diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index 24522b6480..c96f5576a5 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -266,6 +266,7 @@ set(STANDARD_PACKAGES ML-QUIP ML-RANN ML-SNAP + ML-POD MOFFF MOLECULE MOLFILE @@ -432,7 +433,7 @@ if(BUILD_OMP) target_link_libraries(lmp PRIVATE OpenMP::OpenMP_CXX) endif() -if(PKG_MSCG OR PKG_ATC OR PKG_AWPMD OR PKG_ML-QUIP OR PKG_LATTE OR PKG_ELECTRODE) +if(PKG_MSCG OR PKG_ATC OR PKG_AWPMD OR PKG_ML-QUIP OR PKG_ML-POD OR PKG_LATTE OR PKG_ELECTRODE) enable_language(C) if (NOT USE_INTERNAL_LINALG) find_package(LAPACK) @@ -638,7 +639,7 @@ foreach(PKG_LIB POEMS ATC AWPMD H5MD MESONT) endif() endforeach() -if(PKG_ELECTRODE) +if(PKG_ELECTRODE OR PKG_ML-POD) target_link_libraries(lammps PRIVATE ${LAPACK_LIBRARIES}) endif() diff --git a/cmake/presets/all_off.cmake b/cmake/presets/all_off.cmake index 3a7c58eaa3..9127305528 100644 --- a/cmake/presets/all_off.cmake +++ b/cmake/presets/all_off.cmake @@ -56,6 +56,7 @@ set(ALL_PACKAGES ML-HDNNP ML-IAP ML-PACE + ML-POD ML-QUIP ML-RANN ML-SNAP diff --git a/cmake/presets/all_on.cmake b/cmake/presets/all_on.cmake index 8229baf652..0a001bdc56 100644 --- a/cmake/presets/all_on.cmake +++ b/cmake/presets/all_on.cmake @@ -58,6 +58,7 @@ set(ALL_PACKAGES ML-HDNNP ML-IAP ML-PACE + ML-POD ML-QUIP ML-RANN ML-SNAP diff --git a/cmake/presets/mingw-cross.cmake b/cmake/presets/mingw-cross.cmake index c5d9a7bb89..2d74657394 100644 --- a/cmake/presets/mingw-cross.cmake +++ b/cmake/presets/mingw-cross.cmake @@ -47,6 +47,7 @@ set(WIN_PACKAGES MISC ML-HDNNP ML-IAP + ML-POD ML-RANN ML-SNAP MOFFF diff --git a/cmake/presets/most.cmake b/cmake/presets/most.cmake index 4b26a51e23..5dd9a2b78b 100644 --- a/cmake/presets/most.cmake +++ b/cmake/presets/most.cmake @@ -41,6 +41,7 @@ set(ALL_PACKAGES MEAM MISC ML-IAP + ML-POD ML-SNAP MOFFF MOLECULE diff --git a/doc/src/Build_extras.rst b/doc/src/Build_extras.rst index 8a5eeaa485..a3ceb1df4f 100644 --- a/doc/src/Build_extras.rst +++ b/doc/src/Build_extras.rst @@ -48,6 +48,7 @@ This is the list of packages that may require additional steps. * :ref:`ML-HDNNP ` * :ref:`ML-IAP ` * :ref:`ML-PACE ` + * :ref:`ML-POD ` * :ref:`ML-QUIP ` * :ref:`MOLFILE ` * :ref:`MSCG ` @@ -1411,6 +1412,49 @@ at: `https://github.com/ICAMS/lammps-user-pace/ ` * :doc:`hyper ` * :doc:`kim ` + * :doc:`fitpod ` * :doc:`mdi ` * :doc:`ndx2group ` * :doc:`neb ` diff --git a/doc/src/Commands_fix.rst b/doc/src/Commands_fix.rst index b9030e66f6..eece01cb9e 100644 --- a/doc/src/Commands_fix.rst +++ b/doc/src/Commands_fix.rst @@ -70,9 +70,9 @@ OPT. * :doc:`edpd/source ` * :doc:`efield ` * :doc:`ehex ` - * :doc:`electrode/conp (i) ` - * :doc:`electrode/conq (i) ` - * :doc:`electrode/thermo (i) ` + * :doc:`electrode/conp (i) ` + * :doc:`electrode/conq (i) ` + * :doc:`electrode/thermo (i) ` * :doc:`electron/stopping ` * :doc:`electron/stopping/fit ` * :doc:`enforce2d (k) ` diff --git a/doc/src/Commands_pair.rst b/doc/src/Commands_pair.rst index 23930f3f04..3f5deef24a 100644 --- a/doc/src/Commands_pair.rst +++ b/doc/src/Commands_pair.rst @@ -237,6 +237,7 @@ OPT. * :doc:`oxrna2/coaxstk ` * :doc:`pace (k) ` * :doc:`pace/extrapolation ` + * :doc:`pod ` * :doc:`peri/eps ` * :doc:`peri/lps (o) ` * :doc:`peri/pmb (o) ` diff --git a/doc/src/Developer_code_design.rst b/doc/src/Developer_code_design.rst index a5c879de82..786bd51c26 100644 --- a/doc/src/Developer_code_design.rst +++ b/doc/src/Developer_code_design.rst @@ -50,7 +50,7 @@ parallel each MPI process creates such an instance. This can be seen in the ``main.cpp`` file where the core steps of running a LAMMPS simulation are the following 3 lines of code: -.. code-block:: C++ +.. code-block:: c++ LAMMPS *lammps = new LAMMPS(argc, argv, lammps_comm); lammps->input->file(); @@ -232,7 +232,7 @@ macro ``PairStyle()`` will associate the style name "lj/cut" with a factory function creating an instance of the ``PairLJCut`` class. -.. code-block:: C++ +.. code-block:: c++ // from force.h typedef Pair *(*PairCreator)(LAMMPS *); @@ -360,7 +360,7 @@ characters; "{:<8}" would do this as left aligned, "{:^8}" as centered, argument type must be compatible or else the {fmt} formatting code will throw an exception. Some format string examples are given below: -.. code-block:: C +.. code-block:: c++ auto mesg = fmt::format(" CPU time: {:4d}:{:02d}:{:02d}\n", cpuh, cpum, cpus); mesg = fmt::format("{:<8s}| {:<10.5g} | {:<10.5g} | {:<10.5g} |{:6.1f} |{:6.2f}\n", diff --git a/doc/src/Developer_notes.rst b/doc/src/Developer_notes.rst index 2b3375265f..a781737d6f 100644 --- a/doc/src/Developer_notes.rst +++ b/doc/src/Developer_notes.rst @@ -105,7 +105,7 @@ list, where each pair of atoms is listed only once (except when the pairs straddling sub-domains or periodic boundaries will be listed twice). Thus these are the default settings when a neighbor list request is created in: -.. code-block:: C++ +.. code-block:: c++ void Pair::init_style() { @@ -129,7 +129,7 @@ neighbor list request to the specific needs of a style an additional request flag is needed. The :doc:`tersoff ` pair style, for example, needs a "full" neighbor list: -.. code-block:: C++ +.. code-block:: c++ void PairTersoff::init_style() { @@ -141,7 +141,7 @@ When a pair style supports r-RESPA time integration with different cutoff region the request flag may depend on the corresponding r-RESPA settings. Here an example from pair style lj/cut: -.. code-block:: C++ +.. code-block:: c++ void PairLJCut::init_style() { @@ -160,7 +160,7 @@ Granular pair styles need neighbor lists based on particle sizes and not cutoff and also may require to have the list of previous neighbors available ("history"). For example with: -.. code-block:: C++ +.. code-block:: c++ if (use_history) neighbor->add_request(this, NeighConst::REQ_SIZE | NeighConst::REQ_HISTORY); else neighbor->add_request(this, NeighConst::REQ_SIZE); @@ -170,7 +170,7 @@ settings each request can set an id which is then used in the corresponding ``init_list()`` function to assign it to the suitable pointer variable. This is done for example by the :doc:`pair style meam `: -.. code-block:: C++ +.. code-block:: c++ void PairMEAM::init_style() { @@ -189,7 +189,7 @@ just once) and this can also be indicated by a flag. As an example here is the request from the ``FixPeriNeigh`` class which is created internally by :doc:`Peridynamics pair styles `: -.. code-block:: C++ +.. code-block:: c++ neighbor->add_request(this, NeighConst::REQ_FULL | NeighConst::REQ_OCCASIONAL); @@ -198,7 +198,7 @@ than what is usually inferred from the pair style settings (largest cutoff of all pair styles plus neighbor list skin). The following is used in the :doc:`compute rdf ` command implementation: -.. code-block:: C++ +.. code-block:: c++ if (cutflag) neighbor->add_request(this, NeighConst::REQ_OCCASIONAL)->set_cutoff(mycutneigh); @@ -212,7 +212,7 @@ for printing the neighbor list summary the name of the requesting command should be set. Below is the request from the :doc:`delete atoms ` command: -.. code-block:: C++ +.. code-block:: c++ neighbor->add_request(this, "delete_atoms", NeighConst::REQ_FULL); diff --git a/doc/src/Developer_plugins.rst b/doc/src/Developer_plugins.rst index 36fdd010b3..dd5431507e 100644 --- a/doc/src/Developer_plugins.rst +++ b/doc/src/Developer_plugins.rst @@ -95,7 +95,7 @@ a class ``PairMorse2`` in the files ``pair_morse2.h`` and ``pair_morse2.cpp`` with the factory function and initialization function would look like this: -.. code-block:: C++ +.. code-block:: c++ #include "lammpsplugin.h" #include "version.h" @@ -141,7 +141,7 @@ list of argument strings), then the pointer type is ``lammpsplugin_factory2`` and it must be assigned to the *creator.v2* member of the plugin struct. Below is an example for that: -.. code-block:: C++ +.. code-block:: c++ #include "lammpsplugin.h" #include "version.h" @@ -176,7 +176,7 @@ demonstrated in the following example, which also shows that the implementation of the plugin class may be within the same source file as the plugin interface code: -.. code-block:: C++ +.. code-block:: c++ #include "lammpsplugin.h" diff --git a/doc/src/Developer_unittest.rst b/doc/src/Developer_unittest.rst index aff6128e9c..69e29263a6 100644 --- a/doc/src/Developer_unittest.rst +++ b/doc/src/Developer_unittest.rst @@ -194,7 +194,7 @@ macro. These tests operate by capturing the screen output when executing the failing command and then comparing that with a provided regular expression string pattern. Example: -.. code-block:: C++ +.. code-block:: c++ TEST_F(SimpleCommandsTest, UnknownCommand) { @@ -249,7 +249,7 @@ MPI support. These include tests where LAMMPS is run in multi-partition mode or only on a subset of the MPI world communicator. The CMake script code for adding this kind of test looks like this: -.. code-block:: CMake +.. code-block:: cmake if (BUILD_MPI) add_executable(test_library_mpi test_library_mpi.cpp) diff --git a/doc/src/Developer_updating.rst b/doc/src/Developer_updating.rst index 90a138d2cf..c02d6763de 100644 --- a/doc/src/Developer_updating.rst +++ b/doc/src/Developer_updating.rst @@ -61,7 +61,7 @@ header file needs to be updated accordingly. Old: -.. code-block:: C++ +.. code-block:: c++ int PairEAM::pack_comm(int n, int *list, double *buf, int pbc_flag, int *pbc) { @@ -75,7 +75,7 @@ Old: New: -.. code-block:: C++ +.. code-block:: c++ int PairEAM::pack_forward_comm(int n, int *list, double *buf, int pbc_flag, int *pbc) { @@ -112,14 +112,14 @@ Example from a pair style: Old: -.. code-block:: C++ +.. code-block:: c++ if (eflag || vflag) ev_setup(eflag, vflag); else evflag = vflag_fdotr = eflag_global = eflag_atom = 0; New: -.. code-block:: C++ +.. code-block:: c++ ev_init(eflag, vflag); @@ -142,14 +142,14 @@ when they are called from only one or a subset of the MPI processes. Old: -.. code-block:: C++ +.. code-block:: c++ val = force->numeric(FLERR, arg[1]); num = force->inumeric(FLERR, arg[2]); New: -.. code-block:: C++ +.. code-block:: c++ val = utils::numeric(FLERR, true, arg[1], lmp); num = utils::inumeric(FLERR, false, arg[2], lmp); @@ -183,14 +183,14 @@ copy them around for simulations. Old: -.. code-block:: C++ +.. code-block:: c++ fp = force->open_potential(filename); fp = fopen(filename, "r"); New: -.. code-block:: C++ +.. code-block:: c++ fp = utils::open_potential(filename, lmp); @@ -207,7 +207,7 @@ Example: Old: -.. code-block:: C++ +.. code-block:: c++ if (fptr == NULL) { char str[128]; @@ -217,7 +217,7 @@ Old: New: -.. code-block:: C++ +.. code-block:: c++ if (fptr == nullptr) error->one(FLERR, "Cannot open AEAM potential file {}: {}", filename, utils::getsyserror()); @@ -237,7 +237,7 @@ an example from the ``FixWallReflect`` class: Old: -.. code-block:: C++ +.. code-block:: c++ FixWallReflect(class LAMMPS *, int, char **); virtual ~FixWallReflect(); @@ -247,7 +247,7 @@ Old: New: -.. code-block:: C++ +.. code-block:: c++ FixWallReflect(class LAMMPS *, int, char **); ~FixWallReflect() override; @@ -271,7 +271,7 @@ the type of the "this" pointer argument. Old: -.. code-block:: C++ +.. code-block:: c++ comm->forward_comm_pair(this); comm->forward_comm_fix(this); @@ -284,7 +284,7 @@ Old: New: -.. code-block:: C++ +.. code-block:: c++ comm->forward_comm(this); comm->reverse_comm(this); @@ -304,7 +304,7 @@ requests can be :doc:`found here `. Example from the Old: -.. code-block:: C++ +.. code-block:: c++ int irequest = neighbor->request(this,instance_me); neighbor->requests[irequest]->pair = 0; @@ -317,7 +317,7 @@ Old: New: -.. code-block:: C++ +.. code-block:: c++ auto req = neighbor->add_request(this, NeighConst::REQ_OCCASIONAL); if (cutflag) req->set_cutoff(mycutneigh); @@ -340,7 +340,7 @@ these are internal fixes, there is no user visible change. Old: -.. code-block:: C++ +.. code-block:: c++ #include "fix_store.h" @@ -351,7 +351,7 @@ Old: New: -.. code-block:: C++ +.. code-block:: c++ #include "fix_store_peratom.h" @@ -362,7 +362,7 @@ New: Old: -.. code-block:: C++ +.. code-block:: c++ #include "fix_store.h" @@ -373,7 +373,7 @@ Old: New: -.. code-block:: C++ +.. code-block:: c++ #include "fix_store_global.h" @@ -396,7 +396,7 @@ the dump directly. Example: Old: -.. code-block:: C++ +.. code-block:: c++ int idump = output->find_dump(arg[iarg+1]); if (idump < 0) @@ -412,7 +412,7 @@ Old: New: -.. code-block:: C++ +.. code-block:: c++ auto idump = output->get_dump_by_id(arg[iarg+1]); if (!idump) error->all(FLERR,"Dump ID {} in hyper command does not exist", arg[iarg+1]); diff --git a/doc/src/Developer_utils.rst b/doc/src/Developer_utils.rst index 247d972ab4..35c5f96eb2 100644 --- a/doc/src/Developer_utils.rst +++ b/doc/src/Developer_utils.rst @@ -320,7 +320,7 @@ are all "whitespace" characters, i.e. the space character, the tabulator character, the carriage return character, the linefeed character, and the form feed character. -.. code-block:: C++ +.. code-block:: c++ :caption: Tokenizer class example listing entries of the PATH environment variable #include "tokenizer.h" @@ -352,7 +352,7 @@ tokenizer into a ``try`` / ``catch`` block to handle errors. The when a (type of) number is requested as next token that is not compatible with the string representing the next word. -.. code-block:: C++ +.. code-block:: c++ :caption: ValueTokenizer class example with exception handling #include "tokenizer.h" @@ -430,7 +430,7 @@ one or two array indices "[]" with numbers > 0. A typical code segment would look like this: -.. code-block:: C++ +.. code-block:: c++ :caption: Usage example for ArgInfo class int nvalues = 0; @@ -479,7 +479,7 @@ open the file, and will call the :cpp:class:`LAMMPS_NS::Error` class in case of failures to read or to convert numbers, so that LAMMPS will be aborted. -.. code-block:: C++ +.. code-block:: c++ :caption: Use of PotentialFileReader class in pair style coul/streitz PotentialFileReader reader(lmp, file, "coul/streitz"); @@ -558,7 +558,7 @@ chunk size needs to be known in advance, 2) with :cpp:func:`MyPage::vget() its size is registered later with :cpp:func:`MyPage::vgot() `. -.. code-block:: C++ +.. code-block:: c++ :caption: Example of using :cpp:class:`MyPage ` #include "my_page.h" diff --git a/doc/src/Developer_write.rst b/doc/src/Developer_write.rst index bdc6559060..c374ec2e77 100644 --- a/doc/src/Developer_write.rst +++ b/doc/src/Developer_write.rst @@ -26,7 +26,7 @@ constructor with the signature: ``FixPrintVel(class LAMMPS *, int, char **)``. Every fix must be registered in LAMMPS by writing the following lines of code in the header before include guards: -.. code-block:: c +.. code-block:: c++ #ifdef FIX_CLASS // clang-format off @@ -47,7 +47,7 @@ keyword when it parses the input script. Let's write a simple fix which will print the average velocity at the end of each timestep. First of all, implement a constructor: -.. code-block:: C++ +.. code-block:: c++ FixPrintVel::FixPrintVel(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg) @@ -72,7 +72,7 @@ in the Fix class called ``nevery`` which specifies how often the method The next method we need to implement is ``setmask()``: -.. code-block:: C++ +.. code-block:: c++ int FixPrintVel::setmask() { @@ -87,7 +87,7 @@ during execution. The constant ``END_OF_STEP`` corresponds to the are called during a timestep and the order in which they are called are shown in the previous section. -.. code-block:: C++ +.. code-block:: c++ void FixPrintVel::end_of_step() { @@ -143,7 +143,7 @@ The group membership information of an atom is contained in the *mask* property of