diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index 0f15bf02be..08522c6d15 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -73,7 +73,7 @@ Here is a checklist of steps you need to follow to submit a single file or user * If you want your contribution to be added as a user-contributed feature, and it is a single file (actually a `.cpp` and `.h` file) it can be rapidly added to the USER-MISC directory. Include the one-line entry to add to the USER-MISC/README file in that directory, along with the 2 source files. You can do this multiple times if you wish to contribute several individual features. * If you want your contribution to be added as a user-contribution and it is several related features, it is probably best to make it a user package directory with a name like USER-FOO. In addition to your new files, the directory should contain a README text file. The README should contain your name and contact information and a brief description of what your new package does. If your files depend on other LAMMPS style files also being installed (e.g. because your file is a derived class from the other LAMMPS class), then an Install.sh file is also needed to check for those dependencies. See other README and Install.sh files in other USER directories as examples. Send us a tarball of this USER-FOO directory. * Your new source files need to have the LAMMPS copyright, GPL notice, and your name and email address at the top, like other user-contributed LAMMPS source files. They need to create a class that is inside the LAMMPS namespace. If the file is for one of the USER packages, including USER-MISC, then we are not as picky about the coding style (see above). I.e. the files do not need to be in the same stylistic format and syntax as other LAMMPS files, though that would be nice for developers as well as users who try to read your code. -* You **must** also create or extend a documentation file for each new command or style you are adding to LAMMPS. For simplicity and convenience, the documentation of groups of closely related commands or styles may be combined into a single file. This will be one file for a single-file feature. For a package, it might be several files. These are files in the [reStructuredText](https://docutils.sourceforge.io/rst.html) markup language, that are then converted to HTML and PDF. The tools for this conversion are included in the source distribution, and the translation can be as simple as doing "make html pdf" in the doc folder. Thus the documentation source files must be in the same format and style as other `.rst` files in the lammps/doc/src directory for similar commands and styles; use one or more of them as a starting point. An introduction to reStructuredText can be found at [https://docutils.sourceforge.io/docs/user/rst/quickstart.html](https://docutils.sourceforge.io/docs/user/rst/quickstart.html). As appropriate, the text files can include mathematical expressions in MathJAX markup or links to equations (see doc/Eqs/*.tex for examples, we auto-create the associated JPG files), or figures (see doc/JPG for examples), or even additional PDF files with further details (see doc/PDF for examples). The doc page should also include literature citations as appropriate; see the bottom of doc/fix_nh.rst for examples and the earlier part of the same file for how to format the cite itself. The "Restrictions" section of the doc page should indicate that your command is only available if LAMMPS is built with the appropriate USER-MISC or USER-FOO package. See other user package doc files for examples of how to do this. The prerequisite for building the HTML format files are Python 3.x and virtualenv. Please run at least `make html` and `make spelling` and carefully inspect and proofread the resulting HTML format doc page as well as the output produced to the screen. Make sure that all spelling errors are fixed or the necessary false positives are added to the `doc/utils/sphinx-config/false_positives.txt` file. For new styles, those usually also need to be added to lists on the respective overview pages. This can be checked for also with `make style_check`. +* You **must** also create or extend a documentation file for each new command or style you are adding to LAMMPS. For simplicity and convenience, the documentation of groups of closely related commands or styles may be combined into a single file. This will be one file for a single-file feature. For a package, it might be several files. These are files in the [reStructuredText](https://docutils.sourceforge.io/rst.html) markup language, that are then converted to HTML and PDF. The tools for this conversion are included in the source distribution, and the translation can be as simple as doing "make html pdf" in the doc folder. Thus the documentation source files must be in the same format and style as other `.rst` files in the lammps/doc/src directory for similar commands and styles; use one or more of them as a starting point. An introduction to reStructuredText can be found at [https://docutils.sourceforge.io/docs/user/rst/quickstart.html](https://docutils.sourceforge.io/docs/user/rst/quickstart.html). The text files can include mathematical expressions and symbol in ".. math::" sections or ":math:" expressions or figures (see doc/JPG for examples), or even additional PDF files with further details (see doc/PDF for examples). The doc page should also include literature citations as appropriate; see the bottom of doc/fix_nh.rst for examples and the earlier part of the same file for how to format the cite itself. The "Restrictions" section of the doc page should indicate that your command is only available if LAMMPS is built with the appropriate USER-MISC or USER-FOO package. See other user package doc files for examples of how to do this. The prerequisite for building the HTML format files are Python 3.x and virtualenv. Please run at least `make html`, `make pdf` and `make spelling` and carefully inspect and proofread the resulting HTML format doc page as well as the output produced to the screen. Make sure that all spelling errors are fixed or the necessary false positives are added to the `doc/utils/sphinx-config/false_positives.txt` file. For new styles, those usually also need to be added to lists on the respective overview pages. This can be checked for also with `make style_check`. * For a new package (or even a single command) you should include one or more example scripts demonstrating its use. These should run in no more than a couple minutes, even on a single processor, and not require large data files as input. See directories under examples/USER for examples of input scripts other users provided for their packages. These example inputs are also required for validating memory accesses and testing for memory leaks with valgrind * If there is a paper of yours describing your feature (either the algorithm/science behind the feature itself, or its initial usage, or its implementation in LAMMPS), you can add the citation to the *.cpp source file. See src/USER-EFF/atom_vec_electron.cpp for an example. A LaTeX citation is stored in a variable at the top of the file and a single line of code that references the variable is added to the constructor of the class. Whenever a user invokes your feature from their input script, this will cause LAMMPS to output the citation to a log.cite file and prompt the user to examine the file. Note that you should only use this for a paper you or your group authored. E.g. adding a cite in the code for a paper by Nose and Hoover if you write a fix that implements their integrator is not the intended usage. That kind of citation should just be in the doc page you provide. diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index 44c864941c..c2357fa059 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -52,7 +52,13 @@ include(CheckCCompilerFlag) include(CheckIncludeFileCXX) if(${CMAKE_CXX_COMPILER_ID} STREQUAL "Intel") - set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -restrict -std=c++11") + set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -restrict") +endif() + +if(${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU") + if(NOT ("${CMAKE_BUILD_TYPE}" STREQUAL "Debug")) + set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -ffast-math -ftree-vectorize -fexpensive-optimizations") + endif() endif() # we require C++11 @@ -125,12 +131,12 @@ set(LAMMPS_API_DEFINES) set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GRANULAR KSPACE LATTE MANYBODY MC MESSAGE MISC MOLECULE PERI POEMS QEQ REPLICA RIGID SHOCK SPIN SNAP SRD KIM PYTHON MSCG MPIIO VORONOI - USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-MESO USER-CGSDK USER-COLVARS + USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-MESODPD USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD USER-LB USER-MANIFOLD USER-MEAMC USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE - USER-NETCDF USER-PHONON USER-PLUMED USER-PTM USER-QTB USER-REAXC - USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF - USER-VTK USER-QUIP USER-QMMM USER-YAFF USER-ADIOS) + USER-NETCDF USER-PHONON USER-PLUMED USER-PTM USER-QTB USER-REACTION + USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY + USER-UEF USER-VTK USER-QUIP USER-QMMM USER-YAFF USER-ADIOS) set(ACCEL_PACKAGES USER-OMP KOKKOS OPT USER-INTEL GPU) foreach(PKG ${DEFAULT_PACKAGES} ${ACCEL_PACKAGES}) option(PKG_${PKG} "Build ${PKG} Package" OFF) @@ -175,6 +181,7 @@ option(BUILD_MPI "Build MPI version" ${MPI_FOUND}) if(BUILD_MPI) find_package(MPI REQUIRED) include_directories(${MPI_CXX_INCLUDE_PATH}) + add_definitions(-DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1) list(APPEND LAMMPS_LINK_LIBS ${MPI_CXX_LIBRARIES}) option(LAMMPS_LONGLONG_TO_LONG "Workaround if your system or MPI version does not recognize 'long long' data types" OFF) if(LAMMPS_LONGLONG_TO_LONG) diff --git a/doc/src/Commands_pair.rst b/doc/src/Commands_pair.rst index 10873f1203..8624b555bc 100644 --- a/doc/src/Commands_pair.rst +++ b/doc/src/Commands_pair.rst @@ -95,7 +95,7 @@ OPT. * :doc:`eam/fs (gikot) ` * :doc:`edip (o) ` * :doc:`edip/multi ` - * :doc:`edpd ` + * :doc:`edpd ` * :doc:`eff/cut ` * :doc:`eim (o) ` * :doc:`exp6/rx (k) ` @@ -171,8 +171,8 @@ OPT. * :doc:`lubricate/poly (o) ` * :doc:`lubricateU ` * :doc:`lubricateU/poly ` - * :doc:`mdpd ` - * :doc:`mdpd/rhosum ` + * :doc:`mdpd ` + * :doc:`mdpd/rhosum ` * :doc:`meam/c ` * :doc:`meam/spline (o) ` * :doc:`meam/sw/spline ` @@ -242,7 +242,7 @@ OPT. * :doc:`sw (giko) ` * :doc:`table (gko) ` * :doc:`table/rx (k) ` - * :doc:`tdpd ` + * :doc:`tdpd ` * :doc:`tersoff (giko) ` * :doc:`tersoff/mod (gko) ` * :doc:`tersoff/mod/c (o) ` diff --git a/doc/src/Errors_messages.rst b/doc/src/Errors_messages.rst index ec778a0b88..8e13e08f8d 100644 --- a/doc/src/Errors_messages.rst +++ b/doc/src/Errors_messages.rst @@ -509,14 +509,14 @@ Doc page with :doc:`WARNING messages ` *Bond/react: Atom affected by reaction too close to template edge* This means an atom which changes type or connectivity during the - reaction is too close to an 'edge' atom defined in the superimpose + reaction is too close to an 'edge' atom defined in the map file. This could cause incorrect assignment of bonds, angle, etc. Generally, this means you must include more atoms in your templates, such that there are at least two atoms between each atom involved in the reaction and an edge atom. *Bond/react: Fix bond/react needs ghost atoms from farther away* - This is because a processor needs to superimpose the entire unreacted + This is because a processor needs to map the entire unreacted molecule template onto simulation atoms it knows about. The comm\_modify cutoff command can be used to extend the communication range. diff --git a/doc/src/Manual_build.rst b/doc/src/Manual_build.rst index 26c32c0ccb..b401a65ac9 100644 --- a/doc/src/Manual_build.rst +++ b/doc/src/Manual_build.rst @@ -1,22 +1,28 @@ Building the LAMMPS manual ************************** -Depending on how you obtained LAMMPS, the doc directory has 2 or 3 -sub-directories and optionally 2 PDF files and 2 e-book format files: +Depending on how you obtained LAMMPS, the doc directory has up +to 6 sub-directories, 2 Nroff files, and optionally 2 PDF files +plus 2 e-book format files: .. parsed-literal:: src # content files for LAMMPS documentation html # HTML version of the LAMMPS manual (see html/Manual.html) - tools # tools and settings for building the documentation + utils # tools and settings for building the documentation + docenv # virtualenv for processing the manual sources + doctrees # temporary data from processing the manual + mathjax # code and fonts for rendering math in html Manual.pdf # large PDF version of entire manual Developer.pdf # small PDF with info about how LAMMPS is structured LAMMPS.epub # Manual in ePUB e-book format LAMMPS.mobi # Manual in MOBI e-book format + lammps.1 # man page for the lammps command + msi2lmp.1 # man page for the msi2lmp command -If you downloaded LAMMPS as a tarball from the web site, all these -directories and files should be included. +If you downloaded LAMMPS as a tarball from the web site, the html folder +and the PDF files should be included. If you downloaded LAMMPS from the public git repository, then the HTML and PDF files are not included. Instead you need to create them, in one diff --git a/doc/src/Modify_contribute.rst b/doc/src/Modify_contribute.rst index 0fd333b568..4a1377bcf0 100644 --- a/doc/src/Modify_contribute.rst +++ b/doc/src/Modify_contribute.rst @@ -140,8 +140,7 @@ packages in the src directory for examples. If you are uncertain, please ask. and your name and email address at the top, like other user-contributed LAMMPS source files. They need to create a class that is inside the LAMMPS namespace. If the file is for one of the - -* USER packages, including USER-MISC, then we are not as picky about the + USER packages, including USER-MISC, then we are not as picky about the coding style (see above). I.e. the files do not need to be in the same stylistic format and syntax as other LAMMPS files, though that would be nice for developers as well as users who try to read your diff --git a/doc/src/Packages_details.rst b/doc/src/Packages_details.rst index 89157ece6d..00103088a7 100644 --- a/doc/src/Packages_details.rst +++ b/doc/src/Packages_details.rst @@ -81,7 +81,7 @@ page gives those details. * :ref:`USER-LB ` * :ref:`USER-MANIFOLD ` * :ref:`USER-MEAMC ` - * :ref:`USER-MESO ` + * :ref:`USER-MESODPD ` * :ref:`USER-MGPT ` * :ref:`USER-MISC ` * :ref:`USER-MOFFF ` @@ -94,6 +94,7 @@ page gives those details. * :ref:`USER-QMMM ` * :ref:`USER-QTB ` * :ref:`USER-QUIP ` + * :ref:`USER-REACTION ` * :ref:`USER-REAXC ` * :ref:`USER-SCAFACOS ` * :ref:`USER-SDPD ` @@ -1792,10 +1793,10 @@ Sandia. ---------- -.. _PKG-USER-MESO: +.. _PKG-USER-MESODPD: -USER-MESO package ------------------ +USER-MESODPD package +-------------------- **Contents:** @@ -1811,14 +1812,14 @@ algorithm. **Supporting info:** -* src/USER-MESO: filenames -> commands -* src/USER-MESO/README +* src/USER-MESODPD: filenames -> commands +* src/USER-MESODPD/README * :doc:`atom_style edpd ` -* :doc:`pair_style edpd ` -* :doc:`pair_style mdpd ` -* :doc:`pair_style tdpd ` +* :doc:`pair_style edpd ` +* :doc:`pair_style mdpd ` +* :doc:`pair_style tdpd ` * :doc:`fix mvv/dpd ` -* examples/USER/meso +* examples/USER/mesodpd * http://lammps.sandia.gov/movies.html#mesodpd @@ -2180,6 +2181,39 @@ This package has :ref:`specific installation instructions ` on the :d ---------- +.. _PKG-USER-REACTION: + +USER-REACTION package +--------------------- + +**Contents:** + +This package allows for complex bond topology changes (reactions) +during a running MD simulation, when using classical force fields. +Topology changes are defined in pre- and post-reaction molecule +templates and can include creation and deletion of bonds, angles, +dihedrals, impropers, atom types, bond types, angle types, dihedral +types, improper types, and/or atomic charges. Other options currently +available include reaction constraints (e.g. angle and Arrhenius +constraints), deletion of reaction byproducts or other small +molecules, and chiral-sensitive reactions. + +**Author:** Jacob R. Gissinger (CU Boulder) while at NASA Langley Research Center. + +**Supporting info:** + +* src/USER-REACTION: filenames -> commands +* src/USER-REACTION/README +* :doc:`fix bond/react ` +* examples/USER/reaction +* `2017 LAMMPS Workshop `_ +* `2019 LAMMPS Workshop `_ +* disarmmd.org + + +---------- + + .. _PKG-USER-REAXC: USER-REAXC package diff --git a/doc/src/Packages_user.rst b/doc/src/Packages_user.rst index e3f0dba469..3c489564d7 100644 --- a/doc/src/Packages_user.rst +++ b/doc/src/Packages_user.rst @@ -65,7 +65,7 @@ package: +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ | :ref:`USER-MEAMC ` | modified EAM potential (C++) | :doc:`pair_style meam/c ` | meamc | no | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-MESO ` | mesoscale DPD models | :doc:`pair_style edpd ` | USER/meso | no | +| :ref:`USER-MESODPD ` | mesoscale DPD models | :doc:`pair_style edpd ` | USER/mesodpd | no | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ | :ref:`USER-MGPT ` | fast MGPT multi-ion potentials | :doc:`pair_style mgpt ` | USER/mgpt | no | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ @@ -91,6 +91,8 @@ package: +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ | :ref:`USER-QUIP ` | QUIP/libatoms interface | :doc:`pair_style quip ` | USER/quip | ext | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ +| :ref:`USER-REACTION ` | chemical reactions in classical MD | :doc:`fix bond/react ` | USER/reaction | no | ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ | :ref:`USER-REAXC ` | ReaxFF potential (C/C++) | :doc:`pair_style reaxc ` | reax | no | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ | :ref:`USER-SCAFACOS ` | wrapper on ScaFaCoS solver | :doc:`kspace_style scafacos ` | USER/scafacos | ext | diff --git a/doc/src/atom_style.rst b/doc/src/atom_style.rst index d0707559d7..7ae152851f 100644 --- a/doc/src/atom_style.rst +++ b/doc/src/atom_style.rst @@ -338,7 +338,7 @@ The *electron* style is part of the USER-EFF package for :doc:`electronic force The *dpd* style is part of the USER-DPD package for dissipative particle dynamics (DPD). -The *edpd*\ , *mdpd*\ , and *tdpd* styles are part of the USER-MESO package +The *edpd*\ , *mdpd*\ , and *tdpd* styles are part of the USER-MESODPD package for energy-conserving dissipative particle dynamics (eDPD), many-body dissipative particle dynamics (mDPD), and transport dissipative particle dynamics (tDPD), respectively. diff --git a/doc/src/compute_edpd_temp_atom.rst b/doc/src/compute_edpd_temp_atom.rst index e51e70e7f6..f71e04a2c2 100644 --- a/doc/src/compute_edpd_temp_atom.rst +++ b/doc/src/compute_edpd_temp_atom.rst @@ -46,13 +46,13 @@ Restrictions """""""""""" -This compute is part of the USER-MESO package. It is only enabled if +This compute is part of the USER-MESODPD package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. Related commands """""""""""""""" -:doc:`pair_style edpd ` +:doc:`pair_style edpd ` **Default:** none diff --git a/doc/src/compute_tdpd_cc_atom.rst b/doc/src/compute_tdpd_cc_atom.rst index bd3c5df074..ba1a9d5d0f 100644 --- a/doc/src/compute_tdpd_cc_atom.rst +++ b/doc/src/compute_tdpd_cc_atom.rst @@ -48,13 +48,13 @@ Restrictions """""""""""" -This compute is part of the USER-MESO package. It is only enabled if +This compute is part of the USER-MESODPD package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. Related commands """""""""""""""" -:doc:`pair_style tdpd ` +:doc:`pair_style tdpd ` **Default:** none diff --git a/doc/src/fix_bond_react.rst b/doc/src/fix_bond_react.rst index 14d04009e7..1206177ba1 100644 --- a/doc/src/fix_bond_react.rst +++ b/doc/src/fix_bond_react.rst @@ -60,7 +60,7 @@ Syntax Examples """""""" -For unabridged example scripts and files, see examples/USER/misc/bond\_react. +For unabridged example scripts and files, see examples/USER/reaction. .. parsed-literal:: @@ -149,10 +149,9 @@ constant-topology parts of your system separately. The dynamic group contains only atoms not involved in a reaction at a given timestep, and therefore should be used by a subsequent system-wide time integrator such as nvt, npt, or nve, as shown in the second example -above (full examples can be found at examples/USER/misc/bond\_react). -The time integration command should be placed after the fix bond/react -command due to the internal dynamic grouping performed by fix -bond/react. +above (full examples can be found at examples/USER/reaction). The time +integration command should be placed after the fix bond/react command +due to the internal dynamic grouping performed by fix bond/react. .. note:: @@ -295,7 +294,7 @@ either 'none' or 'charges.' Further details are provided in the discussion of the 'update\_edges' keyword. The fifth optional section begins with the keyword 'Constraints' and lists additional criteria that must be satisfied in order for the reaction to occur. Currently, -there are three types of constraints available, as discussed below. +there are four types of constraints available, as discussed below. A sample map file is given below: @@ -371,6 +370,24 @@ the central atom). Angles must be specified in degrees. This constraint can be used to enforce a certain orientation between reacting molecules. +The constraint of type 'dihedral' has the following syntax: + + +.. parsed-literal:: + + dihedral *ID1* *ID2* *ID3* *ID4* *amin* *amax* *amin2* *amax2* + +where 'dihedral' is the required keyword, and *ID1*\ , *ID2*\ , *ID3* +and *ID4* are pre-reaction atom IDs. Dihedral angles are calculated in +the interval (-180,180]. Refer to the :doc:`dihedral style ` +documentation for further details on convention. If *amin* is less +than *amax*, these four atoms must form a dihedral angle greater than +*amin* **and** less than *amax* for the reaction to occur. If *amin* +is greater than *amax*, these four atoms must form a dihedral angle +greater than *amin* **or** less than *amax* for the reaction to occur. +Angles must be specified in degrees. Optionally, a second range of +permissible angles *amin2*-*amax2* can be specified. + The constraint of type 'arrhenius' imposes an additional reaction probability according to the temperature-dependent Arrhenius equation: @@ -516,7 +533,7 @@ Restrictions """""""""""" -This fix is part of the USER-MISC package. It is only enabled if +This fix is part of the USER-REACTION package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. diff --git a/doc/src/fix_dpd_source.rst b/doc/src/fix_dpd_source.rst