom 1 ${name}.dump id x fx +# dump_modify 1 format float %20.15g + +pair_style morse 4.0 +pair_coeff 1 1 ${d0} ${al} ${r0} +pair_coeff 1 1 20.0 ${al} ${r0} +pair_coeff 1 1 20.0 2.0 ${r0} +pair_coeff 1 1 20.0 2.0 1.2 +pair_modify shift yes +run 5 post no +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6 + ghost atom cutoff = 6 + binsize = 3, bins = 4 4 4 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair morse, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.43 | 4.43 | 4.43 Mbytes + Step Temp Press KinEng PotEng TotEng c_pe + 0 0 2683.187147 0 -30.02905654 -30.02905654 -15.01452827 + 1 146.0893547 2514.939772 1.30639385 -31.40065042 -30.09425657 -15.70032521 + 2 485.8091411 2063.804037 4.34431431 -34.55987817 -30.21556386 -17.27993908 + 3 822.0828974 1456.368913 7.351418888 -37.63613582 -30.28471693 -18.81806791 + 4 1018.806679 823.4383177 9.110607565 -39.39265114 -30.28204357 -19.69632557 + 5 1050.331347 253.0262957 9.392514704 -39.63687095 -30.24435625 -19.81843547 +Loop time of 4.2481e-05 on 1 procs for 5 steps with 4 atoms + + +shell rm -f walltest.restart +Total wall time: 0:00:00 diff --git a/examples/wall/log.23Feb23.wall.table.g++.4 b/examples/wall/log.23Feb23.wall.table.g++.4 new file mode 100644 index 0000000000..8b0e9e0902 --- /dev/null +++ b/examples/wall/log.23Feb23.wall.table.g++.4 @@ -0,0 +1,1116 @@ +LAMMPS (8 Feb 2023) + using 1 OpenMP thread(s) per MPI task +units real +atom_style bond +boundary f p p +region box block -5.000000000000001 5.000000000000001 -5 5 -5 5 +create_box 1 box bond/types 1 extra/bond/per/atom 1 extra/special/per/atom 1 +Created orthogonal box = (-5 -5 -5) to (5 5 5) + 1 by 2 by 2 MPI processor grid + +pair_style zero 5.0 +pair_coeff * * +mass * 1.0 +bond_style zero +bond_coeff * 1.0 + +create_atoms 1 single -4.0 0.0 0.0 +Created 1 atoms + using lattice units in orthogonal box = (-5 -5 -5) to (5 5 5) + create_atoms CPU = 0.000 seconds +create_atoms 1 single 4.0 0.0 0.0 +Created 1 atoms + using lattice units in orthogonal box = (-5 -5 -5) to (5 5 5) + create_atoms CPU = 0.000 seconds +create_atoms 1 single -5.0 0.0 0.0 +Created 1 atoms + using lattice units in orthogonal box = (-5 -5 -5) to (5 5 5) + create_atoms CPU = 0.000 seconds +create_atoms 1 single 5.0 0.0 0.0 +Created 1 atoms + using lattice units in orthogonal box = (-5 -5 -5) to (5 5 5) + create_atoms CPU = 0.000 seconds +create_bonds single/bond 1 3 1 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 1 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds +create_bonds single/bond 1 4 2 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 1 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.001 seconds + +group move id 1:2 +2 atoms in group move +write_restart walltest.restart +System init for write_restart ... +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7 + ghost atom cutoff = 7 + binsize = 3.5, bins = 3 3 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard + +variable name string wall-harmonic +include wall.inc + +clear + using 1 OpenMP thread(s) per MPI task +read_restart walltest.restart +Reading restart file ... + restart file = 8 Feb 2023, LAMMPS = 8 Feb 2023 + restoring atom style bond from restart + orthogonal box = (-5 -5 -5) to (5 5 5) + 1 by 2 by 2 MPI processor grid + restoring pair style zero from restart + restoring bond style zero from restart + 4 atoms + 2 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 1 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_restart CPU = 0.001 seconds +# log ${name}.log + +compute ea move pe/atom +compute pe move reduce sum c_ea +special_bonds lj/coul 1.0 1.0 1.0 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 1 1 1 + special bond factors coul: 1 1 1 + 1 = max # of 1-2 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.001 seconds + +thermo_style custom step temp press ke pe etotal c_pe +thermo 1 +thermo_modify format float %14.10g + +fix 0 move nve +# dump 1 all custom 1 ${name}.dump id x fx +# dump_modify 1 format float %20.15g + +fix 1 move wall/harmonic xlo -5.0 100 0.0 4.0 xhi 5.0 100 1.0 4.0 +fix_modify 1 energy yes +run 5 post no +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7 + ghost atom cutoff = 7 + binsize = 3.5, bins = 3 3 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.32 | 4.379 | 4.559 Mbytes + Step Temp Press KinEng PotEng TotEng c_pe + 0 0 0 0 1800 1800 0 + 1 16146.37291 6600.295604 144.3878119 1652.527054 1796.914866 0 + 2 59294.04011 24238.149 530.232812 1258.437705 1788.670517 0 + 3 115302.7492 47133.32419 1031.086781 746.8819904 1777.968771 0 + 4 165817.4572 67782.66799 1482.811029 285.5057515 1768.31678 0 + 5 194283.6024 79419.02582 1737.367544 25.51012833 1762.877672 0 +Loop time of 0.000766029 on 4 procs for 5 steps with 4 atoms + + +variable name string table-harmonic +include wall.inc + +clear + using 1 OpenMP thread(s) per MPI task +read_restart walltest.restart +Reading restart file ... + restart file = 8 Feb 2023, LAMMPS = 8 Feb 2023 + restoring atom style bond from restart + orthogonal box = (-5 -5 -5) to (5 5 5) + 1 by 2 by 2 MPI processor grid + restoring pair style zero from restart + restoring bond style zero from restart + 4 atoms + 2 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 1 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_restart CPU = 0.001 seconds +# log ${name}.log + +compute ea move pe/atom +compute pe move reduce sum c_ea +special_bonds lj/coul 1.0 1.0 1.0 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 1 1 1 + special bond factors coul: 1 1 1 + 1 = max # of 1-2 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + +thermo_style custom step temp press ke pe etotal c_pe +thermo 1 +thermo_modify format float %14.10g + +fix 0 move nve +# dump 1 all custom 1 ${name}.dump id x fx +# dump_modify 1 format float %20.15g + +fix 1 move wall/table linear 1000 xlo -5.0 walltab.dat HARMONIC 4.0 xhi 5.0 walltab.dat HARMONIC 4.0 +Reading fix wall/table table potential file walltab.dat with DATE: 2023-02-23 +Reading fix wall/table table potential file walltab.dat with DATE: 2023-02-23 +fix_modify 1 energy yes +run 5 post no +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7 + ghost atom cutoff = 7 + binsize = 3.5, bins = 3 3 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.32 | 4.379 | 4.559 Mbytes + Step Temp Press KinEng PotEng TotEng c_pe + 0 0 0 0 1800.000356 1800.000356 0 + 1 16146.37291 6600.295604 144.3878119 1652.527723 1796.915535 0 + 2 59294.04011 24238.149 530.232812 1258.437853 1788.670665 0 + 3 115302.7492 47133.32419 1031.086781 746.8824148 1777.969196 0 + 4 165817.4572 67782.66799 1482.811029 285.5061521 1768.317181 0 + 5 194283.6024 79419.02582 1737.367544 25.51090543 1762.878449 0 +Loop time of 0.000395044 on 4 procs for 5 steps with 4 atoms + + +variable name string spline-harmonic +include wall.inc + +clear + using 1 OpenMP thread(s) per MPI task +read_restart walltest.restart +Reading restart file ... + restart file = 8 Feb 2023, LAMMPS = 8 Feb 2023 + restoring atom style bond from restart + orthogonal box = (-5 -5 -5) to (5 5 5) + 1 by 2 by 2 MPI processor grid + restoring pair style zero from restart + restoring bond style zero from restart + 4 atoms + 2 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 1 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_restart CPU = 0.001 seconds +# log ${name}.log + +compute ea move pe/atom +compute pe move reduce sum c_ea +special_bonds lj/coul 1.0 1.0 1.0 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 1 1 1 + special bond factors coul: 1 1 1 + 1 = max # of 1-2 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + +thermo_style custom step temp press ke pe etotal c_pe +thermo 1 +thermo_modify format float %14.10g + +fix 0 move nve +# dump 1 all custom 1 ${name}.dump id x fx +# dump_modify 1 format float %20.15g + +fix 1 move wall/table spline 200 xlo -5.0 walltab.dat HARMONIC 4.0 xhi 5.0 walltab.dat HARMONIC 4.0 +Reading fix wall/table table potential file walltab.dat with DATE: 2023-02-23 +Reading fix wall/table table potential file walltab.dat with DATE: 2023-02-23 +fix_modify 1 energy yes +run 5 post no +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7 + ghost atom cutoff = 7 + binsize = 3.5, bins = 3 3 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.32 | 4.379 | 4.559 Mbytes + Step Temp Press KinEng PotEng TotEng c_pe + 0 0 0 0 1800 1800 0 + 1 16146.37291 6600.295604 144.3878119 1652.527054 1796.914866 0 + 2 59294.04011 24238.149 530.232812 1258.437705 1788.670517 0 + 3 115302.7492 47133.32419 1031.086781 746.8819904 1777.968771 0 + 4 165817.4572 67782.66799 1482.811029 285.5057515 1768.31678 0 + 5 194283.6024 79419.02582 1737.367544 25.51012833 1762.877672 0 +Loop time of 0.00033613 on 4 procs for 5 steps with 4 atoms + + +variable name string bond-harmonic +include wall.inc + +clear + using 1 OpenMP thread(s) per MPI task +read_restart walltest.restart +Reading restart file ... + restart file = 8 Feb 2023, LAMMPS = 8 Feb 2023 + restoring atom style bond from restart + orthogonal box = (-5 -5 -5) to (5 5 5) + 1 by 2 by 2 MPI processor grid + restoring pair style zero from restart + restoring bond style zero from restart + 4 atoms + 2 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 1 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_restart CPU = 0.001 seconds +# log ${name}.log + +compute ea move pe/atom +compute pe move reduce sum c_ea +special_bonds lj/coul 1.0 1.0 1.0 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 1 1 1 + special bond factors coul: 1 1 1 + 1 = max # of 1-2 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + +thermo_style custom step temp press ke pe etotal c_pe +thermo 1 +thermo_modify format float %14.10g + +fix 0 move nve +# dump 1 all custom 1 ${name}.dump id x fx +# dump_modify 1 format float %20.15g + +bond_style harmonic +bond_coeff 1 100 4.0 +run 5 post no +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7 + ghost atom cutoff = 7 + binsize = 3.5, bins = 3 3 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +WARNING: Communication cutoff 7 is shorter than a bond length based estimate of 8. This may lead to errors. (src/comm.cpp:723) +Per MPI rank memory allocation (min/avg/max) = 4.32 | 4.379 | 4.559 Mbytes + Step Temp Press KinEng PotEng TotEng c_pe + 0 0 27427.366 0 1800 1800 900 + 1 16146.37291 36178.74173 144.3878119 1652.527054 1796.914866 826.263527 + 2 59294.04011 58444.6962 530.232812 1258.437705 1788.670517 629.2188524 + 3 115302.7492 83661.44348 1031.086781 746.8819904 1777.968771 373.4409952 + 4 165817.4572 98424.89283 1482.811029 285.5057515 1768.31678 142.7528758 + 5 194283.6024 91313.53086 1737.367544 25.51012833 1762.877672 12.75506417 +Loop time of 0.000380067 on 4 procs for 5 steps with 4 atoms + + +variable name string pair-harmonic +include wall.inc + +clear + using 1 OpenMP thread(s) per MPI task +read_restart walltest.restart +Reading restart file ... + restart file = 8 Feb 2023, LAMMPS = 8 Feb 2023 + restoring atom style bond from restart + orthogonal box = (-5 -5 -5) to (5 5 5) + 1 by 2 by 2 MPI processor grid + restoring pair style zero from restart + restoring bond style zero from restart + 4 atoms + 2 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 1 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_restart CPU = 0.001 seconds +# log ${name}.log + +compute ea move pe/atom +compute pe move reduce sum c_ea +special_bonds lj/coul 1.0 1.0 1.0 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 1 1 1 + special bond factors coul: 1 1 1 + 1 = max # of 1-2 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + +thermo_style custom step temp press ke pe etotal c_pe +thermo 1 +thermo_modify format float %14.10g + +fix 0 move nve +# dump 1 all custom 1 ${name}.dump id x fx +# dump_modify 1 format float %20.15g + +pair_style harmonic/cut +pair_coeff 1 1 100 4.0 +run 5 post no +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6 + ghost atom cutoff = 6 + binsize = 3, bins = 4 4 4 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair harmonic/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.32 | 4.38 | 4.56 Mbytes + Step Temp Press KinEng PotEng TotEng c_pe + 0 0 27427.366 0 1800 1800 900 + 1 16146.37291 36178.74173 144.3878119 1652.527054 1796.914866 826.263527 + 2 59294.04011 58444.6962 530.232812 1258.437705 1788.670517 629.2188524 + 3 115302.7492 83661.44348 1031.086781 746.8819904 1777.968771 373.4409952 + 4 165817.4572 98424.89283 1482.811029 285.5057515 1768.31678 142.7528758 + 5 170540.4005 97560.47089 1525.045619 190.8165235 1715.862142 178.0614593 +Loop time of 0.000337009 on 4 procs for 5 steps with 4 atoms + + +variable eps index 0.02 +variable sig index 2.0 +variable name string wall-lj126 +include wall.inc + +clear + using 1 OpenMP thread(s) per MPI task +read_restart walltest.restart +Reading restart file ... + restart file = 8 Feb 2023, LAMMPS = 8 Feb 2023 + restoring atom style bond from restart + orthogonal box = (-5 -5 -5) to (5 5 5) + 1 by 2 by 2 MPI processor grid + restoring pair style zero from restart + restoring bond style zero from restart + 4 atoms + 2 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 1 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_restart CPU = 0.001 seconds +# log ${name}.log + +compute ea move pe/atom +compute pe move reduce sum c_ea +special_bonds lj/coul 1.0 1.0 1.0 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 1 1 1 + special bond factors coul: 1 1 1 + 1 = max # of 1-2 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + +thermo_style custom step temp press ke pe etotal c_pe +thermo 1 +thermo_modify format float %14.10g + +fix 0 move nve +# dump 1 all custom 1 ${name}.dump id x fx +# dump_modify 1 format float %20.15g + +fix 1 move wall/lj126 xlo -5.0 ${eps} ${sig} 4.0 xhi 5.0 ${eps} ${sig} 4.0 +fix 1 move wall/lj126 xlo -5.0 0.02 ${sig} 4.0 xhi 5.0 ${eps} ${sig} 4.0 +fix 1 move wall/lj126 xlo -5.0 0.02 2.0 4.0 xhi 5.0 ${eps} ${sig} 4.0 +fix 1 move wall/lj126 xlo -5.0 0.02 2.0 4.0 xhi 5.0 0.02 ${sig} 4.0 +fix 1 move wall/lj126 xlo -5.0 0.02 2.0 4.0 xhi 5.0 0.02 2.0 4.0 +fix_modify 1 energy yes +run 5 post no +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7 + ghost atom cutoff = 7 + binsize = 3.5, bins = 3 3 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.32 | 4.379 | 4.559 Mbytes + Step Temp Press KinEng PotEng TotEng c_pe + 0 0 0 0 645.1224609 645.1224609 0 + 1 178153.8707 72825.53278 1593.128544 0.2259591031 1593.354503 0 + 2 178262.3593 72869.88065 1594.098696 -0.02237405364 1594.076322 0 + 3 178259.9436 72868.89314 1594.077094 -0.003385746252 1594.073708 0 + 4 178259.4975 72868.71081 1594.073105 0 1594.073105 0 + 5 178259.4975 72868.71081 1594.073105 0 1594.073105 0 +WARNING: Bond/angle/dihedral extent > half of periodic box length (src/domain.cpp:936) +Loop time of 0.000404521 on 4 procs for 5 steps with 4 atoms + + +variable name string table-lj126 +include wall.inc + +clear + using 1 OpenMP thread(s) per MPI task +read_restart walltest.restart +Reading restart file ... + restart file = 8 Feb 2023, LAMMPS = 8 Feb 2023 + restoring atom style bond from restart + orthogonal box = (-5 -5 -5) to (5 5 5) + 1 by 2 by 2 MPI processor grid + restoring pair style zero from restart + restoring bond style zero from restart + 4 atoms + 2 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 1 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_restart CPU = 0.001 seconds +# log ${name}.log + +compute ea move pe/atom +compute pe move reduce sum c_ea +special_bonds lj/coul 1.0 1.0 1.0 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 1 1 1 + special bond factors coul: 1 1 1 + 1 = max # of 1-2 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + +thermo_style custom step temp press ke pe etotal c_pe +thermo 1 +thermo_modify format float %14.10g + +fix 0 move nve +# dump 1 all custom 1 ${name}.dump id x fx +# dump_modify 1 format float %20.15g + +fix 1 move wall/table linear 1000 xlo -5.0 walltab.dat LJ126 4.0 xhi 5.0 walltab.dat LJ126 4.0 +Reading fix wall/table table potential file walltab.dat with DATE: 2023-02-23 +WARNING: 1 of 400 force values in table are inconsistent with -dE/dr. +WARNING: Should only be flagged at inflection points (src/fix_wall_table.cpp:244) +Reading fix wall/table table potential file walltab.dat with DATE: 2023-02-23 +WARNING: 1 of 400 force values in table are inconsistent with -dE/dr. +WARNING: Should only be flagged at inflection points (src/fix_wall_table.cpp:244) +fix_modify 1 energy yes +run 5 post no +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7 + ghost atom cutoff = 7 + binsize = 3.5, bins = 3 3 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.32 | 4.379 | 4.559 Mbytes + Step Temp Press KinEng PotEng TotEng c_pe + 0 0 0 0 645.2141852 645.2141852 0 + 1 178212.5398 72849.51549 1593.653189 0.2256644171 1593.878854 0 + 2 178320.9331 72893.82438 1594.622489 -0.02236253394 1594.600126 0 + 3 178318.518 72892.83712 1594.600891 -0.0033818408 1594.597509 0 + 4 178318.0722 72892.6549 1594.596905 0 1594.596905 0 + 5 178318.0722 72892.6549 1594.596905 0 1594.596905 0 +WARNING: Bond/angle/dihedral extent > half of periodic box length (src/domain.cpp:936) +Loop time of 0.000334746 on 4 procs for 5 steps with 4 atoms + + +variable name string spline-lj126 +include wall.inc + +clear + using 1 OpenMP thread(s) per MPI task +read_restart walltest.restart +Reading restart file ... + restart file = 8 Feb 2023, LAMMPS = 8 Feb 2023 + restoring atom style bond from restart + orthogonal box = (-5 -5 -5) to (5 5 5) + 1 by 2 by 2 MPI processor grid + restoring pair style zero from restart + restoring bond style zero from restart + 4 atoms + 2 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 1 