and atom and the bit corresponding to a given group is stored in the groupbit variable which is defined in Fix base class: -.. code-block:: C++ +.. code-block:: c++ for (int i = 0; i < nlocal; ++i) { if (atom->mask[i] & groupbit) { @@ -174,7 +174,7 @@ to store positions of atoms from previous timestep, we need to add ``double** xold`` to the header file. Than add allocation code to the constructor: -.. code-block:: C++ +.. code-block:: c++ FixSavePos::FixSavePos(LAMMPS *lmp, int narg, char **arg), xold(nullptr) { @@ -190,7 +190,7 @@ to the constructor: Implement the aforementioned methods: -.. code-block:: C++ +.. code-block:: c++ double FixSavePos::memory_usage() { diff --git a/doc/src/Howto_pylammps.rst b/doc/src/Howto_pylammps.rst index 6c788e2365..a182d4a050 100644 --- a/doc/src/Howto_pylammps.rst +++ b/doc/src/Howto_pylammps.rst @@ -152,14 +152,14 @@ Creating a new instance of PyLammps To create a PyLammps object you need to first import the class from the lammps module. By using the default constructor, a new *lammps* instance is created. -.. code-block:: Python +.. code-block:: python from lammps import PyLammps L = PyLammps() You can also initialize PyLammps on top of this existing *lammps* object: -.. code-block:: Python +.. code-block:: python from lammps import lammps, PyLammps lmp = lammps() @@ -180,14 +180,14 @@ For instance, let's take the following LAMMPS command: In the original interface this command can be executed with the following Python code if *L* was a lammps instance: -.. code-block:: Python +.. code-block:: python L.command("region box block 0 10 0 5 -0.5 0.5") With the PyLammps interface, any command can be split up into arbitrary parts separated by white-space, passed as individual arguments to a region method. -.. code-block:: Python +.. code-block:: python L.region("box block", 0, 10, 0, 5, -0.5, 0.5) @@ -199,14 +199,14 @@ The benefit of this approach is avoiding redundant command calls and easier parameterization. In the original interface parameterization needed to be done manually by creating formatted strings. -.. code-block:: Python +.. code-block:: python L.command("region box block %f %f %f %f %f %f" % (xlo, xhi, ylo, yhi, zlo, zhi)) In contrast, methods of PyLammps accept parameters directly and will convert them automatically to a final command string. -.. code-block:: Python +.. code-block:: python L.region("box block", xlo, xhi, ylo, yhi, zlo, zhi) @@ -256,7 +256,7 @@ LAMMPS variables can be both defined and accessed via the PyLammps interface. To define a variable you can use the :doc:`variable ` command: -.. code-block:: Python +.. code-block:: python L.variable("a index 2") @@ -265,14 +265,14 @@ A dictionary of all variables is returned by L.variables you can access an individual variable by retrieving a variable object from the L.variables dictionary by name -.. code-block:: Python +.. code-block:: python a = L.variables['a'] The variable value can then be easily read and written by accessing the value property of this object. -.. code-block:: Python +.. code-block:: python print(a.value) a.value = 4 @@ -284,7 +284,7 @@ LAMMPS expressions can be immediately evaluated by using the eval method. The passed string parameter can be any expression containing global thermo values, variables, compute or fix data. -.. code-block:: Python +.. code-block:: python result = L.eval("ke") # kinetic energy result = L.eval("pe") # potential energy @@ -298,7 +298,7 @@ All atoms in the current simulation can be accessed by using the L.atoms list. Each element of this list is an object which exposes its properties (id, type, position, velocity, force, etc.). -.. code-block:: Python +.. code-block:: python # access first atom L.atoms[0].id @@ -311,7 +311,7 @@ position, velocity, force, etc.). Some properties can also be used to set: -.. code-block:: Python +.. code-block:: python # set position in 2D simulation L.atoms[0].position = (1.0, 0.0) @@ -328,7 +328,7 @@ after a run via the L.runs list. This list contains a growing list of run data. The first element is the output of the first run, the second element that of the second run. -.. code-block:: Python +.. code-block:: python L.run(1000) L.runs[0] # data of first 1000 time steps @@ -339,14 +339,14 @@ the second run. Each run contains a dictionary of all trajectories. Each trajectory is accessible through its thermo name: -.. code-block:: Python +.. code-block:: python L.runs[0].thermo.Step # list of time steps in first run L.runs[0].thermo.Ke # list of kinetic energy values in first run Together with matplotlib plotting data out of LAMMPS becomes simple: -.. code-block:: Python +.. code-block:: python import matplotlib.plot as plt steps = L.runs[0].thermo.Step @@ -406,7 +406,7 @@ Four atoms are placed in the simulation and the dihedral potential is applied on them using a datafile. Then one of the atoms is rotated along the central axis by setting its position from Python, which changes the dihedral angle. -.. code-block:: Python +.. code-block:: python phi = [d \* math.pi / 180 for d in range(360)] @@ -439,7 +439,7 @@ Initially, a 2D system is created in a state with minimal energy. It is then disordered by moving each atom by a random delta. -.. code-block:: Python +.. code-block:: python random.seed(27848) deltaperturb = 0.2 @@ -458,7 +458,7 @@ It is then disordered by moving each atom by a random delta. Finally, the Monte Carlo algorithm is implemented in Python. It continuously moves random atoms by a random delta and only accepts certain moves. -.. code-block:: Python +.. code-block:: python estart = L.eval("pe") elast = estart @@ -517,7 +517,7 @@ PyLammps can be run in parallel using mpi4py. This python package can be install The following is a short example which reads in an existing LAMMPS input file and executes it in parallel. You can find in.melt in the examples/melt folder. -.. code-block:: Python +.. code-block:: python from mpi4py import MPI from lammps import PyLammps diff --git a/doc/src/Howto_structured_data.rst b/doc/src/Howto_structured_data.rst index 18a5dfd775..3fe630a120 100644 --- a/doc/src/Howto_structured_data.rst +++ b/doc/src/Howto_structured_data.rst @@ -43,7 +43,7 @@ JSON "ke": $(ke) }""" file current_state.json screen no -.. code-block:: JSON +.. code-block:: json :caption: current_state.json { diff --git a/doc/src/Library_config.rst b/doc/src/Library_config.rst index 04b12f35de..481edcee7c 100644 --- a/doc/src/Library_config.rst +++ b/doc/src/Library_config.rst @@ -39,7 +39,7 @@ crashes within LAMMPS may be recovered from by enabling :ref:`exceptions `, avoiding them proactively is a safer approach. -.. code-block:: C +.. code-block:: c :caption: Example for using configuration settings functions #include "library.h" diff --git a/doc/src/Library_create.rst b/doc/src/Library_create.rst index 8ccc2e80ce..546db9b3be 100644 --- a/doc/src/Library_create.rst +++ b/doc/src/Library_create.rst @@ -22,7 +22,7 @@ as the "handle" argument in subsequent function calls until that instance is destroyed by calling :cpp:func:`lammps_close`. Here is a simple example demonstrating its use: -.. code-block:: C +.. code-block:: c #include "library.h" #include diff --git a/doc/src/Library_execute.rst b/doc/src/Library_execute.rst index 201d9c01b0..44b601ba4c 100644 --- a/doc/src/Library_execute.rst +++ b/doc/src/Library_execute.rst @@ -30,7 +30,7 @@ be included in the file or strings, and expansion of variables with ``${name}`` or ``$(expression)`` syntax is performed. Below is a short example using some of these functions. -.. code-block:: C +.. code-block:: c /* define to make the otherwise hidden prototype for "lammps_open()" visible */ #define LAMMPS_LIB_MPI diff --git a/doc/src/Library_properties.rst b/doc/src/Library_properties.rst index dfd72adc95..b3a8f9ea5a 100644 --- a/doc/src/Library_properties.rst +++ b/doc/src/Library_properties.rst @@ -32,7 +32,7 @@ indexed accordingly. Per-atom data can change sizes and ordering at every neighbor list rebuild or atom sort event as atoms migrate between sub-domains and processors. -.. code-block:: C +.. code-block:: c #include "library.h" #include diff --git a/doc/src/Modify_bond.rst b/doc/src/Modify_bond.rst index 682237b8bd..58b08de81b 100644 --- a/doc/src/Modify_bond.rst +++ b/doc/src/Modify_bond.rst @@ -13,24 +13,65 @@ Here is a brief description of common methods you define in your new derived class. See bond.h, angle.h, dihedral.h, and improper.h for details and specific additional methods. -+-----------------------+---------------------------------------------------------------------------------------+ -| init | check if all coefficients are set, calls *init_style* (optional) | -+-----------------------+---------------------------------------------------------------------------------------+ -| init_style | check if style specific conditions are met (optional) | -+-----------------------+---------------------------------------------------------------------------------------+ -| compute | compute the molecular interactions (required) | -+-----------------------+---------------------------------------------------------------------------------------+ -| settings | apply global settings for all types (optional) | -+-----------------------+---------------------------------------------------------------------------------------+ -| coeff | set coefficients for one type (required) | -+-----------------------+---------------------------------------------------------------------------------------+ -| equilibrium_distance | length of bond, used by SHAKE (required, bond only) | -+-----------------------+---------------------------------------------------------------------------------------+ -| equilibrium_angle | opening of angle, used by SHAKE (required, angle only) | -+-----------------------+---------------------------------------------------------------------------------------+ -| write & read_restart | writes/reads coeffs to restart files (required) | -+-----------------------+---------------------------------------------------------------------------------------+ -| single | force (bond only) and energy of a single bond or angle (required, bond or angle only) | -+-----------------------+---------------------------------------------------------------------------------------+ -| memory_usage | tally memory allocated by the style (optional) | -+-----------------------+---------------------------------------------------------------------------------------+ ++-----------------------+---------------------------------------------------------------------+ +| Required | "pure" methods that *must* be overridden in a derived class | ++=======================+=====================================================================+ +| compute | compute the molecular interactions for all listed items | ++-----------------------+---------------------------------------------------------------------+ +| coeff | set coefficients for one type | ++-----------------------+---------------------------------------------------------------------+ +| equilibrium_distance | length of bond, used by SHAKE (bond styles only) | ++-----------------------+---------------------------------------------------------------------+ +| equilibrium_angle | opening of angle, used by SHAKE (angle styles only) | ++-----------------------+---------------------------------------------------------------------+ +| write & read_restart | writes/reads coeffs to restart files | ++-----------------------+---------------------------------------------------------------------+ +| single | force/r (bond styles only) and energy of a single bond or angle | ++-----------------------+---------------------------------------------------------------------+ + + ++--------------------------------+----------------------------------------------------------------------+ +| Optional | methods that have a default or dummy implementation | ++================================+======================================================================+ +| init | check if all coefficients are set, calls init_style() | ++--------------------------------+----------------------------------------------------------------------+ +| init_style | check if style specific conditions are met | ++--------------------------------+----------------------------------------------------------------------+ +| settings | apply global settings for all types | ++--------------------------------+----------------------------------------------------------------------+ +| write & read_restart_settings | writes/reads global style settings to restart files | ++--------------------------------+----------------------------------------------------------------------+ +| write_data | write corresponding Coeffs section(s) in data file | ++--------------------------------+----------------------------------------------------------------------+ +| memory_usage | tally memory allocated by the style | ++--------------------------------+----------------------------------------------------------------------+ +| extract | provide access to internal data (bond or angle styles only) | ++--------------------------------+----------------------------------------------------------------------+ +| reinit | reset all type-based parameters, called by fix adapt (bonds only) | ++--------------------------------+----------------------------------------------------------------------+ +| pack & unpack_forward_comm | copy data to and from buffer in forward communication (bonds only) | ++--------------------------------+----------------------------------------------------------------------+ +| pack & unpack_reverse_comm | copy data to and from buffer in reverse communication (bonds only) | ++--------------------------------+----------------------------------------------------------------------+ + +Here is a list of flags or settings that should be set in the +constructor of the derived class when they differ from the default +setting. + ++---------------------------------+------------------------------------------------------------------------------+---------+ +| Name of flag | Description | default | ++=================================+==============================================================================+=========+ +| writedata | 1 if write_data() is implemented | 1 | ++---------------------------------+------------------------------------------------------------------------------+---------+ +| single_extra | number of extra single values calculated (bond styles only) | 0 | ++---------------------------------+------------------------------------------------------------------------------+---------+ +| partial_flag | 1 if bond type can be set to 0 and deleted (bond styles only) | 0 | ++---------------------------------+------------------------------------------------------------------------------+---------+ +| reinitflag | 1 if style has reinit() and is compatible with fix adapt | 1 | ++---------------------------------+------------------------------------------------------------------------------+---------+ +| comm_forward | size of buffer (in doubles) for forward communication (bond styles only) | 0 | ++---------------------------------+------------------------------------------------------------------------------+---------+ +| comm_reverse | size of buffer (in doubles) for reverse communication (bond styles only) | 0 | ++---------------------------------+------------------------------------------------------------------------------+---------+ +| comm_reverse_off | size of buffer for reverse communication with newton off (bond styles only) | 0 | ++---------------------------------+------------------------------------------------------------------------------+---------+ diff --git a/doc/src/Modify_pair.rst b/doc/src/Modify_pair.rst index 6913204504..38f5ade567 100644 --- a/doc/src/Modify_pair.rst +++ b/doc/src/Modify_pair.rst @@ -1,35 +1,121 @@ Pair styles =========== -Classes that compute pairwise interactions are derived from the Pair -class. In LAMMPS, pairwise calculation include many-body potentials -such as EAM or Tersoff where particles interact without a static bond -topology. New styles can be created to add new pair potentials to -LAMMPS. +Classes that compute pairwise non-bonded interactions are derived from +the Pair class. In LAMMPS, pairwise calculation include many-body +potentials such as EAM, Tersoff, or ReaxFF where particles interact +without an explicit bond topology but include interactions beyond +pairwise non-bonded contributions. New styles can be created to add +support for additional pair potentials to LAMMPS. When the +modifications are small, sometimes it is more effective to derive from +an existing pair style class. This latter approach is also used by +:doc:`Accelerator packages ` where the accelerated style +names differ from their base classes by an appended suffix. -Pair_lj_cut.cpp is a simple example of a Pair class, though it -includes some optional methods to enable its use with rRESPA. +The file ``src/pair_lj_cut.cpp`` is an example of a Pair class with a +very simple potential function. It includes several optional methods to +enable its use with :doc:`run_style respa ` and :doc:`compute +group/group `. -Here is a brief description of the class methods in pair.h: +Here is a brief list of some the class methods in the Pair class that +*must* be or *may* be overridden in a derived class. +---------------------------------+---------------------------------------------------------------------+ +| Required | "pure" methods that *must* be overridden in a derived class | ++=================================+=====================================================================+ | compute | workhorse routine that computes pairwise interactions | +---------------------------------+---------------------------------------------------------------------+ -| settings | reads the input script line with arguments you define | +| settings | processes the arguments to the pair_style command | +---------------------------------+---------------------------------------------------------------------+ -| coeff | set coefficients for one i,j type pair | -+---------------------------------+---------------------------------------------------------------------+ -| init_one | perform initialization for one i,j type pair | -+---------------------------------+---------------------------------------------------------------------+ -| init_style | initialization specific to this pair style | -+---------------------------------+---------------------------------------------------------------------+ -| write & read_restart | write/read i,j pair coeffs to restart files | -+---------------------------------+---------------------------------------------------------------------+ -| write & read_restart_settings | write/read global settings to restart files | -+---------------------------------+---------------------------------------------------------------------+ -| single | force/r and energy of a single pairwise interaction between 2 atoms | -+---------------------------------+---------------------------------------------------------------------+ -| compute_inner/middle/outer | versions of compute used by rRESPA | +| coeff | set coefficients for one i,j type pair, called from pair_coeff | +---------------------------------+---------------------------------------------------------------------+ -The inner/middle/outer routines are optional. ++---------------------------------+----------------------------------------------------------------------+ +| Optional | methods that have a default or dummy implementation | ++=================================+======================================================================+ +| init_one | perform initialization for one i,j type pair | ++---------------------------------+----------------------------------------------------------------------+ +| init_style | style initialization: request neighbor list(s), error checks | ++---------------------------------+----------------------------------------------------------------------+ +| init_list | Neighbor class callback function to pass neighbor list to pair style | ++---------------------------------+----------------------------------------------------------------------+ +| single | force/r and energy of a single pairwise interaction between 2 atoms | ++---------------------------------+----------------------------------------------------------------------+ +| compute_inner/middle/outer | versions of compute used by rRESPA | ++---------------------------------+----------------------------------------------------------------------+ +| memory_usage | return estimated amount of memory used by the pair style | ++---------------------------------+----------------------------------------------------------------------+ +| modify_params | process arguments to pair_modify command | ++---------------------------------+----------------------------------------------------------------------+ +| extract | provide access to internal scalar or per-type data like cutoffs | ++---------------------------------+----------------------------------------------------------------------+ +| extract_peratom | provide access to internal per-atom data | ++---------------------------------+----------------------------------------------------------------------+ +| setup | initialization at the beginning of a run | ++---------------------------------+----------------------------------------------------------------------+ +| finish | called at the end of a run, e.g. to print | ++---------------------------------+----------------------------------------------------------------------+ +| write & read_restart | write/read i,j pair coeffs to restart files | ++---------------------------------+----------------------------------------------------------------------+ +| write & read_restart_settings | write/read global settings to restart files | ++---------------------------------+----------------------------------------------------------------------+ +| write_data | write Pair Coeffs section to data file | ++---------------------------------+----------------------------------------------------------------------+ +| write_data_all | write PairIJ Coeffs section to data file | ++---------------------------------+----------------------------------------------------------------------+ +| pack & unpack_forward_comm | copy data to and from buffer if style uses forward communication | ++---------------------------------+----------------------------------------------------------------------+ +| pack & unpack_reverse_comm | copy data to and from buffer if style uses reverse communication | ++---------------------------------+----------------------------------------------------------------------+ +| reinit | reset all type-based parameters, called by fix adapt for example | ++---------------------------------+----------------------------------------------------------------------+ +| reset_dt | called when the time step is changed by timestep or fix reset/dt | ++---------------------------------+----------------------------------------------------------------------+ + +Here is a list of flags or settings that should be set in the +constructor of the derived pair class when they differ from the default +setting. + ++---------------------------------+-------------------------------------------------------------+---------+ +| Name of flag | Description | default | ++=================================+=============================================================+=========+ +| single_enable | 1 if single() method is implemented, 0 if missing | 1 | ++---------------------------------+-------------------------------------------------------------+---------+ +| respa_enable | 1 if pair style has compute_inner/middle/outer() | 0 | ++---------------------------------+-------------------------------------------------------------+---------+ +| restartinfo | 1 if pair style writes its settings to a restart | 1 | ++---------------------------------+-------------------------------------------------------------+---------+ +| one_coeff | 1 if only a pair_coeff * * command is allowed | 0 | ++---------------------------------+-------------------------------------------------------------+---------+ +| manybody_flag | 1 if pair style is a manybody potential | 0 | ++---------------------------------+-------------------------------------------------------------+---------+ +| unit_convert_flag | value != 0 indicates support for unit conversion | 0 | ++---------------------------------+-------------------------------------------------------------+---------+ +| no_virial_fdotr_compute | 1 if pair style does not call virial_fdotr_compute() | 0 | ++---------------------------------+-------------------------------------------------------------+---------+ +| writedata | 1 if write_data() and write_data_all() are implemented | 0 | ++---------------------------------+-------------------------------------------------------------+---------+ +| comm_forward | size of buffer (in doubles) for forward communication | 0 | ++---------------------------------+-------------------------------------------------------------+---------+ +| comm_reverse | size of buffer (in doubles) for reverse communication | 0 | ++---------------------------------+-------------------------------------------------------------+---------+ +| ghostneigh | 1 if cutghost is set and style uses neighbors of ghosts | 0 | ++---------------------------------+-------------------------------------------------------------+---------+ +| finitecutflag | 1 if cutoff depends on diameter of atoms | 0 | ++---------------------------------+-------------------------------------------------------------+---------+ +| reinitflag | 1 if style has reinit() and is compatible with fix adapt | 0 | ++---------------------------------+-------------------------------------------------------------+---------+ +| ewaldflag | 1 if compatible with kspace_style ewald | 0 | ++---------------------------------+-------------------------------------------------------------+---------+ +| pppmflag | 1 if compatible with kspace_style pppm | 0 | ++---------------------------------+-------------------------------------------------------------+---------+ +| msmflag | 1 if compatible with kspace_style msm | 0 | ++---------------------------------+-------------------------------------------------------------+---------+ +| dispersionflag | 1 if compatible with ewald/disp or pppm/disp | 0 | ++---------------------------------+-------------------------------------------------------------+---------+ +| tip4pflag | 1 if compatible with kspace_style pppm/tip4p | 0 | ++---------------------------------+-------------------------------------------------------------+---------+ +| dipoleflag | 1 if compatible with dipole kspace_style | 0 | ++---------------------------------+-------------------------------------------------------------+---------+ +| spinflag | 1 if compatible with spin kspace_style | 0 | ++---------------------------------+-------------------------------------------------------------+---------+ diff --git a/doc/src/Packages_details.rst b/doc/src/Packages_details.rst index 2a3f5fc391..ecbc54233a 100644 --- a/doc/src/Packages_details.rst +++ b/doc/src/Packages_details.rst @@ -80,6 +80,7 @@ page gives those details. * :ref:`ML-HDNNP ` * :ref:`ML-IAP ` * :ref:`ML-PACE ` + * :ref:`ML-POD ` * :ref:`ML-QUIP ` * :ref:`ML-RANN ` * :ref:`ML-SNAP ` @@ -865,7 +866,7 @@ ELECTRODE package The ELECTRODE package allows the user to enforce a constant potential method for groups of atoms that interact with the remaining atoms as electrolyte. -**Authors:** The ELECTRODE library is written and maintained by Ludwig +**Authors:** The ELECTRODE package is written and maintained by Ludwig Ahrens-Iwers (TUHH, Hamburg, Germany), Shern Tee (UQ, Brisbane, Australia) and Robert Meissner (TUHH, Hamburg, Germany). @@ -878,7 +879,7 @@ This package has :ref:`specific installation instructions ` on the **Supporting info:** -* :doc:`fix electrode/conp ` +* :doc:`fix electrode/conp ` ---------- @@ -1796,6 +1797,39 @@ This package has :ref:`specific installation instructions ` on the ---------- +.. _PKG-ML-POD: + +ML-POD package +------------------- + +**Contents:** + +A pair style and fitpod style for Proper Orthogonal Descriptors +(POD). POD is a methodology for deriving descriptors based on the proper +orthogonal decomposition. The ML-POD package provides an efficient +implementation for running simulations with POD potentials, along with +fitting the potentials natively in LAMMPS. + +**Authors:** + +Ngoc Cuong Nguyen (MIT), Andrew Rohskopf (Sandia) + +.. versionadded:: TBD + +**Install:** + +This package has :ref:`specific installation instructions ` on the +:doc:`Build extras ` page. + +**Supporting info:** + +* src/ML-POD: filenames -> commands +* :doc:`pair_style pod ` +* :doc:`command_style fitpod ` +* examples/PACKAGES/pod + +---------- + .. _PKG-ML-QUIP: ML-QUIP package diff --git a/doc/src/Packages_list.rst b/doc/src/Packages_list.rst index cfe0460d05..ac0ba7728e 100644 --- a/doc/src/Packages_list.rst +++ b/doc/src/Packages_list.rst @@ -155,7 +155,7 @@ whether an extra library is needed to build and use the package: - no * - :ref:`ELECTRODE ` - electrode charges to match potential - - :doc:`fix electrode/conp ` + - :doc:`fix electrode/conp ` - PACKAGES/electrode - no * - :ref:`EXTRA-COMPUTE ` @@ -298,6 +298,11 @@ whether an extra library is needed to build and use the package: - :doc:`pair pace ` - PACKAGES/pace - ext + * - :ref:`ML-POD ` + - Proper orthogonal decomposition potentials + - :doc:`pair pod ` + - pod + - ext * - :ref:`ML-QUIP ` - QUIP/libatoms interface - :doc:`pair_style quip ` diff --git a/doc/src/Python_atoms.rst b/doc/src/Python_atoms.rst index be0d4ff800..2cb5c695e8 100644 --- a/doc/src/Python_atoms.rst +++ b/doc/src/Python_atoms.rst @@ -58,7 +58,7 @@ against invalid accesses. Each element of this list is a :py:class:`Atom ` or :py:class:`Atom2D ` object. The attributes of these objects provide access to their data (id, type, position, velocity, force, etc.): - .. code-block:: Python + .. code-block:: python # access first atom L.atoms[0].id @@ -71,7 +71,7 @@ against invalid accesses. Some attributes can be changed: - .. code-block:: Python + .. code-block:: python # set position in 2D simulation L.atoms[0].position = (1.0, 0.0) diff --git a/doc/src/Python_config.rst b/doc/src/Python_config.rst index 38f0ef0baf..ccbc74a46c 100644 --- a/doc/src/Python_config.rst +++ b/doc/src/Python_config.rst @@ -4,7 +4,7 @@ Configuration information The following methods can be used to query the LAMMPS library about compile time settings and included packages and styles. -.. code-block:: Python +.. code-block:: python :caption: Example