index 368971b1c7..a9ae641a41 100644 --- a/doc/src/fix_dpd_source.rst +++ b/doc/src/fix_dpd_source.rst @@ -82,16 +82,16 @@ Restrictions """""""""""" -This fix is part of the USER-MESO package. It is only enabled if +This fix is part of the USER-MESODPD package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. -Fix *edpd/source* must be used with the :doc:`pair_style edpd ` command. Fix *tdpd/source* must be used with the -:doc:`pair_style tdpd ` command. +Fix *edpd/source* must be used with the :doc:`pair_style edpd ` command. Fix *tdpd/source* must be used with the +:doc:`pair_style tdpd ` command. Related commands """""""""""""""" -:doc:`pair_style edpd `, :doc:`pair_style tdpd `, +:doc:`pair_style edpd `, :doc:`pair_style tdpd `, :doc:`compute edpd/temp/atom `, :doc:`compute tdpd/cc/atom ` **Default:** none diff --git a/doc/src/fix_mvv_dpd.rst b/doc/src/fix_mvv_dpd.rst index 211642e7ec..dbe4231616 100644 --- a/doc/src/fix_mvv_dpd.rst +++ b/doc/src/fix_mvv_dpd.rst @@ -66,15 +66,15 @@ standard velocity-Verlet (VV) scheme. For more details, see :ref:`Groot `. Fix *mvv/dpd* updates the position and velocity of each atom. It can -be used with the :doc:`pair_style mdpd ` command or other +be used with the :doc:`pair_style mdpd ` command or other pair styles such as :doc:`pair dpd `. Fix *mvv/edpd* updates the per-atom temperature, in addition to -position and velocity, and must be used with the :doc:`pair_style edpd ` command. +position and velocity, and must be used with the :doc:`pair_style edpd ` command. Fix *mvv/tdpd* updates the per-atom chemical concentration, in addition to position and velocity, and must be used with the -:doc:`pair_style tdpd ` command. +:doc:`pair_style tdpd ` command. ---------- @@ -92,14 +92,14 @@ Restrictions """""""""""" -This fix is part of the USER-MESO package. It is only enabled if +This fix is part of the USER-MESODPD package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. Related commands """""""""""""""" -:doc:`pair_style mdpd `, :doc:`pair_style edpd `, -:doc:`pair_style tdpd ` +:doc:`pair_style mdpd `, :doc:`pair_style edpd `, +:doc:`pair_style tdpd ` Default """"""" diff --git a/doc/src/min_style.rst b/doc/src/min_style.rst index 0382f0d075..a7453b5a57 100644 --- a/doc/src/min_style.rst +++ b/doc/src/min_style.rst @@ -182,4 +182,4 @@ Jonsson, Mills, Jacobsen. .. _Guenole: **(Guenole)** Guenole, Noehring, Vaid, Houlle, Xie, Prakash, Bitzek, -Comput Mater Sci, (2020), in press (arXiv:190802038). +Comput Mater Sci, 175, 109584 (2020). diff --git a/doc/src/pair_meso.rst b/doc/src/pair_mesodpd.rst similarity index 99% rename from doc/src/pair_meso.rst rename to doc/src/pair_mesodpd.rst index a40ae3db10..f51b1b4a2c 100644 --- a/doc/src/pair_meso.rst +++ b/doc/src/pair_mesodpd.rst @@ -297,7 +297,7 @@ Restrictions """""""""""" The pair styles *edpd*\ , *mdpd*\ , *mdpd/rhosum* and *tdpd* are part of -the USER-MESO package. It is only enabled if LAMMPS was built with +the USER-MESODPD package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. diff --git a/doc/src/pair_style.rst b/doc/src/pair_style.rst index 96d8eb1d04..f2c1ed7c97 100644 --- a/doc/src/pair_style.rst +++ b/doc/src/pair_style.rst @@ -162,7 +162,7 @@ accelerated styles exist. * :doc:`eam/fs ` - Finnis-Sinclair EAM * :doc:`edip ` - three-body EDIP potential * :doc:`edip/multi ` - multi-element EDIP potential -* :doc:`edpd ` - eDPD particle interactions +* :doc:`edpd ` - eDPD particle interactions * :doc:`eff/cut ` - electron force field with a cutoff * :doc:`eim ` - embedded ion method (EIM) * :doc:`exp6/rx ` - reactive DPD potential @@ -239,8 +239,8 @@ accelerated styles exist. * :doc:`lubricate/poly ` - hydrodynamic lubrication forces with polydispersity * :doc:`lubricateU ` - hydrodynamic lubrication forces for Fast Lubrication Dynamics * :doc:`lubricateU/poly ` - hydrodynamic lubrication forces for Fast Lubrication with polydispersity -* :doc:`mdpd ` - mDPD particle interactions -* :doc:`mdpd/rhosum ` - mDPD particle interactions for mass density +* :doc:`mdpd ` - mDPD particle interactions +* :doc:`mdpd/rhosum ` - mDPD particle interactions for mass density * :doc:`meam/c ` - modified embedded atom method (MEAM) in C * :doc:`meam/spline ` - splined version of MEAM * :doc:`meam/sw/spline ` - splined version of MEAM with a Stillinger-Weber term @@ -309,7 +309,7 @@ accelerated styles exist. * :doc:`sw ` - Stillinger-Weber 3-body potential * :doc:`table ` - tabulated pair potential * :doc:`table/rx ` - -* :doc:`tdpd ` - tDPD particle interactions +* :doc:`tdpd ` - tDPD particle interactions * :doc:`tersoff ` - Tersoff 3-body potential * :doc:`tersoff/mod ` - modified Tersoff 3-body potential * :doc:`tersoff/mod/c ` - diff --git a/doc/src/set.rst b/doc/src/set.rst index c633587b25..e7f3620b0f 100644 --- a/doc/src/set.rst +++ b/doc/src/set.rst @@ -462,13 +462,13 @@ value >= 0.0, the internal temperature is set to that value. If it is temperature is set to that value. Keywords *edpd/temp* and *edpd/cv* set the temperature and volumetric -heat capacity of an eDPD particle as defined by the USER-MESO package. +heat capacity of an eDPD particle as defined by the USER-MESODPD package. Currently, only :doc:`atom_style edpd ` defines particles with these attributes. The values for the temperature and heat capacity must be positive. Keyword *cc* sets the chemical concentration of a tDPD particle for a -specified species as defined by the USER-MESO package. Currently, only +specified species as defined by the USER-MESODPD package. Currently, only :doc:`atom_style tdpd ` defines particles with this attribute. An integer for "index" selects a chemical species (1 to Nspecies) where Nspecies is set by the atom\_style command. The value diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index 46af1049db..4192d92a88 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -615,6 +615,7 @@ dipolar dir Direc dirname +disarmmd discoverable discretization discretized @@ -1704,6 +1705,8 @@ Merz meshless meso mesocnt +MESODPD +mesodpd mesoparticle mesoscale mesoscopic @@ -2017,6 +2020,7 @@ Nrecompute Nrepeat nreset Nrho +Nroff nrun Ns Nsample diff --git a/examples/USER/meso/README b/examples/USER/mesodpd/README similarity index 100% rename from examples/USER/meso/README rename to examples/USER/mesodpd/README diff --git a/examples/USER/meso/edpd/in.edpd b/examples/USER/mesodpd/edpd/in.edpd similarity index 100% rename from examples/USER/meso/edpd/in.edpd rename to examples/USER/mesodpd/edpd/in.edpd diff --git a/examples/USER/meso/edpd/log.16Aug17.edpd.g++.1 b/examples/USER/mesodpd/edpd/log.16Aug17.edpd.g++.1 similarity index 100% rename from examples/USER/meso/edpd/log.16Aug17.edpd.g++.1 rename to examples/USER/mesodpd/edpd/log.16Aug17.edpd.g++.1 diff --git a/examples/USER/meso/edpd/log.16Aug17.edpd.g++.4 b/examples/USER/mesodpd/edpd/log.16Aug17.edpd.g++.4 similarity index 100% rename from examples/USER/meso/edpd/log.16Aug17.edpd.g++.4 rename to examples/USER/mesodpd/edpd/log.16Aug17.edpd.g++.4 diff --git a/examples/USER/meso/edpd/temp.profile.16Aug17.edpd.g++.1 b/examples/USER/mesodpd/edpd/temp.profile.16Aug17.edpd.g++.1 similarity index 100% rename from examples/USER/meso/edpd/temp.profile.16Aug17.edpd.g++.1 rename to examples/USER/mesodpd/edpd/temp.profile.16Aug17.edpd.g++.1 diff --git a/examples/USER/meso/edpd/temp.profile.16Aug17.edpd.g++.4 b/examples/USER/mesodpd/edpd/temp.profile.16Aug17.edpd.g++.4 similarity index 100% rename from examples/USER/meso/edpd/temp.profile.16Aug17.edpd.g++.4 rename to examples/USER/mesodpd/edpd/temp.profile.16Aug17.edpd.g++.4 diff --git a/examples/USER/meso/mdpd/in.mdpd b/examples/USER/mesodpd/mdpd/in.mdpd similarity index 100% rename from examples/USER/meso/mdpd/in.mdpd rename to examples/USER/mesodpd/mdpd/in.mdpd diff --git a/examples/USER/meso/mdpd/log.16Aug17.mdpd.g++.1 b/examples/USER/mesodpd/mdpd/log.16Aug17.mdpd.g++.1 similarity index 100% rename from examples/USER/meso/mdpd/log.16Aug17.mdpd.g++.1 rename to examples/USER/mesodpd/mdpd/log.16Aug17.mdpd.g++.1 diff --git a/examples/USER/meso/mdpd/log.16Aug17.mdpd.g++.4 b/examples/USER/mesodpd/mdpd/log.16Aug17.mdpd.g++.4 similarity index 100% rename from examples/USER/meso/mdpd/log.16Aug17.mdpd.g++.4 rename to examples/USER/mesodpd/mdpd/log.16Aug17.mdpd.g++.4 diff --git a/examples/USER/meso/tdpd/cc.profile.16Aug17.tdpd.g++.1 b/examples/USER/mesodpd/tdpd/cc.profile.16Aug17.tdpd.g++.1 similarity index 100% rename from examples/USER/meso/tdpd/cc.profile.16Aug17.tdpd.g++.1 rename to examples/USER/mesodpd/tdpd/cc.profile.16Aug17.tdpd.g++.1 diff --git a/examples/USER/meso/tdpd/cc.profile.16Aug17.tdpd.g++.4 b/examples/USER/mesodpd/tdpd/cc.profile.16Aug17.tdpd.g++.4 similarity index 100% rename from examples/USER/meso/tdpd/cc.profile.16Aug17.tdpd.g++.4 rename to examples/USER/mesodpd/tdpd/cc.profile.16Aug17.tdpd.g++.4 diff --git a/examples/USER/meso/tdpd/in.tdpd b/examples/USER/mesodpd/tdpd/in.tdpd similarity index 100% rename from examples/USER/meso/tdpd/in.tdpd rename to examples/USER/mesodpd/tdpd/in.tdpd diff --git a/examples/USER/meso/tdpd/log.16Aug17.tdpd.g++.1 b/examples/USER/mesodpd/tdpd/log.16Aug17.tdpd.g++.1 similarity index 100% rename from examples/USER/meso/tdpd/log.16Aug17.tdpd.g++.1 rename to examples/USER/mesodpd/tdpd/log.16Aug17.tdpd.g++.1 diff --git a/examples/USER/meso/tdpd/log.16Aug17.tdpd.g++.4 b/examples/USER/mesodpd/tdpd/log.16Aug17.tdpd.g++.4 similarity index 100% rename from examples/USER/meso/tdpd/log.16Aug17.tdpd.g++.4 rename to examples/USER/mesodpd/tdpd/log.16Aug17.tdpd.g++.4 diff --git a/examples/USER/misc/bond_react/nylon,6-6_melt/large_nylon_melt.data.gz b/examples/USER/misc/bond_react/nylon,6-6_melt/large_nylon_melt.data.gz deleted file mode 100644 index c620b879a8..0000000000 Binary files a/examples/USER/misc/bond_react/nylon,6-6_melt/large_nylon_melt.data.gz and /dev/null differ diff --git a/examples/USER/misc/bond_react/nylon,6-6_melt/in.large_nylon_melt b/examples/USER/reaction/nylon,6-6_melt/in.large_nylon_melt similarity index 100% rename from examples/USER/misc/bond_react/nylon,6-6_melt/in.large_nylon_melt rename to examples/USER/reaction/nylon,6-6_melt/in.large_nylon_melt diff --git a/examples/USER/misc/bond_react/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.1 b/examples/USER/reaction/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.1 similarity index 100% rename from examples/USER/misc/bond_react/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.1 rename to examples/USER/reaction/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.1 diff --git a/examples/USER/misc/bond_react/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.4 b/examples/USER/reaction/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.4 similarity index 100% rename from examples/USER/misc/bond_react/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.4 rename to examples/USER/reaction/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.4 diff --git a/examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp1_map b/examples/USER/reaction/nylon,6-6_melt/rxn1_stp1_map similarity index 100% rename from examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp1_map rename to examples/USER/reaction/nylon,6-6_melt/rxn1_stp1_map diff --git a/examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp1_reacted.data_template b/examples/USER/reaction/nylon,6-6_melt/rxn1_stp1_reacted.data_template similarity index 100% rename from examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp1_reacted.data_template rename to examples/USER/reaction/nylon,6-6_melt/rxn1_stp1_reacted.data_template diff --git a/examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp1_unreacted.data_template b/examples/USER/reaction/nylon,6-6_melt/rxn1_stp1_unreacted.data_template similarity index 100% rename from examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp1_unreacted.data_template rename to examples/USER/reaction/nylon,6-6_melt/rxn1_stp1_unreacted.data_template diff --git a/examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp2_map b/examples/USER/reaction/nylon,6-6_melt/rxn1_stp2_map similarity index 100% rename from examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp2_map rename to examples/USER/reaction/nylon,6-6_melt/rxn1_stp2_map diff --git a/examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp2_reacted.data_template b/examples/USER/reaction/nylon,6-6_melt/rxn1_stp2_reacted.data_template similarity index 100% rename from examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp2_reacted.data_template rename to examples/USER/reaction/nylon,6-6_melt/rxn1_stp2_reacted.data_template diff --git a/examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp2_unreacted.data_template b/examples/USER/reaction/nylon,6-6_melt/rxn1_stp2_unreacted.data_template similarity index 100% rename from examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp2_unreacted.data_template rename to examples/USER/reaction/nylon,6-6_melt/rxn1_stp2_unreacted.data_template diff --git a/examples/USER/reaction/tiny_epoxy/in.tiny_epoxy.stabilized b/examples/USER/reaction/tiny_epoxy/in.tiny_epoxy.stabilized new file mode 100644 index 0000000000..0e6e97cd46 --- /dev/null +++ b/examples/USER/reaction/tiny_epoxy/in.tiny_epoxy.stabilized @@ -0,0 +1,49 @@ +# two molecules DGEBA (diepoxy) and one DETA (linker) +# two crosslinking reactions + +units real + +boundary p p p + +atom_style full + +pair_style lj/class2 8 + +angle_style class2 + +bond_style class2 + +dihedral_style class2 + +improper_style class2 + +read_data tiny_epoxy.data + +velocity all create 300.0 4928459 dist gaussian + +molecule mol1 rxn1_stp1_pre.data_template +molecule mol2 rxn1_stp1_post.data_template +molecule mol3 rxn1_stp2_post.data_template +molecule mol4 rxn2_stp1_pre.data_template +molecule mol5 rxn2_stp1_post.data_template +molecule mol6 rxn2_stp2_post.data_template + +thermo 50 + +# dump 1 all xyz 1 test_vis.xyz + +fix rxns all bond/react stabilization yes statted_grp .03 & + react rxn1_stp1 all 1 0.0 5 mol1 mol2 rxn1_stp1.map & + react rxn1_stp2 all 1 0.0 5 mol2 mol3 rxn1_stp2.map & + react rxn2_stp1 all 1 0.0 5 mol4 mol5 rxn2_stp1.map & + react rxn2_stp2 all 1 0.0 5 mol5 mol6 rxn2_stp2.map + + +fix 1 statted_grp_REACT nvt temp 300 300 100 + +thermo_style custom step temp f_rxns[1] f_rxns[2] f_rxns[3] f_rxns[4] + +run 2000 + +# write_restart restart_longrun +# write_data restart_longrun.data nofix diff --git a/examples/USER/reaction/tiny_epoxy/log.20Nov19.tiny_epoxy.stabilized.g++.1 b/examples/USER/reaction/tiny_epoxy/log.20Nov19.tiny_epoxy.stabilized.g++.1 new file mode 100644 index 0000000000..6ca0361513 --- /dev/null +++ b/examples/USER/reaction/tiny_epoxy/log.20Nov19.tiny_epoxy.stabilized.g++.1 @@ -0,0 +1,172 @@ +LAMMPS (20 Nov 2019) + +WARNING-WARNING-WARNING-WARNING-WARNING +This LAMMPS executable was compiled using C++98 compatibility. +Please report the compiler info below at https://github.com/lammps/lammps/issues/1659 +GNU C++ 4.8.5 +WARNING-WARNING-WARNING-WARNING-WARNING + +Reading data file ... + orthogonal box = (10 -10 -15) to (30 20 10) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 118 atoms + scanning bonds ... + 4 = max bonds/atom + scanning angles ... + 6 = max angles/atom + scanning dihedrals ... + 18 = max dihedrals/atom + scanning impropers ... + 4 = max impropers/atom + reading bonds ... + 123 bonds + reading angles ... + 221 angles + reading dihedrals ... + 302 dihedrals + reading impropers ... + 115 impropers +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 4 = max # of 1-2 neighbors + 10 = max # of 1-3 neighbors + 19 = max # of 1-4 neighbors + 22 = max # of special neighbors + special bonds CPU = 0.000286808 secs + read_data CPU = 0.00724107 secs +Read molecule mol1: + 31 atoms with max type 10 + 30 bonds with max type 15 + 53 angles with max type 29 + 66 dihedrals with max type 39 + 31 impropers with max type 5 +Read molecule mol2: + 31 atoms with max type 10 + 30 bonds with max type 17 + 55 angles with max type 36 + 75 dihedrals with max type 51 + 34 impropers with max type 5 +Read molecule mol3: + 31 atoms with max type 11 + 30 bonds with max type 18 + 53 angles with max type 37 + 72 dihedrals with max type 53 + 31 impropers with max type 5 +Read molecule mol4: + 42 atoms with max type 11 + 41 bonds with max type 18 + 73 angles with max type 41 + 96 dihedrals with max type 54 + 43 impropers with max type 5 +Read molecule mol5: + 42 atoms with max type 11 + 41 bonds with max type 18 + 75 angles with max type 37 + 108 dihedrals with max type 53 + 46 impropers with max type 5 +Read molecule mol6: + 42 atoms with max type 11 + 41 bonds with max type 19 + 73 angles with max type 50 + 102 dihedrals with max type 66 + 43 impropers with max type 22 +dynamic group bond_react_MASTER_group defined +dynamic group statted_grp_REACT defined +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 10 + ghost atom cutoff = 10 + binsize = 5, bins = 4 6 5 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) pair lj/class2, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard + (2) fix bond/react, occasional, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +Setting up Verlet run ... + Unit style : real + Current step : 0 + Time step : 1 +Per MPI rank memory allocation (min/avg/max) = 17.28 | 17.28 | 17.28 Mbytes +Step Temp f_rxns[1] f_rxns[2] f_rxns[3] f_rxns[4] + 0 300 0 0 0 0 + 50 391.52956 1 0 0 0 + 100 475.26826 1 1 0 0 + 150 605.26215 1 1 1 0 + 200 545.7485 1 1 1 0 + 250 461.64929 1 1 1 1 + 300 452.10611 1 1 1 1 + 350 379.61671 1 1 1 1 + 400 331.22444 1 1 1 1 + 450 275.63969 1 1 1 1 + 500 316.63407 1 1 1 1 + 550 261.39841 1 1 1 1 + 600 313.70928 1 1 1 1 + 650 294.24011 1 1 1 1 + 700 285.81736 1 1 1 1 + 750 340.37496 1 1 1 1 + 800 333.2496 1 1 1 1 + 850 307.40826 1 1 1 1 + 900 304.68718 1 1 1 1 + 950 328.0289 1 1 1 1 + 1000 290.22808 1 1 1 1 + 1050 272.78518 1 1 1 1 + 1100 291.30546 1 1 1 1 + 1150 320.33992 1 1 1 1 + 1200 330.57057 1 1 1 1 + 1250 300.51008 1 1 1 1 + 1300 293.6209 1 1 1 1 + 1350 324.36604 1 1 1 1 + 1400 331.15408 1 1 1 1 + 1450 302.23396 1 1 1 1 + 1500 297.55562 1 1 1 1 + 1550 277.3187 1 1 1 1 + 1600 289.66052 1 1 1 1 + 1650 281.85404 1 1 1 1 + 1700 293.4999 1 1 1 1 + 1750 306.21866 1 1 1 1 + 1800 283.22696 1 1 1 1 + 1850 295.10473 1 1 1 1 + 1900 317.3843 1 1 1 1 + 1950 305.14825 1 1 1 1 + 2000 289.00911 1 1 1 1 +Loop time of 1.87066 on 1 procs for 2000 steps with 118 atoms + +Performance: 92.374 ns/day, 0.260 hours/ns, 1069.141 timesteps/s +98.4% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.12832 | 0.12832 | 0.12832 | 0.0 | 6.86 +Bond | 0.77458 | 0.77458 | 0.77458 | 0.0 | 41.41 +Neigh | 0.45068 | 0.45068 | 0.45068 | 0.0 | 24.09 +Comm | 0.029785 | 0.029785 | 0.029785 | 0.0 | 1.59 +Output | 0.31635 | 0.31635 | 0.31635 | 0.0 | 16.91 +Modify | 0.16657 | 0.16657 | 0.16657 | 0.0 | 8.90 +Other | | 0.004368 | | | 0.23 + +Nlocal: 118 ave 118 max 118 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 332 ave 332 max 332 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 4338 ave 4338 max 4338 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 4338 +Ave neighs/atom = 36.7627 +Ave special neighs/atom = 10.5763 +Neighbor list builds = 2000 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:02 diff --git a/examples/USER/reaction/tiny_epoxy/log.20Nov19.tiny_epoxy.stabilized.g++.4 b/examples/USER/reaction/tiny_epoxy/log.20Nov19.tiny_epoxy.stabilized.g++.4 new file mode 100644 index 0000000000..4673ba3980 --- /dev/null +++ b/examples/USER/reaction/tiny_epoxy/log.20Nov19.tiny_epoxy.stabilized.g++.4 @@ -0,0 +1,172 @@ +LAMMPS (20 Nov 2019) + +WARNING-WARNING-WARNING-WARNING-WARNING +This LAMMPS executable was compiled using C++98 compatibility. +Please report the compiler info below at https://github.com/lammps/lammps/issues/1659 +GNU C++ 4.8.5 +WARNING-WARNING-WARNING-WARNING-WARNING + +Reading data file ... + orthogonal box = (10 -10 -15) to (30 20 10) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 118 atoms + scanning bonds ... + 4 = max bonds/atom + scanning angles ... + 6 = max angles/atom + scanning dihedrals ... + 18 = max dihedrals/atom + scanning impropers ... + 4 = max impropers/atom + reading bonds ... + 123 bonds + reading angles ... + 221 angles + reading dihedrals ... + 302 dihedrals + reading impropers ... + 115 impropers +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 4 = max # of 1-2 neighbors + 10 = max # of 1-3 neighbors + 19 = max # of 1-4 neighbors + 22 = max # of special neighbors + special bonds CPU = 0.000239905 secs + read_data CPU = 0.0080783 secs +Read molecule mol1: + 31 atoms with max type 10 + 30 bonds with max type 15 + 53 angles with max type 29 + 66 dihedrals with max type 39 + 31 impropers with max type 5 +Read molecule mol2: + 31 atoms with max type 10 + 30 bonds with max type 17 + 55 angles with max type 36 + 75 dihedrals with max type 51 + 34 impropers with max type 5 +Read molecule mol3: + 31 atoms with max type 11 + 30 bonds with max type 18 + 53 angles with max type 37 + 72 dihedrals with max type 53 + 31 impropers with max type 5 +Read molecule mol4: + 42 atoms with max type 11 + 41 bonds with max type 18 + 73 angles with max type 41 + 96 dihedrals with max type 54 + 43 impropers with max type 5 +Read molecule mol5: + 42 atoms with max type 11 + 41 bonds with max type 18 + 75 angles with max type 37 + 108 dihedrals with max type 53 + 46 impropers with max type 5 +Read molecule mol6: + 42 atoms with max type 11 + 41 bonds with max type 19 + 73 angles with max type 50 + 102 dihedrals with max type 66 + 43 impropers with max type 22 +dynamic group bond_react_MASTER_group defined +dynamic group statted_grp_REACT defined +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 10 + ghost atom cutoff = 10 + binsize = 5, bins = 4 6 5 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) pair lj/class2, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard + (2) fix bond/react, occasional, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +Setting up Verlet run ... + Unit style : real + Current step : 0 + Time step : 1 +Per MPI rank memory allocation (min/avg/max) = 16.26 | 16.45 | 16.63 Mbytes +Step Temp f_rxns[1] f_rxns[2] f_rxns[3] f_rxns[4] + 0 300 0 0 0 0 + 50 391.52956 1 0 0 0 + 100 475.26826 1 1 0 0 + 150 605.26215 1 1 1 0 + 200 545.7485 1 1 1 0 + 250 461.64929 1 1 1 1 + 300 452.10611 1 1 1 1 + 350 379.61671 1 1 1 1 + 400 331.22444 1 1 1 1 + 450 275.63969 1 1 1 1 + 500 316.63407 1 1 1 1 + 550 261.39841 1 1 1 1 + 600 313.70928 1 1 1 1 + 650 294.24011 1 1 1 1 + 700 285.81736 1 1 1 1 + 750 340.37496 1 1 1 1 + 800 333.2496 1 1 1 1 + 850 307.40826 1 1 1 1 + 900 304.68718 1 1 1 1 + 950 328.0289 1 1 1 1 + 1000 290.22808 1 1 1 1 + 1050 272.78518 1 1 1 1 + 1100 291.30546 1 1 1 1 + 1150 320.33992 1 1 1 1 + 1200 330.57057 1 1 1 1 + 1250 300.51008 1 1 1 1 + 1300 293.6209 1 1 1 1 + 1350 324.36604 1 1 1 1 + 1400 331.15408 1 1 1 1 + 1450 302.23396 1 1 1 1 + 1500 297.55562 1 1 1 1 + 1550 277.3187 1 1 1 1 + 1600 289.66052 1 1 1 1 + 1650 281.85404 1 1 1 1 + 1700 293.4999 1 1 1 1 + 1750 306.21866 1 1 1 1 + 1800 283.22695 1 1 1 1 + 1850 295.10472 1 1 1 1 + 1900 317.38431 1 1 1 1 + 1950 305.14824 1 1 1 1 + 2000 289.00909 1 1 1 1 +Loop time of 0.689125 on 4 procs for 2000 steps with 118 atoms + +Performance: 250.753 ns/day, 0.096 hours/ns, 2902.231 timesteps/s +100.0% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.02002 | 0.030617 | 0.053133 | 7.7 | 4.44 +Bond | 0.10356 | 0.18908 | 0.22691 | 11.6 | 27.44 +Neigh | 0.16721 | 0.17002 | 0.17247 | 0.5 | 24.67 +Comm | 0.057286 | 0.12002 | 0.21612 | 17.0 | 17.42 +Output | 0.00028991 | 0.00034121 | 0.00049323 | 0.0 | 0.05 +Modify | 0.17626 | 0.17675 | 0.17721 | 0.1 | 25.65 +Other | | 0.002287 | | | 0.33 + +Nlocal: 29.5 ave 41 max 18 min +Histogram: 1 0 0 1 0 0 1 0 0 1 +Nghost: 306 ave 349 max 269 min +Histogram: 1 1 0 0 0 0 1 0 0 1 +Neighs: 1084.5 ave 2154 max 397 min +Histogram: 1 0 1 1 0 0 0 0 0 1 + +Total # of neighbors = 4338 +Ave neighs/atom = 36.7627 +Ave special neighs/atom = 10.5763 +Neighbor list builds = 2000 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:01 diff --git a/examples/USER/reaction/tiny_epoxy/rxn1_stp1.map b/examples/USER/reaction/tiny_epoxy/rxn1_stp1.map new file mode 100644 index 0000000000..fb8720be63 --- /dev/null +++ b/examples/USER/reaction/tiny_epoxy/rxn1_stp1.map @@ -0,0 +1,47 @@ +this is a map file + +1 edgeIDs +31 equivalences + +BondingIDs + +15 +1 + +EdgeIDs + +5 + +Equivalences + +1 1 +2 2 +3 3 +4 4 +5 5 +6 6 +7 7 +8 8 +9 9 +10 10 +11 11 +12 12 +13 13 +14 14 +15 15 +16 16 +17 17 +18 18 +19 19 +20 20 +21 21 +22 22 +23 23 +24 24 +25 25 +26 26 +27 27 +28 28 +29 29 +30 30 +31 31 diff --git a/examples/USER/reaction/tiny_epoxy/rxn1_stp1_post.data_template b/examples/USER/reaction/tiny_epoxy/rxn1_stp1_post.data_template new file mode 100644 index 0000000000..e510883432 --- /dev/null +++ b/examples/USER/reaction/tiny_epoxy/rxn1_stp1_post.data_template @@ -0,0 +1,315 @@ +rxn1_stp1_post + +31 atoms +30 bonds +55 angles +75 dihedrals +34 impropers + +Types + +1 1 +2 6 +3 1 +4 7 +5 4 +6 7 +7 8 +8 8 +9 8 +10 8 +11 8 +12 9 +13 1 +14 1 +15 9 +16 9 +17 1 +18 1 +19 10 +20 8 +21 8 +22 8 +23 8 +24 10 +25 10 +26 10 +27 10 +28 8 +29 8 +30 8 +31 8 + +Charges + +1 0.000000 +2 0.000000 +3 0.000000 +4 0.100000 +5 0.000000 +6 0.000000 +7 0.000000 +8 0.000000 +9 0.000000 +10 0.000000 +11 0.000000 +12 0.000000 +13 0.000000 +14 0.000000 +15 -0.025000 +16 -0.025000 +17 0.000000 +18 0.000000 +19 0.000000 +20 0.000000 +21 0.000000 +22 0.000000 +23 0.000000 +24 0.000000 +25 0.000000 +26 0.000000 +27 0.000000 +28 0.000000 +29 0.000000 +30 0.000000 +31 0.000000 + +Coords + +1 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a/examples/USER/reaction/tiny_epoxy/rxn1_stp2.map b/examples/USER/reaction/tiny_epoxy/rxn1_stp2.map new file mode 100644 index 0000000000..9e39e57310 --- /dev/null +++ b/examples/USER/reaction/tiny_epoxy/rxn1_stp2.map @@ -0,0 +1,47 @@ +this is a map file + +1 edgeIDs +31 equivalences + +BondingIDs + +4 +25 + +EdgeIDs + +5 + +Equivalences + +1 1 +2 2 +3 3 +4 4 +5 5 +6 6 +7 7 +8 8 +9 9 +10 10 +11 11 +12 12 +13 13 +14 14 +15 15 +16 16 +17 17 +18 18 +19 19 +20 20 +21 21 +22 22 +23 23 +24 24 +25 25 +26 26 +27 27 +28 28 +29 29 +30 30 +31 31 diff --git a/examples/USER/reaction/tiny_epoxy/rxn1_stp2_post.data_template b/examples/USER/reaction/tiny_epoxy/rxn1_stp2_post.data_template new file mode 100644 index 0000000000..cbb66a3151 --- /dev/null +++ b/examples/USER/reaction/tiny_epoxy/rxn1_stp2_post.data_template @@ -0,0 +1,307 @@ +rxn1_stp2_post + +31 atoms +30 bonds +53 angles +72 dihedrals +31 impropers + +Types + +1 1 +2 6 +3 1 +4 7 +5 4 +6 7 +7 8 +8 8 +9 8 +10 8 +11 8 +12 9 +13 1 +14 1 +15 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+15 18.354031 10.832100 -1.107140 +16 14.920880 15.018100 -0.201130 +17 16.390551 14.791140 -0.461060 +18 16.852989 13.538490 0.304530 +19 16.264271 12.190330 -1.257620 +20 16.025061 10.195290 0.210910 +21 16.346741 11.269890 1.698950 +22 18.466690 10.092460 0.935470 +23 18.592319 11.941150 0.745170 +24 16.017490 9.805710 -4.329880 +25 20.881861 11.302060 -0.773030 +26 14.344180 14.136430 -0.550280 +27 14.583670 15.922830 -0.748110 +28 16.984310 15.696060 -0.103470 +29 16.562460 14.639560 -1.577590 +30 16.674610 13.686010 1.420370 +31 17.964001 13.363150 0.117750 +32 18.680189 9.134390 -4.183100 +33 18.099751 8.263650 -5.343000 +34 19.081829 7.609610 -6.334180 +35 17.971729 9.827680 -5.367080 +36 20.263880 5.733600 -6.736780 +37 19.414030 6.299980 -5.878960 +38 18.194740 9.091640 -3.210950 +39 19.788940 9.208560 -4.119640 +40 17.399309 7.432220 -5.407800 +41 18.616249 7.545570 -7.316910 +42 19.987049 8.212500 -6.399400 + +Bonds + +1 1 1 8 +2 2 1 2 +3 1 1 7 +4 13 1 15 +5 2 3 2 +6 6 2 9 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27 +41 28 26 16 27 +42 25 18 17 16 +43 26 28 17 16 +44 26 29 17 16 +45 27 18 17 28 +46 27 18 17 29 +47 2 28 17 29 +48 25 17 18 12 +49 26 30 18 12 +50 26 31 18 12 +51 27 17 18 30 +52 27 17 18 31 +53 2 30 18 31 +54 26 39 32 15 +55 47 15 32 33 +56 26 38 32 15 +57 48 39 32 33 +58 2 39 32 38 +59 48 38 32 33 +60 34 32 33 35 +61 32 32 33 34 +62 33 32 33 40 +63 34 34 33 35 +64 35 35 33 40 +65 33 34 33 40 +66 49 37 34 33 +67 48 41 34 33 +68 48 42 34 33 +69 3 37 34 41 +70 3 37 34 42 +71 2 41 34 42 +72 50 24 35 33 +73 22 34 37 36 + +Dihedrals + +1 55 8 1 2 3 +2 3 8 1 2 9 +3 56 8 1 2 4 +4 55 7 1 2 3 +5 3 7 1 2 9 +6 56 7 1 2 4 +7 57 15 1 2 3 +8 58 15 1 2 9 +9 59 15 1 2 4 +10 28 8 1 15 14 +11 28 8 1 15 32 +12 60 2 1 15 14 +13 60 2 1 15 32 +14 28 7 1 15 14 +15 28 7 1 15 32 +16 61 6 3 2 1 +17 55 10 3 2 1 +18 55 11 3 2 1 +19 6 6 3 2 9 +20 3 10 3 2 9 +21 3 11 3 2 9 +22 62 6 3 2 4 +23 56 10 3 2 4 +24 56 11 3 2 4 +25 63 1 2 4 25 +26 63 3 2 4 25 +27 64 9 2 4 25 +28 8 2 3 6 5 +29 7 10 3 6 5 +30 7 11 3 6 5 +31 27 14 13 12 18 +32 28 20 13 12 18 +33 28 21 13 12 18 +34 29 14 13 12 19 +35 30 20 13 12 19 +36 30 21 13 12 19 +37 27 17 18 12 13 +38 28 30 18 12 13 +39 28 31 18 12 13 +40 29 17 18 12 19 +41 30 30 18 12 19 +42 30 31 18 12 19 +43 31 12 13 14 15 +44 32 22 14 13 12 +45 32 23 14 13 12 +46 32 20 13 14 15 +47 33 20 13 14 22 +48 33 20 13 14 23 +49 32 21 13 14 15 +50 33 21 13 14 22 +51 33 21 13 14 23 +52 27 13 14 15 1 +53 27 13 14 15 32 +54 28 22 14 15 1 +55 28 22 14 15 32 +56 28 23 14 15 1 +57 28 23 14 15 32 +58 28 39 32 15 1 +59 46 33 32 15 1 +60 28 38 32 15 1 +61 28 39 32 15 14 +62 46 33 32 15 14 +63 28 38 32 15 14 +64 29 18 17 16 26 +65 30 28 17 16 26 +66 30 29 17 16 26 +67 29 18 17 16 27 +68 30 28 17 16 27 +69 30 29 17 16 27 +70 31 16 17 18 12 +71 32 30 18 17 16 +72 32 31 18 17 16 +73 32 28 17 18 12 +74 33 28 17 18 30 +75 33 28 17 18 31 +76 32 29 17 18 12 +77 33 29 17 18 30 +78 33 29 17 18 31 +79 45 15 32 33 35 +80 43 15 32 33 34 +81 44 15 32 33 40 +82 42 39 32 33 35 +83 40 39 32 33 34 +84 41 39 32 33 40 +85 42 38 32 33 35 +86 40 38 32 33 34 +87 41 38 32 33 40 +88 65 24 35 33 32 +89 65 24 35 33 34 +90 66 24 35 33 40 +91 48 37 34 33 32 +92 40 41 34 33 32 +93 40 42 34 33 32 +94 50 37 34 33 35 +95 42 41 34 33 35 +96 42 42 34 33 35 +97 49 37 34 33 40 +98 41 41 34 33 40 +99 41 42 34 33 40 +100 51 33 34 37 36 +101 7 41 34 37 36 +102 7 42 34 37 36 + +Impropers + +1 4 13 12 18 19 +2 22 1 15 14 32 +3 5 17 16 26 27 +4 1 2 1 8 7 +5 1 2 1 8 15 +6 1 8 1 7 15 +7 1 2 1 7 15 +8 1 1 2 3 9 +9 1 1 2 3 4 +10 1 1 2 4 9 +11 1 3 2 4 9 +12 1 2 3 6 10 +13 1 2 3 6 11 +14 1 2 3 10 11 +15 1 6 3 10 11 +16 1 14 13 20 12 +17 1 14 13 21 12 +18 1 20 13 21 12 +19 1 14 13 20 21 +20 1 13 14 22 15 +21 1 13 14 23 15 +22 1 13 14 22 23 +23 1 22 14 23 15 +24 1 18 17 28 16 +25 1 18 17 29 16 +26 1 28 17 29 16 +27 1 18 17 28 29 +28 1 17 18 30 12 +29 1 17 18 31 12 +30 1 30 18 31 12 +31 1 17 18 30 31 +32 1 39 32 15 33 +33 1 39 32 38 15 +34 1 38 32 15 33 +35 1 39 32 38 33 +36 1 32 33 34 35 +37 1 32 33 35 40 +38 1 32 33 34 40 +39 1 34 33 35 40 +40 1 37 34 41 33 +41 1 37 34 42 33 +42 1 41 34 42 33 +43 1 37 34 41 42 diff --git a/examples/USER/reaction/tiny_epoxy/tiny_epoxy.data b/examples/USER/reaction/tiny_epoxy/tiny_epoxy.data new file mode 100644 index 0000000000..d98006b107 --- /dev/null +++ b/examples/USER/reaction/tiny_epoxy/tiny_epoxy.data @@ -0,0 +1,1582 @@ +# two molecules DGEBA (diepoxy) and one DETA (linker) + +118 atoms +123 bonds +221 angles +302 dihedrals +115 impropers +11 atom types +19 bond types +50 angle types +66 dihedral types +22 improper types +10 30 xlo xhi +-10 20 ylo yhi +-15 10 zlo zhi + +Masses + +1 12.011150 # c2 +2 12.011150 # c3m +3 15.999400 # o3e +4 12.011150 # cp +5 12.011150 # c +6 12.011150 # c3 +7 15.999400 # oc +8 1.007970 # hc +9 14.006700 # na +10 1.007970 # hn +11 1.007970 # ho + +Pair Coeffs # lj/class2/coul/long + +1 0.0540000000 4.0100000000 # c2 +2 0.0540000000 4.0100000000 # c3m +3 0.2400000000 3.5350000000 # o3e +4 0.0640000000 4.0100000000 # cp +5 0.0540000000 4.0100000000 # c +6 0.0540000000 4.0100000000 # c3 +7 0.2400000000 3.5350000000 # oc +8 0.0200000000 2.7000000000 # hc +9 0.0650000000 4.0700000000 # na +10 0.0130000000 1.0980000000 # hn +11 0.0130000000 1.0980000000 # ho + +Bond Coeffs # class2 + +1 1.1010 345.0000 -691.8900 844.6000 # c2-hc +2 1.5300 299.6700 -501.7700 679.8100 # c2-c3m +3 1.4200 400.3954 -835.1951 1313.0142 # c2-oc +4 1.4200 400.3954 -835.1951 1313.0142 # c3m-o3e +5 1.5300 299.6700 -501.7700 679.8100 # c3m-c3m +6 1.1010 345.0000 -691.8900 844.6000 # c3m-hc +7 1.4170 470.8361 -627.6179 1327.6345 # cp-cp +8 1.3768 428.8798 -738.2351 1114.9655 # cp-oc +9 1.0982 372.8251 -803.4526 894.3173 # cp-hc +10 1.5010 321.9021 -521.8208 572.1628 # cp-c +11 1.5300 299.6700 -501.7700 679.8100 # c-c3 +12 1.1010 345.0000 -691.8900 844.6000 # c3-hc +13 1.4570 365.8052 -699.6368 998.4842 # c2-na +14 1.0060 466.7400 -1073.6018 1251.1056 # na-hn +15 1.5300 299.6700 -501.7700 679.8100 # c2-c2 +16 1.5300 299.6700 -501.7700 679.8100 # c2-c3 +17 1.4200 400.3954 -835.1951 1313.0142 # c3-oc +18 0.9650 532.5062 -1282.9050 2004.7658 # oc-ho +19 1.4200 400.3954 -835.1951 1313.0142 # c3m-oc + +Angle Coeffs # class2 + +1 110.7700 41.4530 -10.6040 5.1290 # c3m-c2-hc +2 107.6600 39.6410 -12.9210 -2.4318 # hc-c2-hc +3 108.7280 58.5446 -10.8088 -12.4006 # oc-c2-hc +4 111.2700 54.5381 -8.3642 -13.0838 # c3m-c2-oc +5 111.2700 54.5381 -8.3642 -13.0838 # c2-c3m-o3e +6 112.6700 39.5160 -7.4430 -9.5583 # c2-c3m-c3m +7 110.7700 41.4530 -10.6040 5.1290 # c2-c3m-hc +8 111.2700 54.5381 -8.3642 -13.0838 # c3m-c3m-o3e +9 108.7280 58.5446 -10.8088 -12.4006 # o3e-c3m-hc +10 110.7700 41.4530 -10.6040 5.1290 # c3m-c3m-hc +11 107.6600 39.6410 -12.9210 -2.4318 # hc-c3m-hc +12 104.5000 35.7454 -10.0067 -6.2729 # c3m-o3e-c3m +13 118.9000 61.0226 -34.9931 0.0000 # cp-cp-cp +14 123.4200 73.6781 -21.6787 0.0000 # cp-cp-oc +15 117.9400 35.1558 -12.4682 0.0000 # cp-cp-hc +16 120.0500 44.7148 -22.7352 0.0000 # cp-cp-c +17 108.4000 43.9594 -8.3924 -9.3379 # cp-c-c3 +18 111.0000 44.3234 -9.4454 0.0000 # cp-c-cp +19 112.6700 39.5160 -7.4430 -9.5583 # c3-c-c3 +20 110.7700 41.4530 -10.6040 5.1290 # c-c3-hc +21 107.6600 39.6410 -12.9210 -2.4318 # hc-c3-hc +22 102.9695 38.9739 -6.2595 -8.1710 # c2-oc-cp +23 112.4436 47.2337 -10.6612 -10.2062 # c2-na-c2 +24 110.9538 50.8652 -4.4522 -10.0298 # c2-na-hn +25 111.9100 60.7147 -13.3366 -13.0785 # c2-c2-na +26 110.6204 51.3137 -6.7198 -2.6003 # hc-c2-na +27 110.7700 41.4530 -10.6040 5.1290 # c2-c2-hc +28 107.0671 45.2520 -7.5558 -9.5120 # hn-na-hn +29 112.6700 39.5160 -7.4430 -9.5583 # c3m-c3m-c2 +30 110.7700 41.4530 -10.6040 5.1290 # c3-c2-hc +31 111.9100 60.7147 -13.3366 -13.0785 # c3-c2-na +32 112.6700 39.5160 -7.4430 -9.5583 # c2-c3-c2 +33 110.7700 41.4530 -10.6040 5.1290 # c2-c3-hc +34 111.2700 54.5381 -8.3642 -13.0838 # c2-c3-oc +35 108.7280 58.5446 -10.8088 -12.4006 # oc-c3-hc +36 111.2700 54.5381 -8.3642 -13.0838 # c3-c2-oc +37 105.8000 52.7061 -12.1090 -9.8681 # c3-oc-ho +38 108.7280 58.5446 -10.8088 -12.4006 # hc-c3m-o3e +39 110.7700 41.4530 -10.6040 5.1290 # hc-c3m-c3m +40 111.2700 54.5381 -8.3642 -13.0838 # oc-c2-c3m +41 110.7700 41.4530 -10.6040 5.1290 # hc-c2-c3m +42 111.9100 60.7147 -13.3366 -13.0785 # c3m-c2-na +43 112.6700 39.5160 -7.4430 -9.5583 # c2-c3m-c2 +44 111.2700 54.5381 -8.3642 -13.0838 # c2-c3m-oc +45 108.7280 58.5446 -10.8088 -12.4006 # oc-c3m-hc +46 105.8000 52.7061 -12.1090 -9.8681 # c3m-oc-ho +47 111.9100 60.7147 -13.3366 -13.0785 # na-c2-c3 +48 110.7700 41.4530 -10.6040 5.1290 # hc-c2-c3 +49 111.2700 54.5381 -8.3642 -13.0838 # oc-c2-c3 +50 105.8000 52.7061 -12.1090 -9.8681 # ho-oc-c3 + +Dihedral Coeffs # class2 + +1 -0.1435 0.0000 0.2530 0.0000 -0.0905 0.0000# hc-c2-c3m-o3e +2 0.0000 0.0000 0.0316 0.0000 -0.1681 0.0000# hc-c2-c3m-c3m +3 -0.1432 0.0000 0.0617 0.0000 -0.1083 0.0000# hc-c2-c3m-hc +4 -0.1820 0.0000 -0.1084 0.0000 -0.7047 0.0000# oc-c2-c3m-o3e +5 0.7137 0.0000 0.2660 0.0000 -0.2545 0.0000# oc-c2-c3m-c3m +6 -0.1435 0.0000 0.2530 0.0000 -0.0905 0.0000# oc-c2-c3m-hc +7 0.9513 0.0000 0.1155 0.0000 0.0720 0.0000# hc-c2-oc-cp +8 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000# c3m-c2-oc-cp +9 -0.5203 0.0000 -0.3028 0.0000 -0.3450 0.0000# c2-c3m-o3e-c3m +10 0.5302 0.0000 0.0000 0.0000 -0.3966 0.0000# hc-c3m-o3e-c3m +11 0.7137 0.0000 0.2660 0.0000 -0.2545 0.0000# c2-c3m-c3m-o3e +12 0.0000 0.0000 0.0316 0.0000 -0.1681 0.0000# c2-c3m-c3m-hc +13 -0.1435 0.0000 0.2530 0.0000 -0.0905 0.0000# o3e-c3m-c3m-hc +14 -0.1432 0.0000 0.0617 0.0000 -0.1083 0.0000# hc-c3m-c3m-hc +15 8.3667 0.0000 1.1932 0.0000 0.0000 0.0000# cp-cp-cp-cp +16 0.0000 0.0000 3.9661 0.0000 0.0000 0.0000# cp-cp-cp-hc +17 0.0000 0.0000 4.8498 0.0000 0.0000 0.0000# cp-cp-cp-oc +18 0.0000 0.0000 1.7234 0.0000 0.0000 0.0000# oc-cp-cp-hc +19 0.0000 0.0000 1.5000 0.0000 0.0000 0.0000# cp-cp-oc-c2 +20 0.0000 0.0000 1.8769 0.0000 0.0000 0.0000# hc-cp-cp-hc +21 0.0000 0.0000 4.4072 0.0000 0.0000 0.0000# cp-cp-cp-c +22 0.0000 0.0000 1.5590 0.0000 0.0000 0.0000# c-cp-cp-hc +23 -0.2802 0.0000 -0.0678 0.0000 -0.0122 0.0000# cp-cp-c-c3 +24 -0.2802 0.0000 -0.0678 0.0000 -0.0122 0.0000# cp-cp-c-cp +25 -0.0228 0.0000 0.0280 0.0000 -0.1863 0.0000# cp-c-c3-hc +26 0.0000 0.0000 0.0316 0.0000 -0.1681 0.0000# c3-c-c3-hc +27 -0.1406 0.0000 0.4168 0.0000 0.0150 0.0000# c2-c2-na-c2 +28 0.1904 0.0000 -0.1342 0.0000 -0.2460 0.0000# hc-c2-na-c2 +29 -1.1506 0.0000 -0.6344 0.0000 -0.1845 0.0000# c2-c2-na-hn +30 -0.5187 0.0000 -0.4837 0.0000 -0.1692 0.0000# hc-c2-na-hn +31 0.3805 0.0000 0.3547 0.0000 -0.1102 0.0000# na-c2-c2-na +32 -0.2428 0.0000 0.4065 0.0000 -0.3079 0.0000# hc-c2-c2-na +33 -0.1432 0.0000 0.0617 0.0000 -0.1083 0.0000# hc-c2-c2-hc +34 0.7137 0.0000 0.2660 0.0000 -0.2545 0.0000# c3m-c3m-c2-oc +35 0.0000 0.0000 0.0316 0.0000 -0.1681 0.0000# c3m-c3m-c2-hc +36 -0.1820 0.0000 -0.1084 0.0000 -0.7047 0.0000# o3e-c3m-c2-oc +37 -0.1435 0.0000 0.2530 0.0000 -0.0905 0.0000# o3e-c3m-c2-hc +38 -0.1435 0.0000 0.2530 0.0000 -0.0905 0.0000# hc-c3m-c2-oc +39 -0.1432 0.0000 0.0617 0.0000 -0.1083 0.0000# hc-c3m-c2-hc +40 0.0000 0.0000 0.0316 0.0000 -0.1681 0.0000# hc-c2-c3-c2 +41 -0.1432 0.0000 0.0617 0.0000 -0.1083 0.0000# hc-c2-c3-hc +42 -0.1435 0.0000 0.2530 0.0000 -0.0905 0.0000# hc-c2-c3-oc +43 0.1764 0.0000 0.1766 0.0000 -0.5206 0.0000# na-c2-c3-c2 +44 -0.2428 0.0000 0.4065 0.0000 -0.3079 0.0000# na-c2-c3-hc +45 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000# na-c2-c3-oc +46 -0.1406 0.0000 0.4168 0.0000 0.0150 0.0000# c3-c2-na-c2 +47 -1.1506 0.0000 -0.6344 0.0000 -0.1845 0.0000# c3-c2-na-hn +48 0.7137 0.0000 0.2660 0.0000 -0.2545 0.0000# oc-c2-c3-c2 +49 -0.1435 0.0000 0.2530 0.0000 -0.0905 0.0000# oc-c2-c3-hc +50 -0.1820 0.0000 -0.1084 0.0000 -0.7047 0.0000# oc-c2-c3-oc +51 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000# c3-c2-oc-cp +52 -0.6732 0.0000 -0.4778 0.0000 -0.1670 0.0000# c2-c3-oc-ho +53 0.1863 0.0000 -0.4338 0.0000 -0.2121 0.0000# hc-c3-oc-ho +54 -0.1435 0.0000 0.2530 0.0000 -0.0905 0.0000# hc-c3m-c3m-o3e +55 0.0000 0.0000 0.0316 0.0000 -0.1681 0.0000# hc-c2-c3m-c2 +56 -0.1435 0.0000 0.2530 0.0000 -0.0905 0.0000# hc-c2-c3m-oc +57 0.1764 0.0000 0.1766 0.0000 -0.5206 0.0000# na-c2-c3m-c2 +58 -0.2428 0.0000 0.4065 0.0000 -0.3079 0.0000# na-c2-c3m-hc +59 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000# na-c2-c3m-oc +60 -0.1406 0.0000 0.4168 0.0000 0.0150 0.0000# c3m-c2-na-c2 +61 0.7137 0.0000 0.2660 0.0000 -0.2545 0.0000# oc-c2-c3m-c2 +62 -0.1820 0.0000 -0.1084 0.0000 -0.7047 0.0000# oc-c2-c3m-oc +63 -0.6732 0.0000 -0.4778 0.0000 -0.1670 0.0000# c2-c3m-oc-ho +64 0.1863 0.0000 -0.4338 0.0000 -0.2121 0.0000# hc-c3m-oc-ho +65 -0.6732 0.0000 -0.4778 0.0000 -0.1670 0.0000# ho-oc-c3-c2 +66 0.1863 0.0000 -0.4338 0.0000 -0.2121 0.0000# ho-oc-c3-hc + +Improper Coeffs # class2 + +1 13.0421 0.0000 # cp-cp-cp-oc +2 4.8912 0.0000 # cp-cp-cp-hc +3 7.8153 0.0000 # cp-cp-cp-c +4 0.0000 0.0000 # c2-na-c2-hn +5 0.0000 0.0000 # c2-na-hn-hn +6 0.0000 0.0000 +7 0.0000 0.0000 +8 0.0000 0.0000 +9 0.0000 0.0000 +10 0.0000 0.0000 +11 0.0000 0.0000 +12 0.0000 0.0000 +13 0.0000 0.0000 +14 0.0000 0.0000 +15 0.0000 0.0000 +16 0.0000 0.0000 +17 0.0000 0.0000 +18 0.0000 0.0000 +19 0.0000 0.0000 +20 0.0000 0.0000 +21 0.0000 0.0000 +22 0.0000 0.0000 # c2-na-c2-c2 + +BondBond Coeffs + +1 3.3872 1.5300 1.1010 +2 5.3316 1.1010 1.1010 +3 23.1979 1.4200 1.1010 +4 11.4318 1.5300 1.4200 +5 11.4318 1.5300 1.4200 +6 0.0000 1.5300 1.5300 +7 3.3872 1.5300 1.1010 +8 11.4318 1.5300 1.4200 +9 23.1979 1.4200 1.1010 +10 3.3872 1.5300 1.1010 +11 5.3316 1.1010 1.1010 +12 -7.1131 1.4200 1.4200 +13 68.2856 1.4170 1.4170 +14 48.4754 1.4170 1.3768 +15 1.0795 1.4170 1.0982 +16 12.0676 1.4170 1.5010 +17 0.0000 1.5010 1.5300 +18 0.0000 1.5010 1.5010 +19 0.0000 1.5300 1.5300 +20 3.3872 1.5300 1.1010 +21 5.3316 1.1010 1.1010 +22 0.0000 1.4200 1.3768 +23 -2.1113 1.4570 1.4570 +24 -6.4168 1.4570 1.0060 +25 4.6217 1.5300 1.4570 +26 12.4260 1.1010 1.4570 +27 3.3872 1.5300 1.1010 +28 -1.8749 1.0060 1.0060 +29 0.0000 1.5300 1.5300 +30 3.3872 1.5300 1.1010 +31 4.6217 1.5300 1.4570 +32 0.0000 1.5300 1.5300 +33 3.3872 1.5300 1.1010 +34 11.4318 1.5300 1.4200 +35 23.1979 1.4200 1.1010 +36 11.4318 1.5300 1.4200 +37 -9.6879 1.4200 0.9650 +38 23.1979 1.1010 1.4200 +39 3.3872 1.1010 1.5300 +40 11.4318 1.4200 1.5300 +41 3.3872 1.1010 1.5300 +42 4.6217 1.5300 1.4570 +43 0.0000 1.5300 1.5300 +44 11.4318 1.5300 1.4200 +45 23.1979 1.4200 1.1010 +46 -9.6879 1.4200 0.9650 +47 4.6217 1.4570 1.5300 +48 3.3872 1.1010 1.5300 +49 11.4318 1.4200 1.5300 +50 -9.6879 0.9650 1.4200 + +BondAngle Coeffs + +1 20.7540 11.4210 1.5300 1.1010 +2 18.1030 18.1030 1.1010 1.1010 +3 55.3270 4.6189 1.4200 1.1010 +4 2.6868 20.4033 1.5300 1.4200 +5 2.6868 20.4033 1.5300 1.4200 +6 8.0160 8.0160 1.5300 1.5300 +7 20.7540 11.4210 1.5300 1.1010 +8 2.6868 20.4033 1.5300 1.4200 +9 55.3270 4.6189 1.4200 1.1010 +10 20.7540 11.4210 1.5300 1.1010 +11 18.1030 18.1030 1.1010 1.1010 +12 -2.8112 -2.8112 1.4200 1.4200 +13 28.8708 28.8708 1.4170 1.4170 +14 58.4790 107.6806 1.4170 1.3768 +15 20.0033 24.2183 1.4170 1.0982 +16 31.0771 47.0579 1.4170 1.5010 +17 0.0000 0.0000 1.5010 1.5300 +18 0.0000 0.0000 1.5010 1.5010 +19 8.0160 8.0160 1.5300 1.5300 +20 20.7540 11.4210 1.5300 1.1010 +21 18.1030 18.1030 1.1010 1.1010 +22 0.0000 0.0000 1.4200 1.3768 +23 -7.2229 -7.2229 1.4570 1.4570 +24 31.8096 20.5799 1.4570 1.0060 +25 6.0876 16.5702 1.5300 1.4570 +26 13.4582 42.4332 1.1010 1.4570 +27 20.7540 11.4210 1.5300 1.1010 +28 28.0322 28.0322 1.0060 1.0060 +29 8.0160 8.0160 1.5300 1.5300 +30 20.7540 11.4210 1.5300 1.1010 +31 6.0876 16.5702 1.5300 1.4570 +32 8.0160 8.0160 1.5300 1.5300 +33 20.7540 11.4210 1.5300 1.1010 +34 2.6868 20.4033 1.5300 1.4200 +35 55.3270 4.6189 1.4200 1.1010 +36 2.6868 20.4033 1.5300 1.4200 +37 28.5800 18.9277 1.4200 0.9650 +38 4.6189 55.3270 1.1010 1.4200 +39 11.4210 20.7540 1.1010 1.5300 +40 20.4033 2.6868 1.4200 1.5300 +41 11.4210 20.7540 1.1010 1.5300 +42 6.0876 16.5702 1.5300 1.4570 +43 8.0160 8.0160 1.5300 1.5300 +44 2.6868 20.4033 1.5300 1.4200 +45 55.3270 4.6189 1.4200 1.1010 +46 28.5800 18.9277 1.4200 0.9650 +47 16.5702 6.0876 1.4570 1.5300 +48 11.4210 20.7540 1.1010 1.5300 +49 20.4033 2.6868 1.4200 1.5300 +50 18.9277 28.5800 0.9650 1.4200 + +AngleAngle Coeffs + +1 0.0000 0.0000 0.0000 118.9000 123.4200 123.4200 +2 0.0000 0.0000 0.0000 118.9000 117.9400 117.9400 +3 0.0000 0.0000 0.0000 118.9000 120.0500 120.0500 +4 0.0000 0.0000 0.0000 112.4436 110.9538 110.9538 +5 0.0000 0.0000 0.0000 110.9538 107.0671 110.9538 +6 0.2738 -0.4825 0.2738 110.7700 107.6600 110.7700 +7 0.1689 2.5926 3.9177 111.2700 108.7280 110.7700 +8 2.4259 2.1283 2.4259 108.7280 107.6600 108.7280 +9 -0.8330 -0.8330 -3.5744 112.6700 111.2700 111.2700 +10 0.1689 2.5926 3.9177 111.2700 108.7280 110.7700 +11 -1.3199 -1.3199 0.1184 112.6700 110.7700 110.7700 +12 0.1689 2.5926 3.9177 111.2700 108.7280 110.7700 +13 0.2738 -0.4825 0.2738 110.7700 107.6600 110.7700 +14 2.4259 2.1283 2.4259 108.7280 107.6600 108.7280 +15 0.0000 0.0000 0.0000 108.4000 112.6700 108.4000 +16 0.0000 0.0000 0.0000 111.0000 108.4000 108.4000 +17 0.2738 -0.4825 0.2738 110.7700 107.6600 110.7700 +18 -0.3157 -0.3157 -0.3157 107.6600 107.6600 107.6600 +19 2.4286 0.5381 -2.5301 110.7700 110.6204 111.9100 +20 2.4321 2.4321 -3.5496 107.6600 110.6204 110.6204 +21 0.2738 -0.4825 0.2738 110.7700 107.6600 110.7700 +22 0.0000 0.0000 0.0000 112.4436 112.4436 112.4436 + +AngleAngleTorsion Coeffs + +1 -20.2006 110.7700 111.2700 +2 -16.1640 110.7700 112.6700 +3 -12.5640 110.7700 110.7700 +4 -14.0484 111.2700 111.2700 +5 -29.0420 111.2700 112.6700 +6 -20.2006 111.2700 110.7700 +7 0.0000 108.7280 102.9695 +8 0.0000 111.2700 102.9695 +9 -19.0059 111.2700 104.5000 +10 -16.4438 108.7280 104.5000 +11 -29.0420 112.6700 111.2700 +12 -16.1640 112.6700 110.7700 +13 -20.2006 111.2700 110.7700 +14 -12.5640 110.7700 110.7700 +15 0.0000 118.9000 118.9000 +16 -4.8141 118.9000 117.9400 +17 -21.0247 118.9000 123.4200 +18 4.2296 123.4200 117.9400 +19 0.0000 123.4200 102.9695 +20 0.3598 117.9400 117.9400 +21 -14.4097 118.9000 120.0500 +22 4.4444 120.0500 117.9400 +23 0.0000 120.0500 108.4000 +24 0.0000 120.0500 111.0000 +25 0.0000 108.4000 110.7700 +26 -16.1640 112.6700 110.7700 +27 -24.3818 111.9100 112.4436 +28 -12.5567 110.6204 112.4436 +29 -7.5499 111.9100 110.9538 +30 -10.4258 110.6204 110.9538 +31 -11.2307 111.9100 111.9100 +32 -15.7572 110.7700 111.9100 +33 -12.5640 110.7700 110.7700 +34 -29.0420 112.6700 111.2700 +35 -16.1640 112.6700 110.7700 +36 -14.0484 111.2700 111.2700 +37 -20.2006 111.2700 110.7700 +38 -20.2006 110.7700 111.2700 +39 -12.5640 110.7700 110.7700 +40 -16.1640 110.7700 112.6700 +41 -12.5640 