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_restart CPU = 0.001 seconds +# log ${name}.log + +compute ea move pe/atom +compute pe move reduce sum c_ea +special_bonds lj/coul 1.0 1.0 1.0 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 1 1 1 + special bond factors coul: 1 1 1 + 1 = max # of 1-2 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + +thermo_style custom step temp press ke pe etotal c_pe +thermo 1 +thermo_modify format float %14.10g + +fix 0 move nve +# dump 1 all custom 1 ${name}.dump id x fx +# dump_modify 1 format float %20.15g + +fix 1 move wall/table spline 200 xlo -5.0 walltab.dat LJ126 4.0 xhi 5.0 walltab.dat LJ126 4.0 +Reading fix wall/table table potential file walltab.dat with DATE: 2023-02-23 +WARNING: 1 of 400 force values in table are inconsistent with -dE/dr. +WARNING: Should only be flagged at inflection points (src/fix_wall_table.cpp:244) +Reading fix wall/table table potential file walltab.dat with DATE: 2023-02-23 +WARNING: 1 of 400 force values in table are inconsistent with -dE/dr. +WARNING: Should only be flagged at inflection points (src/fix_wall_table.cpp:244) +fix_modify 1 energy yes +run 5 post no +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7 + ghost atom cutoff = 7 + binsize = 3.5, bins = 3 3 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.32 | 4.379 | 4.559 Mbytes + Step Temp Press KinEng PotEng TotEng c_pe + 0 0 0 0 645.3361317 645.3361317 0 + 1 161871.9611 66169.83266 1447.528705 0.3353251002 1447.86403 0 + 2 162015.342 66228.44376 1448.810879 -0.02581160308 1448.785068 0 + 3 162012.784 66227.39811 1448.788005 -0.004635008226 1448.78337 0 + 4 162012.2554 66227.18201 1448.783278 0 1448.783278 0 + 5 162012.2554 66227.18201 1448.783278 0 1448.783278 0 +WARNING: Bond/angle/dihedral extent > half of periodic box length (src/domain.cpp:936) +Loop time of 0.000345529 on 4 procs for 5 steps with 4 atoms + + +variable name string pair-lj126 +include wall.inc + +clear + using 1 OpenMP thread(s) per MPI task +read_restart walltest.restart +Reading restart file ... + restart file = 8 Feb 2023, LAMMPS = 8 Feb 2023 + restoring atom style bond from restart + orthogonal box = (-5 -5 -5) to (5 5 5) + 1 by 2 by 2 MPI processor grid + restoring pair style zero from restart + restoring bond style zero from restart + 4 atoms + 2 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 1 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_restart CPU = 0.001 seconds +# log ${name}.log + +compute ea move pe/atom +compute pe move reduce sum c_ea +special_bonds lj/coul 1.0 1.0 1.0 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 1 1 1 + special bond factors coul: 1 1 1 + 1 = max # of 1-2 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + +thermo_style custom step temp press ke pe etotal c_pe +thermo 1 +thermo_modify format float %14.10g + +fix 0 move nve +# dump 1 all custom 1 ${name}.dump id x fx +# dump_modify 1 format float %20.15g + +pair_style lj/cut 4.0 +pair_coeff 1 1 ${eps} ${sig} +pair_coeff 1 1 0.02 ${sig} +pair_coeff 1 1 0.02 2.0 +pair_modify shift yes +run 5 post no +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6 + ghost atom cutoff = 6 + binsize = 3, bins = 4 4 4 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.32 | 4.38 | 4.56 Mbytes + Step Temp Press KinEng PotEng TotEng c_pe + 0 0 178343.7047 0 645.1224609 645.1224609 322.5612305 + 1 178153.8707 72925.96146 1593.128544 0.2259591031 1593.354503 0.1129795516 + 2 178262.3593 72867.28485 1594.098696 -0.02237405364 1594.076322 -0.01118702682 + 3 178260.8147 72867.80305 1594.084884 -0.007499601847 1594.077384 -0.005806728722 + 4 176007.6835 72778.53677 1573.936415 2.772305717 1576.708721 2.772305717 + 5 1.132219912e+27 4.628275436e+26 1.012479748e+25 3.761972158e+12 1.012479748e+25 3.761972158e+12 +WARNING: Bond/angle/dihedral extent > half of periodic box length (src/domain.cpp:936) +Loop time of 0.000315196 on 4 procs for 5 steps with 4 atoms + + +variable d0 index 20.0 +variable al index 2.0 +variable r0 index 1.2 + +variable name string wall-morse +include wall.inc + +clear + using 1 OpenMP thread(s) per MPI task +read_restart walltest.restart +Reading restart file ... + restart file = 8 Feb 2023, LAMMPS = 8 Feb 2023 + restoring atom style bond from restart + orthogonal box = (-5 -5 -5) to (5 5 5) + 1 by 2 by 2 MPI processor grid + restoring pair style zero from restart + restoring bond style zero from restart + 4 atoms + 2 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 1 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_restart CPU = 0.001 seconds +# log ${name}.log + +compute ea move pe/atom +compute pe move reduce sum c_ea +special_bonds lj/coul 1.0 1.0 1.0 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 1 1 1 + special bond factors coul: 1 1 1 + 1 = max # of 1-2 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + +thermo_style custom step temp press ke pe etotal c_pe +thermo 1 +thermo_modify format float %14.10g + +fix 0 move nve +# dump 1 all custom 1 ${name}.dump id x fx +# dump_modify 1 format float %20.15g + +fix 1 move wall/morse xlo -5.0 ${d0} ${al} ${r0} 4.0 xhi 5.0 ${d0} ${al} ${r0} 4.0 +fix 1 move wall/morse xlo -5.0 20.0 ${al} ${r0} 4.0 xhi 5.0 ${d0} ${al} ${r0} 4.0 +fix 1 move wall/morse xlo -5.0 20.0 2.0 ${r0} 4.0 xhi 5.0 ${d0} ${al} ${r0} 4.0 +fix 1 move wall/morse xlo -5.0 20.0 2.0 1.2 4.0 xhi 5.0 ${d0} ${al} ${r0} 4.0 +fix 1 move wall/morse xlo -5.0 20.0 2.0 1.2 4.0 xhi 5.0 20.0 ${al} ${r0} 4.0 +fix 1 move wall/morse xlo -5.0 20.0 2.0 1.2 4.0 xhi 5.0 20.0 2.0 ${r0} 4.0 +fix 1 move wall/morse xlo -5.0 20.0 2.0 1.2 4.0 xhi 5.0 20.0 2.0 1.2 4.0 +fix_modify 1 energy yes +run 5 post no +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7 + ghost atom cutoff = 7 + binsize = 3.5, bins = 3 3 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.32 | 4.379 | 4.559 Mbytes + Step Temp Press KinEng PotEng TotEng c_pe + 0 0 0 0 -30.02905654 -30.02905654 0 + 1 146.0893547 59.71823711 1.30639385 -31.40065042 -30.09425657 0 + 2 485.8091411 198.5884977 4.34431431 -34.55987817 -30.21556386 0 + 3 822.0828974 336.0500941 7.351418888 -37.63613582 -30.28471693 0 + 4 1018.806679 416.4666136 9.110607565 -39.39265114 -30.28204357 0 + 5 1050.331347 429.3532307 9.392514704 -39.63687095 -30.24435625 0 +Loop time of 0.000711295 on 4 procs for 5 steps with 4 atoms + + +variable name string table-morse +include wall.inc + +clear + using 1 OpenMP thread(s) per MPI task +read_restart walltest.restart +Reading restart file ... + restart file = 8 Feb 2023, LAMMPS = 8 Feb 2023 + restoring atom style bond from restart + orthogonal box = (-5 -5 -5) to (5 5 5) + 1 by 2 by 2 MPI processor grid + restoring pair style zero from restart + restoring bond style zero from restart + 4 atoms + 2 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 1 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_restart CPU = 0.001 seconds +# log ${name}.log + +compute ea move pe/atom +compute pe move reduce sum c_ea +special_bonds lj/coul 1.0 1.0 1.0 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 1 1 1 + special bond factors coul: 1 1 1 + 1 = max # of 1-2 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + +thermo_style custom step temp press ke pe etotal c_pe +thermo 1 +thermo_modify format float %14.10g + +fix 0 move nve +# dump 1 all custom 1 ${name}.dump id x fx +# dump_modify 1 format float %20.15g + +fix 1 move wall/table linear 1000 xlo -5.0 walltab.dat MORSE 4.0 xhi 5.0 walltab.dat MORSE 4.0 +Reading fix wall/table table potential file walltab.dat with DATE: 2023-02-23 +Reading fix wall/table table potential file walltab.dat with DATE: 2023-02-23 +fix_modify 1 energy yes +run 5 post no +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7 + ghost atom cutoff = 7 + binsize = 3.5, bins = 3 3 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.32 | 4.379 | 4.559 Mbytes + Step Temp Press KinEng PotEng TotEng c_pe + 0 0 0 0 -30.0282104 -30.0282104 0 + 1 146.0967469 59.72125889 1.306459954 -31.40033773 -30.09387777 0 + 2 485.8417772 198.6018386 4.344606156 -34.55851819 -30.21391203 0 + 3 822.1558136 336.0799007 7.352070936 -37.63533573 -30.28326479 0 + 4 1018.904947 416.5067832 9.111486314 -39.39200056 -30.28051425 0 + 5 1050.436268 429.3961205 9.393452958 -39.63643565 -30.24298269 0 +Loop time of 0.000302153 on 4 procs for 5 steps with 4 atoms + + +variable name string spline-morse +include wall.inc + +clear + using 1 OpenMP thread(s) per MPI task +read_restart walltest.restart +Reading restart file ... + restart file = 8 Feb 2023, LAMMPS = 8 Feb 2023 + restoring atom style bond from restart + orthogonal box = (-5 -5 -5) to (5 5 5) + 1 by 2 by 2 MPI processor grid + restoring pair style zero from restart + restoring bond style zero from restart + 4 atoms + 2 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 1 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_restart CPU = 0.001 seconds +# log ${name}.log + +compute ea move pe/atom +compute pe move reduce sum c_ea +special_bonds lj/coul 1.0 1.0 1.0 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 1 1 1 + special bond factors coul: 1 1 1 + 1 = max # of 1-2 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + +thermo_style custom step temp press ke pe etotal c_pe +thermo 1 +thermo_modify format float %14.10g + +fix 0 move nve +# dump 1 all custom 1 ${name}.dump id x fx +# dump_modify 1 format float %20.15g + +fix 1 move wall/table spline 1000 xlo -5.0 walltab.dat MORSE 4.0 xhi 5.0 walltab.dat MORSE 4.0 +Reading fix wall/table table potential file walltab.dat with DATE: 2023-02-23 +Reading fix wall/table table potential file walltab.dat with DATE: 2023-02-23 +fix_modify 1 energy yes +run 5 post no +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7 + ghost atom cutoff = 7 + binsize = 3.5, bins = 3 3 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.32 | 4.379 | 4.559 Mbytes + Step Temp Press KinEng PotEng TotEng c_pe + 0 0 0 0 -30.02905657 -30.02905657 0 + 1 146.0893531 59.71823647 1.306393836 -31.40065068 -30.09425684 0 + 2 485.809133 198.5884944 4.344314238 -34.55987846 -30.21556422 0 + 3 822.0828818 336.0500877 7.351418748 -37.63613601 -30.28471726 0 + 4 1018.80666 416.4666056 9.110607389 -39.39265128 -30.28204389 0 + 5 1050.331328 429.353223 9.392514534 -39.63687099 -30.24435645 0 +Loop time of 0.000295181 on 4 procs for 5 steps with 4 atoms + + +variable name string bond-morse +include wall.inc + +clear + using 1 OpenMP thread(s) per MPI task +read_restart walltest.restart +Reading restart file ... + restart file = 8 Feb 2023, LAMMPS = 8 Feb 2023 + restoring atom style bond from restart + orthogonal box = (-5 -5 -5) to (5 5 5) + 1 by 2 by 2 MPI processor grid + restoring pair style zero from restart + restoring bond style zero from restart + 4 atoms + 2 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 1 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_restart CPU = 0.001 seconds +# log ${name}.log + +compute ea move pe/atom +compute pe move reduce sum c_ea +special_bonds lj/coul 1.0 1.0 1.0 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 1 1 1 + special bond factors coul: 1 1 1 + 1 = max # of 1-2 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + +thermo_style custom step temp press ke pe etotal c_pe +thermo 1 +thermo_modify format float %14.10g + +fix 0 move nve +# dump 1 all custom 1 ${name}.dump id x fx +# dump_modify 1 format float %20.15g + +bond_style morse +bond_coeff 1 ${d0} ${al} ${r0} +bond_coeff 1 20.0 ${al} ${r0} +bond_coeff 1 20.0 2.0 ${r0} +bond_coeff 1 20.0 2.0 1.2 +run 5 post no +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7 + ghost atom cutoff = 7 + binsize = 3.5, bins = 3 3 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.32 | 4.379 | 4.559 Mbytes + Step Temp Press KinEng PotEng TotEng c_pe + 0 0 2683.187147 0 9.675661328 9.675661328 4.837830664 + 1 146.0893547 2514.939772 1.30639385 8.304067455 9.610461305 4.152033728 + 2 485.8091411 2063.804037 4.34431431 5.144839701 9.489154012 2.572419851 + 3 822.0828974 1456.368913 7.351418888 2.06858205 9.420000938 1.034291025 + 4 1018.806679 823.4383177 9.110607565 0.3120667313 9.422674297 0.1560333657 + 5 1050.331347 253.0262957 9.392514704 0.06784692056 9.460361624 0.03392346028 +Loop time of 0.000710295 on 4 procs for 5 steps with 4 atoms + + +variable name string pair-morse +include wall.inc + +clear + using 1 OpenMP thread(s) per MPI task +read_restart walltest.restart +Reading restart file ... + restart file = 8 Feb 2023, LAMMPS = 8 Feb 2023 + restoring atom style bond from restart + orthogonal box = (-5 -5 -5) to (5 5 5) + 1 by 2 by 2 MPI processor grid + restoring pair style zero from restart + restoring bond style zero from restart + 4 atoms + 2 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 1 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_restart CPU = 0.001 seconds +# log ${name}.log + +compute ea move pe/atom +compute pe move reduce sum c_ea +special_bonds lj/coul 1.0 1.0 1.0 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 1 1 1 + special bond factors coul: 1 1 1 + 1 = max # of 1-2 neighbors + 3 = max # of special neighbors + special bonds CPU = 0.000 seconds + +thermo_style custom step temp press ke pe etotal c_pe +thermo 1 +thermo_modify format float %14.10g + +fix 0 move nve +# dump 1 all custom 1 ${name}.dump id x fx +# dump_modify 1 format float %20.15g + +pair_style morse 4.0 +pair_coeff 1 1 ${d0} ${al} ${r0} +pair_coeff 1 1 20.0 ${al} ${r0} +pair_coeff 1 1 20.0 2.0 ${r0} +pair_coeff 1 1 20.0 2.0 1.2 +pair_modify shift yes +run 5 post no +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6 + ghost atom cutoff = 6 + binsize = 3, bins = 4 4 4 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair morse, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.32 | 4.38 | 4.56 Mbytes + Step Temp Press KinEng PotEng TotEng c_pe + 0 0 2683.187147 0 -30.02905654 -30.02905654 -15.01452827 + 1 146.0893547 2514.939772 1.30639385 -31.40065042 -30.09425657 -15.70032521 + 2 485.8091411 2063.804037 4.34431431 -34.55987817 -30.21556386 -17.27993908 + 3 822.0828974 1456.368913 7.351418888 -37.63613582 -30.28471693 -18.81806791 + 4 1018.806679 823.4383177 9.110607565 -39.39265114 -30.28204357 -19.69632557 + 5 1050.331347 253.0262957 9.392514704 -39.63687095 -30.24435625 -19.81843547 +Loop time of 0.000297435 on 4 procs for 5 steps with 4 atoms + + +shell rm -f walltest.restart +Total wall time: 0:00:00 diff --git a/examples/wall/wall.inc b/examples/wall/wall.inc new file mode 100644 index 0000000000..1b36f2c38e --- /dev/null +++ b/examples/wall/wall.inc @@ -0,0 +1,16 @@ + +clear +read_restart walltest.restart +# log ${name}.log + +compute ea move pe/atom +compute pe move reduce sum c_ea +special_bonds lj/coul 1.0 1.0 1.0 + +thermo_style custom step temp press ke pe etotal c_pe +thermo 1 +thermo_modify format float %14.10g + +fix 0 move nve +# dump 1 all custom 1 ${name}.dump id x fx +# dump_modify 1 format float %20.15g diff --git a/examples/wall/walltab.dat b/examples/wall/walltab.dat new file mode 100644 index 0000000000..53b2b42700 --- /dev/null +++ b/examples/wall/walltab.dat @@ -0,0 +1,1212 @@ +# DATE: 2023-02-23 UNITS: real +HARMONIC +N 400 FP 199.99999998802 200.000000002102 + + 1 0.01 1592.01 798 + 2 0.02 1584.04 796 + 3 0.03 1576.09 794 + 4 0.04 1568.16 792 + 5 0.05 1560.25 790 + 6 0.06 1552.36 788 + 7 0.07 1544.49 786 + 8 0.08 1536.64 784 + 9 0.09 1528.81 782 + 10 0.1 1521 780 + 11 0.11 1513.21 778 + 12 0.12 1505.44 776 + 13 0.13 1497.69 774 + 14 0.14 1489.96 772 + 15 0.15 1482.25 770 + 16 0.16 1474.56 768 + 17 0.17 1466.89 766 + 18 0.18 1459.24 764 + 19 0.19 1451.61 762 + 20 0.2 1444 760 + 21 0.21 1436.41 758 + 22 0.22 1428.84 756 + 23 0.23 1421.29 754 + 24 0.24 1413.76 752 + 25 0.25 1406.25 750 + 26 0.26 1398.76 748 + 27 0.27 1391.29 746 + 28 0.28 1383.84 744 + 29 0.29 1376.41 742 + 30 0.3 1369 740 + 31 0.31 1361.61 738 + 32 0.32 1354.24 736 + 33 0.33 1346.89 734 + 34 0.34 1339.56 732 + 35 0.35 1332.25 730 + 36 0.36 1324.96 728 + 37 0.37 1317.69 726 + 38 0.38 1310.44 724 + 39 0.39 1303.21 722 + 40 0.4 1296 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-0.306717065428139 + 399 3.99 -0.150617975739817 -0.30066666145589 + 400 4 -0.147641064738004 -0.29473516163338 diff --git a/lib/gpu/Makefile.cuda b/lib/gpu/Makefile.cuda index e02501d080..be8003e02e 100644 --- a/lib/gpu/Makefile.cuda +++ b/lib/gpu/Makefile.cuda @@ -54,7 +54,7 @@ BIN2C = $(CUDA_HOME)/bin/bin2c CUDR_CPP = mpicxx -DMPI_GERYON -DUCL_NO_EXIT -DMPICH_IGNORE_CXX_SEEK -DOMPI_SKIP_MPICXX=1 -fPIC CUDR_OPTS = -O2 $(LMP_INC) -CUDR = $(CUDR_CPP) $(CUDR_OPTS) $(CUDA_PROXY) $(CUDA_PRECISION) $(CUDA_INCLUDE) \ +CUDR = $(CUDR_CPP) $(CUDR_OPTS) $(CUDA_MPS) $(CUDA_PRECISION) $(CUDA_INCLUDE) \ $(CUDPP_OPT) # Headers for Geryon diff --git a/lib/gpu/Makefile.cuda_mps b/lib/gpu/Makefile.cuda_mps index d7820e4c34..06d2ef0339 100644 --- a/lib/gpu/Makefile.cuda_mps +++ b/lib/gpu/Makefile.cuda_mps @@ -30,7 +30,7 @@ AR = ar BSH = /bin/sh CUDPP_OPT = -CUDA_MPS = -DCUDA_PROXY +CUDA_MPS = -DCUDA_MPS_SUPPORT # device code compiler and settings @@ -53,7 +53,7 @@ BIN2C = $(CUDA_HOME)/bin/bin2c CUDR_CPP = mpicxx -fopenmp -DMPI_GERYON -DUCL_NO_EXIT -DMPICH_IGNORE_CXX_SEEK -DOMPI_SKIP_MPICXX=1 -fPIC CUDR_OPTS = -O2 $(LMP_INC) -CUDR = $(CUDR_CPP) $(CUDR_OPTS) $(CUDA_PROXY) $(CUDA_PRECISION) $(CUDA_INCLUDE) \ +CUDR = $(CUDR_CPP) $(CUDR_OPTS) $(CUDA_MPS) $(CUDA_PRECISION) $(CUDA_INCLUDE) \ $(CUDPP_OPT) # Headers for Geryon diff --git a/lib/gpu/Makefile.oneapi b/lib/gpu/Makefile.oneapi index d0ed78d0c4..9d11a0c4b0 100644 --- a/lib/gpu/Makefile.oneapi +++ b/lib/gpu/Makefile.oneapi @@ -18,7 +18,7 @@ OCL_CPP = mpiicpc -std=c++11 -diag-disable=10441 -DMPICH_IGNORE_CXX_SEEK \ $(LMP_INC) $(OCL_INC) $(CPP_OPT) OCL_LINK = -L$(ONEAPI_ROOT)/compiler/latest/linux/lib -lOpenCL OCL_PREC = -D_SINGLE_DOUBLE -OCL_TUNE = -DMPI_GERYON -DCUDA_PROXY -DGERYON_NUMA_FISSION -DUCL_NO_EXIT +OCL_TUNE = -DMPI_GERYON -DGERYON_NUMA_FISSION -DUCL_NO_EXIT BIN_DIR = ./ OBJ_DIR = ./ diff --git a/lib/gpu/README b/lib/gpu/README index ab7032b64d..51b21960ae 100644 --- a/lib/gpu/README +++ b/lib/gpu/README @@ -205,8 +205,7 @@ $(CUDA_HOME)/lib64/stubs), that can be used for linking. Best performance with the GPU library is typically with multiple MPI processes sharing the same GPU cards. For NVIDIA, this is most efficient with CUDA MPS enabled. To prevent runtime errors for GPUs configured in exclusive process -mode with MPS, the GPU library should be build with either of the equivalent --DCUDA_MPS_SUPPORT or -DCUDA_PROXY flags. +mode with MPS, the GPU library should be build with the -DCUDA_MPS_SUPPORT flag. ------------------------------------------------------------------------------ HIP BUILD NOTES @@ -244,7 +243,6 @@ _SINGLE_SINGLE Build library for single precision mode _SINGLE_DOUBLE Build library for mixed precision mode _DOUBLE_DOUBLE Build library for double precision mode CUDA_MPS_SUPPORT Do not generate errors for exclusive mode for CUDA -CUDA_PROXY Same as above MPI_GERYON Library should use MPI_Abort for unhandled errors GERYON_NUMA_FISSION Accelerators with main memory NUMA are split into multiple virtual accelerators for each NUMA node diff --git a/lib/gpu/lal_device.cpp b/lib/gpu/lal_device.cpp index dd3ce15827..891d67913e 100644 --- a/lib/gpu/lal_device.cpp +++ b/lib/gpu/lal_device.cpp @@ -277,7 +277,7 @@ int DeviceT::init_device(MPI_Comm /*world*/, MPI_Comm replica, const int ngpu, MPI_Comm_split(node_comm,my_gpu,0,&_comm_gpu); MPI_Comm_rank(_comm_gpu,&_gpu_rank); - #if !defined(CUDA_PROXY) && !defined(CUDA_MPS_SUPPORT) + #if !defined(CUDA_MPS_SUPPORT) if (_procs_per_gpu>1 && !gpu->sharing_supported(my_gpu)) return -7; #endif diff --git a/src/.gitignore b/src/.gitignore index ebe2b82f0e..0e13215506 100644 --- a/src/.gitignore +++ b/src/.gitignore @@ -62,6 +62,8 @@ /angle_lepton.h /dihedral_lepton.cpp /dihedral_lepton.h +/fix_wall_lepton.cpp +/fix_wall_lepton.h /lepton_utils.cpp /lepton_utils.h @@ -1465,6 +1467,8 @@ /zstd_file_writer.cpp /zstd_file_writer.h +/compute_pressure_alchemy.cpp +/compute_pressure_alchemy.h /atom_vec_smd.cpp /atom_vec_smd.h /compute_saed.cpp @@ -1531,8 +1535,8 @@ /fix_langevin_drude.h /fix_mol_swap.cpp /fix_mol_swap.h -/fix_pimd.cpp -/fix_pimd.h +/fix_alchemy.cpp +/fix_alchemy.h /fix_pimd_nvt.cpp /fix_pimd_nvt.h /fix_qbmsst.cpp diff --git a/src/COLLOID/fix_wall_colloid.cpp b/src/COLLOID/fix_wall_colloid.cpp index d21856bc60..3160fadb53 100644 --- a/src/COLLOID/fix_wall_colloid.cpp +++ b/src/COLLOID/fix_wall_colloid.cpp @@ -24,7 +24,6 @@ #include using namespace LAMMPS_NS; -using namespace FixConst; /* ---------------------------------------------------------------------- */ diff --git a/src/EXTRA-FIX/fix_wall_ees.cpp b/src/EXTRA-FIX/fix_wall_ees.cpp index bbddd919af..d9bc2a8450 100644 --- a/src/EXTRA-FIX/fix_wall_ees.cpp +++ b/src/EXTRA-FIX/fix_wall_ees.cpp @@ -26,7 +26,6 @@ #include using namespace LAMMPS_NS; -using namespace FixConst; /* ---------------------------------------------------------------------- */ diff --git a/src/EXTRA-FIX/fix_wall_reflect_stochastic.cpp b/src/EXTRA-FIX/fix_wall_reflect_stochastic.cpp index 7899c88473..c0b44530e8 100644 --- a/src/EXTRA-FIX/fix_wall_reflect_stochastic.cpp +++ b/src/EXTRA-FIX/fix_wall_reflect_stochastic.cpp @@ -31,7 +31,6 @@ #include using namespace LAMMPS_NS; -using namespace FixConst; enum{NONE,DIFFUSIVE,MAXWELL,CCL}; diff --git a/src/GRANULAR/fix_wall_gran_region.cpp b/src/GRANULAR/fix_wall_gran_region.cpp index f1bd55a7bc..68afce2b0b 100644 --- a/src/GRANULAR/fix_wall_gran_region.cpp +++ b/src/GRANULAR/fix_wall_gran_region.cpp @@ -29,7 +29,6 @@ #include using namespace LAMMPS_NS; -using namespace FixConst; /* ---------------------------------------------------------------------- */ diff --git a/src/KOKKOS/fix_wall_lj93_kokkos.cpp b/src/KOKKOS/fix_wall_lj93_kokkos.cpp index 03bf6cf8ea..dff47f1c30 100644 --- a/src/KOKKOS/fix_wall_lj93_kokkos.cpp +++ b/src/KOKKOS/fix_wall_lj93_kokkos.cpp @@ -19,7 +19,6 @@ #include "atom_masks.h" using namespace LAMMPS_NS; -using namespace FixConst; /* ---------------------------------------------------------------------- */ diff --git a/src/KOKKOS/fix_wall_reflect_kokkos.cpp b/src/KOKKOS/fix_wall_reflect_kokkos.cpp index 32b9ee61b1..a8a01c1926 100644 --- a/src/KOKKOS/fix_wall_reflect_kokkos.cpp +++ b/src/KOKKOS/fix_wall_reflect_kokkos.cpp @@ -24,7 +24,6 @@ #include using namespace LAMMPS_NS; -using namespace FixConst; enum{XLO=0,XHI=1,YLO=2,YHI=3,ZLO=4,ZHI=5}; enum{NONE=0,EDGE,CONSTANT,VARIABLE}; diff --git a/src/KOKKOS/mliap_unified_couple_kokkos.pyx b/src/KOKKOS/mliap_unified_couple_kokkos.pyx index 37326263d3..5e274d7f36 100644 --- a/src/KOKKOS/mliap_unified_couple_kokkos.pyx +++ b/src/KOKKOS/mliap_unified_couple_kokkos.pyx @@ -115,7 +115,6 @@ cdef create_array(device, void *pointer, shape,is_int): size=1 for i in shape: size = size*i - if ( device == 1): mem = cupy.cuda.UnownedMemory(ptr=int( pointer), owner=None, size=size) memptr = cupy.cuda.MemoryPointer(mem, 0) @@ -146,10 +145,18 @@ cdef class MLIAPDataPy: self.data = NULL def update_pair_energy_cpu(self, eij): - cdef double[:] eij_arr = eij + cdef double[:] eij_arr + try: + eij_arr = eij + except: + eij_arr = eij.detach().numpy().astype(np.double) update_pair_energy(self.data, &eij_arr[0]) def update_pair_energy_gpu(self, eij): - cdef uintptr_t ptr = eij.data.ptr + cdef uintptr_t ptr; + try: + ptr = eij.data.ptr + except: + ptr = eij.data_ptr() update_pair_energy(self.data, ptr) def update_pair_energy(self, eij): if self.data.dev==0: @@ -158,10 +165,18 @@ cdef class MLIAPDataPy: self.update_pair_energy_gpu(eij) def update_pair_forces_cpu(self, fij): - cdef double[:, ::1] fij_arr = fij + cdef double[:, ::1] fij_arr + try: + fij_arr = fij + except: + fij_arr = fij.detach().numpy().astype(np.double) update_pair_forces(self.data, &fij_arr[0][0]) def update_pair_forces_gpu(self, fij): - cdef uintptr_t ptr = fij.data.ptr + cdef uintptr_t ptr + try: + ptr = fij.data.ptr + except: + ptr = fij.data_ptr() update_pair_forces(self.data, ptr) def update_pair_forces(self, fij): if self.data.dev==0: @@ -172,7 +187,8 @@ cdef class MLIAPDataPy: def f(self): if self.data.f is NULL: return None - return cupy.asarray( self.data.f) + return create_array(self.data.dev, self.data.f, [self.ntotal, 3],False) + @property def size_gradforce(self): @@ -205,14 +221,11 @@ cdef class MLIAPDataPy: descriptors_view[:] = value_view print("This code has not been tested or optimized for the GPU, if you are getting this warning optimize descriptors") - @write_only_property - def eatoms(self, value): + @property + def eatoms(self): if self.data.eatoms is NULL: raise ValueError("attempt to set NULL eatoms") - cdef double[:] eatoms_view = &self.data.eatoms[0] - cdef double[:] value_view = value - eatoms_view[:] = value_view - print("This code has not been tested or optimized for the GPU, if you are getting this warning optimize eatoms") + return create_array(self.data.dev, self.data.eatoms, [self.nlistatoms],False) @write_only_property @@ -351,7 +364,7 @@ cdef class MLIAPDataPy: # Interface between C and Python compute functions -cdef class MLIAPUnifiedInterface: +cdef class MLIAPUnifiedInterfaceKokkos: cdef MLIAPDummyModel * model cdef MLIAPDummyDescriptor * descriptor cdef unified_impl @@ -404,7 +417,7 @@ cdef public object mliap_unified_connect_kokkos(char *fname, MLIAPDummyModel * m with open(str_fname, 'rb') as pfile: unified = pickle.load(pfile) - unified_int = MLIAPUnifiedInterface(unified) + unified_int = MLIAPUnifiedInterfaceKokkos(unified) unified_int.model = model unified_int.descriptor = descriptor diff --git a/src/KOKKOS/mliap_unified_kokkos.cpp b/src/KOKKOS/mliap_unified_kokkos.cpp index bfb9193df6..1fdf039473 100644 --- a/src/KOKKOS/mliap_unified_kokkos.cpp +++ b/src/KOKKOS/mliap_unified_kokkos.cpp @@ -269,7 +269,6 @@ MLIAPBuildUnifiedKokkos_t LAMMPS_NS::build_unified(char *unified_fna void LAMMPS_NS::update_pair_energy(MLIAPDataKokkosDevice *data, double *eij) { - double e_total = 0.0; auto d_eatoms = data->eatoms; auto d_pair_i= data->pair_i; const auto nlistatoms = data->nlistatoms; @@ -301,8 +300,13 @@ void LAMMPS_NS::update_pair_forces(MLIAPDataKokkosDevice *data, double *fij) auto j_atoms = data->jatoms; auto vflag = data->vflag; auto rij = data->rij; - int vflag_either=data->pairmliap->vflag_either, vflag_global=data->pairmliap->vflag_global, vflag_atom=data->pairmliap->vflag_atom; + int vflag_global=data->pairmliap->vflag_global, vflag_atom=data->pairmliap->vflag_atom; + if (vflag_atom) { + data->pairmliap->k_vatom.template modify(); + data->pairmliap->k_vatom.template sync(); + } auto d_vatom = data->pairmliap->k_vatom.template view(); + Kokkos::View virial("virial"); Kokkos::parallel_for(data->npairs,KOKKOS_LAMBDA (int ii) { @@ -310,7 +314,6 @@ void LAMMPS_NS::update_pair_forces(MLIAPDataKokkosDevice *data, double *fij) int ii3 = ii * 3; int i = pair_i[ii]; int j = j_atoms[ii]; - // must not count any contribution where i is not a local atom if (i < nlistatoms) { Kokkos::atomic_add(&f[i*3+0], fij[ii3+0]); @@ -335,7 +338,7 @@ void LAMMPS_NS::update_pair_forces(MLIAPDataKokkosDevice *data, double *fij) Kokkos::atomic_add(&virial[4], v[4]); Kokkos::atomic_add(&virial[5], v[5]); } - if (vflag_atom) { + if (vflag_atom ) { Kokkos::atomic_add(&d_vatom(i,0), 0.5*v[0]); Kokkos::atomic_add(&d_vatom(i,1), 0.5*v[1]); Kokkos::atomic_add(&d_vatom(i,2), 0.5*v[2]); @@ -373,15 +376,11 @@ template class MLIAPDummyModelKokkos; template class MLIAPDummyDescriptorKokkos; template MLIAPBuildUnifiedKokkos_t LAMMPS_NS::build_unified(char *unified_fname, MLIAPDataKokkos *data, LAMMPS *lmp, char *coefffilename); -//template void LAMMPS_NS::update_pair_energy(MLIAPDataKokkos *data, double *eij); -//template void LAMMPS_NS::update_pair_forces(MLIAPDataKokkos *data, double *fij); #ifdef LMP_KOKKOS_GPU template class MLIAPDummyModelKokkos; template class MLIAPDummyDescriptorKokkos; template MLIAPBuildUnifiedKokkos_t LAMMPS_NS::build_unified(char *unified_fname, MLIAPDataKokkos *data, LAMMPS *lmp, char *coefffilename); -//template void LAMMPS_NS::update_pair_energy(MLIAPDataKokkos *data, double *eij); -//template void LAMMPS_NS::update_pair_forces(MLIAPDataKokkos *data, double *fij); #endif } #endif diff --git a/src/KOKKOS/pair_mliap_kokkos.cpp b/src/KOKKOS/pair_mliap_kokkos.cpp index 558901c6ff..d19d81e314 100644 --- a/src/KOKKOS/pair_mliap_kokkos.cpp +++ b/src/KOKKOS/pair_mliap_kokkos.cpp @@ -74,7 +74,6 @@ void PairMLIAPKokkos::compute(int eflag, int vflag) int is_kokkos_descriptor = (dynamic_cast*>(descriptor)) != nullptr; auto model_space = is_kokkos_model ? execution_space : Host; auto descriptor_space = is_kokkos_descriptor? execution_space : Host; - // consistency checks if (data->ndescriptors != model->ndescriptors) error->all(FLERR, "Incompatible model and descriptor descriptor count"); @@ -107,12 +106,14 @@ void PairMLIAPKokkos::compute(int eflag, int vflag) k_data->sync(model_space, IELEMS_MASK | DESCRIPTORS_MASK); model->compute_gradients(data); k_data->modified(model_space, BETAS_MASK); - if (eflag_atom) + if (eflag_atom) { k_data->modified(model_space, EATOMS_MASK); + } // calculate force contributions beta_i*dB_i/dR_j atomKK->sync(descriptor_space,F_MASK); k_data->sync(descriptor_space, NUMNEIGHS_MASK | IATOMS_MASK | IELEMS_MASK | ELEMS_MASK | BETAS_MASK | JATOMS_MASK | PAIR_I_MASK | JELEMS_MASK | RIJ_MASK ); + descriptor->compute_forces(data); e_tally(data); @@ -293,7 +294,7 @@ void PairMLIAPKokkos::e_tally(MLIAPData* data) if (eflag_global) eng_vdwl += data->energy; if (eflag_atom) { MLIAPDataKokkos *k_data = static_cast*>(data); - k_data->sync(execution_space, IATOMS_MASK | EATOMS_MASK); + k_data->sync(execution_space, IATOMS_MASK | EATOMS_MASK, true); auto d_iatoms = k_data->k_iatoms.template view(); auto d_eatoms = k_data->k_eatoms.template view(); auto d_eatom = k_eatom.template view(); diff --git a/src/LEPTON/fix_wall_lepton.cpp b/src/LEPTON/fix_wall_lepton.cpp new file mode 100644 index 0000000000..a81d3c4edb --- /dev/null +++ b/src/LEPTON/fix_wall_lepton.cpp @@ -0,0 +1,138 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS development team: developers@lammps.org + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "fix_wall_lepton.h" +#include "atom.h" +#include "error.h" + +#include "Lepton.h" +#include "lepton_utils.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +FixWallLepton::FixWallLepton(LAMMPS *lmp, int narg, char **arg) : FixWall(lmp, narg, arg) +{ + dynamic_group_allow = 1; +} + +/* ---------------------------------------------------------------------- */ + +void FixWallLepton::post_constructor() +{ + // check validity of lepton expression + + for (int m = 0; m < nwall; ++m) { + // remove whitespace and quotes from expression string and then + // check if the expression can be parsed and evaluated without error + std::string exp_one = LeptonUtils::condense(lstr[m]); + try { + auto parsed = Lepton::Parser::parse(LeptonUtils::substitute(exp_one, lmp)); + auto wallpot = parsed.createCompiledExpression(); + auto wallforce = parsed.differentiate("r").createCompiledExpression(); + wallpot.getVariableReference("r") = 0.0; + wallforce.getVariableReference("r") = 0.0; + wallpot.evaluate(); + wallforce.evaluate(); + } catch (std::exception &e) { + error->all(FLERR, e.what()); + } + } +} + +/* ---------------------------------------------------------------------- + compute the potential energy offset so it can be shifted to zero at the cutoff +------------------------------------------------------------------------- */ + +void FixWallLepton::precompute(int m) +{ + std::string exp_one = LeptonUtils::condense(lstr[m]); + auto parsed = Lepton::Parser::parse(LeptonUtils::substitute(exp_one, lmp)); + auto wallpot = parsed.createCompiledExpression(); + + try { + wallpot.getVariableReference("rc") = cutoff[m]; + } catch (std::exception &) { + ; // do nothing + } + + wallpot.getVariableReference("r") = cutoff[m]; + offset[m] = wallpot.evaluate(); +} + +/* ---------------------------------------------------------------------- + interaction of all particles in group with a wall + m = index of wall coeffs + which = xlo,xhi,ylo,yhi,zlo,zhi + error if any particle is on or behind wall +------------------------------------------------------------------------- */ + +void FixWallLepton::wall_particle(int m, int which, double coord) +{ + std::string exp_one = LeptonUtils::condense(lstr[m]); + auto parsed = Lepton::Parser::parse(LeptonUtils::substitute(exp_one, lmp)); + auto wallpot = parsed.createCompiledExpression(); + auto wallforce = parsed.differentiate("r").createCompiledExpression(); + + // set cutoff value, if used + try { + wallpot.getVariableReference("rc") = cutoff[m]; + wallforce.getVariableReference("rc") = cutoff[m]; + } catch (std::exception &) { + ; // do nothing + } + + double delta, fwall, vn; + + double **x = atom->x; + double **f = atom->f; + int *mask = atom->mask; + int nlocal = atom->nlocal; + + int dim = which / 2; + int side = which % 2; + if (side == 0) side = -1; + + int onflag = 0; + + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) { + if (side < 0) + delta = x[i][dim] - coord; + else + delta = coord - x[i][dim]; + if (delta >= cutoff[m]) continue; + if (delta <= 0.0) { + onflag = 1; + continue; + } + wallpot.getVariableReference("r") = delta; + wallforce.getVariableReference("r") = delta; + + fwall = side * wallforce.evaluate(); + f[i][dim] += fwall; + ewall[0] += wallpot.evaluate() - offset[m]; + ewall[m + 1] += fwall; + + if (evflag) { + if (side < 0) + vn = -fwall * delta; + else + vn = fwall * delta; + v_tally(dim, i, vn); + } + } + } + if (onflag) error->one(FLERR, "Particle on or inside fix {} surface", style); +} diff --git a/src/LEPTON/fix_wall_lepton.h b/src/LEPTON/fix_wall_lepton.h new file mode 100644 index 0000000000..4c1df801c7 --- /dev/null +++ b/src/LEPTON/fix_wall_lepton.h @@ -0,0 +1,41 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS development team: developers@lammps.org + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef FIX_CLASS +// clang-format off +FixStyle(wall/lepton,FixWallLepton); +// clang-format on +#else + +#ifndef LMP_FIX_WALL_LEPTON_H +#define LMP_FIX_WALL_LEPTON_H + +#include "fix_wall.h" + +namespace LAMMPS_NS { + +class FixWallLepton : public FixWall { + public: + FixWallLepton(class LAMMPS *, int, char **); + void post_constructor() override; + void precompute(int) override; + void wall_particle(int, int, double) override; + + protected: + double offset[6]; +}; + +} // namespace LAMMPS_NS + +#endif +#endif diff --git a/src/PYTHON/python_impl.cpp b/src/PYTHON/python_impl.cpp index 9177381a35..57f8ea1cf0 100644 --- a/src/PYTHON/python_impl.cpp +++ b/src/PYTHON/python_impl.cpp @@ -35,6 +35,17 @@ // However, that exposes -too many- headers. #include "mliap_model_python_couple.h" #include "mliap_unified_couple.h" +#ifdef LMP_KOKKOS +#include "mliap_model_python_kokkos.h" +#include "mliap_unified_kokkos.h" +// The above should somehow really be included in the next file. +// We could get around this with cython --capi-reexport-cincludes +// However, that exposes -too many- headers. +#include "mliap_model_python_couple_kokkos.h" +#include "mliap_unified_couple_kokkos.h" + + +#endif #endif using namespace LAMMPS_NS; @@ -71,6 +82,16 @@ PythonImpl::PythonImpl(LAMMPS *lmp) : Pointers(lmp) err = PyImport_AppendInittab("mliap_unified_couple", PyInit_mliap_unified_couple); if (err) error->all(FLERR, "Could not register MLIAPPY unified embedded