for using configuration settings functions from lammps import lammps diff --git a/doc/src/Python_create.rst b/doc/src/Python_create.rst index ec4241f36a..939aad2f32 100644 --- a/doc/src/Python_create.rst +++ b/doc/src/Python_create.rst @@ -74,7 +74,7 @@ Here are simple examples using all three Python interfaces: :py:class:`PyLammps ` objects can also be created on top of an existing :py:class:`lammps ` object: - .. code-block:: Python + .. code-block:: python from lammps import lammps, PyLammps ... @@ -113,7 +113,7 @@ Here are simple examples using all three Python interfaces: You can also initialize IPyLammps on top of an existing :py:class:`lammps` or :py:class:`PyLammps` object: - .. code-block:: Python + .. code-block:: python from lammps import lammps, IPyLammps ... @@ -142,7 +142,7 @@ the MPI and/or Kokkos environment if enabled and active. Note that you can create multiple LAMMPS objects in your Python script, and coordinate and run multiple simulations, e.g. -.. code-block:: Python +.. code-block:: python from lammps import lammps lmp1 = lammps() diff --git a/doc/src/Python_error.rst b/doc/src/Python_error.rst index 744a8dd3de..5dbd940723 100644 --- a/doc/src/Python_error.rst +++ b/doc/src/Python_error.rst @@ -7,7 +7,7 @@ current Python process with an error message. C++ exceptions allow capturing them on the C++ side and rethrowing them on the Python side. This way LAMMPS errors can be handled through the Python exception handling mechanism. -.. code-block:: Python +.. code-block:: python from lammps import lammps, MPIAbortException diff --git a/doc/src/Python_execute.rst b/doc/src/Python_execute.rst index 59faa34438..01cf0e920f 100644 --- a/doc/src/Python_execute.rst +++ b/doc/src/Python_execute.rst @@ -60,7 +60,7 @@ it is possible to "compute" what the next LAMMPS command should be. can be executed using with the lammps API with the following Python code if ``lmp`` is an instance of :py:class:`lammps `: - .. code-block:: Python + .. code-block:: python from lammps import lammps @@ -73,7 +73,7 @@ it is possible to "compute" what the next LAMMPS command should be. The arguments of the command can be passed as one string, or individually. - .. code-block:: Python + .. code-block:: python from lammps import PyLammps @@ -93,14 +93,14 @@ it is possible to "compute" what the next LAMMPS command should be. parameterization. In the lammps API parameterization needed to be done manually by creating formatted command strings. - .. code-block:: Python + .. code-block:: python lmp.command("region box block %f %f %f %f %f %f" % (xlo, xhi, ylo, yhi, zlo, zhi)) In contrast, methods of PyLammps accept parameters directly and will convert them automatically to a final command string. - .. code-block:: Python + .. code-block:: python L.region("box block", xlo, xhi, ylo, yhi, zlo, zhi) diff --git a/doc/src/Python_launch.rst b/doc/src/Python_launch.rst index 500a107977..96e43a2d95 100644 --- a/doc/src/Python_launch.rst +++ b/doc/src/Python_launch.rst @@ -56,7 +56,7 @@ and you should see the same output as if you had typed Note that without the mpi4py specific lines from ``test.py`` -.. code-block:: Python +.. code-block:: python from lammps import lammps lmp = lammps() diff --git a/doc/src/Python_objects.rst b/doc/src/Python_objects.rst index 4a1496632e..6e3a329a27 100644 --- a/doc/src/Python_objects.rst +++ b/doc/src/Python_objects.rst @@ -76,7 +76,7 @@ computes, fixes, or variables in LAMMPS using the :py:mod:`lammps` module. To define a variable you can use the :doc:`variable ` command: - .. code-block:: Python + .. code-block:: python L.variable("a index 2") @@ -85,14 +85,14 @@ computes, fixes, or variables in LAMMPS using the :py:mod:`lammps` module. you can access an individual variable by retrieving a variable object from the ``L.variables`` dictionary by name - .. code-block:: Python + .. code-block:: python a = L.variables['a'] The variable value can then be easily read and written by accessing the value property of this object. - .. code-block:: Python + .. code-block:: python print(a.value) a.value = 4 diff --git a/doc/src/Python_properties.rst b/doc/src/Python_properties.rst index 02af03bbb8..227a729622 100644 --- a/doc/src/Python_properties.rst +++ b/doc/src/Python_properties.rst @@ -105,7 +105,7 @@ against invalid accesses. variables, compute or fix data (see :doc:`Howto_output`): - .. code-block:: Python + .. code-block:: python result = L.eval("ke") # kinetic energy result = L.eval("pe") # potential energy diff --git a/doc/src/Python_scatter.rst b/doc/src/Python_scatter.rst index 113b98d354..002a36cc98 100644 --- a/doc/src/Python_scatter.rst +++ b/doc/src/Python_scatter.rst @@ -1,7 +1,7 @@ Scatter/gather operations ========================= -.. code-block:: Python +.. code-block:: python data = lmp.gather_atoms(name,type,count) # return per-atom property of all atoms gathered into data, ordered by atom ID # name = "x", "charge", "type", etc @@ -42,7 +42,7 @@ For the scatter methods, the array of coordinates passed to must be a ctypes vector of ints or doubles, allocated and initialized something like this: -.. code-block:: Python +.. code-block:: python from ctypes import c_double natoms = lmp.get_natoms() diff --git a/doc/src/commands_list.rst b/doc/src/commands_list.rst index 9adc397138..ff2502189d 100644 --- a/doc/src/commands_list.rst +++ b/doc/src/commands_list.rst @@ -42,6 +42,7 @@ Commands echo fix fix_modify + fitpod_command group group2ndx hyper diff --git a/doc/src/fitpod_command.rst b/doc/src/fitpod_command.rst new file mode 100644 index 0000000000..9670bf5dd2 --- /dev/null +++ b/doc/src/fitpod_command.rst @@ -0,0 +1,745 @@ +.. index:: fitpod + +fitpod command +====================== + +Syntax +"""""" + +.. parsed-literal:: + + fitpod Ta_param.pod Ta_data.pod + +* fitpod = style name of this command +* Ta_param.pod = an input file that describes proper orthogonal descriptors (PODs) +* Ta_data.pod = an input file that specifies DFT data used to fit a POD potential + +Examples +"""""""" + +.. code-block:: LAMMPS + + fitpod Ta_param.pod Ta_data.pod + +Description +""""""""""" +.. versionadded:: TBD + +Fit a machine-learning interatomic potential (ML-IAP) based on proper +orthogonal descriptors (POD). Two input files are required for this +command. The first input file describes a POD potential parameter +settings, while the second input file specifies the DFT data used for +the fitting procedure. + +The table below has one-line descriptions of all the keywords that can +be used in the first input file (i.e. ``Ta_param.pod`` in the example +above): + +.. list-table:: + :header-rows: 1 + :widths: auto + + * - Keyword + - Default + - Type + - Description + * - species + - (none) + - STRING + - Chemical symbols for all elements in the system and have to match XYZ training files. + * - pbc + - 1 1 1 + - INT + - three integer constants specify boundary conditions + * - rin + - 1.0 + - REAL + - a real number specifies the inner cut-off radius + * - rcut + - 5.0 + - REAL + - a real number specifies the outer cut-off radius + * - bessel_polynomial_degree + - 3 + - INT + - the maximum degree of Bessel polynomials + * - inverse_polynomial_degree + - 6 + - INT + - the maximum degree of inverse radial basis functions + * - onebody + - 1 + - BOOL + - turns on/off one-body potential + * - twobody_number_radial_basis_functions + - 6 + - INT + - number of radial basis functions for two-body potential + * - threebody_number_radial_basis_functions + - 5 + - INT + - number of radial basis functions for three-body potential + * - threebody_number_angular_basis_functions + - 5 + - INT + - number of angular basis functions for three-body potential + * - fourbody_snap_twojmax + - 0 + - INT + - band limit for SNAP bispectrum components (0,2,4,6,8... allowed) + * - fourbody_snap_chemflag + - 0 + - BOOL + - turns on/off the explicit multi-element variant of the SNAP bispectrum components + * - quadratic_pod_potential + - 0 + - BOOL + - turns on/off quadratic POD potential + +All keywords except *species* have default values. If a keyword is not +set in the input file, its default value is used. The next table +describes all keywords that can be used in the second input file +(i.e. ``Ta_data.pod`` in the example above): + +.. list-table:: + :header-rows: 1 + :widths: auto + + * - Keyword + - Default + - Type + - Description + * - file_format + - extxyz + - STRING + - only the extended xyz format (extxyz) is currently supported + * - file_extension + - xyz + - STRING + - extension of the data files + * - path_to_training_data_set + - (none) + - STRING + - specifies the path to training data files in double quotes + * - path_to_test_data_set + - "" + - STRING + - specifies the path to test data files in double quotes + * - fraction_training_data_set + - 1.0 + - REAL + - a real number (<= 1.0) specifies the fraction of the training set used to fit POD + * - randomize_training_data_set + - 0 + - BOOL + - turns on/off randomization of the training set + * - fitting_weight_energy + - 100.0 + - REAL + - a real constant specifies the weight for energy in the least-squares fit + * - fitting_weight_force + - 1.0 + - REAL + - a real constant specifies the weight for force in the least-squares fit + * - fitting_regularization_parameter + - 1.0e-10 + - REAL + - a real constant specifies the regularization parameter in the least-squares fit + * - error_analysis_for_training_data_set + - 0 + - BOOL + - turns on/off error analysis for the training data set + * - error_analysis_for_test_data_set + - 0 + - BOOL + - turns on/off error analysis for the test data set + * - basename_for_output_files + - pod + - STRING + - a basename string added to the output files + * - precision_for_pod_coefficients + - 8 + - INT + - number of digits after the decimal points for numbers in the coefficient file + +All keywords except *path_to_training_data_set* have default values. If +a keyword is not set in the input file, its default value is used. After +successful training, a number of output files are produced, if enabled: + +* ``_training_errors.pod`` reports the errors in energy and forces for the training data set +* ``_training_analysis.pod`` reports detailed errors for all training configurations +* ``_test_errors.pod`` reports errors for the test data set +* ``_test_analysis.pod`` reports detailed errors for all test configurations +* ``_coefficients.pod`` contains the coefficients of the POD potential + +After training the POD potential, ``Ta_param.pod`` and ``_coefficients.pod`` +are the two files needed to use the POD potential in LAMMPS. See +:doc:`pair_style pod ` for using the POD potential. Examples +about training and using POD potentials are found in the directory +lammps/examples/PACKAGES/pod. + +Parameterized Potential Energy Surface +"""""""""""""""""""""""""""""""""""""" + +We consider a multi-element system of *N* atoms with :math:`N_{\rm e}` +unique elements. We denote by :math:`\boldsymbol r_n` and :math:`Z_n` +position vector and type of an atom *n* in the system, +respectively. Note that we have :math:`Z_n \in \{1, \ldots, N_{\rm e} +\}`, :math:`\boldsymbol R = (\boldsymbol r_1, \boldsymbol r_2, \ldots, +\boldsymbol r_N) \in \mathbb{R}^{3N}`, and :math:`\boldsymbol Z = (Z_1, +Z_2, \ldots, Z_N) \in \mathbb{N}^{N}`. The potential energy surface +(PES) of the system can be expressed as a many-body expansion of the +form + +.. math:: + + E(\boldsymbol R, \boldsymbol Z, \boldsymbol{\eta}, \boldsymbol{\mu}) \ = \ & \sum_{i} V^{(1)}(\boldsymbol r_i, Z_i, \boldsymbol \mu^{(1)} ) + \frac12 \sum_{i,j} V^{(2)}(\boldsymbol r_i, \boldsymbol r_j, Z_i, Z_j, \boldsymbol \eta, \boldsymbol \mu^{(2)}) \\ + & + \frac16 \sum_{i,j,k} V^{(3)}(\boldsymbol r_i, \boldsymbol r_j, \boldsymbol r_k, Z_i, Z_j, Z_k, \boldsymbol \eta, \boldsymbol \mu^{(3)}) + \ldots + +where :math:`V^{(1)}` is the one-body potential often used for +representing external field or energy of isolated elements, and the +higher-body potentials :math:`V^{(2)}, V^{(3)}, \ldots` are symmetric, +uniquely defined, and zero if two or more indices take identical values. +The superscript on each potential denotes its body order. Each *q*-body +potential :math:`V^{(q)}` depends on :math:`\boldsymbol \mu^{(q)}` which +are sets of parameters to fit the PES. Note that :math:`\boldsymbol \mu` +is a collection of all potential parameters :math:`\boldsymbol +\mu^{(1)}`, :math:`\boldsymbol \mu^{(2)}`, :math:`\boldsymbol +\mu^{(3)}`, etc, and that :math:`\boldsymbol \eta` is a set of +hyper-parameters such as inner cut-off radius :math:`r_{\rm in}` and +outer cut-off radius :math:`r_{\rm cut}`. + +Interatomic potentials rely on parameters to learn relationship between +atomic environments and interactions. Since interatomic potentials are +approximations by nature, their parameters need to be set to some +reference values or fitted against data by necessity. Typically, +potential fitting finds optimal parameters, :math:`\boldsymbol \mu^*`, +to minimize a certain loss function of the predicted quantities and +data. Since the fitted potential depends on the data set used to fit it, +different data sets will yield different optimal parameters and thus +different fitted potentials. When fitting the same functional form on +*Q* different data sets, we would obtain *Q* different optimized +potentials, :math:`E(\boldsymbol R,\boldsymbol Z, \boldsymbol \eta, +\boldsymbol \mu_q^*), 1 \le q \le Q`. Consequently, there exist many +different sets of optimized parameters for empirical interatomic +potentials. + +Instead of optimizing the potential parameters, inspired by the reduced +basis method :ref:`(Grepl) ` for parameterized partial +differential equations, we view the parameterized PES as a parametric +manifold of potential energies + +.. math:: + + \mathcal{M} = \{E(\boldsymbol R, \boldsymbol Z, \boldsymbol \eta, \boldsymbol \mu) \ | \ \boldsymbol \mu \in \Omega^{\boldsymbol \mu} \} + +where :math:`\Omega^{\boldsymbol \mu}` is a parameter domain in which +:math:`\boldsymbol \mu` resides. The parametric manifold +:math:`\mathcal{M}` contains potential energy surfaces for all values of +:math:`\boldsymbol \mu \in \Omega^{\boldsymbol \mu}`. Therefore, the +parametric manifold yields a much richer and more transferable atomic +representation than any particular individual PES :math:`E(\boldsymbol +R, \boldsymbol Z, \boldsymbol \eta, \boldsymbol \mu^*)`. + +We propose specific forms of the parameterized potentials for one-body, +two-body, and three-body interactions. We apply the Karhunen-Loeve +expansion to snapshots of the parameterized potentials to obtain sets of +orthogonal basis functions. These basis functions are aggregated +according to the chemical elements of atoms, thus leading to +multi-element proper orthogonal descriptors. + +Proper Orthogonal Descriptors +""""""""""""""""""""""""""""" + +Proper orthogonal descriptors are finger prints characterizing the +radial and angular distribution of a system of atoms. The detailed +mathematical definition is given in the paper by Nguyen and Rohskopf +:ref:`(Nguyen) `. + +The descriptors for the one-body interaction are used to capture energy +of isolated elements and defined as follows + +.. math:: + + D_{ip}^{(1)} = \left\{ + \begin{array}{ll} + 1, & \mbox{if } Z_i = p \\ + 0, & \mbox{if } Z_i \neq p + \end{array} + \right. + +for :math:`1 \le i \le N, 1 \le p \le N_{\rm e}`. The number of one-body +descriptors per