110.7700 110.7700 +42 -20.2006 110.7700 111.2700 +43 -27.3953 111.9100 112.6700 +44 -15.7572 111.9100 110.7700 +45 0.0000 111.9100 111.2700 +46 -24.3818 111.9100 112.4436 +47 -7.5499 111.9100 110.9538 +48 -29.0420 111.2700 112.6700 +49 -20.2006 111.2700 110.7700 +50 -14.0484 111.2700 111.2700 +51 0.0000 111.2700 102.9695 +52 -12.1038 111.2700 105.8000 +53 -10.5093 108.7280 105.8000 +54 -20.2006 110.7700 111.2700 +55 -16.1640 110.7700 112.6700 +56 -20.2006 110.7700 111.2700 +57 -27.3953 111.9100 112.6700 +58 -15.7572 111.9100 110.7700 +59 0.0000 111.9100 111.2700 +60 -24.3818 111.9100 112.4436 +61 -29.0420 111.2700 112.6700 +62 -14.0484 111.2700 111.2700 +63 -12.1038 111.2700 105.8000 +64 -10.5093 108.7280 105.8000 +65 -12.1038 105.8000 111.2700 +66 -10.5093 105.8000 108.7280 + +EndBondTorsion Coeffs + +1 0.9681 0.9551 0.0436 0.5903 0.6669 0.8584 1.1010 1.4200 +2 0.0814 0.0591 0.2219 0.2486 0.2422 -0.0925 1.1010 1.5300 +3 0.2130 0.3120 0.0777 0.2130 0.3120 0.0777 1.1010 1.1010 +4 1.0165 0.7553 -0.4609 1.0165 0.7553 -0.4609 1.4200 1.4200 +5 1.1538 0.8409 -0.9138 -0.3190 0.4411 -0.7174 1.4200 1.5300 +6 0.5903 0.6669 0.8584 0.9681 0.9551 0.0436 1.4200 1.1010 +7 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 1.1010 1.3768 +8 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 1.5300 1.3768 +9 -0.2456 1.0517 -0.7795 0.4741 1.2635 0.5576 1.5300 1.4200 +10 -0.6054 1.3339 0.9648 -0.1620 0.1564 -1.1408 1.1010 1.4200 +11 -0.3190 0.4411 -0.7174 1.1538 0.8409 -0.9138 1.5300 1.4200 +12 0.2486 0.2422 -0.0925 0.0814 0.0591 0.2219 1.5300 1.1010 +13 0.5903 0.6669 0.8584 0.9681 0.9551 0.0436 1.4200 1.1010 +14 0.2130 0.3120 0.0777 0.2130 0.3120 0.0777 1.1010 1.1010 +15 -0.1185 6.3204 0.0000 -0.1185 6.3204 0.0000 1.4170 1.4170 +16 0.0000 -6.8958 0.0000 0.0000 -0.4669 0.0000 1.4170 1.0982 +17 0.0000 0.2655 0.0000 0.0000 4.8905 0.0000 1.4170 1.3768 +18 0.0000 4.2641 0.0000 0.0000 -1.5867 0.0000 1.3768 1.0982 +19 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 1.4170 1.4200 +20 0.0000 -0.6890 0.0000 0.0000 -0.6890 0.0000 1.0982 1.0982 +21 0.0000 -0.6918 0.0000 0.0000 0.2421 0.0000 1.4170 1.5010 +22 0.0000 -1.7970 0.0000 0.0000 -0.4879 0.0000 1.5010 1.0982 +23 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 1.4170 1.5300 +24 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 1.4170 1.5010 +25 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 1.5010 1.1010 +26 0.2486 0.2422 -0.0925 0.0814 0.0591 0.2219 1.5300 1.1010 +27 0.0997 -0.0046 -0.2657 -0.0128 -0.0495 -0.1079 1.5300 1.4570 +28 -0.5892 0.7140 0.3505 0.0628 0.0873 -0.0882 1.1010 1.4570 +29 -0.9466 0.9356 -0.5542 0.0570 0.0625 0.4112 1.5300 1.0060 +30 -1.1685 0.9266 -0.0993 0.0850 0.3061 0.2104 1.1010 1.0060 +31 0.0286 0.0566 -0.0493 0.0286 0.0566 -0.0493 1.4570 1.4570 +32 0.1960 0.7056 0.1120 0.1022 0.2090 0.6433 1.1010 1.4570 +33 0.2130 0.3120 0.0777 0.2130 0.3120 0.0777 1.1010 1.1010 +34 -0.3190 0.4411 -0.7174 1.1538 0.8409 -0.9138 1.5300 1.4200 +35 0.2486 0.2422 -0.0925 0.0814 0.0591 0.2219 1.5300 1.1010 +36 1.0165 0.7553 -0.4609 1.0165 0.7553 -0.4609 1.4200 1.4200 +37 0.5903 0.6669 0.8584 0.9681 0.9551 0.0436 1.4200 1.1010 +38 0.9681 0.9551 0.0436 0.5903 0.6669 0.8584 1.1010 1.4200 +39 0.2130 0.3120 0.0777 0.2130 0.3120 0.0777 1.1010 1.1010 +40 0.0814 0.0591 0.2219 0.2486 0.2422 -0.0925 1.1010 1.5300 +41 0.2130 0.3120 0.0777 0.2130 0.3120 0.0777 1.1010 1.1010 +42 0.9681 0.9551 0.0436 0.5903 0.6669 0.8584 1.1010 1.4200 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1.3768 +9 0.0000 1.5300 1.4200 +10 0.0000 1.1010 1.4200 +11 0.0000 1.5300 1.4200 +12 0.0000 1.5300 1.1010 +13 0.0000 1.4200 1.1010 +14 0.0000 1.1010 1.1010 +15 53.0000 1.4170 1.4170 +16 -6.2741 1.4170 1.0982 +17 -2.2436 1.4170 1.3768 +18 2.0517 1.3768 1.0982 +19 0.0000 1.4170 1.4200 +20 -1.7077 1.0982 1.0982 +21 2.5085 1.4170 1.5010 +22 0.8743 1.5010 1.0982 +23 0.0000 1.4170 1.5300 +24 0.0000 1.4170 1.5010 +25 0.0000 1.5010 1.1010 +26 0.0000 1.5300 1.1010 +27 0.0000 1.5300 1.4570 +28 0.0000 1.1010 1.4570 +29 0.0000 1.5300 1.0060 +30 0.0000 1.1010 1.0060 +31 0.0000 1.4570 1.4570 +32 0.0000 1.1010 1.4570 +33 0.0000 1.1010 1.1010 +34 0.0000 1.5300 1.4200 +35 0.0000 1.5300 1.1010 +36 0.0000 1.4200 1.4200 +37 0.0000 1.4200 1.1010 +38 0.0000 1.1010 1.4200 +39 0.0000 1.1010 1.1010 +40 0.0000 1.1010 1.5300 +41 0.0000 1.1010 1.1010 +42 0.0000 1.1010 1.4200 +43 0.0000 1.4570 1.5300 +44 0.0000 1.4570 1.1010 +45 0.0000 1.4570 1.4200 +46 0.0000 1.5300 1.4570 +47 0.0000 1.5300 1.0060 +48 0.0000 1.4200 1.5300 +49 0.0000 1.4200 1.1010 +50 0.0000 1.4200 1.4200 +51 0.0000 1.5300 1.3768 +52 0.0000 1.5300 0.9650 +53 0.0000 1.1010 0.9650 +54 0.0000 1.1010 1.4200 +55 0.0000 1.1010 1.5300 +56 0.0000 1.1010 1.4200 +57 0.0000 1.4570 1.5300 +58 0.0000 1.4570 1.1010 +59 0.0000 1.4570 1.4200 +60 0.0000 1.5300 1.4570 +61 0.0000 1.4200 1.5300 +62 0.0000 1.4200 1.4200 +63 0.0000 1.5300 0.9650 +64 0.0000 1.1010 0.9650 +65 0.0000 0.9650 1.5300 +66 0.0000 0.9650 1.1010 + +AngleTorsion Coeffs + +1 2.3668 2.4920 -1.0122 -0.1892 0.4918 0.7273 110.7700 111.2700 +2 0.3113 0.4516 -0.1988 -0.2454 0.0000 -0.1136 110.7700 112.6700 +3 -0.8085 0.5569 -0.2466 -0.8085 0.5569 -0.2466 110.7700 110.7700 +4 0.5511 0.9737 -0.6673 0.5511 0.9737 -0.6673 111.2700 111.2700 +5 0.9672 -0.7566 -1.2331 0.5623 -0.3041 -0.4015 111.2700 112.6700 +6 -0.1892 0.4918 0.7273 2.3668 2.4920 -1.0122 111.2700 110.7700 +7 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 108.7280 102.9695 +8 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 111.2700 102.9695 +9 -2.7466 1.4877 -0.8955 0.5676 0.9450 0.0703 111.2700 104.5000 +10 -1.8234 1.6393 0.5144 -0.7777 0.4340 -0.6653 108.7280 104.5000 +11 0.5623 -0.3041 -0.4015 0.9672 -0.7566 -1.2331 112.6700 111.2700 +12 -0.2454 0.0000 -0.1136 0.3113 0.4516 -0.1988 112.6700 110.7700 +13 -0.1892 0.4918 0.7273 2.3668 2.4920 -1.0122 111.2700 110.7700 +14 -0.8085 0.5569 -0.2466 -0.8085 0.5569 -0.2466 110.7700 110.7700 +15 1.9767 1.0239 0.0000 1.9767 1.0239 0.0000 118.9000 118.9000 +16 0.0000 2.5014 0.0000 0.0000 2.7147 0.0000 118.9000 117.9400 +17 0.0000 10.0155 0.0000 0.0000 1.7404 0.0000 118.9000 123.4200 +18 0.0000 2.5706 0.0000 0.0000 1.8729 0.0000 123.4200 117.9400 +19 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 123.4200 102.9695 +20 0.0000 2.4501 0.0000 0.0000 2.4501 0.0000 117.9400 117.9400 +21 0.0000 3.8987 0.0000 0.0000 -4.4683 0.0000 118.9000 120.0500 +22 0.0000 -0.1242 0.0000 0.0000 3.4601 0.0000 120.0500 117.9400 +23 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 120.0500 108.4000 +24 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 120.0500 111.0000 +25 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 108.4000 110.7700 +26 -0.2454 0.0000 -0.1136 0.3113 0.4516 -0.1988 112.6700 110.7700 +27 -2.7883 1.5193 1.4796 1.2031 1.3645 -0.7071 111.9100 112.4436 +28 -2.6321 0.9353 -0.8398 -1.3582 0.1465 -0.5729 110.6204 112.4436 +29 -3.3430 4.4558 -0.0346 0.2873 -0.8072 -0.0960 111.9100 110.9538 +30 -3.9582 2.0063 0.3213 -0.4294 -0.4442 -0.6141 110.6204 110.9538 +31 1.3673 0.4528 -2.7700 1.3673 0.4528 -2.7700 111.9100 111.9100 +32 0.5111 1.6328 -1.0155 -1.1075 0.2820 0.8318 110.7700 111.9100 +33 -0.8085 0.5569 -0.2466 -0.8085 0.5569 -0.2466 110.7700 110.7700 +34 0.5623 -0.3041 -0.4015 0.9672 -0.7566 -1.2331 112.6700 111.2700 +35 -0.2454 0.0000 -0.1136 0.3113 0.4516 -0.1988 112.6700 110.7700 +36 0.5511 0.9737 -0.6673 0.5511 0.9737 -0.6673 111.2700 111.2700 +37 -0.1892 0.4918 0.7273 2.3668 2.4920 -1.0122 111.2700 110.7700 +38 2.3668 2.4920 -1.0122 -0.1892 0.4918 0.7273 110.7700 111.2700 +39 -0.8085 0.5569 -0.2466 -0.8085 0.5569 -0.2466 110.7700 110.7700 +40 0.3113 0.4516 -0.1988 -0.2454 0.0000 -0.1136 110.7700 112.6700 +41 -0.8085 0.5569 -0.2466 -0.8085 0.5569 -0.2466 110.7700 110.7700 +42 2.3668 2.4920 -1.0122 -0.1892 0.4918 0.7273 110.7700 111.2700 +43 2.0125 0.9440 -2.7612 -1.9225 -1.3450 0.2210 111.9100 112.6700 +44 -1.1075 0.2820 0.8318 0.5111 1.6328 -1.0155 111.9100 110.7700 +45 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 111.9100 111.2700 +46 -2.7883 1.5193 1.4796 1.2031 1.3645 -0.7071 111.9100 112.4436 +47 -3.3430 4.4558 -0.0346 0.2873 -0.8072 -0.0960 111.9100 110.9538 +48 0.9672 -0.7566 -1.2331 0.5623 -0.3041 -0.4015 111.2700 112.6700 +49 -0.1892 0.4918 0.7273 2.3668 2.4920 -1.0122 111.2700 110.7700 +50 0.5511 0.9737 -0.6673 0.5511 0.9737 -0.6673 111.2700 111.2700 +51 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 111.2700 102.9695 +52 -3.5903 2.5225 0.4888 0.8726 -0.3577 0.3888 111.2700 105.8000 +53 -3.4060 1.6396 0.0737 0.0000 -0.2810 -0.5944 108.7280 105.8000 +54 2.3668 2.4920 -1.0122 -0.1892 0.4918 0.7273 110.7700 111.2700 +55 0.3113 0.4516 -0.1988 -0.2454 0.0000 -0.1136 110.7700 112.6700 +56 2.3668 2.4920 -1.0122 -0.1892 0.4918 0.7273 110.7700 111.2700 +57 2.0125 0.9440 -2.7612 -1.9225 -1.3450 0.2210 111.9100 112.6700 +58 -1.1075 0.2820 0.8318 0.5111 1.6328 -1.0155 111.9100 110.7700 +59 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 111.9100 111.2700 +60 -2.7883 1.5193 1.4796 1.2031 1.3645 -0.7071 111.9100 112.4436 +61 0.9672 -0.7566 -1.2331 0.5623 -0.3041 -0.4015 111.2700 112.6700 +62 0.5511 0.9737 -0.6673 0.5511 0.9737 -0.6673 111.2700 111.2700 +63 -3.5903 2.5225 0.4888 0.8726 -0.3577 0.3888 111.2700 105.8000 +64 -3.4060 1.6396 0.0737 0.0000 -0.2810 -0.5944 108.7280 105.8000 +65 0.8726 -0.3577 0.3888 -3.5903 2.5225 0.4888 105.8000 111.2700 +66 0.0000 -0.2810 -0.5944 -3.4060 1.6396 0.0737 105.8000 108.7280 + +Atoms # full + +1 1 1 0.000000 25.246496201 -1.871744037 -8.651348114 0 0 0 # c2 +2 1 2 0.000000 25.610639572 -3.288228035 -8.165973663 0 0 0 # c3m +3 1 2 0.000000 24.731319427 -4.483242989 -8.675741196 0 0 0 # c3m +4 1 2 0.000000 18.703355789 9.118826866 -4.174236774 0 0 0 # c3m +5 1 2 0.000000 18.099748611 8.263649940 -5.343001842 0 0 0 # c3m +6 1 1 0.000000 19.081827164 7.609607220 -6.334177017 0 0 0 # c2 +7 1 3 0.100000 26.190139771 -4.295329094 -9.220970154 0 0 0 # o3e +8 1 3 0.100000 17.971729279 9.827675819 -5.367077827 0 0 0 # o3e +9 1 4 0.000000 20.263877869 5.733595848 -6.736782074 0 0 0 # cp +10 1 4 0.000000 19.777191162 4.983679771 -7.809411049 0 0 0 # cp +11 1 4 0.000000 20.667026520 4.390971184 -8.707633972 0 0 0 # cp +12 1 4 0.000000 22.043539047 4.548151016 -8.533248901 0 0 0 # cp +13 1 4 0.000000 22.530214310 5.298062801 -7.460619926 0 0 0 # cp +14 1 4 0.000000 21.640394211 5.890783787 -6.562390804 0 0 0 # cp +15 1 5 0.000000 23.005182266 3.906831026 -9.503917694 0 0 0 # c +16 1 6 0.000000 24.286390305 4.758069992 -9.590908051 0 0 0 # c3 +17 1 6 0.000000 22.342786789 3.812531948 -10.891778946 0 0 0 # c3 +18 1 4 0.000000 23.361906052 2.519830942 -9.029184341 0 0 0 # cp +19 1 4 0.000000 24.458705902 2.330889940 -8.185920715 0 0 0 # cp +20 1 4 0.000000 24.788816452 1.047963977 -7.745534897 0 0 0 # cp +21 1 4 0.000000 24.022008896 -0.046867002 -8.149927139 0 0 0 # cp +22 1 4 0.000000 22.925630569 0.140873000 -8.992565155 0 0 0 # cp +23 1 4 0.000000 22.595729828 1.424777985 -9.432847977 0 0 0 # cp +24 1 7 0.000000 19.414030075 6.299984932 -5.878956795 0 0 0 # oc +25 1 7 0.000000 24.338140488 -1.273216963 -7.729548931 0 0 0 # oc +26 1 8 0.000000 26.150024414 -1.266484976 -8.715751648 0 0 0 # hc +27 1 8 0.000000 24.778566360 -1.933199048 -9.633987427 0 0 0 # hc +28 1 8 0.000000 25.929294586 -2.927781105 -7.187973022 0 0 0 # hc +29 1 8 0.000000 24.549385071 -5.308847904 -7.987242222 0 0 0 # hc +30 1 8 0.000000 23.904827118 -4.254271030 -9.348136902 0 0 0 # hc +31 1 8 0.000000 18.194736481 9.091637611 -3.210949898 0 0 0 # hc +32 1 8 0.000000 19.788938522 9.208558083 -4.119643211 0 0 0 # hc +33 1 8 0.000000 17.399309158 7.432216167 -5.407801151 0 0 0 # hc +34 1 8 0.000000 18.616250992 7.545570850 -7.316913128 0 0 0 # hc +35 1 8 0.000000 19.987047195 8.212498665 -6.399401188 0 0 0 # hc +36 1 8 0.000000 18.713207245 4.862418175 -7.944396973 0 0 0 # hc +37 1 8 0.000000 20.290582657 3.811013937 -9.537291527 0 0 0 # hc +38 1 8 0.000000 23.594188690 5.419342995 -7.325634956 0 0 0 # hc +39 1 8 0.000000 22.016828537 6.470753193 -5.732734203 0 0 0 # hc +40 1 8 0.000000 24.982324600 4.297049999 -10.290958405 0 0 0 # hc +41 1 8 0.000000 24.034254074 5.760886192 -9.936174393 0 0 0 # hc +42 1 8 0.000000 24.749143600 4.819462776 -8.606439590 0 0 0 # hc +43 1 8 0.000000 23.034755707 3.349560976 -11.594371796 0 0 0 # hc +44 1 8 0.000000 21.438467026 3.207982063 -10.822364807 0 0 0 # hc +45 1 8 0.000000 22.084871292 4.811752796 -11.239845276 0 0 0 # hc +46 1 8 0.000000 25.050769806 3.177418947 -7.873311996 0 0 0 # hc +47 1 8 0.000000 25.636974335 0.901705027 -7.093626022 0 0 0 # hc +48 1 8 0.000000 22.333581924 -0.705653012 -9.305183411 0 0 0 # hc +49 1 8 0.000000 21.747369766 1.570054054 -10.084861755 0 0 0 # hc +50 1 1 0.000000 25.222612381 -4.200571060 0.463562995 0 0 0 # c2 +51 1 2 0.000000 25.832977295 -5.360119820 -0.347983003 0 0 0 # c3m +52 1 2 0.000000 27.389345169 -5.551681042 -0.290704012 0 0 0 # c3m +53 1 2 0.000000 20.635538101 8.396902084 -1.535487056 0 0 0 # c3m +54 1 2 0.000000 21.957460403 8.158697128 -0.723941982 0 0 0 # c3m +55 1 1 0.000000 22.041673660 6.895174980 0.154822007 0 0 0 # c2 +56 1 3 0.100000 26.447082520 -6.565405846 0.448491007 0 0 0 # o3e +57 1 3 0.100000 20.959102631 9.287891388 -0.285212994 0 0 0 # o3e +58 1 4 0.000000 22.680345535 4.733430862 0.158248007 0 0 0 # cp +59 1 4 0.000000 23.824728012 4.488029957 0.920358002 0 0 0 # cp +60 1 4 0.000000 23.901163101 3.343113899 1.716701984 0 0 0 # cp +61 1 4 0.000000 22.833225250 2.443607092 1.750934958 0 0 0 # cp +62 1 4 0.000000 21.688846588 2.689002037 0.988831997 0 0 0 # cp +63 1 4 0.000000 21.612403870 3.833913088 0.192488998 0 0 0 # cp +64 1 5 0.000000 22.916360855 1.205785036 2.611289978 0 0 0 # c +65 1 6 0.000000 21.501018524 0.810333014 3.075165987 0 0 0 # c3 +66 1 6 0.000000 23.808341980 1.493147969 3.834667921 0 0 0 # c3 +67 1 4 0.000000 23.514062881 0.070205003 1.817157984 0 0 0 # cp +68 1 4 0.000000 22.684833527 -0.782863975 1.085504055 0 0 0 # cp +69 1 4 0.000000 23.237234116 -1.833225965 0.349765003 0 0 0 # cp +70 1 4 0.000000 24.619955063 -2.031138897 0.346872985 0 0 0 # cp +71 1 4 0.000000 25.449554443 -1.179108977 1.077638030 0 0 0 # cp +72 1 4 0.000000 24.896312714 -0.128257006 1.813575983 0 0 0 # cp +73 1 7 0.000000 22.607131958 5.827101231 -0.602173984 0 0 0 # oc +74 1 7 0.000000 25.147769928 -3.035661936 -0.355791986 0 0 0 # oc +75 1 8 0.000000 24.221906662 -4.476489067 0.794990003 0 0 0 # hc +76 1 8 0.000000 25.849754333 -3.994390965 1.331357956 0 0 0 # hc +77 1 8 0.000000 25.097463608 -5.257826805 -1.146129966 0 0 0 # hc +78 1 8 0.000000 27.892013550 -5.893630028 -1.196079969 0 0 0 # hc +79 1 8 0.000000 27.964216232 -4.855231762 0.319745004 0 0 0 # hc +80 1 8 0.000000 20.720872879 8.854673386 -2.520912886 0 0 0 # hc +81 1 8 0.000000 19.840383530 7.656352043 -1.438712001 0 0 0 # hc +82 1 8 0.000000 23.017726898 8.120765686 -0.970986009 0 0 0 # hc +83 1 8 0.000000 22.669095993 7.097908974 1.022259951 0 0 0 # hc +84 1 8 0.000000 21.041725159 6.616360188 0.486577004 0 0 0 # hc +85 1 8 0.000000 24.650087357 5.183434963 0.894133985 0 0 0 # hc +86 1 8 0.000000 24.786277771 3.153367996 2.306194067 0 0 0 # hc +87 1 8 0.000000 20.863473892 1.993592978 1.015051961 0 0 0 # hc +88 1 8 0.000000 20.727291107 4.023673058 -0.397009999 0 0 0 # hc +89 1 8 0.000000 21.558345795 -0.083162002 3.696341038 0 0 0 # hc +90 1 8 0.000000 21.065618515 1.626867056 3.651936054 0 0 0 # hc +91 1 8 0.000000 20.876825333 0.608124971 2.205033064 0 0 0 # hc +92 1 8 0.000000 23.870355606 0.601037025 4.457283974 0 0 0 # hc +93 1 8 0.000000 24.807676315 1.770614982 3.498578072 0 0 0 # hc +94 1 8 0.000000 23.380037308 2.311306953 4.412462234 0 0 0 # hc +95 1 8 0.000000 21.616291046 -0.629218996 1.087699056 0 0 0 # hc +96 1 8 0.000000 22.596149445 -2.493021011 -0.215893999 0 0 0 # hc +97 1 8 0.000000 26.518102646 -1.332759023 1.075448036 0 0 0 # hc +98 1 8 0.000000 25.538236618 0.531040013 2.379035950 0 0 0 # hc +99 1 9 0.000000 16.072591782 12.338866234 -0.174325004 0 0 0 # na +100 1 1 0.000000 16.557256699 11.130316734 0.587288976 0 0 0 # c2 +101 1 1 0.000000 18.074571609 10.998808861 0.366084993 0 0 0 # c2 +102 1 9 -0.025000 18.353967667 10.832372665 -1.107717037 0 0 0 # na +103 1 9 -0.025000 14.920715332 15.017822266 -0.200534001 0 0 0 # na +104 1 1 0.000000 16.390434265 14.791102409 -0.460442007 0 0 0 # c2 +105 1 1 0.000000 16.852983475 13.538317680 0.304865986 0 0 0 # c2 +106 1 10 0.000000 16.263746262 12.190562248 -1.257431984 0 0 0 # hn +107 1 8 0.000000 16.025363922 10.195071220 0.210473999 0 0 0 # hc +108 1 8 0.000000 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a/examples/USER/misc/bond_react/tiny_nylon/in.tiny_nylon.stabilized b/examples/USER/reaction/tiny_nylon/in.tiny_nylon.stabilized similarity index 100% rename from examples/USER/misc/bond_react/tiny_nylon/in.tiny_nylon.stabilized rename to examples/USER/reaction/tiny_nylon/in.tiny_nylon.stabilized diff --git a/examples/USER/misc/bond_react/tiny_nylon/in.tiny_nylon.unstabilized b/examples/USER/reaction/tiny_nylon/in.tiny_nylon.unstabilized similarity index 100% rename from examples/USER/misc/bond_react/tiny_nylon/in.tiny_nylon.unstabilized rename to examples/USER/reaction/tiny_nylon/in.tiny_nylon.unstabilized diff --git a/examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.stabilized.g++.1 b/examples/USER/reaction/tiny_nylon/log.5Jun19.tiny_nylon.stabilized.g++.1 similarity index 100% rename from examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.stabilized.g++.1 rename to examples/USER/reaction/tiny_nylon/log.5Jun19.tiny_nylon.stabilized.g++.1 diff --git a/examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.stabilized.g++.4 b/examples/USER/reaction/tiny_nylon/log.5Jun19.tiny_nylon.stabilized.g++.4 similarity index 100% rename from examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.stabilized.g++.4 rename to examples/USER/reaction/tiny_nylon/log.5Jun19.tiny_nylon.stabilized.g++.4 diff --git a/examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.unstabilized.g++.1 b/examples/USER/reaction/tiny_nylon/log.5Jun19.tiny_nylon.unstabilized.g++.1 similarity index 100% rename from examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.unstabilized.g++.1 rename to examples/USER/reaction/tiny_nylon/log.5Jun19.tiny_nylon.unstabilized.g++.1 diff --git a/examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.unstabilized.g++.4 b/examples/USER/reaction/tiny_nylon/log.5Jun19.tiny_nylon.unstabilized.g++.4 similarity index 100% rename from examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.unstabilized.g++.4 rename to examples/USER/reaction/tiny_nylon/log.5Jun19.tiny_nylon.unstabilized.g++.4 diff --git a/examples/USER/misc/bond_react/tiny_nylon/rxn1_stp1_map b/examples/USER/reaction/tiny_nylon/rxn1_stp1_map similarity index 100% rename from examples/USER/misc/bond_react/tiny_nylon/rxn1_stp1_map rename to examples/USER/reaction/tiny_nylon/rxn1_stp1_map diff --git a/examples/USER/misc/bond_react/tiny_nylon/rxn1_stp1_reacted.data_template b/examples/USER/reaction/tiny_nylon/rxn1_stp1_reacted.data_template similarity index 100% rename from examples/USER/misc/bond_react/tiny_nylon/rxn1_stp1_reacted.data_template rename to examples/USER/reaction/tiny_nylon/rxn1_stp1_reacted.data_template diff --git a/examples/USER/misc/bond_react/tiny_nylon/rxn1_stp1_unreacted.data_template b/examples/USER/reaction/tiny_nylon/rxn1_stp1_unreacted.data_template similarity index 100% rename from examples/USER/misc/bond_react/tiny_nylon/rxn1_stp1_unreacted.data_template rename to examples/USER/reaction/tiny_nylon/rxn1_stp1_unreacted.data_template diff --git a/examples/USER/misc/bond_react/tiny_nylon/rxn1_stp2_map b/examples/USER/reaction/tiny_nylon/rxn1_stp2_map similarity index 100% rename from examples/USER/misc/bond_react/tiny_nylon/rxn1_stp2_map rename to examples/USER/reaction/tiny_nylon/rxn1_stp2_map diff --git a/examples/USER/misc/bond_react/tiny_nylon/rxn1_stp2_reacted.data_template b/examples/USER/reaction/tiny_nylon/rxn1_stp2_reacted.data_template similarity index 100% rename from examples/USER/misc/bond_react/tiny_nylon/rxn1_stp2_reacted.data_template rename to examples/USER/reaction/tiny_nylon/rxn1_stp2_reacted.data_template diff --git a/examples/USER/misc/bond_react/tiny_nylon/rxn1_stp2_unreacted.data_template b/examples/USER/reaction/tiny_nylon/rxn1_stp2_unreacted.data_template similarity index 100% rename from examples/USER/misc/bond_react/tiny_nylon/rxn1_stp2_unreacted.data_template rename to examples/USER/reaction/tiny_nylon/rxn1_stp2_unreacted.data_template diff --git a/examples/USER/misc/bond_react/tiny_nylon/tiny_nylon.data b/examples/USER/reaction/tiny_nylon/tiny_nylon.data similarity index 100% rename from examples/USER/misc/bond_react/tiny_nylon/tiny_nylon.data rename to examples/USER/reaction/tiny_nylon/tiny_nylon.data diff --git a/examples/USER/reaction/tiny_polystyrene/2styrene_map b/examples/USER/reaction/tiny_polystyrene/2styrene_map new file mode 100644 index 0000000000..be2a789671 --- /dev/null +++ b/examples/USER/reaction/tiny_polystyrene/2styrene_map @@ -0,0 +1,44 @@ +this is a map file + +0 edgeIDs +32 equivalences + +BondingIDs + +4 +30 + +Equivalences + +1 1 +2 2 +3 3 +4 4 +5 5 +6 6 +7 7 +8 8 +9 9 +10 10 +11 11 +12 12 +13 13 +14 14 +15 15 +16 16 +17 17 +18 18 +19 19 +20 20 +21 21 +22 22 +23 23 +24 24 +25 25 +26 26 +27 27 +28 28 +29 29 +30 30 +31 31 +32 32 diff --git a/examples/USER/reaction/tiny_polystyrene/2styrene_reacted.data_template b/examples/USER/reaction/tiny_polystyrene/2styrene_reacted.data_template new file mode 100644 index 0000000000..c4fa646e9f --- /dev/null +++ b/examples/USER/reaction/tiny_polystyrene/2styrene_reacted.data_template @@ -0,0 +1,312 @@ +2styrene_reacted + +32 atoms +33 bonds +54 angles +79 dihedrals +22 impropers + +Types + +1 1 +2 2 +3 1 +4 5 +5 1 +6 2 +7 1 +8 2 +9 1 +10 2 +11 1 +12 2 +13 2 +14 6 +15 2 +16 2 +17 1 +18 2 +19 1 +20 5 +21 1 +22 2 +23 1 +24 2 +25 1 +26 2 +27 1 +28 2 +29 2 +30 6 +31 2 +32 2 + +Charges + +1 -0.129000 +2 0.123700 +3 0.026600 +4 -0.018200 +5 -0.129000 +6 0.123700 +7 -0.173400 +8 0.140300 +9 -0.113400 +10 0.128800 +11 -0.173400 +12 0.140300 +13 0.051600 +14 -0.069600 +15 0.035400 +16 0.035400 +17 -0.129000 +18 0.123700 +19 0.026600 +20 -0.018200 +21 -0.129000 +22 0.123700 +23 -0.173400 +24 0.140300 +25 -0.113400 +26 0.128800 +27 -0.173400 +28 0.140300 +29 0.051600 +30 -0.069600 +31 0.035400 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+27 1 46 44 34 20 +28 1 45 44 46 20 +29 1 45 44 46 34 diff --git a/examples/USER/reaction/tiny_polystyrene/in.tiny_polystyrene.stabilized b/examples/USER/reaction/tiny_polystyrene/in.tiny_polystyrene.stabilized new file mode 100644 index 0000000000..a711f3eaa9 --- /dev/null +++ b/examples/USER/reaction/tiny_polystyrene/in.tiny_polystyrene.stabilized @@ -0,0 +1,56 @@ +# 20 styrene molecules +# three reactions defined + +units real + +boundary p p p + +atom_style full + +kspace_style pppm 1.0e-4 + +pair_style lj/class2/coul/long 8.5 + +angle_style class2 + +bond_style class2 + +dihedral_style class2 + +improper_style class2 + +variable T equal 530 + +read_data tiny_polystyrene.data & + extra/bond/per/atom 5 & + extra/angle/per/atom 15 & + extra/dihedral/per/atom 15 & + extra/improper/per/atom 25 & + extra/special/per/atom 25 + +molecule mol1 2styrene_unreacted.data_template +molecule mol2 2styrene_reacted.data_template +molecule mol3 chain_plus_styrene_unreacted.data_template +molecule mol4 chain_plus_styrene_reacted.data_template +molecule mol5 chain_chain_unreacted.data_template +molecule mol6 chain_chain_reacted.data_template + +thermo 100 + +# dump 1 all xyz 5 test_vis.xyz + +fix rxn1 all bond/react stabilization yes statted_grp .03 & + react rxn1 all 1 0 3.0 mol1 mol2 2styrene_map stabilize_steps 100 & + react rxn2 all 1 0 3.0 mol3 mol4 chain_plus_styrene_map stabilize_steps 100 & + react rxn3 all 1 0 5.0 mol5 mol6 chain_chain_map stabilize_steps 100 + +fix 1 statted_grp_REACT nvt temp $T $T 100 + +fix 4 bond_react_MASTER_group temp/rescale 1 $T $T 1 1 + +thermo_style custom step temp press density f_rxn1[1] f_rxn1[2] f_rxn1[3] + +run 10000 + +# write_restart restart_longrun nofix +# write_data restart_longrun.data diff --git a/examples/USER/reaction/tiny_polystyrene/log.20Nov19.tiny_polystyrene.stabilized.g++.1 b/examples/USER/reaction/tiny_polystyrene/log.20Nov19.tiny_polystyrene.stabilized.g++.1 new file mode 100644 index 0000000000..274c72ece9 --- /dev/null +++ b/examples/USER/reaction/tiny_polystyrene/log.20Nov19.tiny_polystyrene.stabilized.g++.1 @@ -0,0 +1,245 @@ +LAMMPS (20 Nov 2019) + +WARNING-WARNING-WARNING-WARNING-WARNING +This LAMMPS executable was compiled using C++98 compatibility. +Please report the compiler info below at https://github.com/lammps/lammps/issues/1659 +GNU C++ 4.8.5 +WARNING-WARNING-WARNING-WARNING-WARNING + +Reading data file ... + orthogonal box = (1.74267 1.74267 1.74267) to (18.2573 18.2573 18.2573) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 320 atoms + reading velocities ... + 320 velocities + scanning bonds ... + 8 = max bonds/atom + scanning angles ... + 18 = max angles/atom + scanning dihedrals ... + 22 = max dihedrals/atom + scanning impropers ... + 26 = max impropers/atom + reading bonds ... + 320 bonds + reading angles ... + 480 angles + reading dihedrals ... + 640 dihedrals + reading impropers ... + 160 impropers +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 + 6 = max # of 1-3 neighbors + 12 = max # of 1-4 neighbors + 39 = max # of special neighbors + special bonds CPU = 0.000929056 secs + read_data CPU = 0.00930568 secs +Read molecule mol1: + 32 atoms with max type 4 + 32 bonds with max type 6 + 48 angles with max type 8 + 64 dihedrals with max type 9 + 16 impropers with max type 4 +Read molecule mol2: + 32 atoms with max type 6 + 33 bonds with max type 10 + 54 angles with max type 16 + 79 dihedrals with max type 19 + 22 impropers with max type 7 +Read molecule mol3: + 46 atoms with max type 6 + 47 bonds with max type 10 + 75 angles with max type 16 + 105 dihedrals with max type 19 + 29 impropers with max type 7 +Read molecule mol4: + 46 atoms with max type 6 + 48 bonds with max type 13 + 81 angles with max type 22 + 121 dihedrals with max type 36 + 35 impropers with max type 9 +Read molecule mol5: + 50 atoms with max type 6 + 51 bonds with max type 10 + 84 angles with max type 16 + 118 dihedrals with max type 19 + 36 impropers with max type 7 +Read molecule mol6: + 50 atoms with max type 6 + 52 bonds with max type 10 + 90 angles with max type 16 + 135 dihedrals with max type 19 + 42 impropers with max type 5 +dynamic group bond_react_MASTER_group defined +dynamic group statted_grp_REACT defined +PPPM initialization ... +WARNING: System is not charge neutral, net charge = -0.004 (../kspace.cpp:304) + using 12-bit tables for long-range coulomb (../kspace.cpp:323) + G vector (1/distance) = 0.255611 + grid = 6 6 6 + stencil order = 5 + estimated absolute RMS force accuracy = 0.00974692 + estimated relative force accuracy = 2.93525e-05 + using double precision FFTs + 3d grid and FFT values/proc = 1331 216 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 10.5 + ghost atom cutoff = 10.5 + binsize = 5.25, bins = 4 4 4 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) pair lj/class2/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard + (2) fix bond/react, occasional, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +Setting up Verlet run ... + Unit style : real + Current step : 0 + Time step : 1 +Per MPI rank memory allocation (min/avg/max) = 31.14 | 31.14 | 31.14 Mbytes +Step Temp Press Density f_rxn1[1] f_rxn1[2] f_rxn1[3] + 0 320.13638 -376.0844 0.76796752 0 0 0 + 100 520.00782 3952.7008 0.76796752 8 0 0 + 200 499.9174 2360.8219 0.76796752 8 3 1 + 300 583.93895 2453.7374 0.76796752 8 3 2 + 400 560.65536 -2243.3464 0.76796752 8 3 3 + 500 556.27995 3598.7044 0.76796752 8 3 3 + 600 570.8397 -3340.1826 0.76796752 8 4 4 + 700 456.89894 -1087.8081 0.76796752 8 4 4 + 800 572.91817 -776.19188 0.76796752 8 4 4 + 900 530.13621 -246734.46 0.76796752 8 4 5 + 1000 542.34698 1044.0793 0.76796752 8 4 5 + 1100 562.86339 1207.1715 0.76796752 8 4 5 + 1200 520.1559 2725.6523 0.76796752 8 4 5 + 1300 534.01667 951.0972 0.76796752 8 4 5 + 1400 478.68681 1184.9224 0.76796752 8 4 5 + 1500 509.05445 2020.5224 0.76796752 8 4 5 + 1600 549.5382 810.17577 0.76796752 8 4 5 + 1700 549.46882 -6349.7751 0.76796752 8 4 5 + 1800 496.77334 3953.1043 0.76796752 8 4 5 + 1900 522.28719 -2271.7599 0.76796752 8 4 6 + 2000 569.95975 5633.4352 0.76796752 8 4 6 + 2100 590.8418 2355.8447 0.76796752 8 4 6 + 2200 537.64787 6459.6743 0.76796752 8 4 6 + 2300 548.38487 -1566.3528 0.76796752 8 4 6 + 2400 533.50353 6755.664 0.76796752 8 4 6 + 2500 512.57053 325.30968 0.76796752 8 4 6 + 2600 498.4597 -2468.1165 0.76796752 8 4 6 + 2700 559.03937 2428.3446 0.76796752 8 4 6 + 2800 585.85721 -2896.3607 0.76796752 8 4 6 + 2900 523.18635 1391.254 0.76796752 8 4 6 + 3000 524.62076 375.02973 0.76796752 8 4 6 + 3100 534.65688 -1522.7879 0.76796752 8 4 6 + 3200 499.42665 3725.5476 0.76796752 8 4 6 + 3300 514.36972 1725.8329 0.76796752 8 4 6 + 3400 482.52662 4648.5013 0.76796752 8 4 6 + 3500 495.36836 967.3482 0.76796752 8 4 6 + 3600 583.28736 745.21794 0.76796752 8 4 6 + 3700 531.99717 -804.39572 0.76796752 8 4 6 + 3800 555.08359 -2381.363 0.76796752 8 4 6 + 3900 520.1818 -547.34169 0.76796752 8 4 6 + 4000 444.38804 -2488.7881 0.76796752 8 4 6 + 4100 518.65622 -3135.9573 0.76796752 8 4 6 + 4200 484.15227 -1040.2447 0.76796752 8 4 6 + 4300 514.58006 550.14626 0.76796752 8 4 6 + 4400 579.81405 -849.81454 0.76796752 8 4 6 + 4500 522.8698 5222.654 0.76796752 8 4 6 + 4600 490.78275 3251.2892 0.76796752 8 4 6 + 4700 492.64299 3785.3482 0.76796752 8 4 6 + 4800 500.11059 4441.8978 0.76796752 8 4 6 + 4900 536.80009 965.33724 0.76796752 8 4 6 + 5000 516.98575 -3794.4213 0.76796752 8 4 6 + 5100 516.76648 -3593.9106 0.76796752 8 4 6 + 5200 521.6379 -6532.7773 0.76796752 8 4 6 + 5300 535.64798 2931.412 0.76796752 8 4 6 + 5400 559.83266 7628.1659 0.76796752 8 4 6 + 5500 538.91756 2841.6746 0.76796752 8 4 6 + 5600 539.13999 10445.173 0.76796752 8 4 6 + 5700 501.56603 -2106.3309 0.76796752 8 4 6 + 5800 496.72952 -4831.0565 0.76796752 8 4 6 + 5900 536.12979 -3916.8197 0.76796752 8 4 6 + 6000 553.10092 3142.6871 0.76796752 8 4 6 + 6100 558.09546 3154.584 0.76796752 8 4 6 + 6200 523.48472 9807.0034 0.76796752 8 4 6 + 6300 551.80343 -3608.2078 0.76796752 8 4 6 + 6400 484.28359 2255.4675 0.76796752 8 4 6 + 6500 560.68443 -4826.4868 0.76796752 8 4 6 + 6600 604.50797 402.32183 0.76796752 8 4 6 + 6700 538.84714 -7670.3312 0.76796752 8 4 6 + 6800 528.82853 -380.32058 0.76796752 8 4 6 + 6900 579.30919 4438.4574 0.76796752 8 4 6 + 7000 540.3406 3738.0524 0.76796752 8 4 6 + 7100 519.53645 -1825.5563 0.76796752 8 4 6 + 7200 474.136 1657.3863 0.76796752 8 4 6 + 7300 485.55159 -221.84939 0.76796752 8 4 6 + 7400 527.38494 1037.1777 0.76796752 8 4 6 + 7500 517.14767 -2313.5823 0.76796752 8 4 6 + 7600 517.95967 -4763.4709 0.76796752 8 4 6 + 7700 513.63507 4819.0253 0.76796752 8 4 6 + 7800 503.56828 1295.1212 0.76796752 8 4 6 + 7900 520.87804 1506.9417 0.76796752 8 4 6 + 8000 509.46453 -5800.0971 0.76796752 8 4 6 + 8100 566.67059 6065.4607 0.76796752 8 4 6 + 8200 592.53068 1097.2277 0.76796752 8 4 6 + 8300 529.55235 -580.81757 0.76796752 8 4 6 + 8400 518.22587 560.45589 0.76796752 8 4 6 + 8500 521.94561 5325.9459 0.76796752 8 4 6 + 8600 510.54416 -1929.1967 0.76796752 8 4 6 + 8700 562.71252 -629.90392 0.76796752 8 4 6 + 8800 540.23123 -3484.3893 0.76796752 8 4 6 + 8900 513.82411 -5227.152 0.76796752 8 4 6 + 9000 534.3307 -3299.088 0.76796752 8 4 6 + 9100 509.24467 -5676.2775 0.76796752 8 4 6 + 9200 506.3216 -7043.8493 0.76796752 8 4 7 + 9300 480.37682 2380.4696 0.76796752 8 4 7 + 9400 546.15532 1831.0103 0.76796752 8 4 7 + 9500 567.18341 3839.9843 0.76796752 8 4 7 + 9600 536.14883 4258.5304 0.76796752 8 4 7 + 9700 496.04153 3321.3561 0.76796752 8 4 7 + 9800 531.78927 3124.9156 0.76796752 8 4 7 + 9900 530.91395 38.987859 0.76796752 8 4 7 + 10000 551.22761 1027.5706 0.76796752 8 4 7 +Loop time of 57.7096 on 1 procs for 10000 steps with 320 atoms + +Performance: 14.972 ns/day, 1.603 hours/ns, 173.281 timesteps/s +99.9% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 11.621 | 11.621 | 11.621 | 0.0 | 20.14 +Bond | 11.151 | 11.151 | 11.151 | 0.0 | 19.32 +Kspace | 2.2403 | 2.2403 | 2.2403 | 0.0 | 3.88 +Neigh | 25.467 | 25.467 | 25.467 | 0.0 | 44.13 +Comm | 0.90467 | 0.90467 | 0.90467 | 0.0 | 1.57 +Output | 0.0017984 | 0.0017984 | 0.0017984 | 0.0 | 0.00 +Modify | 6.2622 | 6.2622 | 6.2622 | 0.0 | 10.85 +Other | | 0.06192 | | | 0.11 + +Nlocal: 320 ave 320 max 320 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 3240 ave 3240 max 3240 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 54336 ave 54336 max 54336 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 54336 +Ave neighs/atom = 169.8 +Ave special neighs/atom = 11.3063 +Neighbor list builds = 10000 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:58 diff --git a/examples/USER/reaction/tiny_polystyrene/log.20Nov19.tiny_polystyrene.stabilized.g++.4 b/examples/USER/reaction/tiny_polystyrene/log.20Nov19.tiny_polystyrene.stabilized.g++.4 new file mode 100644 index 0000000000..29aae1cd0b --- /dev/null +++ b/examples/USER/reaction/tiny_polystyrene/log.20Nov19.tiny_polystyrene.stabilized.g++.4 @@ -0,0 +1,255 @@ +LAMMPS (20 Nov 2019) + +WARNING-WARNING-WARNING-WARNING-WARNING +This LAMMPS executable was compiled using C++98 compatibility. +Please report the compiler info below at https://github.com/lammps/lammps/issues/1659 +GNU C++ 4.8.5 +WARNING-WARNING-WARNING-WARNING-WARNING + +Reading data file ... + orthogonal box = (1.74267 1.74267 1.74267) to (18.2573 18.2573 18.2573) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 320 atoms + reading velocities ... + 320 velocities + scanning bonds ... + 8 = max bonds/atom + scanning angles ... + 18 = max angles/atom + scanning dihedrals ... + 22 = max dihedrals/atom + scanning impropers ... + 26 = max impropers/atom + reading bonds ... + 320 bonds + reading angles ... + 480 angles + reading dihedrals ... + 640 dihedrals + reading impropers ... + 160 impropers +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 + 6 = max # of 1-3 neighbors + 12 = max # of 1-4 neighbors + 39 = max # of special neighbors + special bonds CPU = 0.000751222 secs + read_data CPU = 0.0268223 secs +Read molecule mol1: + 32 atoms with max type 4 + 32 bonds with max type 6 + 48 angles with max type 8 + 64 dihedrals with max type 9 + 16 impropers with max type 4 +Read molecule mol2: + 32 atoms with max type 6 + 33 bonds with max type 10 + 54 angles with max type 16 + 79 dihedrals with max type 19 + 22 impropers with max type 7 +Read molecule mol3: + 46 atoms with max type 6 + 47 bonds with max type 10 + 75 angles with max type 16 + 105 dihedrals with max type 19 + 29 impropers with max type 7 +Read molecule mol4: + 46 atoms with max type 6 + 48 bonds with max type 13 + 81 angles with max type 22 + 121 dihedrals with max type 36 + 35 impropers with max type 9 +Read molecule mol5: + 50 atoms with max type 6 + 51 bonds with max type 10 + 84 angles with max type 16 + 118 dihedrals with max type 19 + 36 impropers with max type 7 +Read molecule mol6: + 50 atoms with max type 6 + 52 bonds with max type 10 + 90 angles with max type 16 + 135 dihedrals with max type 19 + 42 impropers with max type 5 +dynamic group bond_react_MASTER_group defined +dynamic group statted_grp_REACT defined +PPPM initialization ... +WARNING: System is not charge neutral, net charge = -0.004 (../kspace.cpp:304) + using 12-bit tables for long-range coulomb (../kspace.cpp:323) + G vector (1/distance) = 0.255611 + grid = 6 6 6 + stencil order = 5 + estimated absolute RMS force accuracy = 0.00974692 + estimated relative force accuracy = 2.93525e-05 + using double precision FFTs + 3d grid and FFT values/proc = 704 72 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 10.5 + ghost atom cutoff = 10.5 + binsize = 5.25, bins = 4 4 4 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) pair lj/class2/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard + (2) fix bond/react, occasional, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +Setting up Verlet run ... + Unit style : real + Current step : 0 + Time step : 1 +Per MPI rank memory allocation (min/avg/max) = 30.66 | 30.68 | 30.69 Mbytes +Step Temp Press Density f_rxn1[1] f_rxn1[2] f_rxn1[3] + 0 320.13638 -376.0844 0.76796752 0 0 0 + 100 522.71544 6623.0579 0.76796752 8 0 0 + 200 500.86716 -9439.5519 0.76796752 8 3 2 + 300 594.60588 6714.1323 0.76796752 8 3 3 + 400 598.68768 683.70457 0.76796752 8 3 3 + 500 563.1011 3576.6857 0.76796752 8 3 4 + 600 510.29713 -196148.37 0.76796752 8 3 5 + 700 494.14346 -118517.45 0.76796752 8 3 6 + 800 565.62849 7678.1235 0.76796752 8 3 6 + 900 515.74468 554.84571 0.76796752 8 3 6 + 1000 500.64636 450.15932 0.76796752 8 3 6 + 1100 463.34973 6023.8346 0.76796752 8 3 6 + 1200 529.88483 2748.185 0.76796752 8 3 6 + 1300 546.84049 1353.4891 0.76796752 8 3 6 + 1400 552.27356 1446.5807 0.76796752 8 3 6 + 1500 557.70874 -2745.1523 0.76796752 8 3 6 + 1600 572.0005 629.36722 0.76796752 8 3 6 + 1700 503.96569 5937.0231 0.76796752 8 3 6 + 1800 491.34262 -1175.8104 0.76796752 8 3 6 + 1900 538.24798 -81.197397 0.76796752 8 3 6 + 2000 523.89324 2857.2466 0.76796752 8 3 6 + 2100 515.1424 2288.2405 0.76796752 8 3 6 + 2200 546.80854 3807.1038 0.76796752 8 3 6 + 2300 500.31231 -135.33933 0.76796752 8 4 6 + 2400 497.16354 5516.857 0.76796752 8 4 6 + 2500 545.34187 3485.5645 0.76796752 8 4 6 + 2600 522.70122 3114.1284 0.76796752 8 4 6 + 2700 531.76604 6633.5518 0.76796752 8 4 6 + 2800 521.97643 -279.83682 0.76796752 8 4 6 + 2900 497.29575 7052.9409 0.76796752 8 4 6 + 3000 524.5942 2284.8918 0.76796752 8 4 6 + 3100 567.61329 -3667.4557 0.76796752 8 4 6 + 3200 506.82452 -2934.4936 0.76796752 8 4 6 + 3300 510.8521 313.36263 0.76796752 8 4 6 + 3400 516.70206 3671.1899 0.76796752 8 4 6 + 3500 535.12788 2645.2564 0.76796752 8 4 6 + 3600 580.14214 2604.3079 0.76796752 8 4 6 + 3700 529.77869 2684.0812 0.76796752 8 4 6 + 3800 502.93191 2838.6698 0.76796752 8 4 6 + 3900 585.91492 5308.0828 0.76796752 8 4 6 + 4000 548.89917 5262.5775 0.76796752 8 4 6 + 4100 550.7662 -1066.6807 0.76796752 8 4 6 + 4200 519.19198 2777.5276 0.76796752 8 4 6 + 4300 521.46332 -3429.7171 0.76796752 8 4 6 + 4400 532.64173 2301.3135 0.76796752 8 4 6 + 4500 528.96107 1369.0991 0.76796752 8 4 6 + 4600 564.66443 9687.2531 0.76796752 8 4 6 + 4700 558.49446 2322.6085 0.76796752 8 4 6 + 4800 497.78614 -442.45053 0.76796752 8 4 6 + 4900 511.09435 -10251.159 0.76796752 8 4 6 + 5000 525.6642 -1202.0584 0.76796752 8 4 6 + 5100 521.76974 1821.7811 0.76796752 8 4 6 + 5200 555.9859 7256.9632 0.76796752 8 4 6 + 5300 551.51971 -122893.16 0.76796752 8 4 7 + 5400 524.34705 2905.1033 0.76796752 8 4 7 + 5500 567.09396 2896.4824 0.76796752 8 4 7 + 5600 487.57746 1417.1715 0.76796752 8 4 7 + 5700 547.37304 3900.8734 0.76796752 8 4 7 + 5800 536.17647 -4048.7522 0.76796752 8 4 7 + 5900 536.85051 4497.9847 0.76796752 8 4 7 + 6000 548.58212 -4880.4979 0.76796752 8 4 7 + 6100 500.94692 6004.2105 0.76796752 8 4 7 + 6200 486.82494 402.5875 0.76796752 8 4 7 + 6300 478.09381 6600.767 0.76796752 8 4 7 + 6400 559.90398 2868.0805 0.76796752 8 4 7 + 6500 526.01866 -3398.4788 0.76796752 8 4 7 + 6600 539.68471 -1202.0012 0.76796752 8 4 7 + 6700 507.51217 -378.71164 0.76796752 8 4 7 + 6800 526.15958 -4536.9888 0.76796752 8 4 7 + 6900 511.37134 -2522.3553 0.76796752 8 4 7 + 7000 538.86918 -2028.0323 0.76796752 8 4 7 + 7100 523.25566 2911.9962 0.76796752 8 4 7 + 7200 513.28464 -1000.4758 0.76796752 8 4 7 + 7300 510.19826 5181.7976 0.76796752 8 4 7 + 7400 493.46528 -1166.3996 0.76796752 8 4 7 + 7500 491.51305 5669.2213 0.76796752 8 4 7 + 7600 506.72032 -2840.301 0.76796752 8 4 7 + 7700 513.4319 2802.1719 0.76796752 8 4 7 + 7800 543.7658 -7477.3623 0.76796752 8 4 7 + 7900 527.35619 -3182.3155 0.76796752 8 4 7 + 8000 533.50993 613.16561 0.76796752 8 4 7 + 8100 512.44958 -5037.3414 0.76796752 8 4 7 + 8200 494.88981 1799.3513 0.76796752 8 4 7 + 8300 554.81474 -2436.0507 0.76796752 8 4 7 + 8400 523.22917 364.30593 0.76796752 8 4 7 + 8500 515.12395 525.24581 0.76796752 8 4 7 + 8600 511.6321 -1679.8669 0.76796752 8 4 7 + 8700 531.6327 -1168.1215 0.76796752 8 4 7 + 8800 548.14438 -5222.7573 0.76796752 8 4 7 + 8900 517.72579 2073.9695 0.76796752 8 4 7 + 9000 543.11894 -5307.0759 0.76796752 8 4 7 + 9100 521.13747 -5546.8552 0.76796752 8 4 7 + 9200 509.66142 -1584.019 0.76796752 8 4 7 + 9300 488.73821 -277.85847 0.76796752 8 4 7 + 9400 513.67282 989.60653 0.76796752 8 4 7 + 9500 509.98833 -1754.8786 0.76796752 8 4 7 + 9600 558.72497 5616.6969 0.76796752 8 4 7 + 9700 533.74988 811.48871 0.76796752 8 4 7 + 9800 510.94641 -3136.5876 0.76796752 8 4 7 + 9900 517.80127 -1962.0837 0.76796752 8 4 7 + 10000 477.50428 -3768.1653 0.76796752 8 4 7 +Loop time of 20.9963 on 4 procs for 10000 steps with 320 atoms + +Performance: 41.150 ns/day, 0.583 hours/ns, 476.276 timesteps/s +100.0% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 2.4968 | 3.0329 | 3.3607 | 18.6 | 14.45 +Bond | 2.3164 | 2.8835 | 3.456 | 26.0 | 13.73 +Kspace | 1.3332 | 2.2082 | 3.285 | 48.0 | 10.52 +Neigh | 7.4831 | 7.4922 | 7.5012 | 0.3 | 35.68 +Comm | 1.2809 | 1.3121 | 1.3297 | 1.6 | 6.25 +Output | 0.0012138 | 0.0013506 | 0.0017552 | 0.6 | 0.01 +Modify | 4.0269 | 4.0301 | 4.0335 | 0.1 | 19.19 +Other | | 0.03583 | | | 0.17 + +Nlocal: 80 ave 94 max 66 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 2243.75 ave 2260 max 2221 min +Histogram: 1 0 0 1 0 0 0 0 0 2 +Neighs: 13658.5 ave 17096 max 9421 min +Histogram: 1 0 0 0 0 1 1 0 0 1 + +Total # of neighbors = 54634 +Ave neighs/atom = 170.731 +Ave special neighs/atom = 11.3063 +Neighbor list builds = 10000 +Dangerous builds = 0 +System init for write_data ... +PPPM initialization ... + using 12-bit tables for long-range coulomb (../kspace.cpp:323) + G vector (1/distance) = 0.255611 + grid = 6 6 6 + stencil order = 5 + estimated absolute RMS force accuracy = 0.00974692 + estimated relative force accuracy = 2.93525e-05 + using double precision FFTs + 3d grid and FFT values/proc = 704 72 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:21 diff --git a/examples/USER/reaction/tiny_polystyrene/tiny_polystyrene.data b/examples/USER/reaction/tiny_polystyrene/tiny_polystyrene.data new file mode 100644 index 0000000000..5f0ed4cfa6 --- /dev/null +++ b/examples/USER/reaction/tiny_polystyrene/tiny_polystyrene.data @@ -0,0 +1,2643 @@ +LAMMPS data file via write_data, version 20 Nov 2019, timestep = 25000 + +320 atoms +7 atom types +320 bonds +13 bond types +480 angles +22 angle types +640 dihedrals +36 dihedral types +160 impropers +9 improper types + +1.7426663385337786e+00 1.8257333661465619e+01 xlo xhi +1.7426663385337786e+00 1.8257333661465619e+01 ylo yhi +1.7426663385337786e+00 1.8257333661465619e+01 zlo zhi + +Masses + +1 12.0112 +2 1.00797 +3 12.0112 +4 12.0112 +5 12.0112 +6 12.0112 +7 12.0112 + +Pair Coeffs # lj/class2/coul/long + +1 0.064 4.01 +2 0.02 2.7 +3 0.064 4.01 +4 0.064 3.9 +5 0.054 4.01 +6 0.054 4.01 +7 0.054 4.01 + +Bond Coeffs # class2 + +1 1.0982 372.825 -803.453 894.317 +2 1.417 470.836 -627.618 1327.63 +3 1.501 321.902 -521.821 572.163 +4 1.0883 365.768 -725.54 781.662 +5 1.34 543.99 -1238.2 1644.03 +6 1.0883 365.768 -725.54 781.662 +7 1.501 321.902 -521.821 572.163 +8 1.101 345 -691.89 844.6 +9 1.53 299.67 -501.77 679.81 +10 1.101 345 -691.89 844.6 +11 1.501 321.902 -521.821 572.163 +12 1.101 345 -691.89 844.6 +13 1.53 299.67 -501.77 679.81 + +Angle Coeffs # class2 + +1 117.94 35.1558 -12.4682 0 +2 118.9 61.0226 -34.9931 0 +3 120.05 44.7148 -22.7352 0 +4 111 44.3234 -9.4454 0 +5 108.4 43.9594 -8.3924 -9.3379 +6 124.88 35.2766 -17.774 -1.6215 +7 124.88 35.2766 -17.774 -1.6215 +8 115.49 29.6363 -12.4853 -6.2218 +9 120.05 44.7148 -22.7352 0 +10 111 44.3234 -9.4454 0 +11 108.4 43.9594 -8.3924 -9.3379 +12 110.77 41.453 -10.604 5.129 +13 112.67 39.516 -7.443 -9.5583 +14 110.77 41.453 -10.604 5.129 +15 107.66 39.641 -12.921 -2.4318 +16 112.67 39.516 -7.443 -9.5583 +17 120.05 44.7148 -22.7352 0 +18 111 44.3234 -9.4454 0 +19 108.4 43.9594 -8.3924 -9.3379 +20 110.77 41.453 -10.604 5.129 +21 110.77 41.453 -10.604 5.129 +22 112.67 39.516 -7.443 -9.5583 + +BondBond Coeffs + +1 1.0795 1.417 1.0982 +2 68.2856 1.417 1.417 +3 12.0676 1.417 1.501 +4 2.9168 1.501 1.0883 +5 0 1.501 1.34 +6 10.1047 1.0883 1.34 +7 10.1047 1.0883 1.34 +8 4.8506 1.0883 1.0883 +9 12.0676 1.417 1.501 +10 2.9168 1.501 1.101 +11 0 1.501 1.53 +12 3.3872 1.101 1.53 +13 0 1.53 1.53 +14 3.3872 1.101 1.53 +15 5.3316 1.101 1.101 +16 0 1.53 1.53 +17 12.0676 1.417 1.501 +18 2.9168 1.501 1.101 +19 0 1.501 1.53 +20 3.3872 1.101 1.53 +21 3.3872 1.101 1.53 +22 0 1.53 1.53 + +BondAngle Coeffs + +1 20.0033 24.2183 1.417 1.0982 +2 28.8708 28.8708 1.417 1.417 +3 31.0771 47.0579 1.417 1.501 +4 26.4608 11.7717 1.501 1.0883 +5 0 0 1.501 1.34 +6 19.0592 23.3588 1.0883 1.34 +7 19.0592 23.3588 1.0883 1.34 +8 17.9795 17.9795 1.0883 1.0883 +9 31.0771 47.0579 1.417 1.501 +10 26.4608 11.7717 1.501 1.101 +11 0 0 1.501 1.53 +12 11.421 20.754 1.101 1.53 +13 8.016 8.016 1.53 1.53 +14 11.421 20.754 1.101 1.53 +15 18.103 18.103 1.101 1.101 +16 8.016 8.016 1.53 1.53 +17 31.0771 47.0579 1.417 1.501 +18 26.4608 11.7717 1.501 1.101 +19 0 0 1.501 1.53 +20 11.421 20.754 1.101 1.53 +21 11.421 20.754 1.101 1.53 +22 8.016 8.016 1.53 1.53 + +Dihedral Coeffs # class2 + +1 0 0 1.559 0 0 0 +2 0 0 3.9661 0 0 0 +3 0 0 4.4072 0 0 0 +4 8.3667 0 1.1932 0 0 0 +5 0 0 1.8769 0 0 0 +6 0 0 0 0 0 0 +7 0 0 0 0 0 0 +8 0 0 0 0 0 0 +9 0 0 4.8974 0 0 0 +10 0 0 1.559 0 0 0 +11 0 0 4.4072 0 0 0 +12 -0.2801 0 -0.0678 0 -0.0122 0 +13 -0.2802 0 -0.0678 0 -0.0122 0 +14 -0.0228 0 0.028 0 -0.1863 0 +15 -0.1432 0 0.0617 0 -0.1083 0 +16 0 0 0.0316 0 -0.1681 0 +17 0 0 0 0 0 0 +18 0 0 0.0316 0 -0.1681 0 +19 0 0 0.0514 0 -0.143 0 +20 0 0 1.559 0 0 0 +21 0 0 4.4072 0 0 0 +22 -0.2801 0 -0.0678 0 -0.0122 0 +23 -0.2802 0 -0.0678 0 -0.0122 0 +24 -0.0228 0 0.028 0 -0.1863 0 +25 0 0 0 0 0 0 +26 -0.1432 0 0.0617 0 -0.1083 0 +27 0 0 0.0316 0 -0.1681 0 +28 0 0 0 0 0 0 +29 0 0 0.0316 0 -0.1681 0 +30 0 0 0.0514 0 -0.143 0 +31 -0.0228 0 0.028 0 -0.1863 0 +32 -0.1432 0 0.0617 0 -0.1083 0 +33 0 0 0.0316 0 -0.1681 0 +34 0 0 0 0 0 0 +35 0 0 0.0316 0 -0.1681 0 +36 0 0 0.0514 0 -0.143 0 + +AngleAngleTorsion Coeffs + +1 4.4444 117.94 120.05 +2 -4.8141 118.9 117.94 +3 -14.4097 118.9 120.05 +4 0 118.9 118.9 +5 0.3598 117.94 117.94 +6 0 120.05 111 +7 0 120.05 108.4 +8 0 108.4 124.88 +9 -7.0058 124.88 124.88 +10 4.4444 117.94 120.05 +11 -14.4097 118.9 120.05 +12 -5.8888 120.05 111 +13 0 120.05 108.4 +14 0 108.4 110.77 +15 -12.564 110.77 110.77 +16 -16.164 112.67 110.77 +17 0 108.4 112.67 +18 -16.164 110.77 112.67 +19 -22.045 112.67 112.67 +20 4.4444 117.94 120.05 +21 -14.4097 118.9 120.05 +22 -5.8888 120.05 111 +23 0 120.05 108.4 +24 0 108.4 110.77 +25 0 108.4 112.67 +26 -12.564 110.77 110.77 +27 -16.164 110.77 112.67 +28 0 112.67 108.4 +29 -16.164 112.67 110.77 +30 -22.045 112.67 112.67 +31 0 110.77 108.4 +32 -12.564 110.77 110.77 +33 -16.164 110.77 112.67 +34 0 112.67 108.4 +35 -16.164 112.67 110.77 +36 -22.045 112.67 112.67 + +EndBondTorsion Coeffs + +1 0 -0.4879 0 0 -1.797 0 1.0982 1.501 +2 0 -6.8958 0 0 -0.4669 0 1.417 1.0982 +3 0 -0.6918 0 0 0.2421 0 1.417 1.501 +4 -0.1185 6.3204 0 -0.1185 6.3204 0 1.417 1.417 +5 0 -0.689 0 0 -0.689 0 1.0982 1.0982 +6 0 0 0 0 0 0 1.417 1.0883 +7 0 0 0 0 0 0 1.417 1.34 +8 0 0 0 0 0 0 1.501 1.0883 +9 0.7129 0.5161 0 0.7129 0.5161 0 1.0883 1.0883 +10 0 -0.4879 0 0 -1.797 0 1.0982 1.501 +11 0 -0.6918 0 0 0.2421 0 1.417 1.501 +12 -0.5835 1.122 0.3978 1.3997 0.7756 0 1.417 1.101 +13 0 0 0 0 0 0 1.417 1.53 +14 0 0 0 0 0 0 1.501 1.101 +15 0.213 0.312 0.0777 0.213 0.312 0.0777 1.101 1.101 +16 0.2486 0.2422 -0.0925 0.0814 0.0591 0.2219 1.53 1.101 +17 0 0 0 0 0 0 1.501 1.53 +18 0.0814 0.0591 0.2219 0.2486 0.2422 -0.0925 1.101 1.53 +19 -0.0732 0 0 -0.0732 0 0 1.53 1.53 +20 0 -0.4879 0 0 -1.797 0 1.0982 1.501 +21 0 -0.6918 0 0 0.2421 0 1.417 1.501 +22 -0.5835 1.122 0.3978 1.3997 0.7756 0 1.417 1.101 +23 0 0 0 0 0 0 1.417 1.53 +24 0 0 0 0 0 0 1.501 1.101 +25 0 0 0 0 0 0 1.501 1.53 +26 0.213 0.312 0.0777 0.213 0.312 0.0777 1.101 1.101 +27 0.0814 0.0591 0.2219 0.2486 0.2422 -0.0925 1.101 1.53 +28 0 0 0 0 0 0 1.53 1.501 +29 0.2486 0.2422 -0.0925 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a/lib/gpu/cudpp_mini/cudpp_maximal_launch.cpp b/lib/gpu/cudpp_mini/cudpp_maximal_launch.cpp index 904d101b3b..1a7542e68c 100644 --- a/lib/gpu/cudpp_mini/cudpp_maximal_launch.cpp +++ b/lib/gpu/cudpp_mini/cudpp_maximal_launch.cpp @@ -8,16 +8,7 @@ // in the root directory of this source distribution. // ------------------------------------------------------------- #include "cudpp_maximal_launch.h" - -inline size_t min(size_t x, size_t y) -{ - return (x <= y) ? x : y; -} - -inline size_t max(size_t x, size_t y) -{ - return (x >= y) ? x : y; -} +#include // computes next highest multiple of f from x inline size_t multiple(size_t x, size_t f) @@ -65,7 +56,7 @@ size_t maxBlocks(cudaFuncAttributes &attribs, size_t ctaLimitSMem = smemPerCTA > 0 ? devprop.sharedMemPerBlock / smemPerCTA : maxBlocksPerSM; size_t ctaLimitThreads = maxThreadsPerSM / threadsPerBlock; - return devprop.multiProcessorCount * min(ctaLimitRegs, min(ctaLimitSMem, min(ctaLimitThreads, maxBlocksPerSM))); + return devprop.multiProcessorCount * std::min(ctaLimitRegs, std::min(ctaLimitSMem, std::min(ctaLimitThreads, (size_t)maxBlocksPerSM))); } extern "C" @@ -80,15 +71,15 @@ size_t maxBlocksFromPointer(void* kernel, { err = cudaGetDeviceProperties(&devprop, deviceID); if (err != cudaSuccess) - return -1; + return (size_t)-1; cudaFuncAttributes attr; err = cudaFuncGetAttributes(&attr, (const char*)kernel); if (err != cudaSuccess) - return -1; + return (size_t)-1; return maxBlocks(attr, devprop, bytesDynamicSharedMem, threadsPerBlock); } - return -1; + return (size_t)-1; } diff --git a/lib/gpu/geryon/nvd_kernel.h b/lib/gpu/geryon/nvd_kernel.h index d03a715e1b..9293db2fe4 100644 --- a/lib/gpu/geryon/nvd_kernel.h +++ b/lib/gpu/geryon/nvd_kernel.h @@ -244,7 +244,7 @@ class UCL_Kernel { template inline void add_arg(const dtype* const arg) { #if CUDA_VERSION >= 4000 - _kernel_args[_num_args]=const_cast(arg); + _kernel_args[_num_args]=const_cast(arg); #else _param_size = (_param_size+__alignof(dtype)-1) & ~(__alignof(dtype)-1); CU_SAFE_CALL(cuParamSetv(_kernel,_param_size,(void*)arg,sizeof(dtype))); diff --git a/src/KOKKOS/pair_snap_kokkos.h b/src/KOKKOS/pair_snap_kokkos.h index f20ab34231..2766ac3391 100644 --- a/src/KOKKOS/pair_snap_kokkos.h +++ b/src/KOKKOS/pair_snap_kokkos.h @@ -37,12 +37,16 @@ struct TagPairSNAPBeta{}; struct TagPairSNAPComputeNeigh{}; struct TagPairSNAPPreUi{}; struct TagPairSNAPComputeUi{}; +struct TagPairSNAPComputeUiTot{}; // accumulate ulist into ulisttot separately +struct TagPairSNAPComputeUiCPU{}; struct TagPairSNAPComputeZi{}; struct TagPairSNAPComputeBi{}; struct TagPairSNAPZeroYi{}; struct TagPairSNAPComputeYi{}; struct TagPairSNAPComputeDuidrj{}; +struct TagPairSNAPComputeDuidrjCPU{}; struct TagPairSNAPComputeDeidrj{}; +struct TagPairSNAPComputeDeidrjCPU{}; template class PairSNAPKokkos : public PairSNAP { @@ -74,11 +78,17 @@ public: void operator() (TagPairSNAPComputeNeigh,const typename Kokkos::TeamPolicy::member_type& team) const; KOKKOS_INLINE_FUNCTION - void operator() (TagPairSNAPPreUi,const int& ii) const; + void operator() (TagPairSNAPPreUi,const typename Kokkos::TeamPolicy::member_type& team) const; KOKKOS_INLINE_FUNCTION void operator() (TagPairSNAPComputeUi,const typename Kokkos::TeamPolicy::member_type& team) const; + KOKKOS_INLINE_FUNCTION + void operator() (TagPairSNAPComputeUiTot,const typename Kokkos::TeamPolicy::member_type& team) const; + + KOKKOS_INLINE_FUNCTION + void operator() (TagPairSNAPComputeUiCPU,const typename Kokkos::TeamPolicy::member_type& team) const; + KOKKOS_INLINE_FUNCTION void operator() (TagPairSNAPComputeZi,const int& ii) const; @@ -86,7 +96,7 @@ public: void operator() (TagPairSNAPComputeBi,const typename Kokkos::TeamPolicy::member_type& team) const; KOKKOS_INLINE_FUNCTION - void operator() (TagPairSNAPZeroYi,const int& ii) const; + void operator() (TagPairSNAPZeroYi,const typename Kokkos::TeamPolicy::member_type& team) const; KOKKOS_INLINE_FUNCTION void operator() (TagPairSNAPComputeYi,const int& ii) const; @@ -94,9 +104,15 @@ public: KOKKOS_INLINE_FUNCTION void operator() (TagPairSNAPComputeDuidrj,const typename Kokkos::TeamPolicy::member_type& team) const; + KOKKOS_INLINE_FUNCTION + void operator() (TagPairSNAPComputeDuidrjCPU,const typename Kokkos::TeamPolicy::member_type& team) const; + KOKKOS_INLINE_FUNCTION void operator() (TagPairSNAPComputeDeidrj,const typename Kokkos::TeamPolicy::member_type& team) const; + KOKKOS_INLINE_FUNCTION + void operator() (TagPairSNAPComputeDeidrjCPU,const typename Kokkos::TeamPolicy::member_type& team) const; + KOKKOS_INLINE_FUNCTION void operator() (TagPairSNAPBeta,const typename Kokkos::TeamPolicy::member_type& team) const; diff --git a/src/KOKKOS/pair_snap_kokkos_impl.h b/src/KOKKOS/pair_snap_kokkos_impl.h index 32b63cb776..1156d11c31 100644 --- a/src/KOKKOS/pair_snap_kokkos_impl.h +++ b/src/KOKKOS/pair_snap_kokkos_impl.h @@ -12,7 +12,8 @@ ------------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- - Contributing authors: Christian Trott (SNL), Stan Moore (SNL) + Contributing authors: Christian Trott (SNL), Stan Moore (SNL), + Evan Weinberg (NVIDIA) ------------------------------------------------------------------------- */ #include @@ -29,6 +30,7 @@ #include "kokkos.h" #include "sna.h" + #define MAXLINE 1024 #define MAXWORD 3 @@ -194,7 +196,7 @@ void PairSNAPKokkos::compute(int eflag_in, int vflag_in) if (beta_max < inum) { beta_max = inum; - d_beta = Kokkos::View("PairSNAPKokkos:beta",inum,ncoeff); + d_beta = Kokkos::View("PairSNAPKokkos:beta",ncoeff,inum); d_ninside = Kokkos::View("PairSNAPKokkos:ninside",inum); } @@ -205,6 +207,8 @@ void PairSNAPKokkos::compute(int eflag_in, int vflag_in) EV_FLOAT ev; + int idxu_max = snaKK.idxu_max; + while (chunk_offset < inum) { // chunk up loop to prevent running out of memory EV_FLOAT ev_tmp; @@ -217,15 +221,62 @@ void PairSNAPKokkos::compute(int eflag_in, int vflag_in) Kokkos::parallel_for("ComputeNeigh",policy_neigh,*this); //PreUi - typename Kokkos::RangePolicy policy_preui(0,chunk_size); - Kokkos::parallel_for("PreUi",policy_preui,*this); + { + int vector_length = 1; + int team_size = 1; + if (lmp->kokkos->ngpus != 0) { + vector_length = 32; + team_size = 32;//max_neighs; + int team_size_max = Kokkos::TeamPolicy::team_size_max(*this); + if (team_size*vector_length > team_size_max) + team_size = team_size_max/vector_length; + } + typename Kokkos::TeamPolicy policy_preui((chunk_size+team_size-1)/team_size,team_size,vector_length); + Kokkos::parallel_for("PreUi",policy_preui,*this); + } - //ComputeUi - typename Kokkos::TeamPolicy policy_ui(((chunk_size+team_size-1)/team_size)*max_neighs,team_size,vector_length); - Kokkos::parallel_for("ComputeUi",policy_ui,*this); + // ComputeUI + if (lmp->kokkos->ngpus == 0) { // CPU + // Run a fused calculation of ulist and accumulation into ulisttot using atomics + int vector_length = 1; + int team_size = 1; + + typename Kokkos::TeamPolicy policy_ui_cpu(((chunk_size+team_size-1)/team_size)*max_neighs,team_size,vector_length); + + Kokkos::parallel_for("ComputeUiCPU",policy_ui_cpu,*this); + } else { // GPU, vector parallelism, shared memory, separate ulist and ulisttot to avoid atomics + + // ComputeUi + int vector_length = 32; + int team_size = 4; // need to cap b/c of shared memory reqs + int team_size_max = Kokkos::TeamPolicy::team_size_max(*this); + if (team_size*vector_length > team_size_max) + team_size = team_size_max/vector_length; + + // scratch size: 2 * team_size * (twojmax+1)^2, to cover all `m1`,`m2` values + // 2 is for double buffer + typename Kokkos::TeamPolicy policy_ui(((chunk_size+team_size-1)/team_size)*max_neighs,team_size,vector_length); + + typedef Kokkos::View< SNAcomplex*, + Kokkos::DefaultExecutionSpace::scratch_memory_space, + Kokkos::MemoryTraits > + ScratchViewType; + int scratch_size = ScratchViewType::shmem_size( 2 * team_size * (twojmax+1)*(twojmax+1)); + policy_ui = policy_ui.set_scratch_size(0, Kokkos::PerTeam( scratch_size )); + + Kokkos::parallel_for("ComputeUi",policy_ui,*this); + + // ComputeUitot + vector_length = 1; + team_size = 128; + team_size_max = Kokkos::TeamPolicy::team_size_max(*this); + if (team_size*vector_length > team_size_max) + team_size = team_size_max/vector_length; + + typename Kokkos::TeamPolicy policy_ui_tot(((idxu_max+team_size-1)/team_size)*chunk_size,team_size,vector_length); + Kokkos::parallel_for("ComputeUiTot",policy_ui_tot,*this); + } - //Ulisttot transpose - snaKK.transpose_ulisttot(); //Compute bispectrum if (quadraticflag || eflag) { @@ -237,15 +288,28 @@ void PairSNAPKokkos::compute(int eflag_in, int vflag_in) //ComputeBi typename Kokkos::TeamPolicy policy_bi(chunk_size,team_size,vector_length); Kokkos::parallel_for("ComputeBi",policy_bi,*this); + } //Compute beta = dE_i/dB_i for all i in list typename Kokkos::TeamPolicy policy_beta(chunk_size,team_size,vector_length); Kokkos::parallel_for("ComputeBeta",policy_beta,*this); - //ComputeYi - typename Kokkos::RangePolicy policy_zero_yi(0,chunk_size); - Kokkos::parallel_for("ZeroYi",policy_zero_yi,*this); + //ZeroYi + { + int vector_length = 1; + int team_size = 1; + int team_size_max = Kokkos::TeamPolicy::team_size_max(*this); + +#ifdef KOKKOS_ENABLE_CUDA + team_size = 128; + if (team_size*vector_length > team_size_max) + team_size = team_size_max/vector_length; +#endif + + typename Kokkos::TeamPolicy policy_zero_yi(((idxu_max+team_size-1)/team_size)*chunk_size,team_size,vector_length); + Kokkos::parallel_for("ZeroYi",policy_zero_yi,*this); + } //ComputeYi int idxz_max = snaKK.idxz_max; @@ -253,12 +317,59 @@ void PairSNAPKokkos::compute(int eflag_in, int vflag_in) Kokkos::parallel_for("ComputeYi",policy_yi,*this); //ComputeDuidrj - typename Kokkos::TeamPolicy policy_duidrj(((chunk_size+team_size-1)/team_size)*max_neighs,team_size,vector_length); - Kokkos::parallel_for("ComputeDuidrj",policy_duidrj,*this); + if (lmp->kokkos->ngpus == 0) { // CPU + int vector_length = 1; + int team_size = 1; + + typename Kokkos::TeamPolicy policy_duidrj_cpu(((chunk_size+team_size-1)/team_size)*max_neighs,team_size,vector_length); + snaKK.set_dir(-1); // technically doesn't do anything + Kokkos::parallel_for("ComputeDuidrjCPU",policy_duidrj_cpu,*this); + } else { // GPU, utilize scratch memory and splitting over dimensions + + int team_size_max = Kokkos::TeamPolicy::team_size_max(*this); + int vector_length = 32; + int team_size = 2; // need to cap b/c of shared memory reqs + if (team_size*vector_length > team_size_max) + team_size = team_size_max/vector_length; + + // scratch size: 2 * 2 * team_size * (twojmax+1)^2, to cover all `m1`,`m2` values + // 2 is for double buffer + typedef Kokkos::View< SNAcomplex*, + Kokkos::DefaultExecutionSpace::scratch_memory_space, + Kokkos::MemoryTraits > + ScratchViewType; + + int scratch_size = ScratchViewType::shmem_size( 4 * team_size * (twojmax+1)*(twojmax+1)); + typename Kokkos::TeamPolicy policy_duidrj(((chunk_size+team_size-1)/team_size)*max_neighs,team_size,vector_length); + policy_duidrj = policy_duidrj.set_scratch_size(0, Kokkos::PerTeam( scratch_size )); + // Need to call three times, once for each direction + for (int k = 0; k < 3; k++) { + snaKK.set_dir(k); + Kokkos::parallel_for("ComputeDuidrj",policy_duidrj,*this); + } + } //ComputeDeidrj - typename Kokkos::TeamPolicy policy_deidrj(((chunk_size+team_size-1)/team_size)*max_neighs,team_size,vector_length); - Kokkos::parallel_for("ComputeDeidrj",policy_deidrj,*this); + if (lmp->kokkos->ngpus == 0) { // CPU + int vector_length = 1; + int team_size = 1; + + typename Kokkos::TeamPolicy policy_deidrj_cpu(((chunk_size+team_size-1)/team_size)*max_neighs,team_size,vector_length); + + Kokkos::parallel_for("ComputeDeidrjCPU",policy_deidrj_cpu,*this); + + } else { // GPU, different loop strategy internally + + int team_size_max = Kokkos::TeamPolicy::team_size_max(*this); + int vector_length = 32; // coalescing disaster right now, will fix later + int team_size = 8; + if (team_size*vector_length > team_size_max) + team_size = team_size_max/vector_length; + + typename Kokkos::TeamPolicy policy_deidrj(((chunk_size+team_size-1)/team_size)*max_neighs,team_size,vector_length); + + Kokkos::parallel_for("ComputeDeidrj",policy_deidrj,*this); + } //ComputeForce if (eflag) { @@ -284,6 +395,7 @@ void PairSNAPKokkos::compute(int eflag_in, int vflag_in) } ev += ev_tmp; chunk_offset += chunk_size; + } // end while if (need_dup) @@ -341,18 +453,18 @@ void PairSNAPKokkos::operator() (TagPairSNAPBeta,const typename Kokk d_coeffi(d_coeffelem,ielem,Kokkos::ALL); for (int icoeff = 0; icoeff < ncoeff; icoeff++) - d_beta(ii,icoeff) = d_coeffi[icoeff+1]; + d_beta(icoeff,ii) = d_coeffi[icoeff+1]; if (quadraticflag) { int k = ncoeff+1; for (int icoeff = 0; icoeff < ncoeff; icoeff++) { - double bveci = my_sna.blist(ii,icoeff); - d_beta(ii,icoeff) += d_coeffi[k]*bveci; + double bveci = my_sna.blist(icoeff,ii); + d_beta(icoeff,ii) += d_coeffi[k]*bveci; k++; for (int jcoeff = icoeff+1; jcoeff < ncoeff; jcoeff++) { - double bvecj = my_sna.blist(ii,jcoeff); - d_beta(ii,icoeff) += d_coeffi[k]*bvecj; - d_beta(ii,jcoeff) += d_coeffi[k]*bveci; + double bvecj = my_sna.blist(jcoeff,ii); + d_beta(icoeff,ii) += d_coeffi[k]*bvecj; + d_beta(jcoeff,ii) += d_coeffi[k]*bveci; k++; } } @@ -503,9 +615,14 @@ void PairSNAPKokkos::operator() (TagPairSNAPComputeNeigh,const typen template KOKKOS_INLINE_FUNCTION -void PairSNAPKokkos::operator() (TagPairSNAPPreUi,const int& ii) const { +void PairSNAPKokkos::operator() (TagPairSNAPPreUi,const typename Kokkos::TeamPolicy::member_type& team) const { SNAKokkos my_sna = snaKK; - my_sna.pre_ui(ii); + + // Extract the atom number + const int ii = team.team_rank() + team.team_size() * (team.league_rank() % ((chunk_size+team.team_size()-1)/team.team_size())); + if (ii >= chunk_size) return; + + my_sna.pre_ui(team,ii); } template @@ -514,8 +631,7 @@ void PairSNAPKokkos::operator() (TagPairSNAPComputeUi,const typename SNAKokkos my_sna = snaKK; // Extract the atom number - int ii = team.team_rank() + team.team_size() * (team.league_rank() % - ((chunk_size+team.team_size()-1)/team.team_size())); + int ii = team.team_rank() + team.team_size() * (team.league_rank() % ((chunk_size+team.team_size()-1)/team.team_size())); if (ii >= chunk_size) return; // Extract the neighbor number @@ -528,9 +644,54 @@ void PairSNAPKokkos::operator() (TagPairSNAPComputeUi,const typename template KOKKOS_INLINE_FUNCTION -void PairSNAPKokkos::operator() (TagPairSNAPZeroYi,const int& ii) const { +void PairSNAPKokkos::operator() (TagPairSNAPComputeUiTot,const typename Kokkos::TeamPolicy::member_type& team) const { SNAKokkos my_sna = snaKK; - my_sna.zero_yi(ii); + + // Extract the quantum number + const int idx = team.team_rank() + team.team_size() * (team.league_rank() % ((my_sna.idxu_max+team.team_size()-1)/team.team_size())); + if (idx >= my_sna.idxu_max) return; + + // Extract the atomic index + const int ii = team.league_rank() / ((my_sna.idxu_max+team.team_size()-1)/team.team_size()); + if (ii >= chunk_size) return; + + // Extract the number of neighbors neighbor number + const int ninside = d_ninside(ii); + + my_sna.compute_uitot(team,idx,ii,ninside); +} + +template +KOKKOS_INLINE_FUNCTION +void PairSNAPKokkos::operator() (TagPairSNAPComputeUiCPU,const typename Kokkos::TeamPolicy::member_type& team) const { + SNAKokkos my_sna = snaKK; + + // Extract the atom number + int ii = team.team_rank() + team.team_size() * (team.league_rank() % ((chunk_size+team.team_size()-1)/team.team_size())); + if (ii >= chunk_size) return; + + // Extract the neighbor number + const int jj = team.league_rank() / ((chunk_size+team.team_size()-1)/team.team_size()); + const int ninside = d_ninside(ii); + if (jj >= ninside) return; + + my_sna.compute_ui_cpu(team,ii,jj); +} + +template +KOKKOS_INLINE_FUNCTION +void PairSNAPKokkos::operator() (TagPairSNAPZeroYi,const typename Kokkos::TeamPolicy::member_type& team) const { + SNAKokkos my_sna = snaKK; + + // Extract the quantum number + const int idx = team.team_rank() + team.team_size() * (team.league_rank() % ((my_sna.idxu_max+team.team_size()-1)/team.team_size())); + if (idx >= my_sna.idxu_max) return; + + // Extract the atomic index + const int ii = team.league_rank() / ((my_sna.idxu_max+team.team_size()-1)/team.team_size()); + if (ii >= chunk_size) return; + + my_sna.zero_yi(idx,ii); } template @@ -561,8 +722,7 @@ void PairSNAPKokkos::operator() (TagPairSNAPComputeDuidrj,const type SNAKokkos my_sna = snaKK; // Extract the atom number - int ii = team.team_rank() + team.team_size() * (team.league_rank() % - ((chunk_size+team.team_size()-1)/team.team_size())); + int ii = team.team_rank() + team.team_size() * (team.league_rank() % ((chunk_size+team.team_size()-1)/team.team_size())); if (ii >= chunk_size) return; // Extract the neighbor number @@ -573,14 +733,31 @@ void PairSNAPKokkos::operator() (TagPairSNAPComputeDuidrj,const type my_sna.compute_duidrj(team,ii,jj); } +template +KOKKOS_INLINE_FUNCTION +void PairSNAPKokkos::operator() (TagPairSNAPComputeDuidrjCPU,const typename Kokkos::TeamPolicy::member_type& team) const { + SNAKokkos my_sna = snaKK; + + // Extract the atom number + int ii = team.team_rank() + team.team_size() * (team.league_rank() % ((chunk_size+team.team_size()-1)/team.team_size())); + if (ii >= chunk_size) return; + + // Extract the neighbor number + const int jj = team.league_rank() / ((chunk_size+team.team_size()-1)/team.team_size()); + const int ninside = d_ninside(ii); + if (jj >= ninside) return; + + my_sna.compute_duidrj_cpu(team,ii,jj); +} + + template KOKKOS_INLINE_FUNCTION void PairSNAPKokkos::operator() (TagPairSNAPComputeDeidrj,const typename Kokkos::TeamPolicy::member_type& team) const { SNAKokkos my_sna = snaKK; // Extract the atom number - int ii = team.team_rank() + team.team_size() * (team.league_rank() % - ((chunk_size+team.team_size()-1)/team.team_size())); + int ii = team.team_rank() + team.team_size() * (team.league_rank() % ((chunk_size+team.team_size()-1)/team.team_size())); if (ii >= chunk_size) return; // Extract the neighbor number @@ -591,6 +768,23 @@ void PairSNAPKokkos::operator() (TagPairSNAPComputeDeidrj,const type my_sna.compute_deidrj(team,ii,jj); } +template +KOKKOS_INLINE_FUNCTION +void PairSNAPKokkos::operator() (TagPairSNAPComputeDeidrjCPU,const typename Kokkos::TeamPolicy::member_type& team) const { + SNAKokkos my_sna = snaKK; + + // Extract the atom number + int ii = team.team_rank() + team.team_size() * (team.league_rank() % ((chunk_size+team.team_size()-1)/team.team_size())); + if (ii >= chunk_size) return; + + // Extract the neighbor number + const int jj = team.league_rank() / ((chunk_size+team.team_size()-1)/team.team_size()); + const int ninside = d_ninside(ii); + if (jj >= ninside) return; + + my_sna.compute_deidrj_cpu(team,ii,jj); +} + template template KOKKOS_INLINE_FUNCTION @@ -658,17 +852,17 @@ void PairSNAPKokkos::operator() (TagPairSNAPComputeForce +struct alignas(2*sizeof(real)) SNAComplex +{ + real re,im; + + KOKKOS_FORCEINLINE_FUNCTION SNAComplex() = default; - KOKKOS_INLINE_FUNCTION - SNAcomplex() : re(0),im(0) - {} + KOKKOS_FORCEINLINE_FUNCTION SNAComplex(real re) + : re(re), im(static_cast(0.)) { ; } + + KOKKOS_FORCEINLINE_FUNCTION SNAComplex(real re, real im) + : re(re), im(im) { ; } + + KOKKOS_FORCEINLINE_FUNCTION SNAComplex(const SNAComplex& other) + : re(other.re), im(other.im) { ; } + + KOKKOS_FORCEINLINE_FUNCTION SNAComplex& operator=(const SNAComplex& other) { + re = other.re; im = other.im; + return *this; + } + + KOKKOS_FORCEINLINE_FUNCTION SNAComplex(SNAComplex&& other) + : re(other.re), im(other.im) { ; } + + KOKKOS_FORCEINLINE_FUNCTION SNAComplex& operator=(SNAComplex&& other) { + re = other.re; im = other.im; + return *this; + } + + KOKKOS_FORCEINLINE_FUNCTION