python module."); +#ifdef LMP_KOKKOS + // Inform python intialization scheme of the mliappy module. + // This -must- happen before python is initialized. + err = PyImport_AppendInittab("mliap_model_python_couple_kokkos", PyInit_mliap_model_python_couple_kokkos); + if (err) error->all(FLERR, "Could not register MLIAPPY embedded python module."); + + err = PyImport_AppendInittab("mliap_unified_couple_kokkos", PyInit_mliap_unified_couple_kokkos); + if (err) error->all(FLERR, "Could not register MLIAPPY unified embedded python module."); + +#endif #endif Py_Initialize(); diff --git a/src/REACTION/fix_bond_react.cpp b/src/REACTION/fix_bond_react.cpp index edddac1cb8..eaf4dfd0ec 100644 --- a/src/REACTION/fix_bond_react.cpp +++ b/src/REACTION/fix_bond_react.cpp @@ -216,7 +216,7 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : // this looks excessive // the price of vectorization (all reactions in one command)? - memory->create(rxn_name,nreacts,MAXLINE,"bond/react:rxn_name"); + memory->create(rxn_name,nreacts,MAXNAME,"bond/react:rxn_name"); memory->create(nevery,nreacts,"bond/react:nevery"); memory->create(cutsq,nreacts,2,"bond/react:cutsq"); memory->create(unreacted_mol,nreacts,"bond/react:unreacted_mol"); @@ -287,7 +287,7 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : iarg++; int n = strlen(arg[iarg]) + 1; - if (n > MAXLINE) error->all(FLERR,"Reaction name (react-ID) is too long (limit: 256 characters)"); + if (n > MAXNAME) error->all(FLERR,"Reaction name (react-ID) is too long (limit: 256 characters)"); strcpy(rxn_name[rxn],arg[iarg++]); int groupid = group->find(arg[iarg++]); @@ -545,6 +545,7 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : attempt = nullptr; nattempt = nullptr; allnattempt = 0; + my_num_mega = 0; local_num_mega = 0; ghostly_num_mega = 0; restore = nullptr; @@ -555,6 +556,7 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : glove_counter = 0; guess_branch = new int[MAXGUESS](); pioneer_count = new int[max_natoms]; + my_mega_glove = nullptr; local_mega_glove = nullptr; ghostly_mega_glove = nullptr; global_mega_glove = nullptr; @@ -654,6 +656,7 @@ FixBondReact::~FixBondReact() memory->destroy(restore); memory->destroy(glove); memory->destroy(pioneers); + memory->destroy(my_mega_glove); memory->destroy(local_mega_glove); memory->destroy(ghostly_mega_glove); } @@ -936,7 +939,7 @@ void FixBondReact::post_integrate() if (var_flag[NRATE][rxnID] == 1) { my_nrate = input->variable->compute_equal(var_id[NRATE][rxnID]); } else my_nrate = rate_limit[1][rxnID]; - if (nrxns_delta > my_nrate) rate_limit_flag = 0; + if (nrxns_delta >= my_nrate) rate_limit_flag = 0; } } if ((update->ntimestep % nevery[rxnID]) || @@ -1251,6 +1254,7 @@ void FixBondReact::close_partner() void FixBondReact::superimpose_algorithm() { const int nprocs = comm->nprocs; + my_num_mega = 0; local_num_mega = 0; ghostly_num_mega = 0; @@ -1269,6 +1273,7 @@ void FixBondReact::superimpose_algorithm() memory->destroy(restore); memory->destroy(glove); memory->destroy(pioneers); + memory->destroy(my_mega_glove); memory->destroy(local_mega_glove); memory->destroy(ghostly_mega_glove); } @@ -1277,18 +1282,14 @@ void FixBondReact::superimpose_algorithm() memory->create(restore_pt,MAXGUESS,4,"bond/react:restore_pt"); memory->create(pioneers,max_natoms,"bond/react:pioneers"); memory->create(restore,max_natoms,MAXGUESS*4,"bond/react:restore"); - memory->create(local_mega_glove,max_natoms+1,allnattempt,"bond/react:local_mega_glove"); - memory->create(ghostly_mega_glove,max_natoms+1,allnattempt,"bond/react:ghostly_mega_glove"); + memory->create(my_mega_glove,max_natoms+1,allnattempt,"bond/react:local_mega_glove"); + + for (int i = 0; i < max_natoms+1; i++) + for (int j = 0; j < allnattempt; j++) + my_mega_glove[i][j] = 0; attempted_rxn = 1; - for (int i = 0; i < max_natoms+1; i++) { - for (int j = 0; j < allnattempt; j++) { - local_mega_glove[i][j] = 0; - ghostly_mega_glove[i][j] = 0; - } - } - // let's finally begin the superimpose loop for (rxnID = 0; rxnID < nreacts; rxnID++) { for (lcl_inst = 0; lcl_inst < nattempt[rxnID]; lcl_inst++) { @@ -1335,7 +1336,11 @@ void FixBondReact::superimpose_algorithm() status = REJECT; } else { status = ACCEPT; - glove_ghostcheck(); + my_mega_glove[0][my_num_mega] = rxnID; + for (int i = 0; i < onemol->natoms; i++) { + my_mega_glove[i+1][my_num_mega] = glove[i][1]; + } + my_num_mega++; } } else status = REJECT; } @@ -1378,7 +1383,13 @@ void FixBondReact::superimpose_algorithm() if (status == ACCEPT) { if (fraction[rxnID] < 1.0 && random[rxnID]->uniform() >= fraction[rxnID]) status = REJECT; - else glove_ghostcheck(); + else { + my_mega_glove[0][my_num_mega] = rxnID; + for (int i = 0; i < onemol->natoms; i++) { + my_mega_glove[i+1][my_num_mega] = glove[i][1]; + } + my_num_mega++; + } } hang_catch++; // let's go ahead and catch the simplest of hangs @@ -1394,8 +1405,19 @@ void FixBondReact::superimpose_algorithm() global_megasize = 0; - ghost_glovecast(); // consolidate all mega_gloves to all processors + memory->create(local_mega_glove,max_natoms+1,my_num_mega,"bond/react:local_mega_glove"); + memory->create(ghostly_mega_glove,max_natoms+1,my_num_mega,"bond/react:ghostly_mega_glove"); + + for (int i = 0; i < max_natoms+1; i++) { + for (int j = 0; j < my_num_mega; j++) { + local_mega_glove[i][j] = 0; + ghostly_mega_glove[i][j] = 0; + } + } + dedup_mega_gloves(LOCAL); // make sure atoms aren't added to more than one reaction + glove_ghostcheck(); // split into 'local' and 'global' + ghost_glovecast(); // consolidate all mega_gloves to all processors MPI_Allreduce(&local_rxn_count[0],&reaction_count[0],nreacts,MPI_INT,MPI_SUM,world); @@ -2639,14 +2661,14 @@ void FixBondReact::dedup_mega_gloves(int dedup_mode) { // dedup_mode == LOCAL for local_dedup // dedup_mode == GLOBAL for global_mega_glove - for (int i = 0; i < nreacts; i++) { - if (dedup_mode == LOCAL) local_rxn_count[i] = 0; - if (dedup_mode == GLOBAL) ghostly_rxn_count[i] = 0; - } + + if (dedup_mode == GLOBAL) + for (int i = 0; i < nreacts; i++) + ghostly_rxn_count[i] = 0; int dedup_size = 0; if (dedup_mode == LOCAL) { - dedup_size = local_num_mega; + dedup_size = my_num_mega; } else if (dedup_mode == GLOBAL) { dedup_size = global_megasize; } @@ -2657,7 +2679,7 @@ void FixBondReact::dedup_mega_gloves(int dedup_mode) if (dedup_mode == LOCAL) { for (int i = 0; i < dedup_size; i++) { for (int j = 0; j < max_natoms+1; j++) { - dedup_glove[j][i] = local_mega_glove[j][i]; + dedup_glove[j][i] = my_mega_glove[j][i]; } } } else if (dedup_mode == GLOBAL) { @@ -2671,11 +2693,8 @@ void FixBondReact::dedup_mega_gloves(int dedup_mode) // dedup_mask is size dedup_size and filters reactions that have been deleted // a value of 1 means this reaction instance has been deleted int *dedup_mask = new int[dedup_size]; - int *dup_list = new int[dedup_size]; - for (int i = 0; i < dedup_size; i++) { dedup_mask[i] = 0; - dup_list[i] = 0; } // let's randomly mix up our reaction instances first @@ -2699,60 +2718,40 @@ void FixBondReact::dedup_mega_gloves(int dedup_mode) for (int i = 0; i < dedup_size; i++) { if (dedup_mask[i] == 0) { - int num_dups = 0; int myrxnid1 = dedup_glove[0][i]; onemol = atom->molecules[unreacted_mol[myrxnid1]]; for (int j = 0; j < onemol->natoms; j++) { int check1 = dedup_glove[j+1][i]; for (int ii = i + 1; ii < dedup_size; ii++) { - int already_listed = 0; - for (int jj = 0; jj < num_dups; jj++) { - if (dup_list[jj] == ii) { - already_listed = 1; - break; - } - } - if (dedup_mask[ii] == 0 && already_listed == 0) { + if (dedup_mask[ii] == 0) { int myrxnid2 = dedup_glove[0][ii]; twomol = atom->molecules[unreacted_mol[myrxnid2]]; for (int jj = 0; jj < twomol->natoms; jj++) { int check2 = dedup_glove[jj+1][ii]; if (check2 == check1) { - // add this rxn instance as well - if (num_dups == 0) dup_list[num_dups++] = i; - dup_list[num_dups++] = ii; + dedup_mask[ii] = 1; break; } } } } } - // here we choose random number and therefore reaction instance - int myrand = 1; - if (num_dups > 0) { - myrand = floor(random[0]->uniform()*num_dups); - for (int iii = 0; iii < num_dups; iii++) { - if (iii != myrand) dedup_mask[dup_list[iii]] = 1; - } - } } } // we must update local_mega_glove and local_megasize // we can simply overwrite local_mega_glove column by column if (dedup_mode == LOCAL) { - int new_local_megasize = 0; - for (int i = 0; i < local_num_mega; i++) { + int my_new_megasize = 0; + for (int i = 0; i < my_num_mega; i++) { if (dedup_mask[i] == 0) { - local_rxn_count[(int) dedup_glove[0][i]]++; for (int j = 0; j < max_natoms+1; j++) { - local_mega_glove[j][new_local_megasize] = dedup_glove[j][i]; + my_mega_glove[j][my_new_megasize] = dedup_glove[j][i]; } - new_local_megasize++; + my_new_megasize++; } } - - local_num_mega = new_local_megasize; + my_num_mega = my_new_megasize; } // we must update global_mega_glove and global_megasize @@ -2773,7 +2772,6 @@ void FixBondReact::dedup_mega_gloves(int dedup_mode) memory->destroy(dedup_glove); delete [] dedup_mask; - delete [] dup_list; } /* ---------------------------------------------------------------------- @@ -2826,40 +2824,47 @@ void FixBondReact::glove_ghostcheck() // here we add glove to either local_mega_glove or ghostly_mega_glove // ghostly_mega_glove includes atoms that are ghosts, either of this proc or another // 'ghosts of another' indication taken from comm->sendlist + // also includes local gloves that overlap with ghostly gloves, to get dedup right - int ghostly = 0; -#if !defined(MPI_STUBS) - if (comm->style == Comm::BRICK) { - if (create_atoms_flag[rxnID] == 1) { - ghostly = 1; - } else { - for (int i = 0; i < onemol->natoms; i++) { - int ilocal = atom->map(glove[i][1]); - if (ilocal >= atom->nlocal || localsendlist[ilocal] == 1) { - ghostly = 1; - break; + for (int i = 0; i < nreacts; i++) + local_rxn_count[i] = 0; + + for (int i = 0; i < my_num_mega; i++) { + rxnID = my_mega_glove[0][i]; + onemol = atom->molecules[unreacted_mol[rxnID]]; + int ghostly = 0; + #if !defined(MPI_STUBS) + if (comm->style == Comm::BRICK) { + if (create_atoms_flag[rxnID] == 1) { + ghostly = 1; + } else { + for (int j = 0; j < onemol->natoms; j++) { + int ilocal = atom->map(my_mega_glove[j+1][i]); + if (ilocal >= atom->nlocal || localsendlist[ilocal] == 1) { + ghostly = 1; + break; + } } } + } else { + ghostly = 1; } - } else { - ghostly = 1; - } -#endif + #endif - if (ghostly == 1) { - ghostly_mega_glove[0][ghostly_num_mega] = rxnID; - ghostly_rxn_count[rxnID]++; //for debuginng - for (int i = 0; i < onemol->natoms; i++) { - ghostly_mega_glove[i+1][ghostly_num_mega] = glove[i][1]; + if (ghostly == 1) { + ghostly_mega_glove[0][ghostly_num_mega] = rxnID; + for (int j = 0; j < onemol->natoms+1; j++) { + ghostly_mega_glove[j][ghostly_num_mega] = my_mega_glove[j][i]; + } + ghostly_num_mega++; + } else { + local_mega_glove[0][local_num_mega] = rxnID; + local_rxn_count[rxnID]++; + for (int j = 0; j < onemol->natoms+1; j++) { + local_mega_glove[j][local_num_mega] = my_mega_glove[j][i]; + } + local_num_mega++; } - ghostly_num_mega++; - } else { - local_mega_glove[0][local_num_mega] = rxnID; - local_rxn_count[rxnID]++; //for debuginng - for (int i = 0; i < onemol->natoms; i++) { - local_mega_glove[i+1][local_num_mega] = glove[i][1]; - } - local_num_mega++; } } @@ -3903,6 +3908,7 @@ read map file void FixBondReact::read_map_file(int myrxn) { + int rv; char line[MAXLINE],keyword[MAXLINE]; char *eof,*ptr; @@ -3927,16 +3933,24 @@ void FixBondReact::read_map_file(int myrxn) if (strstr(line,"edgeIDs")) sscanf(line,"%d",&nedge); else if (strstr(line,"equivalences")) { - sscanf(line,"%d",&nequivalent); + rv = sscanf(line,"%d",&nequivalent); + if (rv != 1) error->one(FLERR, "Map file header is incorrectly formatted"); if (nequivalent != onemol->natoms) error->one(FLERR,"Fix bond/react: Number of equivalences in map file must " "equal number of atoms in reaction templates"); } - else if (strstr(line,"deleteIDs")) sscanf(line,"%d",&ndelete); - else if (strstr(line,"createIDs")) sscanf(line,"%d",&ncreate); - else if (strstr(line,"chiralIDs")) sscanf(line,"%d",&nchiral); - else if (strstr(line,"constraints")) { - sscanf(line,"%d",&nconstraints[myrxn]); + else if (strstr(line,"deleteIDs")) { + rv = sscanf(line,"%d",&ndelete); + if (rv != 1) error->one(FLERR, "Map file header is incorrectly formatted"); + } else if (strstr(line,"createIDs")) { + rv = sscanf(line,"%d",&ncreate); + if (rv != 1) error->one(FLERR, "Map file header is incorrectly formatted"); + } else if (strstr(line,"chiralIDs")) { + rv = sscanf(line,"%d",&nchiral); + if (rv != 1) error->one(FLERR, "Map file header is incorrectly formatted"); + } else if (strstr(line,"constraints")) { + rv = sscanf(line,"%d",&nconstraints[myrxn]); + if (rv != 1) error->one(FLERR, "Map file header is incorrectly formatted"); if (maxnconstraints < nconstraints[myrxn]) maxnconstraints = nconstraints[myrxn]; constraints.resize(maxnconstraints, std::vector(nreacts)); } else break; @@ -3956,11 +3970,13 @@ void FixBondReact::read_map_file(int myrxn) if (comm->me == 0) error->warning(FLERR,"Fix bond/react: The BondingIDs section title has been deprecated. Please use InitiatorIDs instead."); bondflag = 1; readline(line); - sscanf(line,"%d",&ibonding[myrxn]); + rv = sscanf(line,"%d",&ibonding[myrxn]); + if (rv != 1) error->one(FLERR, "InitiatorIDs section is incorrectly formatted"); if (ibonding[myrxn] > onemol->natoms) error->one(FLERR,"Fix bond/react: Invalid template atom ID in map file"); readline(line); - sscanf(line,"%d",&jbonding[myrxn]); + rv = sscanf(line,"%d",&jbonding[myrxn]); + if (rv != 1) error->one(FLERR, "InitiatorIDs section is incorrectly formatted"); if (jbonding[myrxn] > onemol->natoms) error->one(FLERR,"Fix bond/react: Invalid template atom ID in map file"); } else if (strcmp(keyword,"EdgeIDs") == 0) { @@ -3991,10 +4007,11 @@ void FixBondReact::EdgeIDs(char *line, int myrxn) { // puts a 1 at edge(edgeID) - int tmp; + int tmp,rv; for (int i = 0; i < nedge; i++) { readline(line); - sscanf(line,"%d",&tmp); + rv = sscanf(line,"%d",&tmp); + if (rv != 1) error->one(FLERR, "EdgeIDs section is incorrectly formatted"); if (tmp > onemol->natoms) error->one(FLERR,"Fix bond/react: Invalid template atom ID in map file"); edge[tmp-1][myrxn] = 1; @@ -4003,11 +4020,11 @@ void FixBondReact::EdgeIDs(char *line, int myrxn) void FixBondReact::Equivalences(char *line, int myrxn) { - int tmp1; - int tmp2; + int tmp1,tmp2,rv; for (int i = 0; i < nequivalent; i++) { readline(line); - sscanf(line,"%d %d",&tmp1,&tmp2); + rv = sscanf(line,"%d %d",&tmp1,&tmp2); + if (rv != 2) error->one(FLERR, "Equivalences section is incorrectly formatted"); if (tmp1 > onemol->natoms || tmp2 > twomol->natoms) error->one(FLERR,"Fix bond/react: Invalid template atom ID in map file"); //equivalences is-> clmn 1: post-reacted, clmn 2: pre-reacted @@ -4021,10 +4038,11 @@ void FixBondReact::Equivalences(char *line, int myrxn) void FixBondReact::DeleteAtoms(char *line, int myrxn) { - int tmp; + int tmp,rv; for (int i = 0; i < ndelete; i++) { readline(line); - sscanf(line,"%d",&tmp); + rv = sscanf(line,"%d",&tmp); + if (rv != 1) error->one(FLERR, "DeleteIDs section is incorrectly formatted"); if (tmp > onemol->natoms) error->one(FLERR,"Fix bond/react: Invalid template atom ID in map file"); delete_atoms[tmp-1][myrxn] = 1; @@ -4034,10 +4052,11 @@ void FixBondReact::DeleteAtoms(char *line, int myrxn) void FixBondReact::CreateAtoms(char *line, int myrxn) { create_atoms_flag[myrxn] = 1; - int tmp; + int tmp,rv; for (int i = 0; i < ncreate; i++) { readline(line); - sscanf(line,"%d",&tmp); + rv = sscanf(line,"%d",&tmp); + if (rv != 1) error->one(FLERR, "CreateIDs section is incorrectly formatted"); create_atoms[tmp-1][myrxn] = 1; } if (twomol->xflag == 0) @@ -4055,10 +4074,11 @@ void FixBondReact::CustomCharges(int ifragment, int myrxn) void FixBondReact::ChiralCenters(char *line, int myrxn) { - int tmp; + int tmp,rv; for (int i = 0; i < nchiral; i++) { readline(line); - sscanf(line,"%d",&tmp); + rv = sscanf(line,"%d",&tmp); + if (rv != 1) error->one(FLERR, "ChiralIDs section is incorrectly formatted"); if (tmp > onemol->natoms) error->one(FLERR,"Fix bond/react: Invalid template atom ID in map file"); chiral_atoms[tmp-1][0][myrxn] = 1; @@ -4088,6 +4108,7 @@ void FixBondReact::ChiralCenters(char *line, int myrxn) void FixBondReact::ReadConstraints(char *line, int myrxn) { + int rv; double tmp[MAXCONARGS]; char **strargs,*ptr,*lptr; memory->create(strargs,MAXCONARGS,MAXLINE,"bond/react:strargs"); @@ -4129,10 +4150,12 @@ void FixBondReact::ReadConstraints(char *line, int myrxn) } if ((ptr = strchr(lptr,')'))) *ptr = '\0'; - sscanf(line,"%s",constraint_type); + rv = sscanf(line,"%s",constraint_type); + if (rv != 1) error->one(FLERR, "Constraints section is incorrectly formatted"); if (strcmp(constraint_type,"distance") == 0) { constraints[i][myrxn].type = DISTANCE; - sscanf(line,"%*s %s %s %lg %lg",strargs[0],strargs[1],&tmp[0],&tmp[1]); + rv = sscanf(line,"%*s %s %s %lg %lg",strargs[0],strargs[1],&tmp[0],&tmp[1]); + if (rv != 4) error->one(FLERR, "Distance constraint is incorrectly formatted"); readID(strargs[0], i, myrxn, 0); readID(strargs[1], i, myrxn, 1); // cutoffs @@ -4140,7 +4163,8 @@ void FixBondReact::ReadConstraints(char *line, int myrxn) constraints[i][myrxn].par[1] = tmp[1]*tmp[1]; } else if (strcmp(constraint_type,"angle") == 0) { constraints[i][myrxn].type = ANGLE; - sscanf(line,"%*s %s %s %s %lg %lg",strargs[0],strargs[1],strargs[2],&tmp[0],&tmp[1]); + rv = sscanf(line,"%*s %s %s %s %lg %lg",strargs[0],strargs[1],strargs[2],&tmp[0],&tmp[1]); + if (rv != 5) error->one(FLERR, "Angle constraint is incorrectly formatted"); readID(strargs[0], i, myrxn, 0); readID(strargs[1], i, myrxn, 1); readID(strargs[2], i, myrxn, 2); @@ -4150,8 +4174,9 @@ void FixBondReact::ReadConstraints(char *line, int myrxn) constraints[i][myrxn].type = DIHEDRAL; tmp[2] = 181.0; // impossible range tmp[3] = 182.0; - sscanf(line,"%*s %s %s %s %s %lg %lg %lg %lg",strargs[0],strargs[1], + rv = sscanf(line,"%*s %s %s %s %s %lg %lg %lg %lg",strargs[0],strargs[1], strargs[2],strargs[3],&tmp[0],&tmp[1],&tmp[2],&tmp[3]); + if (!