atom is equal to the number of elements. The one-body +descriptors are independent of atom positions, but dependent on atom +types. The one-body descriptors are active only when the keyword +*onebody* is set to 1. + +We adopt the usual assumption that the direct interaction between two +atoms vanishes smoothly when their distance is greater than the outer +cutoff distance :math:`r_{\rm cut}`. Furthermore, we assume that two +atoms can not get closer than the inner cutoff distance :math:`r_{\rm +in}` due to the Pauli repulsion principle. Let :math:`r \in (r_{\rm in}, +r_{\rm cut})`, we introduce the following parameterized radial functions + +.. math:: + + \phi(r, r_{\rm in}, r_{\rm cut}, \alpha, \beta) = \frac{\sin (\alpha \pi x) }{r - r_{\rm in}}, \qquad \varphi(r, \gamma) = \frac{1}{r^\gamma} , + +where the scaled distance function :math:`x` is defined below to enrich the two-body manifold + +.. math:: + + x(r, r_{\rm in}, r_{\rm cut}, \beta) = \frac{e^{-\beta(r - r_{\rm in})/(r_{\rm cut} - r_{\rm in})} - 1}{e^{-\beta} - 1} . + +We introduce the following function as a convex combination of the two functions + +.. math:: + + \psi(r, r_{\rm in}, r_{\rm cut}, \alpha, \beta, \gamma, \kappa) = \kappa \phi(r, r_{\rm in}, r_{\rm cut}, \alpha, \beta) + (1- \kappa) \varphi(r, \gamma) . + +We see that :math:`\psi` is a function of distance :math:`r`, cut-off +distances :math:`r_{\rm in}` and :math:`r_{\rm cut}`, and parameters +:math:`\alpha, \beta, \gamma, \kappa`. Together these parameters allow +the function :math:`\psi` to characterize a diverse spectrum of two-body +interactions within the cut-off interval :math:`(r_{\rm in}, r_{\rm +cut})`. + +Next, we introduce the following parameterized potential + +.. math:: + + W^{(2)}(r_{ij}, \boldsymbol \eta, \boldsymbol \mu^{(2)}) = f_{\rm c}(r_{ij}, \boldsymbol \eta) \psi(r_{ij}, \boldsymbol \eta, \boldsymbol \mu^{(2)}) + +where :math:`\eta_1 = r_{\rm in}, \eta_2 = r_{\rm cut}, \mu_1^{(2)} = +\alpha, \mu_2^{(2)} = \beta, \mu_3^{(2)} = \gamma`, and +:math:`\mu_4^{(2)} = \kappa`. Here the cut-off function :math:`f_{\rm +c}(r_{ij}, \boldsymbol \eta)` proposed in [refs] is used to ensure the +smooth vanishing of the potential and its derivative for :math:`r_{ij} +\ge r_{\rm cut}`: + +.. math:: + + f_{\rm c}(r_{ij}, r_{\rm in}, r_{\rm cut}) = \exp \left(1 -\frac{1}{\sqrt{\left(1 - \frac{(r-r_{\rm in})^3}{(r_{\rm cut} - r_{\rm in})^3} \right)^2 + 10^{-6}}} \right) + +Based on the parameterized potential, we form a set of snapshots as +follows. We assume that we are given :math:`N_{\rm s}` parameter tuples +:math:`\boldsymbol \mu^{(2)}_\ell, 1 \le \ell \le N_{\rm s}`. We +introduce the following set of snapshots on :math:`(r_{\rm in}, r_{\rm +cut})`: + +.. math:: + + \xi_\ell(r_{ij}, \boldsymbol \eta) = W^{(2)}(r_{ij}, \boldsymbol \eta, \boldsymbol \mu^{(2)}_\ell), \quad \ell = 1, \ldots, N_{\rm s} . + +To ensure adequate sampling of the PES for different parameters, we +choose :math:`N_{\rm s}` parameter points :math:`\boldsymbol +\mu^{(2)}_\ell = (\alpha_\ell, \beta_\ell, \gamma_\ell, \kappa_\ell), 1 +\le \ell \le N_{\rm s}` as follows. The parameters :math:`\alpha \in [1, +N_\alpha]` and :math:`\gamma \in [1, N_\gamma]` are integers, where +:math:`N_\alpha` and :math:`N_\gamma` are the highest degrees for +:math:`\alpha` and :math:`\gamma`, respectively. We next choose +:math:`N_\beta` different values of :math:`\beta` in the interval +:math:`[\beta_{\min}, \beta_{\max}]`, where :math:`\beta_{\min} = 0` and +:math:`\beta_{\max} = 4`. The parameter :math:`\kappa` can be set either +0 or 1. Hence, the total number of parameter points is :math:`N_{\rm s} += N_\alpha N_\beta + N_\gamma`. Although :math:`N_\alpha, N_\beta, +N_\gamma` can be chosen conservatively large, we find that +:math:`N_\alpha = 6, N_\beta = 3, N_\gamma = 8` are adequate for most +problems. Note that :math:`N_\alpha` and :math:`N_\gamma` correspond to +*bessel_polynomial_degree* and *inverse_polynomial_degree*, +respectively. + +We employ the Karhunen-Loeve (KL) expansion to generate an orthogonal +basis set which is known to be optimal for representation of the +snapshot family :math:`\{\xi_\ell\}_{\ell=1}^{N_{\rm s}}`. The two-body +orthogonal basis functions are computed as follows + +.. math:: + + U^{(2)}_m(r_{ij}, \boldsymbol \eta) = \sum_{\ell = 1}^{N_{\rm s}} A_{\ell m}(\boldsymbol \eta) \, \xi_\ell(r_{ij}, \boldsymbol \eta), \qquad m = 1, \ldots, N_{\rm 2b} , + +where the matrix :math:`\boldsymbol A \in \mathbb{R}^{N_{\rm s} \times +N_{\rm s}}` consists of eigenvectors of the eigenvalue problem + +.. math:: + + \boldsymbol C \boldsymbol a = \lambda \boldsymbol a + +with the entries of :math:`\boldsymbol C \in \mathbb{R}^{N_{\rm s} \times N_{\rm s}}` being given by + +.. math:: + + C_{ij} = \frac{1}{N_{\rm s}} \int_{r_{\rm in}}^{r_{\rm cut}} \xi_i(x, \boldsymbol \eta) \xi_j(x, \boldsymbol \eta) dx, \quad 1 \le i, j \le N_{\rm s} + +Note that the eigenvalues :math:`\lambda_\ell, 1 \le \ell \le N_{\rm +s}`, are ordered such that :math:`\lambda_1 \ge \lambda_2 \ge \ldots \ge +\lambda_{N_{\rm s}}`, and that the matrix :math:`\boldsymbol A` is +pe-computed and stored for any given :math:`\boldsymbol \eta`. Owing to +the rapid convergence of the KL expansion, only a small number of +orthogonal basis functions is needed to obtain accurate +approximation. The value of :math:`N_{\rm 2b}` corresponds to +*twobody_number_radial_basis_functions*. + +The two-body proper orthogonal descriptors at each atom *i* are computed +by summing the orthogonal basis functions over the neighbors of atom *i* +and numerating on the atom types as follows + +.. math:: + + D^{(2)}_{im l(p, q) }(\boldsymbol \eta) = \left\{ + \begin{array}{ll} + \displaystyle \sum_{\{j | Z_j = q\}} U^{(2)}_m(r_{ij}, \boldsymbol \eta), & \mbox{if } Z_i = p \\ + 0, & \mbox{if } Z_i \neq p + \end{array} + \right. + +for :math:`1 \le i \le N, 1 \le m \le N_{\rm 2b}, 1 \le q, p \le N_{\rm +e}`. Here :math:`l(p,q)` is a symmetric index mapping such that + +.. math:: + + l(p,q) = \left\{ + \begin{array}{ll} + q + (p-1) N_{\rm e} - p(p-1)/2, & \mbox{if } q \ge p \\ + p + (q-1) N_{\rm e} - q(q-1)/2, & \mbox{if } q < p . + \end{array} + \right. + +The number of two-body descriptors per atom is thus :math:`N_{\rm 2b} +N_{\rm e}(N_{\rm e}+1)/2`. + +It is important to note that the orthogonal basis functions do not +depend on the atomic numbers :math:`Z_i` and :math:`Z_j`. Therefore, the +cost of evaluating the basis functions and their derivatives with +respect to :math:`r_{ij}` is independent of the number of elements +:math:`N_{\rm e}`. Consequently, even though the two-body proper +orthogonal descriptors depend on :math:`\boldsymbol Z`, their +computational complexity is independent of :math:`N_{\rm e}`. + +In order to provide proper orthogonal descriptors for three-body +interactions, we need to introduce a three-body parameterized +potential. In particular, the three-body potential is defined as a +product of radial and angular functions as follows + +.. math:: + + W^{(3)}(r_{ij}, r_{ik}, \theta_{ijk}, \boldsymbol \eta, \boldsymbol \mu^{(3)}) = \psi(r_{ij}, r_{\rm min}, r_{\rm max}, \alpha, \beta, \gamma, \kappa) f_{\rm c}(r_{ij}, r_{\rm min}, r_{\rm max}) \\ + \psi(r_{ik}, r_{\rm min}, r_{\rm max}, \alpha, \beta, \gamma, \kappa) f_{\rm c}(r_{ik}, r_{\rm min}, r_{\rm max}) \\ + \cos (\sigma \theta_{ijk} + \zeta) + +where :math:`\sigma` is the periodic multiplicity, :math:`\zeta` is the +equilibrium angle, :math:`\boldsymbol \mu^{(3)} = (\alpha, \beta, +\gamma, \kappa, \sigma, \zeta)`. The three-body potential provides an +angular fingerprint of the atomic environment through the bond angles +:math:`\theta_{ijk}` formed with each pair of neighbors :math:`j` and +:math:`k`. Compared to the two-body potential, the three-body potential +has two extra parameters :math:`(\sigma, \zeta)` associated with the +angular component. + +Let :math:`\boldsymbol \varrho = (\alpha, \beta, \gamma, \kappa)`. We +assume that we are given :math:`L_{\rm r}` parameter tuples +:math:`\boldsymbol \varrho_\ell, 1 \le \ell \le L_{\rm r}`. We +introduce the following set of snapshots on :math:`(r_{\min}, +r_{\max})`: + +.. math:: + + \zeta_\ell(r_{ij}, r_{\rm min}, r_{\rm max} ) = \psi(r_{ij}, r_{\rm min}, r_{\rm max}, \boldsymbol \varrho_\ell) f_{\rm c}(r_{ij}, r_{\rm min}, r_{\rm max}), \quad 1 \le \ell \le L_{\rm r} . + +We apply the Karhunen-Loeve (KL) expansion to this set of snapshots to +obtain orthogonal basis functions as follows + +.. math:: + + U^{r}_m(r_{ij}, r_{\rm min}, r_{\rm max} ) = \sum_{\ell = 1}^{L_{\rm r}} A_{\ell m} \, \zeta_\ell(r_{ij}, r_{\rm min}, r_{\rm max} ), \qquad m = 1, \ldots, N_{\rm r} , + +where the matrix :math:`\boldsymbol A \in \mathbb{R}^{L_{\rm r} \times L_{\rm r}}` consists +of eigenvectors of the eigenvalue problem. For the parameterized angular function, +we consider angular basis functions + +.. math:: + + U^{a}_n(\theta_{ijk}) = \cos ((n-1) \theta_{ijk}), \qquad n = 1,\ldots, N_{\rm a}, + +where :math:`N_{\rm a}` is the number of angular basis functions. The orthogonal +basis functions for the parameterized potential are computed as follows + +.. math:: + + U^{(3)}_{mn}(r_{ij}, r_{ik}, \theta_{ijk}, \boldsymbol \eta) = U^{r}_m(r_{ij}, \boldsymbol \eta) U^{r}_m(r_{ik}, \boldsymbol \eta) U^{a}_n(\theta_{ijk}), + +for :math:`1 \le m \le N_{\rm r}, 1 \le n \le N_{\rm a}`. The number of three-body +orthogonal basis functions is equal to :math:`N_{\rm 3b} = N_{\rm r} N_{\rm a}` and +independent of the number of elements. The value of :math:`N_{\rm r}` corresponds to +*threebody_number_radial_basis_functions*, while that of :math:`N_{\rm a}` to +*threebody_number_angular_basis_functions*. + +The three-body proper orthogonal descriptors at each atom *i* +are obtained by summing over the neighbors *j* and *k* of atom *i* as + +.. math:: + + D^{(3)}_{imn \ell(p, q, s)}(\boldsymbol \eta) = \left\{ + \begin{array}{ll} + \displaystyle \sum_{\{j | Z_j = q\}} \sum_{\{k | Z_k = s\}} U^{(3)}_{mn}(r_{ij}, r_{ik}, \theta_{ijk}, \boldsymbol \eta), & \mbox{if } Z_i = p \\ + 0, & \mbox{if } Z_i \neq p + \end{array} + \right. + +for :math:`1 \le i \le N, 1 \le m \le N_{\rm r}, 1 \le n \le N_{\rm a}, 1 \le q, p, s \le N_{\rm e}`, +where + +.. math:: + + \ell(p,q,s) = \left\{ + \begin{array}{ll} + s + (q-1) N_{\rm e} - q(q-1)/2 + (p-1)N_{\rm e}(1+N_{\rm e})/2 , & \mbox{if } s \ge q \\ + q + (s-1) N_{\rm e} - s(s-1)/2 + (p-1)N_{\rm e}(1+N_{\rm e})/2, & \mbox{if } s < q . + \end{array} + \right. + +The number of three-body descriptors per atom is thus :math:`N_{\rm 3b} N_{\rm e}^2(N_{\rm e}+1)/2`. +While the number of three-body PODs is cubic function of the number of elements, +the computational complexity of the three-body PODs is independent of the number of elements. + +Four-Body SNAP Descriptors +"""""""""""""""""""""""""" + +In addition to the proper orthogonal descriptors described above, we also employ +the spectral neighbor analysis potential (SNAP) descriptors. SNAP uses bispectrum components +to characterize the local neighborhood of each atom in a very general way. The mathematical definition +of the bispectrum calculation and its derivatives w.r.t. atom positions is described in +:doc:`compute snap `. In SNAP, the +total energy is decomposed into a sum over atom energies. The energy of +atom *i* is expressed as a weighted sum over bispectrum components. + +.. math:: + + E_i^{\rm SNAP} = \sum_{k=1}^{N_{\rm 4b}} \sum_{p=1}^{N_{\rm e}} c_{kp}^{(4)} D_{ikp}^{(4)} + + +where the SNAP descriptors are related to the bispectrum components by + +.. math:: + + D^{(4)}_{ikp} = \left\{ + \begin{array}{ll} + \displaystyle B_{ik}, & \mbox{if } Z_i = p \\ + 0, & \mbox{if } Z_i \neq p + \end{array} + \right. + +Here :math:`B_{ik}` is the *k*\ -th bispectrum component of atom *i*. The number of +bispectrum components :math:`N_{\rm 4b}` depends on the value of *fourbody_snap_twojmax* :math:`= 2 J_{\rm max}` +and *fourbody_snap_chemflag*. If *fourbody_snap_chemflag* = 0 +then :math:`N_{\rm 4b} = (J_{\rm max}+1)(J_{\rm max}+2)(J_{\rm max}+1.5)/3`. +If *fourbody_snap_chemflag* = 1 then :math:`N_{\rm 4b} = N_{\rm e}^3 (J_{\rm max}+1)(J_{\rm max}+2)(J_{\rm max}+1.5)/3`. +The bispectrum calculation is described in more detail in :doc:`compute sna/atom `. + +Linear Proper Orthogonal Descriptor Potentials +"""""""""""""""""""""""""""""""""""""""""""""" + +The proper orthogonal descriptors and SNAP descriptors are used to define the atomic energies +in the following expansion + +.. math:: + + E_{i}(\boldsymbol \eta) = \sum_{p=1}^{N_{\rm e}} c^{(1)}_p D^{(1)}_{ip} + \sum_{m=1}^{N_{\rm 2b}} \sum_{l=1}^{N_{\rm e}(N_{\rm e}+1)/2} c^{(2)}_{ml} D^{(2)}_{iml}(\boldsymbol \eta) + \sum_{m=1}^{N_{\rm r}} \sum_{n=1}^{N_{\rm a}} \sum_{\ell=1}^{N_{\rm e}^2(N_{\rm e}+1)/2} c^{(3)}_{mn\ell} D^{(3)}_{imn\ell}(\boldsymbol \eta) + \sum_{k=1}^{N_{\rm 4b}} \sum_{p=1}^{N_{\rm e}} c_{kp}^{(4)} D_{ikp}^{(4)}(\boldsymbol \eta), + +where :math:`D^{(1)}_{ip}, D^{(2)}_{iml}, D^{(3)}_{imn\ell}, D^{(4)}_{ikp}` are the one-body, two-body, three-body, four-body descriptors, +respectively, and :math:`c^{(1)}_p, c^{(2)}_{ml}, c^{(3)}_{mn\ell}, c^{(4)}_{kp}` are their respective expansion +coefficients. In a more compact notation that implies summation over descriptor indices +the atomic energies can be written as + +.. math:: + + E_i(\boldsymbol \eta) = \sum_{m=1}^{N_{\rm e}} c^{(1)}_m D^{(1)}_{im} + \sum_{m=1}^{N_{\rm d}^{(2)}} c^{(2)}_k D^{(2)}_{im} + \sum_{m=1}^{N_{\rm d}^{(3)}} c^{(3)}_m D^{(3)}_{im} + \sum_{m=1}^{N_{\rm d}^{(4)}} c^{(4)}_m D^{(4)}_{im} + +where :math:`N_{\rm d}^{(2)} = N_{\rm 2b} N_{\rm e} (N_{\rm e}+1)/2`, +:math:`N_{\rm d}^{(3)} = N_{\rm 3b} N_{\rm e}^2 (N_{\rm e}+1)/2`, and +:math:`N_{\rm d}^{(4)} = N_{\rm 4b} N_{\rm e}` are +the number of two-body, three-body, and four-body descriptors, respectively. + +The potential energy is then obtained by summing local atomic energies :math:`E_i` +for all atoms :math:`i` in the system + +.. math:: + + E(\boldsymbol \eta) = \sum_{i}^N E_{i}(\boldsymbol \eta) + +Because the descriptors are one-body, two-body, and three-body terms, +the resulting POD potential is a three-body PES. We can express the potential +energy as a linear combination of the global descriptors as follows + +.. math:: + + E(\boldsymbol \eta) = \sum_{m=1}^{N_{\rm e}} c^{(1)}_m d^{(1)}_{m} + \sum_{m=1}^{N_{\rm d}^{(2)}} c^{(2)}_m d^{(2)}_{m} + \sum_{m=1}^{N_{\rm d}^{(3)}} c^{(3)}_m d^{(3)}_{m} + \sum_{m=1}^{N_{\rm d}^{(4)}} c^{(4)}_m d^{(4)}_{m} + +where the global descriptors are given by + +.. math:: + + d_{m}^{(1)}(\boldsymbol \eta) = \sum_{i=1}^N D_{im}^{(1)}(\boldsymbol \eta), \quad d_{m}^{(2)}(\boldsymbol \eta) = \sum_{i=1}^N D_{im}^{(2)}(\boldsymbol \eta), \quad d_{m}^{(3)}(\boldsymbol \eta) = \sum_{i=1}^N D_{im}^{(3)}(\boldsymbol \eta), \quad d_{m}^{(4)}(\boldsymbol \eta) = \sum_{i=1}^N D_{im}^{(4)}(\boldsymbol \eta) + +Hence, we obtain the atomic forces as + +.. math:: + + \boldsymbol F = -\nabla E(\boldsymbol \eta) = - \sum_{m=1}^{N_{\rm d}^{(2)}} c^{(2)}_m \nabla d_m^{(2)} - \sum_{m=1}^{N_{\rm d}^{(3)}} c^{(3)}_m \nabla d_m^{(3)} - \sum_{m=1}^{N_{\rm d}^{(4)}} c^{(4)}_m \nabla d_m^{(4)} + +where :math:`\nabla d_m^{(2)}`, :math:`\nabla d_m^{(3)}` and :math:`\nabla d_m^{(4)}` are derivatives of the two-body +three-body, and four-body global descriptors with respect to atom positions, respectively. +Note that since the first-body global