SNAComplex operator+(SNAComplex const& other) { + return SNAComplex(re + other.re, im + other.im); + } + + KOKKOS_FORCEINLINE_FUNCTION SNAComplex& operator+=(SNAComplex const& other) { + re += other.re; im += other.im; + return *this; + } - KOKKOS_INLINE_FUNCTION - SNAcomplex(SNAreal real_in, SNAreal imag_in) - :re(real_in),im(imag_in) - {} }; +template +KOKKOS_FORCEINLINE_FUNCTION SNAComplex operator*(const real& r, const SNAComplex& self) { + return SNAComplex(r*self.re, r*self.im); +} + +typedef SNAComplex SNAcomplex; + //struct SNAKK_ZINDICES { // int j1, j2, j, ma1min, ma2max, mb1min, mb2max, na, nb, jju; //}; @@ -58,6 +92,7 @@ public: typedef Kokkos::View > t_sna_1d_atomic; typedef Kokkos::View t_sna_2i; typedef Kokkos::View t_sna_2d; + typedef Kokkos::View t_sna_2d_ll; typedef Kokkos::View t_sna_3d; typedef Kokkos::View t_sna_4d; typedef Kokkos::View t_sna_3d3; @@ -66,32 +101,15 @@ public: typedef Kokkos::View t_sna_1c; typedef Kokkos::View > t_sna_1c_atomic; typedef Kokkos::View t_sna_2c; + typedef Kokkos::View t_sna_2c_ll; typedef Kokkos::View t_sna_2c_lr; typedef Kokkos::View t_sna_3c; + typedef Kokkos::View t_sna_3c_ll; typedef Kokkos::View t_sna_4c; + typedef Kokkos::View t_sna_4c_ll; typedef Kokkos::View t_sna_3c3; typedef Kokkos::View t_sna_5c; -// Helper class to get ulisttot_r - -template -class UlisttotHelper { -public: - inline - static void transpose(T1 &ulisttot_lr, const T2 &ulisttot) { - Kokkos::deep_copy(ulisttot_lr,ulisttot); - } -}; - -template -class UlisttotHelper { -public: - inline - static void transpose(T1 &ulisttot_lr, const T2 &ulisttot) { - ulisttot_lr = ulisttot; - } -}; - inline SNAKokkos() {}; KOKKOS_INLINE_FUNCTION @@ -113,20 +131,21 @@ inline int ncoeff; -inline - void transpose_ulisttot(); - // functions for bispectrum coefficients KOKKOS_INLINE_FUNCTION - void pre_ui(const int&); // ForceSNAP + void pre_ui(const typename Kokkos::TeamPolicy::member_type& team,const int&); // ForceSNAP KOKKOS_INLINE_FUNCTION void compute_ui(const typename Kokkos::TeamPolicy::member_type& team, int, int); // ForceSNAP KOKKOS_INLINE_FUNCTION + void compute_ui_cpu(const typename Kokkos::TeamPolicy::member_type& team, int, int); // ForceSNAP + KOKKOS_INLINE_FUNCTION void compute_ui_orig(const typename Kokkos::TeamPolicy::member_type& team, int, int); // ForceSNAP KOKKOS_INLINE_FUNCTION + void compute_uitot(const typename Kokkos::TeamPolicy::member_type& team, int, int, int); // ForceSNAP + KOKKOS_INLINE_FUNCTION void compute_zi(const int&); // ForceSNAP KOKKOS_INLINE_FUNCTION - void zero_yi(const int&); + void zero_yi(const int&,const int&); // ForceSNAP KOKKOS_INLINE_FUNCTION void compute_yi(int, const Kokkos::View &beta); // ForceSNAP @@ -138,12 +157,29 @@ inline KOKKOS_INLINE_FUNCTION void compute_duidrj(const typename Kokkos::TeamPolicy::member_type& team, int, int); //ForceSNAP KOKKOS_INLINE_FUNCTION + void compute_duidrj_cpu(const typename Kokkos::TeamPolicy::member_type& team, int, int); //ForceSNAP + KOKKOS_INLINE_FUNCTION void compute_deidrj(const typename Kokkos::TeamPolicy::member_type& team, int, int); // ForceSNAP KOKKOS_INLINE_FUNCTION + void compute_deidrj_cpu(const typename Kokkos::TeamPolicy::member_type& team, int, int); // ForceSNAP + KOKKOS_INLINE_FUNCTION double compute_sfac(double, double); // add_uarraytot, compute_duarray KOKKOS_INLINE_FUNCTION double compute_dsfac(double, double); // compute_duarray + // efficient complex FMA + // efficient caxpy (i.e., y += a x) + static KOKKOS_FORCEINLINE_FUNCTION + void caxpy(const SNAcomplex& a, const SNAcomplex& x, SNAcomplex& y); + + // efficient complex FMA, conjugate of scalar + static KOKKOS_FORCEINLINE_FUNCTION + void caconjxpy(const SNAcomplex& a, const SNAcomplex& x, SNAcomplex& y); + + // Set the direction for split ComputeDuidrj + KOKKOS_INLINE_FUNCTION + void set_dir(int); + #ifdef TIMING_INFO double* timers; timespec starttime, endtime; @@ -165,17 +201,16 @@ inline void grow_rij(int, int); int twojmax, diagonalstyle; + + t_sna_2d_ll blist; + t_sna_2c_ll ulisttot; + t_sna_2c_ll zlist; - t_sna_2d blist; - t_sna_2c ulisttot; - t_sna_2c_lr ulisttot_lr; - t_sna_2c zlist; - - t_sna_3c ulist; - t_sna_2c_lr ylist; + t_sna_3c_ll ulist; + t_sna_2c_ll ylist; // derivatives of data - t_sna_4c dulist; + t_sna_4c_ll dulist; int idxcg_max, idxu_max, idxz_max, idxb_max; @@ -212,10 +247,7 @@ inline inline void init_rootpqarray(); // init() - KOKKOS_INLINE_FUNCTION - void zero_uarraytot(const int&); // compute_ui - KOKKOS_INLINE_FUNCTION - void addself_uarraytot(const int&, const double&); // compute_ui + KOKKOS_INLINE_FUNCTION void add_uarraytot(const typename Kokkos::TeamPolicy::member_type& team, int, int, double, double, double); // compute_ui @@ -223,6 +255,12 @@ inline void compute_uarray(const typename Kokkos::TeamPolicy::member_type& team, int, int, double, double, double, double, double); // compute_ui + KOKKOS_INLINE_FUNCTION + void compute_uarray_cpu(const typename Kokkos::TeamPolicy::member_type& team, int, int, + double, double, double, + double, double); // compute_ui_cpu + + inline double deltacg(int, int, int); // init_clebsch_gordan @@ -232,6 +270,10 @@ inline void compute_duarray(const typename Kokkos::TeamPolicy::member_type& team, int, int, double, double, double, // compute_duidrj double, double, double, double, double); + KOKKOS_INLINE_FUNCTION + void compute_duarray_cpu(const typename Kokkos::TeamPolicy::member_type& team, int, int, + double, double, double, // compute_duidrj + double, double, double, double, double); // Sets the style for the switching function // 0 = none @@ -243,6 +285,9 @@ inline int bzero_flag; // 1 if bzero subtracted from barray Kokkos::View bzero; // array of B values for isolated atoms + + // for per-direction dulist calculation, specify the direction. + int dir; }; } diff --git a/src/KOKKOS/sna_kokkos_impl.h b/src/KOKKOS/sna_kokkos_impl.h index 8d5a4a21be..c8c9a07e3e 100644 --- a/src/KOKKOS/sna_kokkos_impl.h +++ b/src/KOKKOS/sna_kokkos_impl.h @@ -224,16 +224,19 @@ void SNAKokkos::grow_rij(int newnatom, int newnmax) rcutij = t_sna_2d("sna:rcutij",natom,nmax); dedr = t_sna_3d("sna:dedr",natom,nmax,3); - blist = t_sna_2d("sna:blist",natom,idxb_max); - ulisttot = t_sna_2c("sna:ulisttot",natom,idxu_max); - if (!Kokkos::Impl::is_same::value) - ulisttot_lr = t_sna_2c_lr("sna:ulisttot_lr",natom,idxu_max); - zlist = t_sna_2c("sna:zlist",natom,idxz_max); + blist = t_sna_2d_ll("sna:blist",idxb_max,natom); + //ulisttot = t_sna_2c("sna:ulisttot",natom,idxu_max); + ulisttot = t_sna_2c_ll("sna:ulisttot",idxu_max,natom); - ulist = t_sna_3c("sna:ulist",natom,nmax,idxu_max); - ylist = t_sna_2c_lr("sna:ylist",natom,idxu_max); + zlist = t_sna_2c_ll("sna:zlist",idxz_max,natom); - dulist = t_sna_4c("sna:dulist",natom,nmax,idxu_max); + //ulist = t_sna_3c("sna:ulist",natom,nmax,idxu_max); + ulist = t_sna_3c_ll("sna:ulist",idxu_max,natom,nmax); + //ylist = t_sna_2c_lr("sna:ylist",natom,idxu_max); + ylist = t_sna_2c_ll("sna:ylist",idxu_max,natom); + + //dulist = t_sna_4c("sna:dulist",natom,nmax,idxu_max); + dulist = t_sna_4c_ll("sna:dulist",idxu_max,natom,nmax); } /* ---------------------------------------------------------------------- @@ -242,19 +245,31 @@ void SNAKokkos::grow_rij(int newnatom, int newnmax) template KOKKOS_INLINE_FUNCTION -void SNAKokkos::pre_ui(const int& iatom) +void SNAKokkos::pre_ui(const typename Kokkos::TeamPolicy::member_type& team, const int& iatom) { - //if(team.team_rank() == 0) { - zero_uarraytot(iatom); - //Kokkos::single(Kokkos::PerThread(team), [&] (){ - addself_uarraytot(iatom,wself); - //}); - //} - //team.team_barrier(); + for (int j = 0; j <= twojmax; j++) { + const int jju = idxu_block(j); + + // Only diagonal elements get initialized + // for (int m = 0; m < (j+1)*(j+1); m++) + Kokkos::parallel_for(Kokkos::ThreadVectorRange(team, (j+1)*(j+1)), + [&] (const int m) { + + const int jjup = jju + m; + + // if m is on the "diagonal", initialize it with the self energy. + // Otherwise zero it out + SNAcomplex init = {0., 0.}; + if (m % (j+2) == 0) { init = {wself, 0.0}; } + + ulisttot(jjup, iatom) = init; + }); + } + } /* ---------------------------------------------------------------------- - compute Ui by summing over neighbors j + compute Ui by summing over bispectrum components ------------------------------------------------------------------------- */ template @@ -280,11 +295,72 @@ void SNAKokkos::compute_ui(const typename Kokkos::TeamPolicy +KOKKOS_INLINE_FUNCTION +void SNAKokkos::compute_ui_cpu(const typename Kokkos::TeamPolicy::member_type& team, int iatom, int jnbor) +{ + double rsq, r, x, y, z, z0, theta0; + + // utot(j,ma,mb) = 0 for all j,ma,ma + // utot(j,ma,ma) = 1 for all j,ma + // for j in neighbors of i: + // compute r0 = (x,y,z,z0) + // utot(j,ma,mb) += u(r0;j,ma,mb) for all j,ma,mb + + x = rij(iatom,jnbor,0); + y = rij(iatom,jnbor,1); + z = rij(iatom,jnbor,2); + rsq = x * x + y * y + z * z; + r = sqrt(rsq); + + theta0 = (r - rmin0) * rfac0 * MY_PI / (rcutij(iatom,jnbor) - rmin0); + // theta0 = (r - rmin0) * rscale0; + z0 = r / tan(theta0); + + compute_uarray_cpu(team, iatom, jnbor, x, y, z, z0, r); add_uarraytot(team, iatom, jnbor, r, wj(iatom,jnbor), rcutij(iatom,jnbor)); + +} + +/* ---------------------------------------------------------------------- + compute UiTot by summing over neighbors +------------------------------------------------------------------------- */ + +template +KOKKOS_INLINE_FUNCTION +void SNAKokkos::compute_uitot(const typename Kokkos::TeamPolicy::member_type& team, int idx, int iatom, int ninside) +{ + // fuse initialize in, avoid this load? + SNAcomplex utot = ulisttot(idx, iatom); + for (int jnbor = 0; jnbor < ninside; jnbor++) { + + const auto x = rij(iatom,jnbor,0); + const auto y = rij(iatom,jnbor,1); + const auto z = rij(iatom,jnbor,2); + const auto rsq = x * x + y * y + z * z; + const auto r = sqrt(rsq); + + const double wj_local = wj(iatom, jnbor); + const double rcut = rcutij(iatom, jnbor); + const double sfac = compute_sfac(r, rcut) * wj_local; + + auto ulist_local = ulist(idx, iatom, jnbor); + utot.re += sfac * ulist_local.re; + utot.im += sfac * ulist_local.im; + } + + ulisttot(idx, iatom) = utot; + } /* ---------------------------------------------------------------------- compute Zi by summing over products of Ui + not updated yet ------------------------------------------------------------------------- */ template @@ -306,8 +382,8 @@ void SNAKokkos::compute_zi(const int& iter) const double* cgblock = cglist.data() + idxcg_block(j1,j2,j); - zlist(iatom,jjz).re = 0.0; - zlist(iatom,jjz).im = 0.0; + zlist(jjz,iatom).re = 0.0; + zlist(jjz,iatom).im = 0.0; int jju1 = idxu_block[j1] + (j1+1)*mb1min; int jju2 = idxu_block[j2] + (j2+1)*mb2max; @@ -321,15 +397,15 @@ void SNAKokkos::compute_zi(const int& iter) int ma2 = ma2max; int icga = ma1min*(j2+1) + ma2max; for(int ia = 0; ia < na; ia++) { - suma1_r += cgblock[icga] * (ulisttot(iatom,jju1+ma1).re * ulisttot(iatom,jju2+ma2).re - ulisttot(iatom,jju1+ma1).im * ulisttot(iatom,jju2+ma2).im); - suma1_i += cgblock[icga] * (ulisttot(iatom,jju1+ma1).re * ulisttot(iatom,jju2+ma2).im + ulisttot(iatom,jju1+ma1).im * ulisttot(iatom,jju2+ma2).re); + suma1_r += cgblock[icga] * (ulisttot(jju1+ma1,iatom).re * ulisttot(jju2+ma2,iatom).re - ulisttot(jju1+ma1,iatom).im * ulisttot(jju2+ma2,iatom).im); + suma1_i += cgblock[icga] * (ulisttot(jju1+ma1,iatom).re * ulisttot(jju2+ma2,iatom).im + ulisttot(jju1+ma1,iatom).im * ulisttot(jju2+ma2,iatom).re); ma1++; ma2--; icga += j2; } // end loop over ia - zlist(iatom,jjz).re += cgblock[icgb] * suma1_r; - zlist(iatom,jjz).im += cgblock[icgb] * suma1_i; + zlist(jjz,iatom).re += cgblock[icgb] * suma1_r; + zlist(jjz,iatom).im += cgblock[icgb] * suma1_i; jju1 += j1+1; jju2 -= j2+1; @@ -343,10 +419,9 @@ void SNAKokkos::compute_zi(const int& iter) template KOKKOS_INLINE_FUNCTION -void SNAKokkos::zero_yi(const int& iatom) +void SNAKokkos::zero_yi(const int& idx, const int& iatom) { - for (int j = 0; j < idxu_max; j++) - ylist(iatom,j) = {0.0,0.0}; + ylist(idx,iatom) = {0.0, 0.0}; } /* ---------------------------------------------------------------------- @@ -393,8 +468,8 @@ void SNAKokkos::compute_yi(int iter, int icga = ma1min*(j2+1) + ma2max; for(int ia = 0; ia < na; ia++) { - suma1_r += cgblock[icga] * (ulisttot_lr(iatom,jju1+ma1).re * ulisttot_lr(iatom,jju2+ma2).re - ulisttot_lr(iatom,jju1+ma1).im * ulisttot_lr(iatom,jju2+ma2).im); - suma1_i += cgblock[icga] * (ulisttot_lr(iatom,jju1+ma1).re * ulisttot_lr(iatom,jju2+ma2).im + ulisttot_lr(iatom,jju1+ma1).im * ulisttot_lr(iatom,jju2+ma2).re); + suma1_r += cgblock[icga] * (ulisttot(jju1+ma1,iatom).re * ulisttot(jju2+ma2,iatom).re - ulisttot(jju1+ma1,iatom).im * ulisttot(jju2+ma2,iatom).im); + suma1_i += cgblock[icga] * (ulisttot(jju1+ma1,iatom).re * ulisttot(jju2+ma2,iatom).im + ulisttot(jju1+ma1,iatom).im * ulisttot(jju2+ma2,iatom).re); ma1++; ma2--; icga += j2; @@ -417,20 +492,20 @@ void SNAKokkos::compute_yi(int iter, if (j >= j1) { const int jjb = idxb_block(j1,j2,j); if (j1 == j) { - if (j2 == j) betaj = 3*beta(iatom,jjb); - else betaj = 2*beta(iatom,jjb); - } else betaj = beta(iatom,jjb); + if (j2 == j) betaj = 3*beta(jjb,iatom); + else betaj = 2*beta(jjb,iatom); + } else betaj = beta(jjb,iatom); } else if (j >= j2) { const int jjb = idxb_block(j,j2,j1); - if (j2 == j) betaj = 2*beta(iatom,jjb)*(j1+1)/(j+1.0); - else betaj = beta(iatom,jjb)*(j1+1)/(j+1.0); + if (j2 == j) betaj = 2*beta(jjb,iatom)*(j1+1)/(j+1.0); + else betaj = beta(jjb,iatom)*(j1+1)/(j+1.0); } else { const int jjb = idxb_block(j2,j,j1); - betaj = beta(iatom,jjb)*(j1+1)/(j+1.0); + betaj = beta(jjb,iatom)*(j1+1)/(j+1.0); } - Kokkos::atomic_add(&(ylist(iatom,jju).re), betaj*ztmp_r); - Kokkos::atomic_add(&(ylist(iatom,jju).im), betaj*ztmp_i); + Kokkos::atomic_add(&(ylist(jju,iatom).re), betaj*ztmp_r); + Kokkos::atomic_add(&(ylist(jju,iatom).im), betaj*ztmp_i); } /* ---------------------------------------------------------------------- @@ -441,18 +516,81 @@ template KOKKOS_INLINE_FUNCTION void SNAKokkos::compute_deidrj(const typename Kokkos::TeamPolicy::member_type& team, int iatom, int jnbor) { - t_scalar3 sum; + t_scalar3 final_sum; + // Like in ComputeUi/ComputeDuidrj, regular loop over j. + for (int j = 0; j <= twojmax; j++) { + int jju = idxu_block(j); + + // Flatten loop over ma, mb, reduce w/in + + const int n_ma = j+1; + // for (int mb = 0; 2*mb <= j; mb++) + const int n_mb = j/2+1; + + const int total_iters = n_ma * n_mb; + + t_scalar3 sum; + + //for (int m = 0; m < total_iters; m++) { + Kokkos::parallel_reduce(Kokkos::ThreadVectorRange(team, total_iters), + [&] (const int m, t_scalar3& sum_tmp) { + + // ma fast, mb slow + int ma = m % n_ma; + int mb = m / n_ma; + + // get index + const int jju_index = jju+mb+mb*j+ma; + + // get ylist, rescale last element by 0.5 + SNAcomplex y_local = ylist(jju_index,iatom); + + const SNAcomplex du_x = dulist(jju_index,iatom,jnbor,0); + const SNAcomplex du_y = dulist(jju_index,iatom,jnbor,1); + const SNAcomplex du_z = dulist(jju_index,iatom,jnbor,2); + + if (j % 2 == 0 && 2*mb == j) { + if (ma == mb) { y_local = 0.5*y_local; } + else if (ma > mb) { y_local = { 0., 0. }; } + // else the ma < mb gets "double counted", cancelling the 0.5. + } + + sum_tmp.x += du_x.re * y_local.re + du_x.im * y_local.im; + sum_tmp.y += du_y.re * y_local.re + du_y.im * y_local.im; + sum_tmp.z += du_z.re * y_local.re + du_z.im * y_local.im; + + }, sum); // end loop over flattened ma,mb + + final_sum.x += sum.x; + final_sum.y += sum.y; + final_sum.z += sum.z; + } + + Kokkos::single(Kokkos::PerThread(team), [&] () { + dedr(iatom,jnbor,0) = final_sum.x*2.0; + dedr(iatom,jnbor,1) = final_sum.y*2.0; + dedr(iatom,jnbor,2) = final_sum.z*2.0; + }); + +} + +template +KOKKOS_INLINE_FUNCTION +void SNAKokkos::compute_deidrj_cpu(const typename Kokkos::TeamPolicy::member_type& team, int iatom, int jnbor) +{ + t_scalar3 final_sum; + + //for(int j = 0; j <= twojmax; j++) { Kokkos::parallel_reduce(Kokkos::ThreadVectorRange(team,twojmax+1), [&] (const int& j, t_scalar3& sum_tmp) { - //for(int j = 0; j <= twojmax; j++) { int jju = idxu_block[j]; for(int mb = 0; 2*mb < j; mb++) for(int ma = 0; ma <= j; ma++) { - sum_tmp.x += dulist(iatom,jnbor,jju,0).re * ylist(iatom,jju).re + dulist(iatom,jnbor,jju,0).im * ylist(iatom,jju).im; - sum_tmp.y += dulist(iatom,jnbor,jju,1).re * ylist(iatom,jju).re + dulist(iatom,jnbor,jju,1).im * ylist(iatom,jju).im; - sum_tmp.z += dulist(iatom,jnbor,jju,2).re * ylist(iatom,jju).re + dulist(iatom,jnbor,jju,2).im * ylist(iatom,jju).im; + sum_tmp.x += dulist(jju,iatom,jnbor,0).re * ylist(jju,iatom).re + dulist(jju,iatom,jnbor,0).im * ylist(jju,iatom).im; + sum_tmp.y += dulist(jju,iatom,jnbor,1).re * ylist(jju,iatom).re + dulist(jju,iatom,jnbor,1).im * ylist(jju,iatom).im; + sum_tmp.z += dulist(jju,iatom,jnbor,2).re * ylist(jju,iatom).re + dulist(jju,iatom,jnbor,2).im * ylist(jju,iatom).im; jju++; } //end loop over ma mb @@ -462,25 +600,24 @@ void SNAKokkos::compute_deidrj(const typename Kokkos::TeamPolicy::compute_bi(const typename Kokkos::TeamPolicy::compute_bi(const typename Kokkos::TeamPolicy::compute_bi(const typename Kokkos::TeamPolicy::compute_bi(const typename Kokkos::TeamPolicy::compute_duidrj(const typename Kokkos::TeamPolicy KOKKOS_INLINE_FUNCTION -void SNAKokkos::zero_uarraytot(const int& iatom) +void SNAKokkos::compute_duidrj_cpu(const typename Kokkos::TeamPolicy::member_type& team, int iatom, int jnbor) { - { - //Kokkos::parallel_for(Kokkos::ThreadVectorRange(team,ulisttot.extent(1)), - // [&] (const int& i) { - for (int i = 0; i < ulisttot.extent(1); i++) { - ulisttot(iatom,i).re = 0.0; - ulisttot(iatom,i).im = 0.0; - } - //}); - } -} + double rsq, r, x, y, z, z0, theta0, cs, sn; + double dz0dr; -/* ---------------------------------------------------------------------- */ + x = rij(iatom,jnbor,0); + y = rij(iatom,jnbor,1); + z = rij(iatom,jnbor,2); + rsq = x * x + y * y + z * z; + r = sqrt(rsq); + double rscale0 = rfac0 * MY_PI / (rcutij(iatom,jnbor) - rmin0); + theta0 = (r - rmin0) * rscale0; + cs = cos(theta0); + sn = sin(theta0); + z0 = r * cs / sn; + dz0dr = z0 / r - (r*rscale0) * (rsq + z0 * z0) / rsq; -template -KOKKOS_INLINE_FUNCTION -void SNAKokkos::addself_uarraytot(const int& iatom, const double& wself_in) -{ - //Kokkos::parallel_for(Kokkos::ThreadVectorRange(team,twojmax+1), - // [&] (const int& j) { - for (int j = 0; j <= twojmax; j++) { - int jju = idxu_block[j]; - for (int ma = 0; ma <= j; ma++) { - ulisttot(iatom,jju).re = wself_in; - ulisttot(iatom,jju).im = 0.0; - jju += j+2; - } - }//}); + compute_duarray_cpu(team, iatom, jnbor, x, y, z, z0, r, dz0dr, wj(iatom,jnbor), rcutij(iatom,jnbor)); } /* ---------------------------------------------------------------------- @@ -639,10 +763,10 @@ void SNAKokkos::add_uarraytot(const typename Kokkos::TeamPolicy::compute_uarray(const typename Kokkos::TeamPolicy::member_type& team, int iatom, int jnbor, double x, double y, double z, double z0, double r) +{ + // define size of scratch memory buffer + const int max_m_tile = (twojmax+1)*(twojmax+1); + const int team_rank = team.team_rank(); + + // get scratch memory double buffer + SNAcomplex* buf1 = (SNAcomplex*)team.team_shmem( ).get_shmem(team.team_size()*max_m_tile*sizeof(SNAcomplex), 0); + SNAcomplex* buf2 = (SNAcomplex*)team.team_shmem( ).get_shmem(team.team_size()*max_m_tile*sizeof(SNAcomplex), 0); + + // compute Cayley-Klein parameters for unit quaternion, + // pack into complex number + double r0inv = 1.0 / sqrt(r * r + z0 * z0); + SNAcomplex a = { r0inv * z0, -r0inv * z }; + SNAcomplex b = { r0inv * y, -r0inv * x }; + + // VMK Section 4.8.2 + + // All writes go to global memory and shared memory + // so we can avoid all global memory reads + Kokkos::single(Kokkos::PerThread(team), [=]() { + ulist(0,iatom,jnbor) = { 1.0, 0.0 }; + buf1[max_m_tile*team_rank] = {1.,0.}; + }); + + for (int j = 1; j <= twojmax; j++) { + const int jju = idxu_block[j]; + int jjup = idxu_block[j-1]; + + // fill in left side of matrix layer from previous layer + + // Flatten loop over ma, mb, need to figure out total + // number of iterations + + // for (int ma = 0; ma <= j; ma++) + const int n_ma = j+1; + // for (int mb = 0; 2*mb <= j; mb++) + const int n_mb = j/2+1; + + const int total_iters = n_ma * n_mb; + + //for (int m = 0; m < total_iters; m++) { + Kokkos::parallel_for(Kokkos::ThreadVectorRange(team, total_iters), + [&] (const int m) { + + // ma fast, mb slow + int ma = m % n_ma; + int mb = m / n_ma; + + // index into global memory array + const int jju_index = jju+mb+mb*j+ma; + + // index into shared memory buffer for previous level + const int jju_shared_idx = max_m_tile*team_rank+mb+mb*j+ma; + + // index into shared memory buffer for next level + const int jjup_shared_idx = max_m_tile*team_rank+mb*j+ma; + + SNAcomplex u_accum = {0., 0.}; + + // VMK recursion relation: grab contribution which is multiplied by a* + const double rootpq1 = rootpqarray(j - ma, j - mb); + const SNAcomplex u_up1 = (ma < j)?rootpq1*buf1[jjup_shared_idx]:SNAcomplex(0.,0.); + caconjxpy(a, u_up1, u_accum); + + // VMK recursion relation: grab contribution which is multiplied by b* + const double rootpq2 = -rootpqarray(ma, j - mb); + const SNAcomplex u_up2 = (ma > 0)?rootpq2*buf1[jjup_shared_idx-1]:SNAcomplex(0.,0.); + caconjxpy(b, u_up2, u_accum); + + ulist(jju_index,iatom,jnbor) = u_accum; + + // We no longer accumulate into ulisttot in this kernel. + // Instead, we have a separate kernel which avoids atomics. + // Running two separate kernels is net faster. + + // back up into shared memory for next iter + if (j != twojmax) buf2[jju_shared_idx] = u_accum; + + // copy left side to right side with inversion symmetry VMK 4.4(2) + // u[ma-j,mb-j] = (-1)^(ma-mb)*Conj([u[ma,mb)) + // We can avoid this if we're on the last row for an integer j + if (!