(rv == 6 || rv == 8)) error->one(FLERR, "Dihedral constraint is incorrectly formatted"); readID(strargs[0], i, myrxn, 0); readID(strargs[1], i, myrxn, 1); readID(strargs[2], i, myrxn, 2); @@ -4163,7 +4188,8 @@ void FixBondReact::ReadConstraints(char *line, int myrxn) } else if (strcmp(constraint_type,"arrhenius") == 0) { constraints[i][myrxn].type = ARRHENIUS; constraints[i][myrxn].par[0] = narrhenius++; - sscanf(line,"%*s %lg %lg %lg %lg",&tmp[0],&tmp[1],&tmp[2],&tmp[3]); + rv = sscanf(line,"%*s %lg %lg %lg %lg",&tmp[0],&tmp[1],&tmp[2],&tmp[3]); + if (rv != 4) error->one(FLERR, "Arrhenius constraint is incorrectly formatted"); constraints[i][myrxn].par[1] = tmp[0]; constraints[i][myrxn].par[2] = tmp[1]; constraints[i][myrxn].par[3] = tmp[2]; @@ -4171,7 +4197,8 @@ void FixBondReact::ReadConstraints(char *line, int myrxn) } else if (strcmp(constraint_type,"rmsd") == 0) { constraints[i][myrxn].type = RMSD; strcpy(strargs[0],"0"); - sscanf(line,"%*s %lg %s",&tmp[0],strargs[0]); + rv = sscanf(line,"%*s %lg %s",&tmp[0],strargs[0]); + if (!(rv == 1 || rv == 2)) error->one(FLERR, "RMSD constraint is incorrectly formatted"); constraints[i][myrxn].par[0] = tmp[0]; // RMSDmax constraints[i][myrxn].id[0] = -1; // optional molecule fragment if (isalpha(strargs[0][0])) { @@ -4411,8 +4438,8 @@ void FixBondReact::write_restart(FILE *fp) for (int i = 0; i < nreacts; i++) { set[i].reaction_count_total = reaction_count_total[i]; - strncpy(set[i].rxn_name,rxn_name[i],MAXLINE-1); - set[i].rxn_name[MAXLINE-1] = '\0'; + strncpy(set[i].rxn_name,rxn_name[i],MAXNAME-1); + set[i].rxn_name[MAXNAME-1] = '\0'; } int rbufcount = max_rate_limit_steps*nreacts; @@ -4449,13 +4476,16 @@ void FixBondReact::restart(char *buf) Set *set_restart = (Set *) &buf[n*sizeof(int)]; r_nreacts = set_restart[0].nreacts; + n2cpy = 0; if (revision > 0) { r_max_rate_limit_steps = set_restart[0].max_rate_limit_steps; - ibufcount = r_max_rate_limit_steps*r_nreacts; - memory->create(ibuf,r_max_rate_limit_steps,r_nreacts,"bond/react:ibuf"); - memcpy(&ibuf[0][0],&buf[sizeof(int)+r_nreacts*sizeof(Set)],sizeof(int)*ibufcount); - n2cpy = r_max_rate_limit_steps; - } else n2cpy = 0; + if (r_max_rate_limit_steps > 0) { + ibufcount = r_max_rate_limit_steps*r_nreacts; + memory->create(ibuf,r_max_rate_limit_steps,r_nreacts,"bond/react:ibuf"); + memcpy(&ibuf[0][0],&buf[sizeof(int)+r_nreacts*sizeof(Set)],sizeof(int)*ibufcount); + n2cpy = r_max_rate_limit_steps; + } + } if (max_rate_limit_steps < n2cpy) n2cpy = max_rate_limit_steps; for (int i = 0; i < r_nreacts; i++) { @@ -4468,7 +4498,7 @@ void FixBondReact::restart(char *buf) } } } - if (revision > 0) memory->destroy(ibuf); + if (revision > 0 && r_max_rate_limit_steps > 0) memory->destroy(ibuf); } /* ---------------------------------------------------------------------- diff --git a/src/REACTION/fix_bond_react.h b/src/REACTION/fix_bond_react.h index b434699ec7..66a5e4d6a0 100644 --- a/src/REACTION/fix_bond_react.h +++ b/src/REACTION/fix_bond_react.h @@ -33,7 +33,8 @@ namespace LAMMPS_NS { class FixBondReact : public Fix { public: - enum { MAXLINE = 256 }; // max length of line read from files + enum { MAXLINE = 1024 }; // max length of line read from files + enum { MAXNAME = 256 }; // max character length of react-ID enum { MAXCONIDS = 4 }; // max # of IDs used by any constraint enum { MAXCONPAR = 5 }; // max # of constraint parameters @@ -154,13 +155,15 @@ class FixBondReact : public Fix { int pion, neigh, trace; // important indices for various loops. required for restore points int lcl_inst; // reaction instance tagint **glove; // 1st colmn: pre-reacted template, 2nd colmn: global IDs - // for all mega_gloves and global_mega_glove: first row is the ID of bond/react - tagint **local_mega_glove; // consolidation local of reaction instances - tagint **ghostly_mega_glove; // consolidation nonlocal of reaction instances + // for all mega_gloves: first row is the ID of bond/react + tagint **my_mega_glove; // local + ghostly reaction instances + tagint **local_mega_glove; // consolidation of local reaction instances + tagint **ghostly_mega_glove; // consolidation of nonlocal reaction instances tagint **global_mega_glove; // consolidation (inter-processor) of gloves // containing nonlocal atoms int *localsendlist; // indicates ghosts of other procs + int my_num_mega; // local + ghostly reaction instances (on this proc) int local_num_mega; // num of local reaction instances int ghostly_num_mega; // num of ghostly reaction instances int global_megasize; // num of reaction instances in global_mega_glove @@ -216,7 +219,7 @@ class FixBondReact : public Fix { // store restart data struct Set { int nreacts; - char rxn_name[MAXLINE]; + char rxn_name[MAXNAME]; int reaction_count_total; int max_rate_limit_steps; }; diff --git a/src/REPLICA/compute_pressure_alchemy.cpp b/src/REPLICA/compute_pressure_alchemy.cpp new file mode 100644 index 0000000000..d19ea1b893 --- /dev/null +++ b/src/REPLICA/compute_pressure_alchemy.cpp @@ -0,0 +1,102 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS development team: developers@lammps.org + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "compute_pressure_alchemy.h" + +#include "domain.h" +#include "error.h" +#include "fix.h" +#include "modify.h" +#include "update.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +ComputePressureAlchemy::ComputePressureAlchemy(LAMMPS *lmp, int narg, char **arg) : + Compute(lmp, narg, arg) +{ + if (narg != 4) error->all(FLERR, "Illegal compute pressure/alchemy command"); + if (igroup) error->all(FLERR, "Compute pressure/alchemy must use group all"); + + scalar_flag = vector_flag = 1; + size_vector = 6; + extscalar = 0; + extvector = 0; + pressflag = 1; + timeflag = 1; + + id_fix = arg[3]; + if (!modify->get_fix_by_id(id_fix)) + error->all(FLERR, "Could not find compute pressure/alchemy fix ID {} for fix alchemy", id_fix); + + vector = new double[size_vector]; +} + +/* ---------------------------------------------------------------------- */ + +ComputePressureAlchemy::~ComputePressureAlchemy() +{ + delete[] vector; +} + +/* ---------------------------------------------------------------------- */ + +void ComputePressureAlchemy::init() +{ + + fix = modify->get_fix_by_id(id_fix); + if (!fix) + error->all(FLERR, "Could not find compute pressure/alchemy fix ID {} for fix alchemy", id_fix); + + int dim = 0; + void *ptr = fix->extract("pressure", dim); + if (!ptr || (dim != 1)) error->all(FLERR, "Could not extract pressure from fix alchemy"); +} + +/* ---------------------------------------------------------------------- + compute total pressure from tensor, averaged over Pxx, Pyy, Pzz +------------------------------------------------------------------------- */ + +double ComputePressureAlchemy::compute_scalar() +{ + invoked_scalar = update->ntimestep; + if (update->vflag_global != invoked_scalar) + error->all(FLERR, "Virial was not tallied on needed timestep"); + + compute_vector(); + + if (domain->dimension == 3) { + scalar = (vector[0] + vector[1] + vector[2]) / 3.0; + } else { + scalar = (vector[0] + vector[1]) / 2.0; + } + return scalar; +} + +/* ---------------------------------------------------------------------- + extract compute combined system pressure tensor from alchemy fix +------------------------------------------------------------------------- */ + +void ComputePressureAlchemy::compute_vector() +{ + invoked_vector = update->ntimestep; + if (update->vflag_global != invoked_vector) + error->all(FLERR, "Virial was not tallied on needed timestep"); + + int dim = 0; + double *pressure = (double *) fix->extract("pressure", dim); + if (!pressure || (dim != 1)) error->all(FLERR, "Could not extract pressure from fix alchemy"); + + for (int i = 0; i < 6; i++) vector[i] = pressure[i]; +} diff --git a/src/REPLICA/compute_pressure_alchemy.h b/src/REPLICA/compute_pressure_alchemy.h new file mode 100644 index 0000000000..0ce0039587 --- /dev/null +++ b/src/REPLICA/compute_pressure_alchemy.h @@ -0,0 +1,41 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS development team: developers@lammps.org + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef COMPUTE_CLASS +// clang-format off +ComputeStyle(pressure/alchemy,ComputePressureAlchemy); +// clang-format on +#else + +#ifndef LMP_COMPUTE_PRESSURE_ALCHEMY_H +#define LMP_COMPUTE_PRESSURE_ALCHEMY_H + +#include "compute.h" + +namespace LAMMPS_NS { + +class ComputePressureAlchemy : public Compute { + public: + ComputePressureAlchemy(class LAMMPS *, int, char **); + ~ComputePressureAlchemy() override; + void init() override; + double compute_scalar() override; + void compute_vector() override; + + protected: + class Fix *fix; + std::string id_fix; +}; +} // namespace LAMMPS_NS +#endif +#endif diff --git a/src/REPLICA/fix_alchemy.cpp b/src/REPLICA/fix_alchemy.cpp new file mode 100644 index 0000000000..2f99f667b6 --- /dev/null +++ b/src/REPLICA/fix_alchemy.cpp @@ -0,0 +1,265 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS development team: developers@lammps.org + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "fix_alchemy.h" + +#include "atom.h" +#include "comm.h" +#include "compute.h" +#include "domain.h" +#include "error.h" +#include "input.h" +#include "memory.h" +#include "modify.h" +#include "respa.h" +#include "universe.h" +#include "update.h" +#include "variable.h" + +#include + +using namespace LAMMPS_NS; +using namespace FixConst; + +/* ---------------------------------------------------------------------- */ + +FixAlchemy::FixAlchemy(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg), commbuf(nullptr) +{ + if (narg != 4) error->all(FLERR, "Incorrect number of arguments for fix alchemy"); + if (universe->nworlds != 2) error->all(FLERR, "Must use exactly two partitions"); + if (utils::strmatch(arg[3], "^v_")) + id_lambda = arg[3] + 2; + else + error->all(FLERR, "Must use variable as lambda argument to fix alchemy"); + + lambda = epot[0] = epot[1] = epot[2] = 0.0; + progress = 0; + for (int i = 0; i < 6; ++i) pressure[i] = 0.0; + + no_change_box = 1; + time_depend = 1; + scalar_flag = 1; + extscalar = 0; + vector_flag = 1; + size_vector = 3; + extvector = 1; + ilevel_respa = 0; + nmax = 6; + sync_box = 0; + + // set up rank-to-rank communicator for inter-partition communication + + int color = comm->me; + int key = universe->iworld; + MPI_Comm_split(universe->uworld, color, key, &samerank); + + // check that we have the same domain decomposition on all ranks + + int my_nlocal[2] = {0, 0}; + int all_nlocal[2] = {0, 0}; + my_nlocal[universe->iworld] = atom->nlocal; + MPI_Allreduce(my_nlocal, all_nlocal, 2, MPI_INT, MPI_SUM, samerank); + int fail = (all_nlocal[0] == all_nlocal[1]) ? 0 : 1; + int allfail = 0; + MPI_Allreduce(&fail, &allfail, 1, MPI_INT, MPI_MAX, universe->uworld); + if (allfail) + error->all(FLERR, "Number of atoms and domain decomposition must match for both partitions"); + + id_pe = std::string(id) + "_pe"; + pe = modify->add_compute(id_pe + " all pe"); + pe->addstep(update->ntimestep); + id_temp = std::string(id) + "_temp"; + temp = modify->add_compute(id_temp + " all temp"); + temp->addstep(update->ntimestep); + id_press = std::string(id) + "_press"; + press = modify->add_compute(id_press + " all pressure " + id_temp); + press->addstep(update->ntimestep); +} + +/* ---------------------------------------------------------------------- */ + +FixAlchemy::~FixAlchemy() +{ + MPI_Comm_free(&samerank); + modify->delete_compute(id_pe); + modify->delete_compute(id_temp); + modify->delete_compute(id_press); + memory->destroy(commbuf); +} + +/* ---------------------------------------------------------------------- */ + +int FixAlchemy::setmask() +{ + int mask = 0; + mask |= POST_INTEGRATE; + mask |= POST_FORCE; + return mask; +} + +/* ---------------------------------------------------------------------- */ + +static void synchronize_box(Domain *domain, MPI_Comm samerank) +{ + MPI_Bcast(&domain->boxlo[0], 3, MPI_DOUBLE, 0, samerank); + MPI_Bcast(&domain->boxhi[0], 3, MPI_DOUBLE, 0, samerank); + MPI_Bcast(&domain->yz, 1, MPI_DOUBLE, 0, samerank); + MPI_Bcast(&domain->xz, 1, MPI_DOUBLE, 0, samerank); + MPI_Bcast(&domain->xy, 1, MPI_DOUBLE, 0, samerank); + domain->set_global_box(); + domain->set_local_box(); +} + +/* ---------------------------------------------------------------------- */ + +void FixAlchemy::init() +{ + int onenmax = MAX(nmax, 3 * atom->nmax); + MPI_Allreduce(&onenmax, &nmax, 1, MPI_INT, MPI_MAX, universe->uworld); + memory->destroy(commbuf); + memory->create(commbuf, sizeof(double) * nmax, "alchemy:nmax"); + + if (modify->get_fix_by_style("^balance").size() > 0) + error->all(FLERR, "Fix alchemy is not compatible with load balancing"); + + if (modify->get_fix_by_style("^alchemy").size() > 1) + error->all(FLERR, "There may only one fix alchemy at a time"); + + ivar = input->variable->find(id_lambda.c_str()); + if (ivar < 0) + error->universe_one(FLERR, fmt::format("Variable {} for fix alchemy does not exist", id_lambda)); + if (!input->variable->equalstyle(ivar)) + error->universe_one(FLERR, + fmt::format("Variable {} for fix alchemy is invalid style", id_lambda)); + lambda = input->variable->compute_equal(ivar); + + // synchronize box dimensions, determine if resync during run will be needed. + + synchronize_box(domain, samerank); + + sync_box = 0; + for (auto ifix : modify->get_fix_list()) + if (ifix->box_change) sync_box = 1; +} + +/* ---------------------------------------------------------------------- */ + +void FixAlchemy::setup(int vflag) +{ + if (utils::strmatch(update->integrate_style, "^respa")) { + auto respa = dynamic_cast(update->integrate); + respa->copy_flevel_f(ilevel_respa); + post_force_respa(vflag, ilevel_respa, 0); + respa->copy_f_flevel(ilevel_respa); + } else { + post_force(vflag); + } + + if (universe->me == 0) { + double delta = update->ntimestep - update->beginstep; + if ((delta != 0.0) && (update->beginstep != update->endstep)) + delta /= update->endstep - update->beginstep; + progress = static_cast(delta*100.0); + auto msg = fmt::format("Starting alchemical transformation at {:>3d}%\n", progress); + if (universe->uscreen) fmt::print(universe->uscreen, msg); + if (universe->ulogfile) fmt::print(universe->ulogfile, msg); + } +} + +/* ---------------------------------------------------------------------- */ + +void FixAlchemy::post_integrate() +{ + // synchronize atom positions + + const int nall = atom->nlocal + atom->nghost; + MPI_Bcast(&atom->x[0][0], 3 * nall, MPI_DOUBLE, 0, samerank); + + // synchronize box dimensions, if needed + + if (sync_box) synchronize_box(domain, samerank); +} + +/* ---------------------------------------------------------------------- */ + +void FixAlchemy::post_force(int /*vflag*/) +{ + if (3 * atom->nmax > nmax) { + nmax = 3 * atom->nmax; + memory->grow(commbuf, sizeof(double) * atom->nmax, "alchemy:commbuf"); + } + + const int nall = 3 * atom->nlocal; + double *f = &atom->f[0][0]; + lambda = input->variable->compute_equal(ivar); + + for (int i = 0; i < nall; ++i) commbuf[i] = f[i] * lambda; + MPI_Allreduce(commbuf, f, nall, MPI_DOUBLE, MPI_SUM, samerank); + + // sum up potential energy + + const double scalefac = 1.0 / comm->nprocs; + commbuf[0] = commbuf[1] = commbuf[2] = 0.0; + commbuf[universe->iworld] = scalefac * pe->compute_scalar(); + commbuf[2] = lambda * scalefac * pe->compute_scalar(); + MPI_Allreduce(commbuf, epot, 3, MPI_DOUBLE, MPI_SUM, universe->uworld); + pe->addstep(update->ntimestep + 1); + + // sum up pressure + + press->compute_vector(); + for (int i = 0; i < 6; ++i) commbuf[i] = lambda * scalefac * press->vector[i]; + MPI_Allreduce(commbuf, pressure, 6, MPI_DOUBLE, MPI_SUM, universe->uworld); + press->addstep(update->ntimestep + 1); + + // print progress info + + if (universe->me == 0) { + double delta = update->ntimestep - update->beginstep; + if ((delta != 0.0) && (update->beginstep != update->endstep)) + delta /= update->endstep - update->beginstep; + int status = static_cast(delta*100.0); + if ((status / 10) > (progress / 10)) { + progress = status; + auto msg = fmt::format(" Alchemical transformation progress: {:>3d}%\n", progress); + if (universe->uscreen) fmt::print(universe->uscreen, msg); + if (universe->ulogfile) fmt::print(universe->ulogfile, msg); + } + } +} + +/* ---------------------------------------------------------------------- */ + +double FixAlchemy::compute_scalar() +{ + return lambda; +} + +/* ---------------------------------------------------------------------- */ + +double FixAlchemy::compute_vector(int n) +{ + return epot[n]; +} + +/* ---------------------------------------------------------------------- */ + +void *FixAlchemy::extract(const char *str, int &dim) +{ + dim = 0; + if (strcmp(str, "lambda") == 0) { return λ } + if (strcmp(str, "pe") == 0) { return &epot[2]; } + dim = 1; + if (strcmp(str, "pressure") == 0) { return pressure; } + return nullptr; +} diff --git a/src/REPLICA/fix_alchemy.h b/src/REPLICA/fix_alchemy.h new file mode 100644 index 0000000000..677a29b643 --- /dev/null +++ b/src/REPLICA/fix_alchemy.h @@ -0,0 +1,58 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS development team: developers@lammps.org + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef FIX_CLASS +// clang-format off +FixStyle(alchemy,FixAlchemy); +// clang-format on +#else + +#ifndef LMP_FIX_ALCHEMY_H +#define LMP_FIX_ALCHEMY_H + +#include "fix.h" + +namespace LAMMPS_NS { + +class FixAlchemy : public Fix { + public: + FixAlchemy(class LAMMPS *, int, char **); + ~FixAlchemy() override; + + int setmask() override; + void init() override; + void setup(int) override; + void post_integrate() override; + void post_force(int) override; + double compute_scalar() override; + double compute_vector(int) override; + void *extract(const char *, int &) override; + + protected: + MPI_Comm samerank; + double *commbuf; + class Compute *pe, *temp, *press; + std::string id_pe, id_temp, id_press, id_lambda; + double lambda; // scaling prefactor for combining the partitions + double epot[3]; // last (unscaled) potential energy from each replica and combined energy + double pressure[6]; // joined pressure + int progress; // for progress indicator + int sync_box; // 1 of box dimensions need to be synchronized + int ilevel_respa; + int nmax; + int ivar; +}; +} // namespace LAMMPS_NS + +#endif +#endif diff --git a/src/SHOCK/fix_wall_piston.cpp b/src/SHOCK/fix_wall_piston.cpp index 82cec907f4..cb20e2d683 100644 --- a/src/SHOCK/fix_wall_piston.cpp +++ b/src/SHOCK/fix_wall_piston.cpp @@ -13,17 +13,19 @@ ------------------------------------------------------------------------- */ #include "fix_wall_piston.h" + +#include "atom.h" +#include "comm.h" +#include "domain.h" +#include "error.h" +#include "force.h" +#include "lattice.h" +#include "math_const.h" +#include "random_mars.h" +#include "update.h" + #include #include -#include "atom.h" -#include "domain.h" -#include "lattice.h" -#include "update.h" -#include "error.h" -#include "random_mars.h" -#include "force.h" -#include "comm.h" -#include "math_const.