descriptors are constant, their derivatives are zero. + +Quadratic Proper Orthogonal Descriptor Potentials +""""""""""""""""""""""""""""""""""""""""""""""""" + +We recall two-body PODs :math:`D^{(2)}_{ik}, 1 \le k \le N_{\rm d}^{(2)}`, +and three-body PODs :math:`D^{(3)}_{im}, 1 \le m \le N_{\rm d}^{(3)}`, +with :math:`N_{\rm d}^{(2)} = N_{\rm 2b} N_{\rm e} (N_{\rm e}+1)/2` and +:math:`N_{\rm d}^{(3)} = N_{\rm 3b} N_{\rm e}^2 (N_{\rm e}+1)/2` being +the number of descriptors per atom for the two-body PODs and three-body PODs, +respectively. We employ them to define a new set of atomic descriptors as follows + +.. math:: + + D^{(2*3)}_{ikm} = \frac{1}{2N}\left( D^{(2)}_{ik} \sum_{j=1}^N D^{(3)}_{jm} + D^{(3)}_{im} \sum_{j=1}^N D^{(2)}_{jk} \right) + +for :math:`1 \le i \le N, 1 \le k \le N_{\rm d}^{(2)}, 1 \le m \le N_{\rm d}^{(3)}`. +The new descriptors are four-body because they involve central atom :math:`i` together +with three neighbors :math:`j, k` and :math:`l`. The total number of new descriptors per atom is equal to + +.. math:: + + N_{\rm d}^{(2*3)} = N_{\rm d}^{(2)} * N_{\rm d}^{(3)} = N_{\rm 2b} N_{\rm 3b} N_{\rm e}^3 (N_{\rm e}+1)^2/4 . + +The new global descriptors are calculated as + +.. math:: + + d^{(2*3)}_{km} = \sum_{i=1}^N D^{(2*3)}_{ikm} = \left( \sum_{i=1}^N D^{(2)}_{ik} \right) \left( \sum_{i=1}^N D^{(3)}_{im} \right) = d^{(2)}_{k} d^{(3)}_m, + +for :math:`1 \le k \le N_{\rm d}^{(2)}, 1 \le m \le N_{\rm d}^{(3)}`. Hence, the gradient +of the new global descriptors with respect to atom positions is calculated as + +.. math:: + + \nabla d^{(2*3)}_{km} = d^{(3)}_m \nabla d^{(2)}_{k} + d^{(2)}_{k} \nabla d^{(3)}_m, \quad 1 \le k \le N_{\rm d}^{(2)}, 1 \le m \le N_{\rm d}^{(3)} . + +The quadratic POD potential is defined as a linear combination of the +original and new global descriptors as follows + +.. math:: + + E^{(2*3)} = \sum_{k=1}^{N_{\rm 2d}^{(2*3)}} \sum_{m=1}^{N_{\rm 3d}^{(2*3)}} c^{(2*3)}_{km} d^{(2*3)}_{km} . + +It thus follows that + +.. math:: + + E^{(2*3)} = 0.5 \sum_{k=1}^{N_{\rm 2d}^{(2*3)}} \left( \sum_{m=1}^{N_{\rm 3d}^{(2*3)}} c^{(2*3)}_{km} d_m^{(3)} \right) d_k^{(2)} + 0.5 \sum_{m=1}^{N_{\rm 3d}^{(2*3)}} \left( \sum_{k=1}^{N_{\rm 2d}^{(2*3)}} c^{(2*3)}_{km} d_k^{(2)} \right) d_m^{(3)} , + +which is simplified to + +.. math:: + + E^{(2*3)} = 0.5 \sum_{k=1}^{N_{\rm 2d}^{(2*3)}} b_k^{(2)} d_k^{(2)} + 0.5 \sum_{m=1}^{N_{\rm 3d}^{(2*3)}} b_m^{(3)} d_m^{(3)} + +where + +.. math:: + + b_k^{(2)} & = \sum_{m=1}^{N_{\rm 3d}^{(2*3)}} c^{(2*3)}_{km} d_m^{(3)}, \quad k = 1,\ldots, N_{\rm 2d}^{(2*3)}, \\ + b_m^{(3)} & = \sum_{k=1}^{N_{\rm 2d}^{(2*3)}} c^{(2*3)}_{km} d_k^{(2)}, \quad m = 1,\ldots, N_{\rm 3d}^{(2*3)} . + +The quadratic POD potential results in the following atomic forces + +.. math:: + + \boldsymbol F^{(2*3)} = - \sum_{k=1}^{N_{\rm 2d}^{(2*3)}} \sum_{m=1}^{N_{\rm 3d}^{(2*3)}} c^{(2*3)}_{km} \nabla d^{(2*3)}_{km} . + +It can be shown that + +.. math:: + + \boldsymbol F^{(2*3)} = - \sum_{k=1}^{N_{\rm 2d}^{(2*3)}} b^{(2)}_k \nabla d_k^{(2)} - \sum_{m=1}^{N_{\rm 3d}^{(2*3)}} b^{(3)}_m \nabla d_m^{(3)} . + +The calculation of the atomic forces for the quadratic POD potential +only requires the extra calculation of :math:`b_k^{(2)}` and :math:`b_m^{(3)}` which can be negligible. +As a result, the quadratic POD potential does not increase the computational complexity. + + +Training +"""""""" + +POD potentials are trained using the least-squares regression against +density functional theory (DFT) data. Let :math:`J` be the number of +training configurations, with :math:`N_j` being the number of atoms in +the j-th configuration. Let :math:`\{E^{\star}_j\}_{j=1}^{J}` and +:math:`\{\boldsymbol F^{\star}_j\}_{j=1}^{J}` be the DFT energies and +forces for :math:`J` configurations. Next, we calculate the global +descriptors and their derivatives for all training configurations. Let +:math:`d_{jm}, 1 \le m \le M`, be the global descriptors associated with +the j-th configuration, where :math:`M` is the number of global +descriptors. We then form a matrix :math:`\boldsymbol A \in +\mathbb{R}^{J \times M}` with entries :math:`A_{jm} = d_{jm}/ N_j` for +:math:`j=1,\ldots,J` and :math:`m=1,\ldots,M`. Moreover, we form a +matrix :math:`\boldsymbol B \in \mathbb{R}^{\mathcal{N} \times M}` by +stacking the derivatives of the global descriptors for all training +configurations from top to bottom, where :math:`\mathcal{N} = +3\sum_{j=1}^{J} N_j`. + +The coefficient vector :math:`\boldsymbol c` of the POD potential is +found by solving the following least-squares problem + +.. math:: + + {\min}_{\boldsymbol c \in \mathbb{R}^{M}} \ w_E \|\boldsymbol A(\boldsymbol \eta) \boldsymbol c - \bar{\boldsymbol E}^{\star} \|^2 + w_F \|\boldsymbol B(\boldsymbol \eta) \boldsymbol c + \boldsymbol F^{\star} \|^2 + w_R \|\boldsymbol c \|^2, + +where :math:`w_E` and :math:`w_F` are weights for the energy +(*fitting_weight_energy*) and force (*fitting_weight_force*), +respectively; and :math:`w_R` is the regularization parameter (*fitting_regularization_parameter*). Here :math:`\bar{\boldsymbol E}^{\star} \in +\mathbb{R}^{J}` is a vector of with entries :math:`\bar{E}^{\star}_j = +E^{\star}_j/N_j` and :math:`\boldsymbol F^{\star}` is a vector of +:math:`\mathcal{N}` entries obtained by stacking :math:`\{\boldsymbol +F^{\star}_j\}_{j=1}^{J}` from top to bottom. + +The training procedure is the same for both the linear and quadratic POD +potentials. However, since the quadratic POD potential has a +significantly larger number of the global descriptors, it is more +expensive to train the linear POD potential. This is because the +training of the quadratic POD potential still requires us to calculate +and store the quadratic global descriptors and their +gradient. Furthermore, the quadratic POD potential may require more +training data in order to prevent over-fitting. In order to reduce the +computational cost of fitting the quadratic POD potential and avoid +over-fitting, we can use subsets of two-body and three-body PODs for +constructing the new descriptors. + + +Restrictions +"""""""""""" + +This command is part of the ML-POD package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package +` page for more info. + +Related commands +"""""""""""""""" + +:doc:`pair_style pod ` + +Default +""""""" + +The keyword defaults are also given in the description of the input files. + +---------- + +.. _Grepl20072: + +**(Grepl)** Grepl, Maday, Nguyen, and Patera, ESAIM: Mathematical Modelling and Numerical Analysis 41(3), 575-605, (2007). + +.. _Nguyen20222: + +**(Nguyen)** Nguyen and Rohskopf, arXiv preprint arXiv:2209.02362 (2022). diff --git a/doc/src/fix.rst b/doc/src/fix.rst index 5a082da38c..30dd996e4b 100644 --- a/doc/src/fix.rst +++ b/doc/src/fix.rst @@ -222,9 +222,9 @@ accelerated styles exist. * :doc:`edpd/source ` - add heat source to eDPD simulations * :doc:`efield ` - impose electric field on system * :doc:`ehex ` - enhanced heat exchange algorithm -* :doc:`electrode/conp ` - impose electric potential -* :doc:`electrode/conq ` - impose total electric charge -* :doc:`electrode/thermo ` - apply thermo-potentiostat +* :doc:`electrode/conp ` - impose electric potential +* :doc:`electrode/conq ` - impose total electric charge +* :doc:`electrode/thermo ` - apply thermo-potentiostat * :doc:`electron/stopping ` - electronic stopping power as a friction force * :doc:`electron/stopping/fit ` - electronic stopping power as a friction force * :doc:`enforce2d ` - zero out *z*-dimension velocity and force diff --git a/doc/src/fix_electrode.rst b/doc/src/fix_electrode.rst new file mode 100644 index 0000000000..9da8dcbdf9 --- /dev/null +++ b/doc/src/fix_electrode.rst @@ -0,0 +1,421 @@ +.. index:: fix electrode/conp +.. index:: fix electrode/conq +.. index:: fix electrode/thermo +.. index:: fix electrode/conp/intel +.. index:: fix electrode/conq/intel +.. index:: fix electrode/thermo/intel + +fix electrode/conp command +========================== + +Accelerator Variant: *electrode/conp/intel* + +fix electrode/conq command +========================== + +Accelerator Variant: *electrode/conq/intel* + +fix electrode/thermo command +============================ + +Accelerator Variant: *electrode/thermo/intel* + +Syntax +"""""" + +.. code-block:: LAMMPS + + fix ID group-ID style args keyword value ... + +* ID, group-ID are documented in :doc:`fix ` command +* style = *electrode/conp* or *electrode/conq* or *electrode/thermo* +* args = arguments used by a particular style + + .. parsed-literal:: + + *electrode/conp* args = potential eta + *electrode/conq* args = charge eta + *electrode/thermo* args = potential eta *temp* values + potential = electrode potential + charge = electrode charge + eta = reciprocal width of electrode charge smearing + *temp* values = T_v tau_v rng_v + T_v = temperature of thermo-potentiostat + tau_v = time constant of thermo-potentiostat + rng_v = integer used to initialize random number generator + +* zero or more keyword/value pairs may be appended +* keyword = *algo* or *symm* or *couple* or *etypes* or *ffield* or *write_mat* or *write_inv* or *read_mat* or *read_inv* + +.. parsed-literal:: + + *algo* values = *mat_inv* or *mat_cg* tol or *cg* tol + specify the algorithm used to compute the electrode charges + *symm* value = *on* or *off* + turn on/off charge neutrality constraint for the electrodes + *couple* values = group-ID val + group-ID = group of atoms treated as additional electrode + val = electric potential or charge on this electrode + *etypes* value = *on* or *off* + turn on/off type-based optimized neighbor lists (electrode and electrolyte types may not overlap) + *ffield* value = *on* or *off* + turn on/off finite-field implementation + *write_mat* value = filename + filename = file to which to write elastance matrix + *write_inv* value = filename + filename = file to which to write inverted matrix + *read_mat* value = filename + filename = file from which to read elastance matrix + *read_inv* value = filename + filename = file from which to read inverted matrix + +Examples +"""""""" + +.. code-block:: LAMMPS + + fix fxconp bot electrode/conp -1.0 1.805 couple top 1.0 couple ref 0.0 write_inv inv.csv symm on + fix fxconp electrodes electrode/conq 0.0 1.805 algo cg 1e-5 + fix fxconp bot electrode/thermo -1.0 1.805 temp 298 100 couple top 1.0 + +Description +""""""""""" + +The *electrode* fixes implement the constant potential method (CPM) +(:ref:`Siepmann `, :ref:`Reed `), and modern variants, +to accurately model electrified, conductive electrodes. This is +primarily useful for studying electrode-electrolyte interfaces, +especially at high potential differences or ionicities, with non-planar +electrodes such as nanostructures or nanopores, and to study dynamic +phenomena such as charging or discharging time scales or conductivity or +ionic diffusivities. + +Each *electrode* fix allows users to set additional electrostatic +relationships between the specified groups which model useful +electrostatic configurations: + +* *electrode/conp* sets potentials or potential differences between electrodes + + * (resulting in changing electrode total charges) + +* *electrode/conq* sets the total charge on each electrode + + * (resulting in changing electrode potentials) + +* *electrode/thermo* sets a thermopotentiostat + :ref:`(Deissenbeck)` between two electrodes + + * (resulting in changing charges and potentials with appropriate + average potential difference and thermal variance) + +The first group-ID provided to each fix specifies the first electrode +group, and more group(s) are added using the *couple* keyword for each +additional group. While *electrode/thermo* only accepts two groups, +*electrode/conp* and *electrode/conq* accept any number of groups, up to +LAMMPS's internal restrictions (see Restrictions below). Electrode +groups must not overlap, i.e. the fix will issue an error if any +particle is detected to belong to at least two electrode groups. + +CPM involves updating charges on groups of electrode particles, per time +step, so that the system's total energy is minimized with respect to +those charges. From basic electrostatics, this is equivalent to making +each group conductive, or imposing an equal electrostatic potential on +every particle in the same group (hence the name CPM). The charges are +usually modelled as a Gaussian distribution to make the charge-charge +interaction matrix invertible (:ref:`Gingrich `). The keyword +*eta* specifies the distribution's width in units of inverse length. + +.. versionadded:: TBD + +Three algorithms are available to minimize the energy, varying in how +matrices are pre-calculated before a run to provide computational +speedup. These algorithms can be selected using the keyword *algo*: + +* *algo mat_inv* pre-calculates the capacitance matrix and obtains the + charge configuration in one matrix-vector calculation per time step + +* *algo mat_cg* pre-calculates the elastance matrix (inverse of + capacitance matrix) and obtains the charge configuration using a + conjugate gradient solver in multiple matrix-vector calculations per + time step + +* *algo cg* does not perform any pre-calculation and obtains the charge + configuration using a conjugate gradient solver and multiple + calculations of the electric potential per time step. + +For both *cg* methods, the command must specify the conjugate gradient +tolerance. *fix electrode/thermo* currently only supports the *mat_inv* +algorithm. + +The keyword *symm* can be set *on* (or *off*) to turn on (or turn off) +the capacitance matrix constraint that sets total electrode charge to be +zero. This has slightly different effects for each *fix electrode* +variant. For *fix electrode/conp*, with *symm off*, the potentials +specified are absolute potentials, but the charge configurations +satisfying them may add up to an overall non-zero, varying charge for +the electrodes (and thus the simulation box). With *symm on*, the total +charge over all electrode groups is constrained to zero, and potential +differences rather than absolute potentials are the physically relevant +quantities. + +For *fix electrode/conq*, with *symm off*, overall neutrality is +explicitly obeyed or violated by the user input (which is not +checked!). With *symm on*, overall neutrality is ensured by ignoring the +user-input charge for the last listed electrode (instead, its charge +will always be minus the total sum of all other electrode charges). For +*fix electrode/thermo*, overall neutrality is always automatically +imposed for any setting of *symm*, but *symm on* allows finite-field +mode (*ffield on*, described below) for faster simulations. + +For all three fixes, any potential (or charge for *conq*) can be +specified as an equal-style variable prefixed with "v\_". For example, +the following code will ramp the potential difference between electrodes +from 0.0V to 2.0V over the course of the simulation: + +.. code-block:: LAMMPS + + fix fxconp bot electrode/conp 0.0 1.805 couple top v_v symm on + variable v equal ramp(0.0, 2.0) + +Note that these fixes only parse their supplied variable name when +starting a run, and so these fixes will accept equal-style variables +defined *after* the fix definition, including variables dependent on the +fix's own output. This is useful, for example, in the fix's internal +finite-field commands (see below). For an advanced example of this see +the