(n_ma % 2 == 1 && (mb+1) == n_mb)) { + + int sign_factor = ((ma%2==0)?1:-1)*(mb%2==0?1:-1); + const int jjup_flip = jju+(j+1-mb)*(j+1)-(ma+1); + const int jju_shared_flip = max_m_tile*team_rank+(j+1-mb)*(j+1)-(ma+1); + + if (sign_factor == 1) { + u_accum.im = -u_accum.im; + } else { + u_accum.re = -u_accum.re; + } + ulist(jjup_flip,iatom,jnbor) = u_accum; + if (j != twojmax) buf2[jju_shared_flip] = u_accum; + } + }); + // In CUDA backend, + // ThreadVectorRange has a __syncwarp (appropriately masked for + // vector lengths < 32) implict at the end + + // swap double buffers + auto tmp = buf1; buf1 = buf2; buf2 = tmp; + //std::swap(buf1, buf2); // throws warnings + + } +} + +// CPU version +template +KOKKOS_INLINE_FUNCTION +void SNAKokkos::compute_uarray_cpu(const typename Kokkos::TeamPolicy::member_type& team, int iatom, int jnbor, + double x, double y, double z, + double z0, double r) { double r0inv; double a_r, b_r, a_i, b_i; @@ -670,8 +907,8 @@ void SNAKokkos::compute_uarray(const typename Kokkos::TeamPolicy::compute_uarray(const typename Kokkos::TeamPolicy::compute_uarray(const typename Kokkos::TeamPolicy::compute_uarray(const typename Kokkos::TeamPolicy -void SNAKokkos::transpose_ulisttot() -{ - UlisttotHelper::transpose(ulisttot_lr,ulisttot); -} - /* ---------------------------------------------------------------------- compute derivatives of Wigner U-functions for one neighbor see comments in compute_uarray() @@ -755,7 +986,150 @@ void SNAKokkos::compute_duarray(const typename Kokkos::TeamPolicy 0)?rootpq2*ulist_buf1[jjup_shared_idx-1]:SNAcomplex(0.,0.); + caconjxpy(b, u_up2, u_accum); + + // No need to save u_accum to global memory + if (j != twojmax) ulist_buf2[jju_shared_idx] = u_accum; + + // Next, spin up du_accum + const SNAcomplex du_up1 = (ma < j) ? rootpq1*dulist_buf1[jjup_shared_idx] : SNAcomplex(0.,0.); + caconjxpy(da, u_up1, du_accum); + caconjxpy(a, du_up1, du_accum); + + const SNAcomplex du_up2 = (ma > 0) ? rootpq2*dulist_buf1[jjup_shared_idx-1] : SNAcomplex(0.,0.); + caconjxpy(db, u_up2, du_accum); + caconjxpy(b, du_up2, du_accum); + + dulist(jju_index,iatom,jnbor,dir) = ((dsfac * u)*u_accum) + (sfac*du_accum); + + if (j != twojmax) dulist_buf2[jju_shared_idx] = du_accum; + + // copy left side to right side with inversion symmetry VMK 4.4(2) + // u[ma-j][mb-j] = (-1)^(ma-mb)*Conj([u[ma][mb]) + + int sign_factor = ((ma%2==0)?1:-1)*(mb%2==0?1:-1); + const int jjup_flip = jju+(j+1-mb)*(j+1)-(ma+1); + const int jju_shared_flip = max_m_tile*team_rank+(j+1-mb)*(j+1)-(ma+1); + + if (sign_factor == 1) { + //ulist_alt(iatom,jnbor,jjup_flip).re = u_accum.re; + //ulist_alt(iatom,jnbor,jjup_flip).im = -u_accum.im; + u_accum.im = -u_accum.im; + du_accum.im = -du_accum.im; + } else { + //ulist_alt(iatom,jnbor,jjup_flip).re = -u_accum.re; + //ulist_alt(iatom,jnbor,jjup_flip).im = u_accum.im; + u_accum.re = -u_accum.re; + du_accum.re = -du_accum.re; + } + + dulist(jjup_flip,iatom,jnbor,dir) = ((dsfac * u)*u_accum) + (sfac*du_accum); + + if (j != twojmax) { + ulist_buf2[jju_shared_flip] = u_accum; + dulist_buf2[jju_shared_flip] = du_accum; + } + + }); + + // swap buffers + auto tmp = ulist_buf1; ulist_buf1 = ulist_buf2; ulist_buf2 = tmp; + tmp = dulist_buf1; dulist_buf1 = dulist_buf2; dulist_buf2 = tmp; + } +} + +template +KOKKOS_INLINE_FUNCTION +void SNAKokkos::compute_duarray_cpu(const typename Kokkos::TeamPolicy::member_type& team, int iatom, int jnbor, + double x, double y, double z, + double z0, double r, double dz0dr, + double wj, double rcut) +{ +double r0inv; double a_r, a_i, b_r, b_i; double da_r[3], da_i[3], db_r[3], db_i[3]; double dz0[3], dr0inv[3], dr0invdr; @@ -772,7 +1146,7 @@ void SNAKokkos::compute_duarray(const typename Kokkos::TeamPolicy::compute_duarray(const typename Kokkos::TeamPolicy::compute_duarray(const typename Kokkos::TeamPolicy::compute_duarray(const typename Kokkos::TeamPolicy::compute_duarray(const typename Kokkos::TeamPolicy::compute_dsfac(double r, double rcut) return 0.0; } +/* ---------------------------------------------------------------------- */ + +// efficient complex FMA (i.e., y += a x) +template +KOKKOS_FORCEINLINE_FUNCTION +void SNAKokkos::caxpy(const SNAcomplex& a, const SNAcomplex& x, SNAcomplex& y) { + y.re += a.re * x.re; + y.re -= a.im * x.im; + y.im += a.im * x.re; + y.im += a.re * x.im; +} + +/* ---------------------------------------------------------------------- */ + +// efficient complex FMA, conjugate of scalar (i.e.) y += (a.re - i a.im) x) +template +KOKKOS_FORCEINLINE_FUNCTION +void SNAKokkos::caconjxpy(const SNAcomplex& a, const SNAcomplex& x, SNAcomplex& y) { + y.re += a.re * x.re; + y.re += a.im * x.im; + y.im -= a.im * x.re; + y.im += a.re * x.im; +} + +/* ---------------------------------------------------------------------- */ + +// set direction of batched Duidrj +template +KOKKOS_FORCEINLINE_FUNCTION +void SNAKokkos::set_dir(int dir_) { + dir = dir_; +} + /* ---------------------------------------------------------------------- memory usage of arrays ------------------------------------------------------------------------- */ diff --git a/src/MANYBODY/pair_adp.cpp b/src/MANYBODY/pair_adp.cpp index 64c778659c..e730466fcb 100644 --- a/src/MANYBODY/pair_adp.cpp +++ b/src/MANYBODY/pair_adp.cpp @@ -927,7 +927,7 @@ void PairADP::grab(FILE *fp, char *filename, int n, double *list) while (i < n) { utils::sfgets(FLERR,line,MAXLINE,fp,filename,error); ptr = strtok(line," \t\n\r\f"); - list[i++] = atof(ptr); + if (ptr) list[i++] = atof(ptr); while ((ptr = strtok(NULL," \t\n\r\f"))) list[i++] = atof(ptr); } } diff --git a/src/MANYBODY/pair_eam.cpp b/src/MANYBODY/pair_eam.cpp index d1b864d9e4..a1bc6e1eb4 100644 --- a/src/MANYBODY/pair_eam.cpp +++ b/src/MANYBODY/pair_eam.cpp @@ -797,7 +797,7 @@ void PairEAM::grab(FILE *fptr, int n, double *list) while (i < n) { utils::sfgets(FLERR,line,MAXLINE,fptr,NULL,error); ptr = strtok(line," \t\n\r\f"); - list[i++] = atof(ptr); + if (ptr) list[i++] = atof(ptr); while ((ptr = strtok(NULL," \t\n\r\f"))) list[i++] = atof(ptr); } } diff --git a/src/Makefile b/src/Makefile index 5ca583aa11..bce5089500 100644 --- a/src/Makefile +++ b/src/Makefile @@ -60,10 +60,10 @@ PACKAGE = asphere body class2 colloid compress coreshell dipole gpu \ PACKUSER = user-adios user-atc user-awpmd user-bocs user-cgdna user-cgsdk user-colvars \ user-diffraction user-dpd user-drude user-eff user-fep user-h5md \ - user-intel user-lb user-manifold user-meamc user-meso \ + user-intel user-lb user-manifold user-meamc user-mesodpd \ user-mgpt user-misc user-mofff user-molfile \ user-netcdf user-omp user-phonon user-plumed user-ptm user-qmmm \ - user-qtb user-quip user-reaxc user-scafacos user-smd user-smtbq \ + user-qtb user-quip user-reaction user-reaxc user-scafacos user-smd user-smtbq \ user-sdpd user-sph user-tally user-uef user-vtk user-yaff PACKLIB = compress gpu kim kokkos latte message mpiio mscg poems \ diff --git a/src/USER-MESO/README b/src/USER-MESODPD/README similarity index 100% rename from src/USER-MESO/README rename to src/USER-MESODPD/README diff --git a/src/USER-MESO/atom_vec_edpd.cpp b/src/USER-MESODPD/atom_vec_edpd.cpp similarity index 100% rename from src/USER-MESO/atom_vec_edpd.cpp rename to src/USER-MESODPD/atom_vec_edpd.cpp diff --git a/src/USER-MESO/atom_vec_edpd.h b/src/USER-MESODPD/atom_vec_edpd.h similarity index 100% rename from src/USER-MESO/atom_vec_edpd.h rename to src/USER-MESODPD/atom_vec_edpd.h diff --git a/src/USER-MESO/atom_vec_mdpd.cpp b/src/USER-MESODPD/atom_vec_mdpd.cpp similarity index 100% rename from src/USER-MESO/atom_vec_mdpd.cpp rename to src/USER-MESODPD/atom_vec_mdpd.cpp diff --git a/src/USER-MESO/atom_vec_mdpd.h b/src/USER-MESODPD/atom_vec_mdpd.h similarity index 100% rename from src/USER-MESO/atom_vec_mdpd.h rename to src/USER-MESODPD/atom_vec_mdpd.h diff --git a/src/USER-MESO/atom_vec_tdpd.cpp b/src/USER-MESODPD/atom_vec_tdpd.cpp similarity index 100% rename from src/USER-MESO/atom_vec_tdpd.cpp rename to src/USER-MESODPD/atom_vec_tdpd.cpp diff --git a/src/USER-MESO/atom_vec_tdpd.h b/src/USER-MESODPD/atom_vec_tdpd.h similarity index 100% rename from src/USER-MESO/atom_vec_tdpd.h rename to src/USER-MESODPD/atom_vec_tdpd.h diff --git a/src/USER-MESO/compute_edpd_temp_atom.cpp b/src/USER-MESODPD/compute_edpd_temp_atom.cpp similarity index 100% rename from src/USER-MESO/compute_edpd_temp_atom.cpp rename to src/USER-MESODPD/compute_edpd_temp_atom.cpp diff --git a/src/USER-MESO/compute_edpd_temp_atom.h b/src/USER-MESODPD/compute_edpd_temp_atom.h similarity index 100% rename from src/USER-MESO/compute_edpd_temp_atom.h rename to src/USER-MESODPD/compute_edpd_temp_atom.h diff --git a/src/USER-MESO/compute_tdpd_cc_atom.cpp b/src/USER-MESODPD/compute_tdpd_cc_atom.cpp similarity index 100% rename from src/USER-MESO/compute_tdpd_cc_atom.cpp rename to src/USER-MESODPD/compute_tdpd_cc_atom.cpp diff --git a/src/USER-MESO/compute_tdpd_cc_atom.h b/src/USER-MESODPD/compute_tdpd_cc_atom.h similarity index 100% rename from src/USER-MESO/compute_tdpd_cc_atom.h rename to src/USER-MESODPD/compute_tdpd_cc_atom.h diff --git a/src/USER-MESO/fix_edpd_source.cpp b/src/USER-MESODPD/fix_edpd_source.cpp similarity index 100% rename from src/USER-MESO/fix_edpd_source.cpp rename to src/USER-MESODPD/fix_edpd_source.cpp diff --git a/src/USER-MESO/fix_edpd_source.h b/src/USER-MESODPD/fix_edpd_source.h similarity index 100% rename from src/USER-MESO/fix_edpd_source.h rename to src/USER-MESODPD/fix_edpd_source.h diff --git a/src/USER-MESO/fix_mvv_dpd.cpp b/src/USER-MESODPD/fix_mvv_dpd.cpp similarity index 100% rename from src/USER-MESO/fix_mvv_dpd.cpp rename to src/USER-MESODPD/fix_mvv_dpd.cpp diff --git a/src/USER-MESO/fix_mvv_dpd.h b/src/USER-MESODPD/fix_mvv_dpd.h similarity index 100% rename from src/USER-MESO/fix_mvv_dpd.h rename to src/USER-MESODPD/fix_mvv_dpd.h diff --git a/src/USER-MESO/fix_mvv_edpd.cpp b/src/USER-MESODPD/fix_mvv_edpd.cpp similarity index 100% rename from src/USER-MESO/fix_mvv_edpd.cpp rename to src/USER-MESODPD/fix_mvv_edpd.cpp diff --git a/src/USER-MESO/fix_mvv_edpd.h b/src/USER-MESODPD/fix_mvv_edpd.h similarity index 100% rename from src/USER-MESO/fix_mvv_edpd.h rename to src/USER-MESODPD/fix_mvv_edpd.h diff --git a/src/USER-MESO/fix_mvv_tdpd.cpp b/src/USER-MESODPD/fix_mvv_tdpd.cpp similarity index 100% rename from src/USER-MESO/fix_mvv_tdpd.cpp rename to src/USER-MESODPD/fix_mvv_tdpd.cpp diff --git a/src/USER-MESO/fix_mvv_tdpd.h b/src/USER-MESODPD/fix_mvv_tdpd.h similarity index 100% rename from src/USER-MESO/fix_mvv_tdpd.h rename to src/USER-MESODPD/fix_mvv_tdpd.h diff --git a/src/USER-MESO/fix_tdpd_source.cpp b/src/USER-MESODPD/fix_tdpd_source.cpp similarity index 100% rename from src/USER-MESO/fix_tdpd_source.cpp rename to src/USER-MESODPD/fix_tdpd_source.cpp diff --git a/src/USER-MESO/fix_tdpd_source.h b/src/USER-MESODPD/fix_tdpd_source.h similarity index 100% rename from src/USER-MESO/fix_tdpd_source.h rename to src/USER-MESODPD/fix_tdpd_source.h diff --git a/src/USER-MESO/pair_edpd.cpp b/src/USER-MESODPD/pair_edpd.cpp similarity index 100% rename from src/USER-MESO/pair_edpd.cpp rename to src/USER-MESODPD/pair_edpd.cpp diff --git a/src/USER-MESO/pair_edpd.h b/src/USER-MESODPD/pair_edpd.h similarity index 100% rename from src/USER-MESO/pair_edpd.h rename to src/USER-MESODPD/pair_edpd.h diff --git a/src/USER-MESO/pair_mdpd.cpp b/src/USER-MESODPD/pair_mdpd.cpp similarity index 100% rename from src/USER-MESO/pair_mdpd.cpp rename to src/USER-MESODPD/pair_mdpd.cpp diff --git a/src/USER-MESO/pair_mdpd.h b/src/USER-MESODPD/pair_mdpd.h similarity index 100% rename from src/USER-MESO/pair_mdpd.h rename to src/USER-MESODPD/pair_mdpd.h diff --git a/src/USER-MESO/pair_mdpd_rhosum.cpp b/src/USER-MESODPD/pair_mdpd_rhosum.cpp similarity index 100% rename from src/USER-MESO/pair_mdpd_rhosum.cpp rename to src/USER-MESODPD/pair_mdpd_rhosum.cpp diff --git a/src/USER-MESO/pair_mdpd_rhosum.h b/src/USER-MESODPD/pair_mdpd_rhosum.h similarity index 100% rename from src/USER-MESO/pair_mdpd_rhosum.h rename to src/USER-MESODPD/pair_mdpd_rhosum.h diff --git a/src/USER-MESO/pair_tdpd.cpp b/src/USER-MESODPD/pair_tdpd.cpp similarity index 100% rename from src/USER-MESO/pair_tdpd.cpp rename to src/USER-MESODPD/pair_tdpd.cpp diff --git a/src/USER-MESO/pair_tdpd.h b/src/USER-MESODPD/pair_tdpd.h similarity index 100% rename from src/USER-MESO/pair_tdpd.h rename to src/USER-MESODPD/pair_tdpd.h diff --git a/src/USER-MISC/README b/src/USER-MISC/README index 9fdc18fbe5..6f16912d9c 100644 --- a/src/USER-MISC/README +++ b/src/USER-MISC/README @@ -48,7 +48,6 @@ dihedral_style table, Andrew Jewett, jewett.aij@gmail.com, 10 Jan 12 dihedral_style table/cut, Mike Salerno, ksalerno@pha.jhu.edu, 11 May 18 fix addtorque, Laurent Joly (U Lyon), ljoly.ulyon at gmail.com, 8 Aug 11 fix ave/correlate/long, Jorge Ramirez (UPM Madrid), jorge.ramirez at upm.es, 21 Oct 2015 -fix bond/react, Jacob Gissinger (CU Boulder), info at disarmmd.org, 24 Feb 2018 fix electron/stopping, Konstantin Avchaciov, k.avchachov at gmail.com, 26 Feb 2019 fix ffl, David Wilkins (EPFL Lausanne), david.wilkins @ epfl.ch, 28 Sep 2018 fix filter/corotate, Lukas Fath (KIT), lukas.fath at kit.edu, 15 Mar 2017 diff --git a/src/USER-REACTION/README b/src/USER-REACTION/README new file mode 100644 index 0000000000..f099ace103 --- /dev/null +++ b/src/USER-REACTION/README @@ -0,0 +1,23 @@ +This package implements the DisARMMD protocol (disarmmd.org) as +"fix bond/react." This fix allows for complex topology changes +during a running MD simulation, when using classical force fields. +Topology changes are defined in pre- and post-reaction molecule +templates and can include creation and deletion of bonds, angles, +dihedrals, impropers, atom types, bond types, angle types, +dihedral types, improper types, and/or atomic charges. + +The DisARMMD protocol is a method for modeling chemical reactions in +classical molecular dynamics simulations. It was developed to build +physically-realistic initial configurations for amorphous or +crosslinked materials. Any number of competing or reversible reaction +pathways can be specified, and reacting sites can be stabilized. Other +advanced options currently available include reaction constraints +(e.g. angle and Arrhenius constraints), deletion of reaction +byproducts or other small molecules, and chiral-sensitive reactions. + +The DisARMMD methodology is detailed in: + Gissinger et al., Polymer 128, 211-217 (2017) + https://doi.org/10.1016/j.polymer.2017.09.038 + +This package was created by Jacob Gissinger (info@disarmmd.org), +while at the NASA Langley Research Center. diff --git a/src/USER-MISC/fix_bond_react.cpp b/src/USER-REACTION/fix_bond_react.cpp similarity index 97% rename from src/USER-MISC/fix_bond_react.cpp rename to src/USER-REACTION/fix_bond_react.cpp index b14139afff..b2bb66b288 100644 --- a/src/USER-MISC/fix_bond_react.cpp +++ b/src/USER-REACTION/fix_bond_react.cpp @@ -60,7 +60,7 @@ static const char cite_fix_bond_react[] = #define BIG 1.0e20 #define DELTA 16 #define MAXGUESS 20 // max # of guesses allowed by superimpose algorithm -#define MAXCONARGS 7 // max # of arguments for any type of constraint + rxnID +#define MAXCONARGS 10 // max # of arguments for any type of constraint + rxnID // various statuses of superimpose algorithm: // ACCEPT: site successfully matched to pre-reacted template @@ -72,7 +72,7 @@ static const char cite_fix_bond_react[] = enum{ACCEPT,REJECT,PROCEED,CONTINUE,GUESSFAIL,RESTORE}; // types of available reaction constraints -enum{DISTANCE,ANGLE,ARRHENIUS}; +enum{DISTANCE,ANGLE,DIHEDRAL,ARRHENIUS}; /* ---------------------------------------------------------------------- */ @@ -1654,10 +1654,15 @@ evaluate constraints: return 0 if any aren't satisfied int FixBondReact::check_constraints() { - tagint atom1,atom2,atom3; + tagint atom1,atom2,atom3,atom4; double delx,dely,delz,rsq; double delx1,dely1,delz1,delx2,dely2,delz2; double rsq1,rsq2,r1,r2,c,t,prrhob; + // for computation of dihedrals + double vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z,vb2xm,vb2ym,vb2zm; + double ax,ay,az,bx,by,bz,rasq,rbsq,rgsq,rg,ra2inv,rb2inv,rabinv; + double s,phi; + int ANDgate; double **x = atom->x; @@ -1699,6 +1704,69 @@ int FixBondReact::check_constraints() if (c > 1.0) c = 1.0; if (c < -1.0) c = -1.0; if (acos(c) < constraints[i][5] || acos(c) > constraints[i][6]) return 0; + } else if (constraints[i][1] == DIHEDRAL) { + // phi calculation from dihedral style harmonic + atom1 = atom->map(glove[(int) constraints[i][2]-1][1]); + atom2 = atom->map(glove[(int) constraints[i][3]-1][1]); + atom3 = atom->map(glove[(int) constraints[i][4]-1][1]); + atom4 = atom->map(glove[(int) constraints[i][5]-1][1]); + + vb1x = x[atom1][0] - x[atom2][0]; + vb1y = x[atom1][1] - x[atom2][1]; + vb1z = x[atom1][2] - x[atom2][2]; + domain->minimum_image(vb1x,vb1y,vb1z); + + vb2x = x[atom3][0] - x[atom2][0]; + vb2y = x[atom3][1] - x[atom2][1]; + vb2z = x[atom3][2] - x[atom2][2]; + domain->minimum_image(vb2x,vb2y,vb2z); + + vb2xm = -vb2x; + vb2ym = -vb2y; + vb2zm = -vb2z; + domain->minimum_image(vb2xm,vb2ym,vb2zm); + + vb3x = x[atom4][0] - x[atom3][0]; + vb3y = x[atom4][1] - x[atom3][1]; + vb3z = x[atom4][2] - x[atom3][2]; + domain->minimum_image(vb3x,vb3y,vb3z); + + ax = vb1y*vb2zm - vb1z*vb2ym; + ay = vb1z*vb2xm - vb1x*vb2zm; + az = vb1x*vb2ym - vb1y*vb2xm; + bx = vb3y*vb2zm - vb3z*vb2ym; + by = vb3z*vb2xm - vb3x*vb2zm; + bz = vb3x*vb2ym - vb3y*vb2xm; + + rasq = ax*ax + ay*ay + az*az; + rbsq = bx*bx + by*by + bz*bz; + rgsq = vb2xm*vb2xm + vb2ym*vb2ym + vb2zm*vb2zm; + rg = sqrt(rgsq); + + ra2inv = rb2inv = 0.0; + if (rasq > 0) ra2inv = 1.0/rasq; + if (rbsq > 0) rb2inv = 1.0/rbsq; + rabinv = sqrt(ra2inv*rb2inv); + + c = (ax*bx + ay*by + az*bz)*rabinv; + s = rg*rabinv*(ax*vb3x + ay*vb3y + az*vb3z); + + if (c > 1.0) c = 1.0; + if (c < -1.0) c = -1.0; + phi = atan2(s,c); + + ANDgate = 0; + if (constraints[i][6] < constraints[i][7]) { + if (phi > constraints[i][6] && phi < constraints[i][7]) ANDgate = 1; + } else { + if (phi > constraints[i][6] || phi < constraints[i][7]) ANDgate = 1; + } + if (constraints[i][8] < constraints[i][9]) { + if (phi > constraints[i][8] && phi < constraints[i][9]) ANDgate = 1; + } else { + if (phi > constraints[i][8] || phi < constraints[i][9]) ANDgate = 1; + } + if (ANDgate != 1) return 0; } else if (constraints[i][1] == ARRHENIUS) { t = get_temperature(); prrhob = constraints[i][3]*pow(t,constraints[i][4])* @@ -3110,6 +3178,23 @@ void FixBondReact::Constraints(char *line, int myrxn) constraints[nconstraints][4] = tmp[2]; constraints[nconstraints][5] = tmp[3]/180.0 * MY_PI; constraints[nconstraints][6] = tmp[4]/180.0 * MY_PI; + } else if (strcmp(constraint_type,"dihedral") == 0) { + constraints[nconstraints][1] = DIHEDRAL; + tmp[6] = 181.0; // impossible range + tmp[7] = 182.0; + sscanf(line,"%*s %lg %lg %lg %lg %lg %lg %lg %lg",&tmp[0],&tmp[1], + &tmp[2],&tmp[3],&tmp[4],&tmp[5],&tmp[6],&tmp[7]); + if (tmp[0] > onemol->natoms || tmp[1] > onemol->natoms || + tmp[2] > onemol->natoms || tmp[3] > onemol->natoms) + error->one(FLERR,"Bond/react: Invalid template atom ID in map file"); + constraints[nconstraints][2] = tmp[0]; + constraints[nconstraints][3] = tmp[1]; + constraints[nconstraints][4] = tmp[2]; + constraints[nconstraints][5] = tmp[3]; + constraints[nconstraints][6] = tmp[4]/180.0 * MY_PI; + constraints[nconstraints][7] = tmp[5]/180.0 * MY_PI; + constraints[nconstraints][8] = tmp[6]/180.0 * MY_PI; + constraints[nconstraints][9] = tmp[7]/180.0 * MY_PI; } else if (strcmp(constraint_type,"arrhenius") == 0) { constraints[nconstraints][1] = ARRHENIUS; constraints[nconstraints][2] = narrhenius++; diff --git a/src/USER-MISC/fix_bond_react.h b/src/USER-REACTION/fix_bond_react.h similarity index 94% rename from src/USER-MISC/fix_bond_react.h rename to src/USER-REACTION/fix_bond_react.h index 1dba13283b..84cb9401f8 100644 --- a/src/USER-MISC/fix_bond_react.h +++ b/src/USER-REACTION/fix_bond_react.h @@ -239,18 +239,17 @@ Atom IDs in molecule templates range from 1 to the number of atoms in the templa E or W: Bond/react: Atom affected by reaction %s too close to template edge This means an atom which changes type or connectivity during the -reaction is too close to an 'edge' atom defined in the superimpose -file. This could cause incorrect assignment of bonds, angle, etc. -Generally, this means you must include more atoms in your templates, -such that there are at least two atoms between each atom involved in -the reaction and an edge atom. +reaction is too close to an 'edge' atom defined in the map file. This +could cause incorrect assignment of bonds, angle, etc. Generally, this +means you must include more atoms in your templates, such that there +are at least two atoms between each atom involved in the reaction and +an edge atom. E: Bond/react: Fix bond/react needs ghost atoms from farther away -This is because a processor needs to superimpose the entire unreacted -molecule template onto simulation atoms it knows about. The -comm_modify cutoff command can be used to extend the communication -range. +This is because a processor needs to map the entire unreacted molecule +template onto simulation atoms it knows about. The comm_modify cutoff +command can be used to extend the communication range. E: Bond/react: A deleted atom cannot remain bonded to an atom that is not deleted diff --git a/src/min_fire.cpp b/src/min_fire.cpp index 4aeeddf6b2..0b0a9d801b 100644 --- a/src/min_fire.cpp +++ b/src/min_fire.cpp @@ -87,6 +87,7 @@ void MinFire::setup_style() for (int i = 0; i < nlocal; i++) v[i][0] = v[i][1] = v[i][2] = 0.0; + flagv0 = 1; } /* ---------------------------------------------------------------------- @@ -259,14 +260,40 @@ int MinFire::iterate(int maxiter) if (halfstepback_flag) { for (int i = 0; i < nlocal; i++) { - x[i][0] -= 0.5 * dtv * v[i][0]; - x[i][1] -= 0.5 * dtv * v[i][1]; - x[i][2] -= 0.5 * dtv * v[i][2]; + x[i][0] -= 0.5 * dt * v[i][0]; + x[i][1] -= 0.5 * dt * v[i][1]; + x[i][2] -= 0.5 * dt * v[i][2]; } } for (int i = 0; i < nlocal; i++) v[i][0] = v[i][1] = v[i][2] = 0.0; + flagv0 = 1; + } + + // evaluates velocties to estimate wether dtv has to be limited + // required when v have been reset + + if (flagv0) { + dtf = dt * force->ftm2v; + energy_force(0); + neval++; + + if (rmass) { + for (int i = 0; i < nlocal; i++) { + dtfm = dtf / rmass[i]; + v[i][0] = dtfm * f[i][0]; + v[i][1] = dtfm * f[i][1]; + v[i][2] = dtfm * f[i][2]; + } + } else { + for (int i = 0; i < nlocal; i++) { + dtfm = dtf / mass[type[i]]; + v[i][0] = dtfm * f[i][0]; + v[i][1] = dtfm * f[i][1]; + v[i][2] = dtfm * f[i][2]; + } + } } // limit timestep so no particle moves further than dmax @@ -281,6 +308,13 @@ int MinFire::iterate(int maxiter) MPI_Allreduce(&dtvone,&dtv,1,MPI_DOUBLE,MPI_MIN,world); + // reset velocities when necessary + + if (flagv0) { + for (int i = 0; i < nlocal; i++) + v[i][0] = v[i][1] = v[i][2] = 0.0; + } + // min dtv over replicas, if necessary // this communicator would be invalid for multiprocess replicas @@ -438,6 +472,10 @@ int MinFire::iterate(int maxiter) neval++; } + // velocities have been evaluated + + flagv0 = 0; + // energy tolerance criterion // only check after delaystep elapsed since velocties reset to 0 // sync across replicas if running multi-replica minimization diff --git a/src/min_fire.h b/src/min_fire.h index 0c4be968dc..79e5cb7c14 100644 --- a/src/min_fire.h +++ b/src/min_fire.h @@ -37,7 +37,7 @@ class MinFire : public Min { double dt,dtmax,dtmin; double alpha; bigint last_negative,ntimestep_start; - int vdotf_negatif; + int vdotf_negatif,flagv0; }; }