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/SRD/fix_wall_srd.cpp b/src/SRD/fix_wall_srd.cpp index ccce252e5d..d9e55a49f2 100644 --- a/src/SRD/fix_wall_srd.cpp +++ b/src/SRD/fix_wall_srd.cpp @@ -27,7 +27,6 @@ #include using namespace LAMMPS_NS; -using namespace FixConst; enum { XLO, XHI, YLO, YHI, ZLO, ZHI }; enum { NONE, EDGE, CONSTANT, VARIABLE }; diff --git a/src/create_bonds.cpp b/src/create_bonds.cpp index c6d3f1838e..5355ce2b7c 100644 --- a/src/create_bonds.cpp +++ b/src/create_bonds.cpp @@ -319,8 +319,6 @@ void CreateBonds::many() void CreateBonds::single_bond() { - int m; - // check that 2 atoms exist const int nlocal = atom->nlocal; @@ -341,7 +339,8 @@ void CreateBonds::single_bond() int **bond_type = atom->bond_type; tagint **bond_atom = atom->bond_atom; - if ((m = idx1) >= 0) { + int m = idx1; + if ((m >= 0) && (m < nlocal)) { if (num_bond[m] == atom->bond_per_atom) error->one(FLERR, "New bond exceeded bonds per atom in create_bonds"); bond_type[m][num_bond[m]] = btype; @@ -352,7 +351,8 @@ void CreateBonds::single_bond() if (force->newton_bond) return; - if ((m = idx2) >= 0) { + m = idx2; + if ((m >= 0) && (m < nlocal)) { if (num_bond[m] == atom->bond_per_atom) error->one(FLERR, "New bond exceeded bonds per atom in create_bonds"); bond_type[m][num_bond[m]] = btype; @@ -365,8 +365,6 @@ void CreateBonds::single_bond() void CreateBonds::single_angle() { - int m; - // check that 3 atoms exist const int nlocal = atom->nlocal; @@ -391,7 +389,8 @@ void CreateBonds::single_angle() tagint **angle_atom2 = atom->angle_atom2; tagint **angle_atom3 = atom->angle_atom3; - if ((m = idx2) >= 0) { + int m = idx2; + if ((m >= 0) && (m < nlocal)) { if (num_angle[m] == atom->angle_per_atom) error->one(FLERR, "New angle exceeded angles per atom in create_bonds"); angle_type[m][num_angle[m]] = atype; @@ -404,7 +403,8 @@ void CreateBonds::single_angle() if (force->newton_bond) return; - if ((m = idx1) >= 0) { + m = idx1; + if ((m >= 0) && (m < nlocal)) { if (num_angle[m] == atom->angle_per_atom) error->one(FLERR, "New angle exceeded angles per atom in create_bonds"); angle_type[m][num_angle[m]] = atype; @@ -414,7 +414,8 @@ void CreateBonds::single_angle() num_angle[m]++; } - if ((m = idx3) >= 0) { + m = idx3; + if ((m >= 0) && (m < nlocal)) { if (num_angle[m] == atom->angle_per_atom) error->one(FLERR, "New angle exceeded angles per atom in create_bonds"); angle_type[m][num_angle[m]] = atype; @@ -429,8 +430,6 @@ void CreateBonds::single_angle() void CreateBonds::single_dihedral() { - int m; - // check that 4 atoms exist const int nlocal = atom->nlocal; @@ -458,7 +457,8 @@ void CreateBonds::single_dihedral() tagint **dihedral_atom3 = atom->dihedral_atom3; tagint **dihedral_atom4 = atom->dihedral_atom4; - if ((m = idx2) >= 0) { + int m = idx2; + if ((m >= 0) && (m < nlocal)) { if (num_dihedral[m] == atom->dihedral_per_atom) error->one(FLERR, "New dihedral exceeded dihedrals per atom in create_bonds"); dihedral_type[m][num_dihedral[m]] = dtype; @@ -472,7 +472,8 @@ void CreateBonds::single_dihedral() if (force->newton_bond) return; - if ((m = idx1) >= 0) { + m = idx1; + if ((m >= 0) && (m < nlocal)) { if (num_dihedral[m] == atom->dihedral_per_atom) error->one(FLERR, "New dihedral exceeded dihedrals per atom in create_bonds"); dihedral_type[m][num_dihedral[m]] = dtype; @@ -483,7 +484,8 @@ void CreateBonds::single_dihedral() num_dihedral[m]++; } - if ((m = idx3) >= 0) { + m = idx3; + if ((m >= 0) && (m < nlocal)) { if (num_dihedral[m] == atom->dihedral_per_atom) error->one(FLERR, "New dihedral exceeded dihedrals per atom in create_bonds"); dihedral_type[m][num_dihedral[m]] = dtype; @@ -494,7 +496,8 @@ void CreateBonds::single_dihedral() num_dihedral[m]++; } - if ((m = idx4) >= 0) { + m = idx4; + if ((m >= 0) && (m < nlocal)) { if (num_dihedral[m] == atom->dihedral_per_atom) error->one(FLERR, "New dihedral exceeded dihedrals per atom in create_bonds"); dihedral_type[m][num_dihedral[m]] = dtype; @@ -510,8 +513,6 @@ void CreateBonds::single_dihedral() void CreateBonds::single_improper() { - int m; - // check that 4 atoms exist const int nlocal = atom->nlocal; @@ -539,7 +540,8 @@ void CreateBonds::single_improper() tagint **improper_atom3 = atom->improper_atom3; tagint **improper_atom4 = atom->improper_atom4; - if ((m = idx2) >= 0) { + int m = idx2; + if ((m >= 0) && (m < nlocal)) { if (num_improper[m] == atom->improper_per_atom) error->one(FLERR, "New improper exceeded impropers per atom in create_bonds"); improper_type[m][num_improper[m]] = dtype; @@ -553,7 +555,8 @@ void CreateBonds::single_improper() if (force->newton_bond) return; - if ((m = idx1) >= 0) { + m = idx1; + if ((m >= 0) && (m < nlocal)) { if (num_improper[m] == atom->improper_per_atom) error->one(FLERR, "New improper exceeded impropers per atom in create_bonds"); improper_type[m][num_improper[m]] = dtype; @@ -564,7 +567,8 @@ void CreateBonds::single_improper() num_improper[m]++; } - if ((m = idx3) >= 0) { + m = idx3; + if ((m >= 0) && (m < nlocal)) { if (num_improper[m] == atom->improper_per_atom) error->one(FLERR, "New improper exceeded impropers per atom in create_bonds"); improper_type[m][num_improper[m]] = dtype; @@ -575,7 +579,8 @@ void CreateBonds::single_improper() num_improper[m]++; } - if ((m = idx4) >= 0) { + m = idx4; + if ((m >= 0) && (m < nlocal)) { if (num_improper[m] == atom->improper_per_atom) error->one(FLERR, "New improper exceeded impropers per atom in create_bonds"); improper_type[m][num_improper[m]] = dtype; diff --git a/src/fix_wall.cpp b/src/fix_wall.cpp index d624ee9ff7..4c4406a34c 100644 --- a/src/fix_wall.cpp +++ b/src/fix_wall.cpp @@ -1,4 +1,3 @@ -// clang-format off /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories @@ -28,14 +27,14 @@ using namespace LAMMPS_NS; using namespace FixConst; -enum{XLO=0,XHI=1,YLO=2,YHI=3,ZLO=4,ZHI=5}; -enum{NONE=0,EDGE,CONSTANT,VARIABLE}; +enum { XLO = 0, XHI = 1, YLO = 2, YHI = 3, ZLO = 4, ZHI = 5 }; +enum { NONE = 0, EDGE, CONSTANT, VARIABLE }; + +static const char *wallpos[] = {"xlo", "xhi", "ylo", "yhi", "zlo", "zhi"}; /* ---------------------------------------------------------------------- */ -FixWall::FixWall(LAMMPS *lmp, int narg, char **arg) : - Fix(lmp, narg, arg), - nwall(0) +FixWall::FixWall(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg), nwall(0) { scalar_flag = 1; vector_flag = 1; @@ -53,111 +52,145 @@ FixWall::FixWall(LAMMPS *lmp, int narg, char **arg) : fldflag = 0; int pbcflag = 0; - for (int i = 0; i < 6; i++) xstr[i] = estr[i] = sstr[i] = nullptr; + for (int i = 0; i < 6; i++) xstr[i] = estr[i] = sstr[i] = lstr[i] = fstr[i] = kstr[i] = nullptr; int iarg = 3; + if (utils::strmatch(style, "^wall/table")) iarg = 5; + while (iarg < narg) { - if ((strcmp(arg[iarg],"xlo") == 0) || (strcmp(arg[iarg],"xhi") == 0) || - (strcmp(arg[iarg],"ylo") == 0) || (strcmp(arg[iarg],"yhi") == 0) || - (strcmp(arg[iarg],"zlo") == 0) || (strcmp(arg[iarg],"zhi") == 0)) { - if (iarg+5 > narg) error->all(FLERR,"Illegal fix wall command"); + int wantargs = 5; + if (utils::strmatch(style, "^wall/lepton")) wantargs = 4; + if (utils::strmatch(style, "^wall/morse")) wantargs = 6; + + if ((strcmp(arg[iarg], "xlo") == 0) || (strcmp(arg[iarg], "xhi") == 0) || + (strcmp(arg[iarg], "ylo") == 0) || (strcmp(arg[iarg], "yhi") == 0) || + (strcmp(arg[iarg], "zlo") == 0) || (strcmp(arg[iarg], "zhi") == 0)) { + if (iarg + wantargs > narg) error->all(FLERR, "Missing argument for fix {} command", style); int newwall; - if (strcmp(arg[iarg],"xlo") == 0) newwall = XLO; - else if (strcmp(arg[iarg],"xhi") == 0) newwall = XHI; - else if (strcmp(arg[iarg],"ylo") == 0) newwall = YLO; - else if (strcmp(arg[iarg],"yhi") == 0) newwall = YHI; - else if (strcmp(arg[iarg],"zlo") == 0) newwall = ZLO; - else if (strcmp(arg[iarg],"zhi") == 0) newwall = ZHI; - - for (int m = 0; (m < nwall) && (m < 6); m++) + if (strcmp(arg[iarg], "xlo") == 0) { + newwall = XLO; + } else if (strcmp(arg[iarg], "xhi") == 0) { + newwall = XHI; + } else if (strcmp(arg[iarg], "ylo") == 0) { + newwall = YLO; + } else if (strcmp(arg[iarg], "yhi") == 0) { + newwall = YHI; + } else if (strcmp(arg[iarg], "zlo") == 0) { + newwall = ZLO; + } else if (strcmp(arg[iarg], "zhi") == 0) { + newwall = ZHI; + } + for (int m = 0; (m < nwall) && (m < 6); m++) { if (newwall == wallwhich[m]) - error->all(FLERR,"Wall defined twice in fix wall command"); - + error->all(FLERR, "{} wall defined twice in fix {} command", wallpos[newwall], style); + } wallwhich[nwall] = newwall; - if (strcmp(arg[iarg+1],"EDGE") == 0) { + + if (strcmp(arg[iarg + 1], "EDGE") == 0) { xstyle[nwall] = EDGE; int dim = wallwhich[nwall] / 2; int side = wallwhich[nwall] % 2; - if (side == 0) coord0[nwall] = domain->boxlo[dim]; - else coord0[nwall] = domain->boxhi[dim]; - } else if (utils::strmatch(arg[iarg+1],"^v_")) { + if (side == 0) { + coord0[nwall] = domain->boxlo[dim]; + } else { + coord0[nwall] = domain->boxhi[dim]; + } + } else if (utils::strmatch(arg[iarg + 1], "^v_")) { xstyle[nwall] = VARIABLE; - xstr[nwall] = utils::strdup(arg[iarg+1]+2); + xstr[nwall] = utils::strdup(arg[iarg + 1] + 2); } else { xstyle[nwall] = CONSTANT; - coord0[nwall] = utils::numeric(FLERR,arg[iarg+1],false,lmp); + coord0[nwall] = utils::numeric(FLERR, arg[iarg + 1], false, lmp); } - if (utils::strmatch(arg[iarg+2],"^v_")) { - estr[nwall] = utils::strdup(arg[iarg+2]+2); - estyle[nwall] = VARIABLE; + if (utils::strmatch(style, "^wall/lepton")) { + estyle[nwall] = sstyle[nwall] = CONSTANT; + lstr[nwall] = utils::strdup(arg[iarg + 2]); + cutoff[nwall] = utils::numeric(FLERR, arg[iarg + 3], false, lmp); + } else if (utils::strmatch(style, "^wall/table")) { + estyle[nwall] = sstyle[nwall] = CONSTANT; + fstr[nwall] = utils::strdup(arg[iarg + 2]); + kstr[nwall] = utils::strdup(arg[iarg + 3]); + cutoff[nwall] = utils::numeric(FLERR, arg[iarg + 4], false, lmp); } else { - epsilon[nwall] = utils::numeric(FLERR,arg[iarg+2],false,lmp); - estyle[nwall] = CONSTANT; - } + if (iarg + 5 > narg) error->all(FLERR, "Missing argument for fix {} command", style); - if (utils::strmatch(style,"^wall/morse")) { - if (utils::strmatch(arg[iarg+3],"^v_")) { - astr[nwall] = utils::strdup(arg[iarg+3]+2); - astyle[nwall] = VARIABLE; + if (utils::strmatch(arg[iarg + 2], "^v_")) { + estr[nwall] = utils::strdup(arg[iarg + 2] + 2); + estyle[nwall] = VARIABLE; } else { - alpha[nwall] = utils::numeric(FLERR,arg[iarg+3],false,lmp); - astyle[nwall] = CONSTANT; + epsilon[nwall] = utils::numeric(FLERR, arg[iarg + 2], false, lmp); + estyle[nwall] = CONSTANT; } - ++iarg; - } - if (utils::strmatch(arg[iarg+3],"^v_")) { - sstr[nwall] = utils::strdup(arg[iarg+3]+2); - sstyle[nwall] = VARIABLE; - } else { - sigma[nwall] = utils::numeric(FLERR,arg[iarg+3],false,lmp); - sstyle[nwall] = CONSTANT; - } + if (utils::strmatch(style, "^wall/morse")) { + if (utils::strmatch(arg[iarg + 3], "^v_")) { + astr[nwall] = utils::strdup(arg[iarg + 3] + 2); + astyle[nwall] = VARIABLE; + } else { + alpha[nwall] = utils::numeric(FLERR, arg[iarg + 3], false, lmp); + astyle[nwall] = CONSTANT; + } + // adjust so we can share the regular code path + ++iarg; + --wantargs; + } - cutoff[nwall] = utils::numeric(FLERR,arg[iarg+4],false,lmp); + if (utils::strmatch(arg[iarg + 3], "^v_")) { + sstr[nwall] = utils::strdup(arg[iarg + 3] + 2); + sstyle[nwall] = VARIABLE; + } else { + sigma[nwall] = utils::numeric(FLERR, arg[iarg + 3], false, lmp); + sstyle[nwall] = CONSTANT; + } + cutoff[nwall] = utils::numeric(FLERR, arg[iarg + 4], false, lmp); + } nwall++; - iarg += 5; - - } else if (strcmp(arg[iarg],"units") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal fix wall command"); - if (strcmp(arg[iarg+1],"box") == 0) scaleflag = 0; - else if (strcmp(arg[iarg+1],"lattice") == 0) scaleflag = 1; - else error->all(FLERR,"Illegal fix wall command"); + iarg += wantargs; + } else if (strcmp(arg[iarg], "units") == 0) { + if (iarg + 2 > narg) error->all(FLERR, "Illegal fix {} command", style); + if (strcmp(arg[iarg + 1], "box") == 0) + scaleflag = 0; + else if (strcmp(arg[iarg + 1], "lattice") == 0) + scaleflag = 1; + else + error->all(FLERR, "Illegal fix {} command", style); iarg += 2; - } else if (strcmp(arg[iarg],"fld") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal fix wall command"); - fldflag = utils::logical(FLERR,arg[iarg+1],false,lmp); + } else if (strcmp(arg[iarg], "fld") == 0) { + if (iarg + 2 > narg) error->all(FLERR, "Illegal fix {} command", style); + fldflag = utils::logical(FLERR, arg[iarg + 1], false, lmp); iarg += 2; - } else if (strcmp(arg[iarg],"pbc") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal fix wall command"); - pbcflag = utils::logical(FLERR,arg[iarg+1],false,lmp); + } else if (strcmp(arg[iarg], "pbc") == 0) { + if (iarg + 2 > narg) error->all(FLERR, "Illegal fix {} command", style); + pbcflag = utils::logical(FLERR, arg[iarg + 1], false, lmp); iarg += 2; - } else error->all(FLERR,"Illegal fix wall command"); + } else + error->all(FLERR, "Illegal fix {} command", style); } size_vector = nwall; // error checks - if (nwall == 0) error->all(FLERR,"Illegal fix wall command"); - for (int m = 0; m < nwall; m++) + if (nwall == 0) error->all(FLERR, "Illegal fix {} command: no walls defined", style); + for (int m = 0; m < nwall; m++) { if (cutoff[m] <= 0.0) - error->all(FLERR,"Fix wall cutoff <= 0.0"); + error->all(FLERR, "Fix {} cutoff <= 0.0 for {} wall", style, wallpos[wallwhich[m]]); + } for (int m = 0; m < nwall; m++) if ((wallwhich[m] == ZLO || wallwhich[m] == ZHI) && domain->dimension == 2) - error->all(FLERR,"Cannot use fix wall zlo/zhi for a 2d simulation"); + error->all(FLERR, "Cannot use fix {} zlo/zhi for a 2d simulation", style); if (!pbcflag) { for (int m = 0; m < nwall; m++) { if ((wallwhich[m] == XLO || wallwhich[m] == XHI) && domain->xperiodic) - error->all(FLERR,"Cannot use fix wall in periodic dimension"); + error->all(FLERR, "Cannot use {} wall in periodic x dimension", wallpos[wallwhich[m]]); if ((wallwhich[m] == YLO || wallwhich[m] == YHI) && domain->yperiodic) - error->all(FLERR,"Cannot use fix wall in periodic dimension"); + error->all(FLERR, "Cannot use {} wall in periodic y dimension", wallpos[wallwhich[m]]); if ((wallwhich[m] == ZLO || wallwhich[m] == ZHI) && domain->zperiodic) - error->all(FLERR,"Cannot use fix wall in periodic dimension"); + error->all(FLERR, "Cannot use {} wall in periodic z dimension", wallpos[wallwhich[m]]); } } @@ -172,14 +205,17 @@ FixWall::FixWall(LAMMPS *lmp, int narg, char **arg) : xscale = domain->lattice->xlattice; yscale = domain->lattice->ylattice; zscale = domain->lattice->zlattice; - } - else xscale = yscale = zscale = 1.0; + } else + xscale = yscale = zscale = 1.0; for (int m = 0; m < nwall; m++) { if (xstyle[m] != CONSTANT) continue; - if (wallwhich[m] < YLO) coord0[m] *= xscale; - else if (wallwhich[m] < ZLO) coord0[m] *= yscale; - else coord0[m] *= zscale; + if (wallwhich[m] < YLO) + coord0[m] *= xscale; + else if (wallwhich[m] < ZLO) + coord0[m] *= yscale; + else + coord0[m] *= zscale; } } @@ -191,8 +227,10 @@ FixWall::FixWall(LAMMPS *lmp, int narg, char **arg) : for (int m = 0; m < nwall; m++) { if (xstyle[m] == VARIABLE) xflag = 1; if (xflag || estyle[m] == VARIABLE || sstyle[m] == VARIABLE) varflag = 1; - if (estyle[m] == VARIABLE || sstyle[m] == VARIABLE) wstyle[m] = VARIABLE; - else wstyle[m] = CONSTANT; + if (estyle[m] == VARIABLE || sstyle[m] == VARIABLE) + wstyle[m] = VARIABLE; + else + wstyle[m] = CONSTANT; } eflag = 0; @@ -206,9 +244,12 @@ FixWall::~FixWall() if (copymode) return; for (int m = 0; m < nwall; m++) { - delete [] xstr[m]; - delete [] estr[m]; - delete [] sstr[m]; + delete[] xstr[m]; + delete[] estr[m]; + delete[] sstr[m]; + delete[] lstr[m]; + delete[] fstr[m]; + delete[] kstr[m]; } } @@ -220,8 +261,10 @@ int FixWall::setmask() // FLD implicit needs to invoke wall forces before pair style - if (fldflag) mask |= PRE_FORCE; - else mask |= POST_FORCE; + if (fldflag) + mask |= PRE_FORCE; + else + mask |= POST_FORCE; mask |= POST_FORCE_RESPA; mask |= MIN_POST_FORCE; @@ -235,24 +278,21 @@ void FixWall::init() for (int m = 0; m < nwall; m++) { if (xstyle[m] == VARIABLE) { xindex[m] = input->variable->find(xstr[m]); - if (xindex[m] < 0) - error->all(FLERR,"Variable name for fix wall does not exist"); + if (xindex[m] < 0) error->all(FLERR, "Variable name for fix wall does not exist"); if (!input->variable->equalstyle(xindex[m])) - error->all(FLERR,"Variable for fix wall is invalid style"); + error->all(FLERR, "Variable for fix wall is invalid style"); } if (estyle[m] == VARIABLE) { eindex[m] = input->variable->find(estr[m]); - if (eindex[m] < 0) - error->all(FLERR,"Variable name for fix wall does not exist"); + if (eindex[m] < 0) error->all(FLERR, "Variable name for fix wall does not exist"); if (!input->variable->equalstyle(eindex[m])) - error->all(FLERR,"Variable for fix wall is invalid style"); + error->all(FLERR, "Variable for fix wall is invalid style"); } if (sstyle[m] == VARIABLE) { sindex[m] = input->variable->find(sstr[m]); - if (sindex[m] < 0) - error->all(FLERR,"Variable name for fix wall does not exist"); + if (sindex[m] < 0) error->all(FLERR, "Variable name for fix wall does not exist"); if (!input->variable->equalstyle(sindex[m])) - error->all(FLERR,"Variable for fix wall is invalid style"); + error->all(FLERR, "Variable for fix wall is invalid style"); } } @@ -260,9 +300,9 @@ void FixWall::init() for (int m = 0; m < nwall; m++) precompute(m); - if (utils::strmatch(update->integrate_style,"^respa")) { - ilevel_respa = (dynamic_cast(update->integrate))->nlevels-1; - if (respa_level >= 0) ilevel_respa = MIN(respa_level,ilevel_respa); + if (utils::strmatch(update->integrate_style, "^respa")) { + ilevel_respa = (dynamic_cast(update->integrate))->nlevels - 1; + if (respa_level >= 0) ilevel_respa = MIN(respa_level, ilevel_respa); } } @@ -270,11 +310,11 @@ void FixWall::init() void FixWall::setup(int vflag) { - if (utils::strmatch(update->integrate_style,"^verlet")) { + if (utils::strmatch(update->integrate_style, "^verlet")) { if (!fldflag) post_force(vflag); } else { (dynamic_cast(update->integrate))->copy_flevel_f(ilevel_respa); - post_force_respa(vflag,ilevel_respa,0); + post_force_respa(vflag, ilevel_respa, 0); (dynamic_cast(update->integrate))->copy_f_flevel(ilevel_respa); } } @@ -319,25 +359,27 @@ void FixWall::post_force(int vflag) for (int m = 0; m < nwall; m++) { if (xstyle[m] == VARIABLE) { coord = input->variable->compute_equal(xindex[m]); - if (wallwhich[m] < YLO) coord *= xscale; - else if (wallwhich[m] < ZLO) coord *= yscale; - else coord *= zscale; - } else coord = coord0[m]; + if (wallwhich[m] < YLO) + coord *= xscale; + else if (wallwhich[m] < ZLO) + coord *= yscale; + else + coord *= zscale; + } else + coord = coord0[m]; if (wstyle[m] == VARIABLE) { if (estyle[m] == VARIABLE) { epsilon[m] = input->variable->compute_equal(eindex[m]); - if (epsilon[m] < 0.0) - error->all(FLERR,"Variable evaluation in fix wall gave bad value"); + if (epsilon[m] < 0.0) error->all(FLERR, "Variable evaluation in fix wall gave bad value"); } if (sstyle[m] == VARIABLE) { sigma[m] = input->variable->compute_equal(sindex[m]); - if (sigma[m] < 0.0) - error->all(FLERR,"Variable evaluation in fix wall gave bad value"); + if (sigma[m] < 0.0) error->all(FLERR, "Variable evaluation in fix wall gave bad value"); } precompute(m); } - wall_particle(m,wallwhich[m],coord); + wall_particle(m, wallwhich[m], coord); } if (varflag) modify->addstep_compute(update->ntimestep + 1); @@ -366,7 +408,7 @@ double FixWall::compute_scalar() // only sum across procs one time if (eflag == 0) { - MPI_Allreduce(ewall,ewall_all,nwall+1,MPI_DOUBLE,MPI_SUM,world); + MPI_Allreduce(ewall, ewall_all, nwall + 1, MPI_DOUBLE, MPI_SUM, world); eflag = 1; } return ewall_all[0]; @@ -381,8 +423,8 @@ double FixWall::compute_vector(int n) // only sum across procs one time if (eflag == 0) { - MPI_Allreduce(ewall,ewall_all,nwall+1,MPI_DOUBLE,MPI_SUM,world); + MPI_Allreduce(ewall, ewall_all, nwall + 1, MPI_DOUBLE, MPI_SUM, world); eflag = 1; } - return ewall_all[n+1]; + return ewall_all[n + 1]; } diff --git a/src/fix_wall.h b/src/fix_wall.h index 32fccea2b3..12ceb17b49 100644 --- a/src/fix_wall.h +++ b/src/fix_wall.h @@ -50,8 +50,8 @@ class FixWall : public Fix { double xscale, yscale, zscale; int estyle[6], sstyle[6], astyle[6], wstyle[6]; int eindex[6], sindex[6]; - char *estr[6], *sstr[6], *astr[6]; - int varflag; // 1 if any wall position,epsilon,sigma is a var + char *estr[6], *sstr[6], *astr[6], *lstr[6], *fstr[6], *kstr[6]; + int varflag; // 1 if any wall position,epsilon,sigma is a variable int eflag; // per-wall flag for energy summation int ilevel_respa; int fldflag; diff --git a/src/fix_wall_harmonic.cpp b/src/fix_wall_harmonic.cpp index a8e4127523..0e8fa22684 100644 --- a/src/fix_wall_harmonic.cpp +++ b/src/fix_wall_harmonic.cpp @@ -16,7 +16,6 @@ #include "error.h" using namespace LAMMPS_NS; -using namespace FixConst; /* ---------------------------------------------------------------------- */ diff --git a/src/fix_wall_lj126.cpp b/src/fix_wall_lj126.cpp index 78d9656e7f..f7458448be 100644 --- a/src/fix_wall_lj126.cpp +++ b/src/fix_wall_lj126.cpp @@ -18,7 +18,6 @@ #include "error.h" using namespace LAMMPS_NS; -using namespace FixConst; /* ---------------------------------------------------------------------- */ diff --git a/src/fix_wall_lj93.cpp b/src/fix_wall_lj93.cpp index 1e02b61fe1..7c4db056f9 100644 --- a/src/fix_wall_lj93.cpp +++ b/src/fix_wall_lj93.cpp @@ -18,7 +18,6 @@ #include "error.h" using namespace LAMMPS_NS; -using namespace FixConst; /* ---------------------------------------------------------------------- */ diff --git a/src/fix_wall_morse.cpp b/src/fix_wall_morse.cpp index a1427b380f..6c5eee885d 100644 --- a/src/fix_wall_morse.cpp +++ b/src/fix_wall_morse.cpp @@ -18,7 +18,6 @@ #include using namespace LAMMPS_NS; -using namespace FixConst; /* ---------------------------------------------------------------------- */ @@ -72,7 +71,7 @@ void FixWallMorse::wall_particle(int m, int which, double coord) } double dr = delta - sigma[m]; double dexp = exp(-alpha[m] * dr); - fwall = side * coeff1[m] * (dexp * dexp - dexp) / delta; + fwall = side * coeff1[m] * (dexp * dexp - dexp); ewall[0] += epsilon[m] * (dexp * dexp - 2.0 * dexp) - offset[m]; f[i][dim] -= fwall; ewall[m + 1] += fwall; diff --git a/src/fix_wall_table.cpp b/src/fix_wall_table.cpp new file mode 100644 index 0000000000..dc1dda4504 --- /dev/null +++ b/src/fix_wall_table.cpp @@ -0,0 +1,472 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS development team: developers@lammps.org + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "fix_wall_table.h" +#include "atom.h" +#include "comm.h" +#include "error.h" +#include "memory.h" +#include "table_file_reader.h" +#include "tokenizer.h" + +#include + +using namespace LAMMPS_NS; + +enum { NONE, LINEAR, SPLINE }; + +static constexpr double BIGNUM = 1.0e300; + +/* ---------------------------------------------------------------------- */ + +FixWallTable::FixWallTable(LAMMPS *lmp, int narg, char **arg) : + FixWall(lmp, narg, arg), tables(nullptr) +{ + dynamic_group_allow = 1; + tabstyle = NONE; + if (strcmp(arg[3], "linear") == 0) + tabstyle = LINEAR; + else if (strcmp(arg[3], "spline") == 0) + tabstyle = SPLINE; + else + error->all(FLERR, "Unknown table style {} in fix {}", arg[3], style); + + tablength = utils::inumeric(FLERR, arg[4], false, lmp); + if (tablength < 2) error->all(FLERR, "Illegal number of fix {} table entries", style); +} + +/* ---------------------------------------------------------------------- */ + +void FixWallTable::post_constructor() +{ + memory->sfree(tables); + tables = (Table *) memory->smalloc(nwall * sizeof(Table), "wall:tables"); + + for (int m = 0; m < nwall; ++m) { + Table &tb = tables[m]; + null_table(tb); + + if (comm->me == 0) read_table(tb, fstr[m], kstr[m]); + bcast_table(tb); + + // error check on table parameters + if (tb.ninput <= 1) error->all(FLERR, "Invalid fix {} table length: {}", style, tb.ninput); + tb.lo = tb.rfile[0]; + tb.hi = tb.rfile[tb.ninput - 1]; + if (tb.lo >= tb.hi) error->all(FLERR, "Fix {} table distance values do not increase", style); + if (cutoff[m] > tb.hi) + error->all(FLERR, "Fix {} wall cutoff {} is larger than table outer cutoff {}", style, + cutoff[m], tb.hi); + + // spline read-in data and compute r,e,f arrays within table + spline_table(tb); + compute_table(tb); + } +} + +/* ---------------------------------------------------------------------- */ + +FixWallTable::~FixWallTable() +{ + for (int m = 0; m < nwall; m++) free_table(tables[m]); + memory->sfree(tables); +} + +/* ---------------------------------------------------------------------- + compute the potential energy offset so it can be shifted to zero at the cutoff +------------------------------------------------------------------------- */ + +void FixWallTable::precompute(int m) +{ + double u, mdu; + + // always use linear interpolation to determine the offset, since we may be at the + // outer table cutoff and spline interpolation would cause out-of-bounds array accesses + int savedtabstyle = tabstyle; + tabstyle = LINEAR; + uf_lookup(m, cutoff[m], u, mdu); + offset[m] = u; + tabstyle = savedtabstyle; +} + +/* ---------------------------------------------------------------------- + interaction of all particles in group with a wall + m = index of wall coeffs + which = xlo,xhi,ylo,yhi,zlo,zhi + error if any particle is on or behind wall +------------------------------------------------------------------------- */ + +void FixWallTable::wall_particle(int m, int which, double coord) +{ + double delta, fwall, vn, u, mdu; + + double **x = atom->x; + double **f = atom->f; + int *mask = atom->mask; + int nlocal = atom->nlocal; + + int dim = which / 2; + int side = which % 2; + if (side == 0) side = -1; + + int onflag = 0; + + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit) { + if (side < 0) + delta = x[i][dim] - coord; + else + delta = coord - x[i][dim]; + if (delta >= cutoff[m]) continue; + if (delta <= 0.0) { + onflag = 1; + continue; + } + + uf_lookup(m, delta, u, mdu); + fwall = side * mdu; + f[i][dim] -= fwall; + ewall[0] += u - offset[m]; + ewall[m + 1] += fwall; + + if (evflag) { + if (side < 0) + vn = -fwall * delta; + else + vn = fwall * delta; + v_tally(dim, i, vn); + } + } + + if (onflag) error->one(FLERR, "Particle on or inside fix {} surface", style); +} + +/* ---------------------------------------------------------------------- */ + +void FixWallTable::null_table(Table &tb) +{ + tb.rfile = tb.efile = tb.ffile = nullptr; + tb.e2file = tb.f2file = nullptr; + tb.r = tb.e = tb.de = nullptr; + tb.f = tb.df = tb.e2 = tb.f2 = nullptr; +} + +/* ---------------------------------------------------------------------- */ + +void FixWallTable::free_table(Table &tb) +{ + memory->destroy(tb.rfile); + memory->destroy(tb.efile); + memory->destroy(tb.ffile); + memory->destroy(tb.e2file); + memory->destroy(tb.f2file); + + memory->destroy(tb.r); + memory->destroy(tb.e); + memory->destroy(tb.de); + memory->destroy(tb.f); + memory->destroy(tb.df); + memory->destroy(tb.e2); + memory->destroy(tb.f2); +} + +/* ---------------------------------------------------------------------- */ + +void FixWallTable::read_table(Table &tb, const std::string &tabfile, const std::string &keyword) +{ + TableFileReader reader(lmp, tabfile, "fix wall/table"); + + char *line = reader.find_section_start(keyword); + if (!line) error->one(FLERR, "Did not find keyword {} in table file", keyword); + + // read args on 2nd line of section + // allocate table arrays for file values + + line = reader.next_line(); + param_extract(tb, line); + memory->create(tb.rfile, tb.ninput, "wall:rfile"); + memory->create(tb.efile, tb.ninput, "wall:efile"); + memory->create(tb.ffile, tb.ninput, "wall:ffile"); + + // read r,e,f table values from file + + reader.skip_line(); + for (int i = 0; i < tb.ninput; i++) { + line = reader.next_line(); + if (!line) + error->one(FLERR, "Data missing when parsing wall table '{}' line {} of {}.", keyword, i + 1, + tb.ninput); + try { + ValueTokenizer values(line); + values.next_int(); + tb.rfile[i] = values.next_double(); + tb.efile[i] = values.next_double(); + tb.ffile[i] = values.next_double(); + } catch (TokenizerException &e) { + error->one(FLERR, "Error parsing wall table '{}' line {} of {}. {}\nLine was: {}", keyword, + i + 1, tb.ninput, e.what(), line); + } + } + + // warn if force != dE/dr at any point that is not an inflection point + // check via secant approximation to dE/dr + // skip two end points since do not have surrounding secants + // inflection point is where curvature changes sign + + double r, e, f, rprev, rnext, eprev, enext, fleft, fright; + + int ferror = 0; + for (int i = 1; i < tb.ninput - 1; i++) { + r = tb.rfile[i]; + rprev = tb.rfile[i - 1]; + rnext = tb.rfile[i + 1]; + e = tb.efile[i]; + eprev = tb.efile[i - 1]; + enext = tb.efile[i + 1]; + f = tb.ffile[i]; + fleft = -(e - eprev) / (r - rprev); + fright = -(enext - e) / (rnext - r); + if (f < fleft && f < fright) ferror++; + if (f > fleft && f > fright) ferror++; + } + + if (ferror) + error->warning(FLERR, + "{} of {} force values in table are inconsistent with -dE/dr.\n" + "WARNING: Should only be flagged at inflection points", + ferror, tb.ninput); +} + +/* ---------------------------------------------------------------------- + build spline representation of e,f over entire range of read-in table + this function sets these values in e2file,f2file +------------------------------------------------------------------------- */ + +void FixWallTable::spline_table(Table &tb) +{ + memory->create(tb.e2file, tb.ninput, "wall:e2file"); + memory->create(tb.f2file, tb.ninput, "wall:f2file"); + + double ep0 = -tb.ffile[0]; + double epn = -tb.ffile[tb.ninput - 1]; + spline(tb.rfile, tb.efile, tb.ninput, ep0, epn, tb.e2file); + + if (tb.fpflag == 0) { + tb.fplo = (tb.ffile[1] - tb.ffile[0]) / (tb.rfile[1] - tb.rfile[0]); + tb.fphi = (tb.ffile[tb.ninput - 1] - tb.ffile[tb.ninput - 2]) / + (tb.rfile[tb.ninput - 1] - tb.rfile[tb.ninput - 2]); + } + + double fp0 = tb.fplo; + double fpn = tb.fphi; + spline(tb.rfile, tb.ffile, tb.ninput, fp0, fpn, tb.f2file); +} + +/* ---------------------------------------------------------------------- + compute r,e,f vectors from splined values +------------------------------------------------------------------------- */ + +void FixWallTable::compute_table(Table &tb) +{ + // delta = table spacing for N-1 bins + int tlm1 = tablength - 1; + + tb.delta = (tb.hi - tb.lo) / tlm1; + tb.invdelta = 1.0 / tb.delta; + tb.deltasq6 = tb.delta * tb.delta / 6.0; + + // N-1 evenly spaced bins in r from min to max + // r,e,f = value at lower edge of bin + // de,df values = delta values of e,f + // r,e,f are N in length so de,df arrays can compute difference + + memory->create(tb.r, tablength, "wall:r"); + memory->create(tb.e, tablength, "wall:e"); + memory->create(tb.de, tablength, "wall:de"); + memory->create(tb.f, tablength, "wall:f"); + memory->create(tb.df, tablength, "wall:df"); + memory->create(tb.e2, tablength, "wall:e2"); + memory->create(tb.f2, tablength, "wall:f2"); + + double a; + for (int i = 0; i < tablength; i++) { + a = tb.lo + i * tb.delta; + tb.r[i] = a; + tb.e[i] = splint(tb.rfile, tb.efile, tb.e2file, tb.ninput, a); + tb.f[i] = splint(tb.rfile, tb.ffile, tb.f2file, tb.ninput, a); + } + + for (int i = 0; i < tlm1; i++) { + tb.de[i] = tb.e[i + 1] - tb.e[i]; + tb.df[i] = tb.f[i + 1] - tb.f[i]; + } + // get final elements from linear extrapolation + tb.de[tlm1] = 2.0 * tb.de[tlm1 - 1] - tb.de[tlm1 - 2]; + tb.df[tlm1] = 2.0 * tb.df[tlm1 - 1] - tb.df[tlm1 - 2]; + + double ep0 = -tb.f[0]; + double epn = -tb.f[tlm1]; + spline(tb.r, tb.e, tablength, ep0, epn, tb.e2); + spline(tb.r, tb.f, tablength, tb.fplo, tb.fphi, tb.f2); +} + +/* ---------------------------------------------------------------------- + extract attributes from parameter line in table section + format of line: N value FP fplo fphi + N is required, other params are optional +------------------------------------------------------------------------- */ + +void FixWallTable::param_extract(Table &tb, char *line) +{ + tb.ninput = 0; + tb.fpflag = 0; + + try { + ValueTokenizer values(line); + + while (values.has_next()) { + std::string word = values.next_string(); + + if (word == "N") { + tb.ninput = values.next_int(); + } else if (word == "FP") { + tb.fpflag = 1; + tb.fplo = values.next_double(); + tb.fphi = values.next_double(); + } else { + error->one(FLERR, "Invalid keyword {} in fix {} table parameters", word, style); + } + } + } catch (TokenizerException &e) { + error->one(FLERR, e.what()); + } + + if (tb.ninput == 0) error->one(FLERR, "Fix {} parameters did not set N", style); +} + +/* ---------------------------------------------------------------------- + broadcast read-in table info from proc 0 to other procs + this function communicates these values in Table: + ninput,rfile,efile,ffile,fpflag,fplo,fphi +------------------------------------------------------------------------- */ + +void FixWallTable::bcast_table(Table &tb) +{ + MPI_Bcast(&tb.ninput, 1, MPI_INT, 0, world); + + if (comm->me > 0) { + memory->create(tb.rfile, tb.ninput, "wall:rfile"); + memory->create(tb.efile, tb.ninput, "wall:efile"); + memory->create(tb.ffile, tb.ninput, "wall:ffile"); + } + + MPI_Bcast(tb.rfile, tb.ninput, MPI_DOUBLE, 0, world); + MPI_Bcast(tb.efile, tb.ninput, MPI_DOUBLE, 0, world); + MPI_Bcast(tb.ffile, tb.ninput, MPI_DOUBLE, 0, world); + + MPI_Bcast(&tb.fpflag, 1, MPI_INT, 0, world); + if (tb.fpflag) { + MPI_Bcast(&tb.fplo, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&tb.fphi, 1, MPI_DOUBLE, 