in.conq2 input file in the directory +``examples/PACKAGES/electrode/graph-il``. + +This fix necessitates the use of a long range solver that calculates and +provides the matrix of electrode-electrode interactions and a vector of +electrode-electrolyte interactions. The Kspace styles +*ewald/electrode*, *pppm/electrode* and *pppm/electrode/intel* are +created specifically for this task :ref:`(Ahrens-Iwers) `. + +For systems with non-periodic boundaries in one or two directions dipole +corrections are available with the :doc:`kspace_modify `. +For ewald/electrode a two-dimensional Ewald summation :ref:`(Hu) ` +can be used by setting "slab ew2d": + +.. code-block:: LAMMPS + + kspace_modify slab + kspace_modify wire + kspace_modify slab ew2d + +Two implementations for the calculation of the elastance matrix are +available with pppm and can be selected using the *amat onestep/twostep* +keyword. *onestep* is the default; *twostep* can be faster for large +electrodes and a moderate mesh size but requires more memory. + +.. code-block:: LAMMPS + + kspace_modify amat onestep/twostep + +For all versions of the fix, the keyword-value *ffield on* enables the +finite-field mode (:ref:`Dufils `, :ref:`Tee `), which uses +an electric field across a periodic cell instead of non-periodic +boundary conditions to impose a potential difference between the two +electrodes bounding the cell. The fix (with name *fix-ID*) detects which +of the two electrodes is "on top" (has the larger maximum *z*-coordinate +among all particles). Assuming the first electrode group is on top, it +then issues the following commands internally: + +.. code-block:: LAMMPS + + variable fix-ID_ffield_zfield equal (f_fix-ID[2]-f_fix-ID[1])/lz + efield fix-ID_efield all efield 0.0 0.0 v_fix-ID_ffield_zfield + +which implements the required electric field as the potential difference +divided by cell length. The internal commands use variable so that the +electric field will correctly vary with changing potentials in the +correct way (for example with equal-style potential difference or with +*fix electrode/conq*). This keyword requires two electrodes and will +issue an error with any other number of electrodes. This keyword +requires electroneutrality to be imposed (*symm on*) and will issue an +error otherwise. + +.. versionchanged:: TBD + +For all versions of the fix, the keyword-value *etypes on* enables +type-based optimized neighbor lists. With this feature enabled, LAMMPS +provides the fix with an occasional neighbor list restricted to +electrode-electrode interactions for calculating the electrode matrix, +and a perpetual neighbor list restricted to electrode-electrolyte +interactions for calculating the electrode potentials, using particle +types to list only desired interactions, and typically resulting in +5--10\% less computational time. Without this feature the fix will +simply use the active pair style's neighbor list. This feature cannot +be enabled if any electrode particle has the same type as any +electrolyte particle (which would be unusual in a typical simulation) +and the fix will issue an error in that case. + +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +This fix currently does not write any information to restart files. + +The *fix_modify tf* option enables the Thomas-Fermi metallicity model +(:ref:`Scalfi `) and allows parameters to be set for each atom type. + +.. code-block:: LAMMPS + + fix_modify ID tf type length voronoi + + +If this option is used parameters must be set for all atom types of the +electrode. + +The *fix_modify timer* option turns on (off) additional timer outputs in the log +file, for code developers to track optimization. + +.. code-block:: LAMMPS + + fix_modify ID timer on/off + +---------- + +These fixes compute a global (extensive) scalar, a global (intensive) +vector, and a global array, which can be accessed by various +:doc:`output commands `. + +The global scalar outputs the energy added to the system by this fix, +which is the negative of the total charge on each electrode multiplied +by that electrode's potential. + +The global vector outputs the potential on each electrode (and thus has +*N* entries if the fix manages *N* electrode groups), in :doc:`units +` of electric field multiplied by distance (thus volts for *real* +and *metal* units). The electrode groups' ordering follows the order in +which they were input in the fix command using *couple*. The global +vector output is useful for *fix electrode/conq* and *fix +electrode/thermo*, where potential is dynamically updated based on +electrolyte configuration instead of being directly set. + +The global array has *N* rows and *2N+1* columns, where the fix manages +*N* electrode groups managed by the fix. For the *I*-th row of the +array, the elements are: + +* array[I][1] = total charge that group *I* would have had *if it were + at 0 V applied potential* * array[I][2 to *N* + 1] = the *N* entries + of the *I*-th row of the electrode capacitance matrix (definition + follows) * array[I][*N* + 2 to *2N* + 1] = the *N* entries of the + *I*-th row of the electrode elastance matrix (the inverse of the + electrode capacitance matrix) + +The :math:`N \times N` electrode capacitance matrix, denoted :math:`\mathbf{C}` +in the following equation, summarizes how the total charge induced on each +electrode (:math:`\mathbf{Q}` as an *N*-vector) is related to the potential on +each electrode, :math:`\mathbf{V}`, and the charge-at-0V :math:`\mathbf{Q}_{0V}` +(which is influenced by the local electrolyte structure): + +.. math:: + + \mathbf{Q} = \mathbf{Q}_{0V} + \mathbf{C} \cdot \mathbf{V} + +The charge-at-0V, electrode capacitance and elastance matrices are internally +used to calculate the potentials required to induce the specified total +electrode charges in *fix electrode/conq* and *fix electrode/thermo*. With the +*symm on* option, the electrode capacitance matrix would be singular, and thus +its last row is replaced with *N* copies of its top-left entry +(:math:`\mathbf{C}_{11}`) for invertibility. + +The global array output is mainly useful for quickly determining the 'vacuum +capacitance' of the system (capacitance with only electrodes, no electrolyte), +and can also be used for advanced simulations setting the potential as some +function of the charge-at-0V (such as the ``in.conq2`` example mentioned above). + +Please cite :ref:`(Ahrens-Iwers2022) ` in any publication that +uses this implementation. Please cite also the publication on the combination +of the CPM with PPPM if you use *pppm/electrode* :ref:`(Ahrens-Iwers) +`. + +---------- + +Restrictions +"""""""""""" + +For algorithms that use a matrix for the electrode-electrode +interactions, positions of electrode particles have to be immobilized at +all times. + +With *ffield off* (i.e. the default), the box geometry is expected to be +*z*-non-periodic (i.e. *boundary p p f*), and this fix will issue an +error if the box is *z*-periodic. With *ffield on*, the box geometry is +expected to be *z*-periodic, and this fix will issue an error if the box +is *z*-non-periodic. + +The parallelization for the fix works best if electrode atoms are evenly +distributed across processors. For a system with two electrodes at the bottom +and top of the cell this can be achieved with *processors * * 2*, or with the +line + +.. code-block:: LAMMPS + + if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2" + +which avoids an error if the script is run on an odd number of +processors (such as on just one processor for testing). + +The fix creates an additional group named *[fix-ID]_group* which is the +union of all electrode groups supplied to LAMMPS. This additional group +counts towards LAMMPS's limitation on the total number of groups +(currently 32), which may not allow scripts that use that many groups to +run with this fix. + +The matrix-based algorithms (*algo mat_inv* and *algo mat_cg*) currently +store an interaction matrix (either elastance or capacitance) of *N* by +*N* doubles for each MPI process. This memory requirement may be +prohibitive for large electrode groups. The fix will issue a warning if +it expects to use more than 0.5 GiB of memory. + +Default +""""""" + +The default keyword-option settings are *algo mat_inv*, *symm off*, +*etypes off* and *ffield off*. + +---------- + +.. include:: accel_styles.rst + +---------- + +.. _Siepmann: + +**(Siepmann)** Siepmann and Sprik, J. Chem. Phys. 102, 511 (1995). + +.. _Reed3: + +**(Reed)** Reed *et al.*, J. Chem. Phys. 126, 084704 (2007). + +.. _Deissenbeck: + +**(Deissenbeck)** Deissenbeck *et al.*, Phys. Rev. Letters 126, 136803 (2021). + +.. _Gingrich: + +**(Gingrich)** Gingrich, `MSc thesis` ` (2010). + +.. _Ahrens-Iwers: + +**(Ahrens-Iwers)** Ahrens-Iwers and Meissner, J. Chem. Phys. 155, 104104 (2021). + +.. _Hu: + +**(Hu)** Hu, J. Chem. Theory Comput. 10, 5254 (2014). + +.. _Dufils: + +**(Dufils)** Dufils *et al.*, Phys. Rev. Letters 123, 195501 (2019). + +.. _Tee: + +**(Tee)** Tee and Searles, J. Chem. Phys. 156, 184101 (2022). + +.. _Scalfi: + +**(Scalfi)** Scalfi *et al.*, J. Chem. Phys., 153, 174704 (2020). + +.. _Ahrens-Iwers2: + +**(Ahrens-Iwers2022)** Ahrens-Iwers *et al.*, J. Chem. Phys. 157, 084801 (2022). diff --git a/doc/src/fix_electrode_conp.rst b/doc/src/fix_electrode_conp.rst deleted file mode 100644 index e070433c07..0000000000 --- a/doc/src/fix_electrode_conp.rst +++ /dev/null @@ -1,230 +0,0 @@ -.. index:: fix electrode/conp -.. index:: fix electrode/conq -.. index:: fix electrode/thermo -.. index:: fix electrode/conp/intel -.. index:: fix electrode/conq/intel -.. index:: fix electrode/thermo/intel - -fix electrode/conp command -========================== - -Accelerator Variant: *electrode/conp/intel* - -fix electrode/conq command -========================== - -Accelerator Variant: *electrode/conq/intel* - -fix electrode/thermo command -============================ - -Accelerator Variant: *electrode/thermo/intel* - -Syntax -"""""" - -.. parsed-literal:: - - fix ID group-ID style args keyword value ... - -* ID, group-ID are documented in :doc:`fix ` command -* style = *electrode/conp* or *electrode/conq* or *electrode/thermo* -* args = arguments used by a particular style - - .. parsed-literal:: - - *electrode/conp* args = potential eta - *electrode/conq* args = charge eta - *electrode/thermo* args = potential eta *temp* values - potential = electrode potential - charge = electrode charge - eta = reciprocal width of electrode charge smearing - *temp* values = T_v tau_v rng_v - T_v = temperature of thermo-potentiostat - tau_v = time constant of thermo-potentiostat - rng_v = integer used to initialize random number generator - -* zero or more keyword/value pairs may be appended -* keyword = *symm* or *couple* or *etypes* or *ffield* or *write_mat* or *write_inv* or *read_mat* or *read_inv* - -.. parsed-literal:: - - *symm* value = *on* or *off* - turn on/off charge neutrality constraint for the electrodes - *couple* values = group-ID val - group-ID = group of atoms treated as additional electrode - val = electric potential or charge on this electrode - *etypes* values = type - type = atom type (can be a range) exclusive to the electrode for optimized neighbor lists - *ffield* value = *on* or *off* - turn on/off finite-field implementation - *write_mat* value = filename - filename = file to which to write elastance matrix - *write_inv* value = filename - filename = file to which to write inverted matrix - *read_mat* value = filename - filename = file from which to read elastance matrix - *read_inv* value = filename - filename = file from which to read inverted matrix - -Examples -"""""""" - -.. code-block:: LAMMPS - - fix fxconp bot electrode/conp -1.0 1.805 couple top 1.0 couple ref 0.0 write_inv inv.csv symm on - fix fxconp electrodes electrode/conq 0.0 1.805 - fix fxconp bot electrode/thermo -1.0 1.805 temp 298 100 couple top 1.0 - -Description -""""""""""" - -fix electrode/conp mode implements a constant potential method (CPM) -(:ref:`Siepmann `, :ref:`Reed `). Charges of groups specified -via group-ID and optionally with the `couple` keyword are adapted to meet their respective -potential at every time step. An arbitrary number of electrodes can be set but -the respective groups may not overlap. Electrode charges have a Gaussian charge -distribution with reciprocal width eta. The energy minimization is achieved via -matrix inversion :ref:`(Wang) `. - -fix electrode/conq enforces a total charge specified in the input on each electrode. The energy is -minimized w.r.t. the charge distribution within the electrode. - -fix electrode/thermo implements a thermo-potentiostat :ref:`(Deissenbeck) -`. Temperature and time constant of the thermo-potentiostat need -to be specified using the temp keyword. Currently, only two electrodes are possible with -this style. - -This fix necessitates the use of a long range solver that calculates and provides the matrix -of electrode-electrode interactions and a vector of electrode-electrolyte -interactions. The Kspace styles *ewald/electrode*, *pppm/electrode* and -*pppm/electrode/intel* are created specifically for this task -:ref:`(Ahrens-Iwers) `. - -For systems with non-periodic boundaries in one or two directions dipole -corrections are available with the :doc:`kspace_modify `. For -ewald/electrode a two-dimensional Ewald summation :ref:`(Hu) ` can be used -by setting "slab ew2d": - -.. code-block:: LAMMPS - - kspace_modify slab - kspace_modify wire - kspace_modify slab ew2d - -Two implementations for the calculation of the elastance matrix are available -with pppm and can be selected using the *amat onestep/twostep* keyword. -*onestep* is the default; *twostep* can be faster for large electrodes and a -moderate mesh size but requires more memory. - -.. code-block:: LAMMPS - - kspace_modify amat onestep/twostep - - -The *fix_modify tf* option enables the Thomas-Fermi metallicity model -(:ref:`Scalfi `) and allows parameters to be set for each atom type. - -.. code-block:: LAMMPS - - fix_modify ID tf type length voronoi - - -If this option is used parameters must be set for all atom types of the electrode. - -The *fix_modify timer* option turns on (off) additional timer outputs in the log -file, for code developers to track optimization. - -.. code-block:: LAMMPS - - fix_modify ID timer on/off - -The *fix_modify set* options allow calculated quantities to be accessed via -internal variables. Currently four types of quantities can be accessed: - -.. code-block:: LAMMPS - - fix-modify ID set v group-ID variablename - fix-modify ID set qsb group-ID variablename - fix-modify ID set mc group-ID1 group-ID2 variablename - fix-modify ID set me group-ID1 group-ID2 variablename - -One use case is to output the potential that is internally calculated and -applied to each electrode group by *fix electrode/conq* or *fix electrode/thermo*. -For that case the *v* option makes *fix electrode* update the variable -*variablename* with the potential applied to group *group-ID*, where *group-ID* -must be a group whose charges are updated by *fix electrode* and *variablename* -must be an internal-style variable: - -.. code-block:: LAMMPS - - fix conq bot electrode/conq -1.0 1.979 couple top 1.0 - variable vbot internal 0.0 - fix_modify conq set v bot vbot - -The *qsb* option similarly outputs the total updated charge of the group if its -potential were 0.0V. The *mc* option requires two *group-IDs*, and outputs the -entry \{*group-ID1*, *group-ID2*\} of the (symmetric) *macro-capacitance* matrix -(MC) which relates the electrodes' applied potentials (V), total charges (Q), and -total charges at 0.0 V (Qsb): - -.. math:: - - \mathbf{Q} = \mathbf{Q}_{SB} + \mathbf{MC} \cdot \mathbf{V} - -Lastly, the *me* option also requires two *group-IDs* and outputs the entry -\{*group-ID1*, *group-ID2*\} of the *macro-elastance* matrix, which is the -inverse of the macro-capacitance matrix. (As the names denote, the -macro-capacitance matrix gives electrode charges from potentials, and the -macro-elastance matrix gives electrode potentials from charges). - -.. warning:: - - Positions of electrode particles have to be immobilized at all times. - -The parallelization for the fix works best if electrode atoms are evenly -distributed across processors. For a system with two electrodes at the bottom -and top of the cell this can be achieved with *processors * * 2*, or with the -line - -.. code-block:: LAMMPS - - if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2" - -which avoids an error if the script is run on an odd number of processors (such -as on just one processor for testing). - ----------- - -.. include:: accel_styles.rst - ----------- - -.. _Siepmann: - -**(Siepmann)** Siepmann and Sprik, J. Chem. Phys. 102, 511 (1995). - -.. _Reed3: - -**(Reed)** Reed *et al.