0, world); + } +} + +/* ---------------------------------------------------------------------- + spline and splint routines modified from Numerical Recipes +------------------------------------------------------------------------- */ + +void FixWallTable::spline(double *x, double *y, int n, double yp1, double ypn, double *y2) +{ + int i, k; + double p, qn, sig, un; + auto u = new double[n]; + + if (yp1 > BIGNUM) + y2[0] = u[0] = 0.0; + else { + y2[0] = -0.5; + u[0] = (3.0 / (x[1] - x[0])) * ((y[1] - y[0]) / (x[1] - x[0]) - yp1); + } + for (i = 1; i < n - 1; i++) { + sig = (x[i] - x[i - 1]) / (x[i + 1] - x[i - 1]); + p = sig * y2[i - 1] + 2.0; + y2[i] = (sig - 1.0) / p; + u[i] = (y[i + 1] - y[i]) / (x[i + 1] - x[i]) - (y[i] - y[i - 1]) / (x[i] - x[i - 1]); + u[i] = (6.0 * u[i] / (x[i + 1] - x[i - 1]) - sig * u[i - 1]) / p; + } + if (ypn > BIGNUM) + qn = un = 0.0; + else { + qn = 0.5; + un = (3.0 / (x[n - 1] - x[n - 2])) * (ypn - (y[n - 1] - y[n - 2]) / (x[n - 1] - x[n - 2])); + } + y2[n - 1] = (un - qn * u[n - 2]) / (qn * y2[n - 2] + 1.0); + for (k = n - 2; k >= 0; k--) y2[k] = y2[k] * y2[k + 1] + u[k]; + + delete[] u; +} + +/* ---------------------------------------------------------------------- */ + +double FixWallTable::splint(double *xa, double *ya, double *y2a, int n, double x) +{ + int klo, khi, k; + double h, b, a, y; + + klo = 0; + khi = n - 1; + while (khi - klo > 1) { + k = (khi + klo) >> 1; + if (xa[k] > x) + khi = k; + else + klo = k; + } + h = xa[khi] - xa[klo]; + a = (xa[khi] - x) / h; + b = (x - xa[klo]) / h; + y = a * ya[klo] + b * ya[khi] + + ((a * a * a - a) * y2a[klo] + (b * b * b - b) * y2a[khi]) * (h * h) / 6.0; + return y; +} + +/* ---------------------------------------------------------------------- + calculate potential u and force f at distance x + ensure x is between wall min/max, exit with error if not +------------------------------------------------------------------------- */ + +void FixWallTable::uf_lookup(int m, double x, double &u, double &f) +{ + double fraction, a, b; + const Table &tb = tables[m]; + const int itable = static_cast((x - tb.lo) * tb.invdelta); + if (itable < 0) + error->one(FLERR, "Particle / wall distance < table inner cutoff: {:.8}", x); + else if (itable >= tablength) + error->one(FLERR, "Particle / wall distance > table outer cutoff: {:.8}", x); + + if (tabstyle == LINEAR) { + fraction = (x - tb.r[itable]) * tb.invdelta; + u = tb.e[itable] + fraction * tb.de[itable]; + f = tb.f[itable] + fraction * tb.df[itable]; + } else if (tabstyle == SPLINE) { + fraction = (x - tb.r[itable]) * tb.invdelta; + + b = (x - tb.r[itable]) * tb.invdelta; + a = 1.0 - b; + u = a * tb.e[itable] + b * tb.e[itable + 1] + + ((a * a * a - a) * tb.e2[itable] + (b * b * b - b) * tb.e2[itable + 1]) * tb.deltasq6; + f = a * tb.f[itable] + b * tb.f[itable + 1] + + ((a * a * a - a) * tb.f2[itable] + (b * b * b - b) * tb.f2[itable + 1]) * tb.deltasq6; + } +} diff --git a/src/fix_wall_table.h b/src/fix_wall_table.h new file mode 100644 index 0000000000..368c2e3cd1 --- /dev/null +++ b/src/fix_wall_table.h @@ -0,0 +1,67 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS development team: developers@lammps.org + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef FIX_CLASS +// clang-format off +FixStyle(wall/table,FixWallTable); +// clang-format on +#else + +#ifndef LMP_FIX_WALL_TABLE_H +#define LMP_FIX_WALL_TABLE_H + +#include "fix_wall.h" + +namespace LAMMPS_NS { + +class FixWallTable : public FixWall { + public: + FixWallTable(class LAMMPS *, int, char **); + ~FixWallTable() override; + + void post_constructor() override; + void precompute(int) override; + void wall_particle(int, int, double) override; + + protected: + double offset[6]; + + int tabstyle, tablength; + struct Table { + int ninput, fpflag; + double fplo, fphi; + double lo, hi; + double *rfile, *efile, *ffile; + double *e2file, *f2file; + double delta, invdelta, deltasq6; + double *r, *e, *de, *f, *df, *e2, *f2; + }; + Table *tables; + + void null_table(Table &); + void free_table(Table &); + void read_table(Table &, const std::string &, const std::string &); + void bcast_table(Table &); + void spline_table(Table &); + void compute_table(Table &); + + void param_extract(Table &, char *); + void spline(double *, double *, int, double, double, double *); + double splint(double *, double *, double *, int, double); + void uf_lookup(int, double, double &, double &); +}; + +} // namespace LAMMPS_NS + +#endif +#endif diff --git a/tools/tabulate/README.md b/tools/tabulate/README.md index fb23e260a1..6f63d03a80 100644 --- a/tools/tabulate/README.md +++ b/tools/tabulate/README.md @@ -6,13 +6,14 @@ table, and angle style table To create tables, you need to define your energy and - optionally - force functions and then an instance of either the PairTabulate(), -BondTabulate(), AngleTabulate(), or DihedralTabulate() class from the -tabulate module and call its run() method to generate the table. Most -of the settings (number of points, minimum, maximum etc.) are provided -as command line flags. The run() method may be called multiple times to -generate multiple tables, for instance after changing parameters of the -energy/force functions. If the force function is not provided, the -force will be determined through numerical differentiation. +BondTabulate(), AngleTabulate(), DihedralTabulate(), or WallTabulate() +class from the tabulate module and call its run() method to generate the +table. Most of the settings (number of points, minimum, maximum etc.) +are provided as command line flags. The run() method may be called +multiple times to generate multiple tables, for instance after changing +parameters of the energy/force functions. If the force function is not +provided, the force will be determined from the energy function through +numerical differentiation. Please see the individual tabulation scripts in this folder for examples: @@ -24,7 +25,8 @@ Please see the individual tabulation scripts in this folder for examples: | angle_harmonic_tabulate.py | creates a table for a harmonic angle potential table | | dihedral_harmonic_tabulate.py | creates a table for a harmonic dihedral potential table | | pair_hybrid_tabulate.py | creates a Morse/Lennard-Jones hybrid potential table with smooth switching | -| pair_zbladd_tabulate.py | creates a table for hybrid/overlay to use ZBL repulsion with an EAM potential | +| wall_harmonic_tabulate.py | creates a table for fix wall/table with a simple repulsive harmonic potential | +| wall_multi_tabulate.py | creates a table for fix wall/table with multiple tables | | ------------------------------|-------------------------------------------------------------------------------| Common command line flags: diff --git a/tools/tabulate/tabulate.py b/tools/tabulate/tabulate.py index 3bba7c2ecf..c3cb3a256f 100755 --- a/tools/tabulate/tabulate.py +++ b/tools/tabulate/tabulate.py @@ -279,6 +279,53 @@ class DihedralTabulate(Tabulate): if self.args.filename != '-': self.fp.close() +################################################################################ +# create tabulation for fix wall/table +class WallTabulate(Tabulate): + def __init__(self, efunc, ffunc=None, units=None, comment=None): + super(WallTabulate, self).__init__('wall', efunc, ffunc, units, comment) + self.parser.add_argument('--eshift', '-e', dest='eshift', default=False, + action='store_true', + help="Shift potential energy to be zero at outer cutoff") + idx = [a.dest for a in self.parser._actions].index('xmin') + self.parser._actions[idx].required=False + self.parser._actions[idx].default=0.0 + try: + self.args = self.parser.parse_args() + except argparse.ArgumentError: + sys.exit() + + def run(self, label): + # sanity checks + if self.args.num < 2: + self.helpexit('Expect 2 or more points in table for tabulation') + if self.args.xmin < 0.0: + self.helpexit('Inner cutoff must not be negative') + + self.diff = self.args.diff + if not self.forcefunc: + self.diff = True + + table, xzero = mktable(self.tstyle, label, self.args.num, self.args.xmin, self.args.xmax, + self.energyfunc, self.args.diff, self.forcefunc) + print("# Minimum energy of tabulated potential is at %g" % xzero) + offset = 0.0 + if self.args.eshift: + offset=self.energyfunc(self.args.xmax) + + self.openfile(label) + + if self.forcefunc: + diffmin = -numdiff(self.args.xmin, self.forcefunc) + diffmax = -numdiff(self.args.xmax, self.forcefunc) + self.fp.write("N %d FP %- 22.15g %- 22.15g\n\n" % (self.args.num, diffmin, diffmax)) + else: + self.fp.write("N %d\n\n" % (self.args.num)) + + self.writetable(table, offset) + if self.args.filename != '-': + self.fp.close() + ################################################################################ if __name__ == "__main__": sys.exit("The tabulate module is not meant to be executed directly") diff --git a/tools/tabulate/wall_harmonic_tabulate.py b/tools/tabulate/wall_harmonic_tabulate.py new file mode 100755 index 0000000000..9424856dbf --- /dev/null +++ b/tools/tabulate/wall_harmonic_tabulate.py @@ -0,0 +1,25 @@ +#!/usr/bin/env python + +from tabulate import WallTabulate + +################################################################################ +import math + +k = 100.0 +rzero = 4.0 + +def harmonic_force(r): + dr = r - rzero + f = -2.0 * k * dr + return f + +def harmonic_energy(r): + dr = r - rzero + f = k * dr * dr + return f + +################################################################################ + +if __name__ == "__main__": + wtable = WallTabulate(harmonic_energy, harmonic_force, units='real') + wtable.run('HARMONIC') diff --git a/tools/tabulate/wall_multi_tabulate.py b/tools/tabulate/wall_multi_tabulate.py new file mode 100755 index 0000000000..576889cf75 --- /dev/null +++ b/tools/tabulate/wall_multi_tabulate.py @@ -0,0 +1,64 @@ +#!/usr/bin/env python + +from tabulate import WallTabulate +import os, sys +################################################################################ +import math + +k = 100.0 +rzero = 4.0 +epsilon = 0.02 +sigma = 2.0 +depth = 20.0 +width = 2.0 +r0 = 1.2 + +def harmonic_force(r): + dr = r - rzero + f = -2.0 * k * dr + return f + +def harmonic_energy(r): + dr = r - rzero + f = k * dr * dr + return f + +def lj126_force(r): + f = -4.0*epsilon*(-12.0*math.pow(sigma/r,12.0)/r + 6.0*math.pow(sigma/r,6.0)/r) + return f + +def lj126_energy(r): + f = 4.0*epsilon*(math.pow(sigma/r,12.0) - math.pow(sigma/r,6.0)) + return f + +def morse_energy(r): + ralpha = math.exp(-width*(r-r0)) + f = depth * (-1.0 + (1.0 - ralpha) * (1.0 - ralpha)) + return f + +def morse_force(r): + ralpha = math.exp(-width*(r-r0)) + f = -2.0 * depth * width * (1.0 -ralpha) * ralpha + return f + + +################################################################################ + +if __name__ == "__main__": + fname = 'walltab.dat' + if os.path.exists(fname): + os.remove(fname) + sys.argv.append('--filename') + sys.argv.append(fname) + sys.argv.append('--num-points') + sys.argv.append('400') + sys.argv.append('--inner') + sys.argv.append('0.01') + sys.argv.append('--outer') + sys.argv.append('4.0') + wtable = WallTabulate(harmonic_energy, harmonic_force, units='real') + wtable.run('HARMONIC') + wtable = WallTabulate(lj126_energy, lj126_force, units='real') + wtable.run('LJ126') + wtable = WallTabulate(morse_energy, morse_force, units='real') + wtable.run('MORSE') diff --git a/unittest/force-styles/tests/fix-timestep-wall_lepton_const.yaml b/unittest/force-styles/tests/fix-timestep-wall_lepton_const.yaml new file mode 100644 index 0000000000..947bc6a95a --- /dev/null +++ b/unittest/force-styles/tests/fix-timestep-wall_lepton_const.yaml @@ -0,0 +1,82 @@ +--- +lammps_version: 8 Feb 2023 +date_generated: Thu Feb 23 00:40:51 2023 +epsilon: 4e-14 +skip_tests: +prerequisites: ! | + atom full + fix wall/lepton +pre_commands: ! | + boundary p f p +post_commands: ! | + fix move all nve + fix test solute wall/lepton ylo EDGE "k*(r-rc)^2;k=100.0" 5.0 yhi EDGE "k*(r-rc)^2;k=100.0" 5.0 + fix_modify test virial yes +input_file: in.fourmol +natoms: 29 +run_stress: ! |2- + 0.0000000000000000e+00 -7.2422093200265749e+02 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 +global_scalar: 42.69977443532441 +global_vector: ! |- + 2 0 -161.92409617466126 +run_pos: ! |2 + 1 -2.7051715090682593e-01 2.4891718422041942e+00 -1.6687343912524535e-01 + 2 3.1037661579862175e-01 2.9347166386691113e+00 -8.5496435221221156e-01 + 3 -7.0402515865264603e-01 1.2304739304383521e+00 -6.2777422080240730e-01 + 4 -1.5818156002522876e+00 1.4837443919066966e+00 -1.2538703954644463e+00 + 5 -9.0719963033698159e-01 9.2651871779341399e-01 3.9954137559444142e-01 + 6 2.4831695467823400e-01 2.8312974957866005e-01 -1.2314232372542311e+00 + 7 3.4143527599853957e-01 -2.2646552136496162e-02 -2.5292291409504188e+00 + 8 1.1743552256787158e+00 -4.8863229191571117e-01 -6.3783432834416876e-01 + 9 1.3800524227031346e+00 -2.5274721005121037e-01 2.8353985882456578e-01 + 10 2.0510765220197009e+00 -1.4604063740411815e+00 -9.8323745080488900e-01 + 11 1.7878031944407509e+00 -1.9921863272886073e+00 -1.8890602447598965e+00 + 12 3.0063007038317027e+00 -4.9013350489718083e-01 -1.6231898106978369e+00 + 13 4.0515402959160571e+00 -8.9202011606485665e-01 -1.6400005529914481e+00 + 14 2.6066963345462244e+00 -4.1789253964874307e-01 -2.6634003608727506e+00 + 15 2.9695287185264685e+00 5.5422613167055734e-01 -1.2342022021669503e+00 + 16 2.6747029695037297e+00 -2.4124119054292041e+00 -2.3435746152831470e-02 + 17 2.2153577785010934e+00 -2.0897985186506944e+00 1.1963150794337314e+00 + 18 2.1369701704267587e+00 3.0158507413153752e+00 -3.5179348337454122e+00 + 19 1.5355837136075348e+00 2.6255292355297897e+00 -4.2353987779858038e+00 + 20 2.7727573003201997e+00 3.6923910440705336e+00 -3.9330842459619779e+00 + 21 4.9040128073837339e+00 -4.0752348170758461e+00 -3.6210314709795299e+00 + 22 4.3582355554510048e+00 -4.2126119427061379e+00 -4.4612844196307497e+00 + 23 5.7439382849366911e+00 -3.5821957939240279e+00 -3.8766361295959513e+00 + 24 2.0689243582618388e+00 3.1513346906720905e+00 3.1550389755134005e+00 + 25 1.3045351331892774e+00 3.2665125705550957e+00 2.5111855258151388e+00 + 26 2.5809237402747862e+00 4.0117602605470681e+00 3.2212060529139430e+00 + 27 -1.9611343130344261e+00 -4.3563411931314180e+00 2.1098293115505782e+00 + 28 -2.7473562684511403e+00 -4.0200819932374339e+00 1.5830052163432258e+00 + 29 -1.3126000191357743e+00 -3.5962518039473323e+00 2.2746342468733483e+00 +run_vel: ! |2 + 1 8.0432349631399738e-03 1.4401841389211066e-02 4.9594370365888983e-03 + 2 6.1330361195047721e-03 -2.0880295268721639e-02 -2.0467529305087918e-03 + 3 -8.3074380171099371e-03 -1.3074180712034015e-02 -4.0925567431707903e-03 + 4 -3.7694367867060264e-03 -6.5650784618522711e-03 -1.1170951231990144e-03 + 5 -1.1026343955717478e-02 -9.8958287307442973e-03 -2.8423479505575396e-03 + 6 -3.9677127674597606e-02 4.6816039080495052e-02 3.7148638820894170e-02 + 7 9.1033730239907995e-04 -1.0128528243740664e-02 -5.1568250829251872e-02 + 8 7.9064772413549398e-03 -3.3507427942055241e-03 3.4557101116794005e-02 + 9 1.5644169779778431e-03 3.7365552198096001e-03 1.5047408727814703e-02 + 10 2.9201446825927662e-02 -2.9249578944835361e-02 -1.5018077412006624e-02 + 11 -4.7835961594766378e-03 -3.7481385002840358e-03 -2.3464104088049835e-03 + 12 2.2696449755579846e-03 -3.4774139663753189e-04 -3.0640769495163746e-03 + 13 2.7531740375147718e-03 5.8171061651960147e-03 -7.9467453772151639e-04 + 14 3.5246182201851889e-03 -5.7939995452846414e-03 -3.9478431035191398e-03 + 15 -1.8547944555517633e-03 -5.8554729566882438e-03 6.2938485388423842e-03 + 16 1.8681499934669346e-02 -1.3262466149576239e-02 -4.5638651461858082e-02 + 17 -1.2896270037715950e-02 9.7527666092669853e-03 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a/unittest/force-styles/tests/fix-timestep-wall_morse_const.yaml b/unittest/force-styles/tests/fix-timestep-wall_morse_const.yaml index 89290d9d7d..391070609f 100644 --- a/unittest/force-styles/tests/fix-timestep-wall_morse_const.yaml +++ b/unittest/force-styles/tests/fix-timestep-wall_morse_const.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 17 Feb 2022 -date_generated: Fri Mar 18 22:18:01 2022 +lammps_version: 8 Feb 2023 +date_generated: Thu Feb 23 15:26:55 2023 epsilon: 4e-14 skip_tests: prerequisites: ! | @@ -15,68 +15,68 @@ post_commands: ! | input_file: in.fourmol natoms: 29 run_stress: ! |2- - 0.0000000000000000e+00 -1.6447328969000660e+03 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 -global_scalar: -715.4154062573953 + 0.0000000000000000e+00 -7.4088044731917480e+03 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 +global_scalar: -860.4604684981359 global_vector: ! |- - 2 0 -362.76807567062644 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/dev/null +++ b/unittest/force-styles/tests/fix-timestep-wall_table_linear.yaml @@ -0,0 +1,82 @@ +--- +lammps_version: 8 Feb 2023 +date_generated: Thu Feb 23 00:56:30 2023 +epsilon: 4e-14 +skip_tests: +prerequisites: ! | + atom full + fix wall/table +pre_commands: ! | + boundary p f p +post_commands: ! | + fix move all nve + fix test solute wall/table linear 2000 ylo EDGE ${input_dir}/wall.table HARMONIC 4.0 yhi EDGE ${input_dir}/wall.table HARMONIC 4.0 + fix_modify test virial yes +input_file: in.fourmol +natoms: 29 +run_stress: ! |2- + 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 +global_scalar: 0 +global_vector: ! |- + 2 0 0 +run_pos: ! |2 + 1 -2.7045559775384032e-01 2.4912159905679729e+00 -1.6695851791541888e-01 + 2 3.1004029573899528e-01 2.9612354631094391e+00 -8.5466363037021464e-01 + 3 -7.0398551400789477e-01 1.2305509955830618e+00 -6.2777526944456274e-01 + 4 -1.5818159336499285e+00 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