*, J. Chem. Phys. 126, 084704 (2007). - -.. _Wang5: - -**(Wang)** Wang *et al.*, J. Chem. Phys. 141, 184102 (2014). - -.. _Deissenbeck: - -**(Deissenbeck)** Deissenbeck *et al.*, Phys. Rev. Letters 126, 136803 (2021). - -.. _Ahrens-Iwers: - -**(Ahrens-Iwers)** Ahrens-Iwers and Meissner, J. Chem. Phys. 155, 104104 (2021). - -.. _Hu: - -**(Hu)** Hu, J. Chem. Theory Comput. 10, 5254 (2014). - -.. _Scalfi: - -**(Scalfi)** Scalfi *et al.*, J. Chem. Phys., 153, 174704 (2020). - diff --git a/doc/src/kspace_style.rst b/doc/src/kspace_style.rst index cbaa82d547..38a6fce375 100644 --- a/doc/src/kspace_style.rst +++ b/doc/src/kspace_style.rst @@ -283,7 +283,7 @@ parameters and how to choose them is described in ---------- The *electrode* styles add methods that are required for the constant potential -method implemented in :doc:`fix electrode/* `. The styles +method implemented in :doc:`fix electrode/* `. The styles *ewald/electrode*, *pppm/electrode* and *pppm/electrode/intel* are available. These styles do not support the `kspace_modify slab nozforce` command. diff --git a/doc/src/pair_pod.rst b/doc/src/pair_pod.rst new file mode 100644 index 0000000000..0aa6250dab --- /dev/null +++ b/doc/src/pair_pod.rst @@ -0,0 +1,97 @@ +.. index:: pair_style pod + +pair_style pod command +======================== + +Syntax +"""""" + +.. code-block:: LAMMPS + + pair_style pod + +Examples +"""""""" + +.. code-block:: LAMMPS + + pair_style pod + pair_coeff * * Ta_param.pod Ta_coefficients.pod Ta + +Description +""""""""""" + +.. versionadded:: TBD + +Pair style *pod* defines the proper orthogonal descriptor (POD) +potential :ref:`(Nguyen) `. The mathematical definition of +the POD potential is described from :doc:`fitpod `, which is +used to fit the POD potential to *ab initio* energy and force data. + +Only a single pair_coeff command is used with the *pod* style which +specifies a POD parameter file followed by a coefficient file. + +The coefficient file (``Ta_coefficients.pod``) contains coefficients for the +POD potential. The top of the coefficient file can contain any number of +blank and comment lines (start with #), but follows a strict format +after that. The first non-blank non-comment line must contain: + +* POD_coefficients: *ncoeff* + +This is followed by *ncoeff* coefficients, one per line. The coefficient +file is generated after training the POD potential using :doc:`fitpod +`. + +The POD parameter file (``Ta_param.pod``) can contain blank and comment lines +(start with #) anywhere. Each non-blank non-comment line must contain +one keyword/value pair. See :doc:`fitpod ` for the description +of all the keywords that can be assigned in the parameter file. + +As an example, if a LAMMPS indium phosphide simulation has 4 atoms +types, with the first two being indium and the third and fourth being +phophorous, the pair_coeff command would look like this: + +.. code-block:: LAMMPS + + pair_coeff * * pod InP_param.pod InP_coefficients.pod In In P P + +The first 2 arguments must be \* \* so as to span all LAMMPS atom types. +The two filenames are for the parameter and coefficient files, respectively. +The two trailing 'In' arguments map LAMMPS atom types 1 and 2 to the +POD 'In' element. The two trailing 'P' arguments map LAMMPS atom types +3 and 4 to the POD 'P' element. + +If a POD mapping value is specified as NULL, the mapping is not +performed. This can be used when a *pod* potential is used as part of +the *hybrid* pair style. The NULL values are placeholders for atom +types that will be used with other potentials. + +Examples about training and using POD potentials are found in the +directory lammps/examples/PACKAGES/pod. + +---------- + +Restrictions +"""""""""""" + +This style is part of the ML-POD package. It is only enabled if LAMMPS +was built with that package. See the :doc:`Build package +` page for more info. + +This pair style does not compute per-atom energies and per-atom stresses. + +Related commands +"""""""""""""""" + +:doc:`fitpod `, + +Default +""""""" + +none + +---------- + +.. _Nguyen20221: + +**(Nguyen)** Nguyen and Rohskopf, arXiv preprint arXiv:2209.02362 (2022). diff --git a/doc/src/pair_style.rst b/doc/src/pair_style.rst index 2249eb3c58..48daf34f17 100644 --- a/doc/src/pair_style.rst +++ b/doc/src/pair_style.rst @@ -314,6 +314,7 @@ accelerated styles exist. * :doc:`oxrna2/xstk ` - * :doc:`pace ` - Atomic Cluster Expansion (ACE) machine-learning potential * :doc:`pace/extrapolation ` - Atomic Cluster Expansion (ACE) machine-learning potential with extrapolation grades +* :doc:`pod ` - Proper orthogonal decomposition (POD) machine-learning potential * :doc:`peri/eps ` - peridynamic EPS potential * :doc:`peri/lps ` - peridynamic LPS potential * :doc:`peri/pmb ` - peridynamic PMB potential diff --git a/doc/utils/check-packages.py b/doc/utils/check-packages.py old mode 100755 new mode 100644 diff --git a/doc/utils/check-styles.py b/doc/utils/check-styles.py old mode 100755 new mode 100644 diff --git a/doc/utils/converters/lammpsdoc/doc_anchor_check.py b/doc/utils/converters/lammpsdoc/doc_anchor_check.py old mode 100755 new mode 100644 diff --git a/doc/utils/converters/lammpsdoc/rst_anchor_check.py b/doc/utils/converters/lammpsdoc/rst_anchor_check.py old mode 100755 new mode 100644 diff --git a/doc/utils/converters/lammpsdoc/txt2html.py b/doc/utils/converters/lammpsdoc/txt2html.py old mode 100755 new mode 100644 diff --git a/doc/utils/converters/lammpsdoc/txt2rst.py b/doc/utils/converters/lammpsdoc/txt2rst.py old mode 100755 new mode 100644 diff --git a/doc/utils/fixup_headers.py b/doc/utils/fixup_headers.py old mode 100755 new mode 100644 diff --git a/doc/utils/sphinx-config/LAMMPSLexer.py b/doc/utils/sphinx-config/LAMMPSLexer.py index 524d7bf1fa..c8826a9ed6 100644 --- a/doc/utils/sphinx-config/LAMMPSLexer.py +++ b/doc/utils/sphinx-config/LAMMPSLexer.py @@ -1,25 +1,33 @@ from pygments.lexer import RegexLexer, words, include, default from pygments.token import * -LAMMPS_COMMANDS = ("angle_coeff", "angle_style", "atom_modify", "atom_style", -"balance", "bond_coeff", "bond_style", "bond_write", "boundary", "box", -"clear", "comm_modify", "comm_style", -"compute_modify", "create_atoms", "create_bonds", "create_box", "delete_atoms", -"delete_bonds", "dielectric", "dihedral_coeff", "dihedral_style", "dimension", -"displace_atoms", "dump_modify", "dynamical_matrix", "echo", "elif", "else", -"fix_modify", "group2ndx", "hyper", "if", "improper_coeff", -"improper_style", "include", "info", "jump", "kim", -"kspace_modify", "kspace_style", "label", "labelmap", "lattice", "log", -"mass", "mdi", "message", "minimize", "min_modify", "min_style", "molecule", -"ndx2group", "neb", "neb/spin", "neighbor", "neigh_modify", "newton", "next", -"package", "pair_coeff", "pair_modify", "pair_style", "pair_write", -"partition", "prd", "print", "processors", "python", "quit", "read_data", -"read_dump", "read_restart", "replicate", "rerun", "reset_ids", -"reset_timestep", "restart", "run", "run_style", "server", "set", "shell", -"special_bonds", "suffix", "tad", "temper", "temper/grem", "temper/npt", "then", -"thermo", "thermo_modify", "thermo_style", "third_order", "timer", "timestep", -"units", "velocity", "write_coeff", -"write_data", "write_restart") +LAMMPS_COMMANDS = ("angle_coeff", "angle_style", "atom_modify", + "atom_style", "balance", "bond_coeff", "bond_style", + "bond_write", "boundary", "clear", "comm_modify", + "comm_style", "compute_modify", "create_atoms", + "create_bonds", "create_box", "delete_atoms", + "delete_bonds", "dielectric", "dihedral_coeff", + "dihedral_style", "dimension", "displace_atoms", + "dump_modify", "dynamical_matrix", "echo", "elif", + "else", "fix_modify", "group2ndx", "hyper", "if", + "improper_coeff", "improper_style", "include", + "info", "jump", "kim", "kspace_modify", + "kspace_style", "label", "labelmap", "lattice", + "log", "mass", "mdi", "message", "minimize", + "min_modify", "min_style", "molecule", "ndx2group", + "neb", "neb/spin", "neighbor", "neigh_modify", + "newton", "next", "package", "pair_coeff", + "pair_modify", "pair_style", "pair_write", + "partition", "plugin", "prd", "print", "processors", + "python", "quit", "read_data", "read_dump", + "read_restart", "replicate", "rerun", "reset_atoms", + "reset_timestep", "restart", "run", "run_style", + "server", "set", "shell", "special_bonds", "suffix", + "tad", "temper", "temper/grem", "temper/npt", "then", + "thermo", "thermo_modify", "thermo_style", + "third_order", "timer", "timestep", "units", + "velocity", "write_coeff", "write_data", + "write_restart") #fix ID group-ID style args #compute ID group-ID style args diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index b1ef6e575b..834962f7f4 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -228,6 +228,7 @@ Bartels Bartelt barycenter barye +basename Bashford bashrc Baskes @@ -256,6 +257,7 @@ berlin Berne Bertotti Bessarab +bessel Beutler Bext Bfrac @@ -448,6 +450,7 @@ checkbox checkmark checkqeq checksum +chemflag chemistries Chemnitz Cheng @@ -612,6 +615,7 @@ curv Cusentino customIDs cutbond +cutghost cuthi cutinner cutlo @@ -742,6 +746,7 @@ diel Dietz differentiable diffusively +diffusivities diffusivity dihedral dihedrals @@ -753,6 +758,7 @@ dimensionality dimensioned dimgray dipolar +dipoleflag dir Direc dirname @@ -761,6 +767,7 @@ discretization discretized discretizing disp +dispersionflag dissipative Dissipative distharm @@ -824,6 +831,7 @@ du dU Ducastelle Dudarev +Dufils Duin Dullweber dumpfile @@ -911,6 +919,7 @@ elastance Electroneg electronegative electronegativity +electroneutrality Eleftheriou ElementN elementset @@ -1027,12 +1036,14 @@ evirials ew ewald Ewald +ewaldflag excitations excv exe executables extep extrema +extxyz exy ey ez @@ -1099,8 +1110,10 @@ Fincham Fint fingerprintconstants fingerprintsperelement +finitecutflag Finnis Fiorin +fitpod fixID fj Fji @@ -1143,6 +1156,7 @@ Forschungszentrum fortran Fortran Fosado +fourbody fourier fp fphi @@ -1278,6 +1292,7 @@ greenyellow Greffet grem gREM +Grepl Grest Grigera Grimme @@ -1519,6 +1534,9 @@ inumeric inv invariants inversed +invertible +invertibility +ionicities ionizable ionocovalent iostreams @@ -1640,6 +1658,7 @@ Kalia Kamberaj Kantorovich Kapfer +Karhunen Karls Karlsruhe Karniadakis @@ -1894,6 +1913,7 @@ ln localhost localTemp localvectors +Loeve Loewen logfile logfreq @@ -1945,6 +1965,7 @@ Mackrodt MacOS Macromolecules macroparticle +Maday Madura Magda Magdeburg @@ -2209,6 +2230,7 @@ msd msi MSI msm +msmflag msse msst Mtchell @@ -2288,6 +2310,8 @@ nanometer nanometers nanoparticle nanoparticles +nanopores +nanostructures nanotube Nanotube nanotubes @@ -2567,6 +2591,7 @@ Omelyan omp OMP oneAPI +onebody onelevel oneway onlysalt @@ -2650,6 +2675,7 @@ Pastewka pathangle pathname pathnames +Patera Patomtrans Pattnaik Pavese @@ -2792,6 +2818,7 @@ PowerShell ppme ppn pppm +pppmflag Prakash Praprotnik prd @@ -2946,6 +2973,7 @@ Rcmx Rcmy Rco Rcut +rcut rcutfac rdc rdf @@ -2971,6 +2999,7 @@ refactoring reflectionstyle Reinders reinit +reinitflag relaxbox relink relres @@ -3038,6 +3067,7 @@ Rij RIj Rik Rin +rin Rinaldi Rino RiRj @@ -3174,6 +3204,7 @@ sdpd SDPD se seagreen +Searles Secor sectoring sed @@ -3304,6 +3335,7 @@ SPH spica SPICA Spickermann +spinflag splined spparks Sprik @@ -3491,6 +3523,7 @@ thermo thermochemical thermochemistry thermodynamically +thermopotentiostat Thermophysical thermostatted thermostatting @@ -3858,6 +3891,7 @@ workflows Workum Worley Wriggers +writedata Wuppertal Wurtzite www diff --git a/examples/PACKAGES/electrode/README b/examples/PACKAGES/electrode/README index 652194670b..b0c64d496b 100644 --- a/examples/PACKAGES/electrode/README +++ b/examples/PACKAGES/electrode/README @@ -1,14 +1,14 @@ These examples demonstrate the use of the ELECTRODE package for constant potential molecular dynamics. planar/ - au-vac.data -- gold electrodes with vacuum + data.au-vac -- gold electrodes with vacuum in.planar* -- comparison of gold electrodes with vacuum to theoretical capacitance of planar capacitor -- 5x, further labeled by long-range solver (ewald / pppm) and boundary correction (ew2d / ew3dc / ffield) -- the pppm-ew2d combination would not give correct results and will throw an error if selected test.sh -- run all in.planar files and check charge at 1.2V and %difference from theoretical (last column) graph-il/ - graph-il.data -- graphene electrodes with electrolyte (coarse-grained BMIm-PF6) + data.graph-il -- graphene electrodes with electrolyte (coarse-grained BMIm-PF6) in.conp -- reference run at constant potential in.etypes -- type-based smart neighborlists in.ffield -- finite field method with fully periodic cell @@ -18,10 +18,22 @@ graph-il/ in.thermo -- thermalize electrolyte with thermopotentiostat instead of NVT au-aq/ - au-aq.data -- gold electrodes with electrolyte (SPC water + NaCl) + data.au-aq -- gold electrodes with electrolyte (SPC water + NaCl) in.ffield -- finite field method with fully periodic cell in.tf -- Thomas-Fermi metallicity model with more delocalized charges +madelung/ + data.au-elyt -- tiny electrodes with two electrolyte atoms in between + settings.mod -- common settings + in.* -- setup KSpace and fix electrode/conp + plate_cap.py -- compute reference energy and charges from Madelung style sum + eval.py -- compare output of reference and Lammps job (used by test.sh) + test.sh -- run all in.* files and check charge at 1 V and %difference from theoretical (last column) + +piston/ + data.piston -- two electrodes with water + in.piston -- equilibrate distance between rigid electrodes + # future work: # in.cylinder -- comparison of carbon nanotube to theoretical induced charge for charge near circular conductor diff --git a/examples/PACKAGES/electrode/au-aq/in.ffield b/examples/PACKAGES/electrode/au-aq/in.ffield index 094fc39144..de594f8c9a 100644 --- a/examples/PACKAGES/electrode/au-aq/in.ffield +++ b/examples/PACKAGES/electrode/au-aq/in.ffield @@ -4,7 +4,7 @@ boundary p p p # ffield uses periodic z-boundary and no slab include settings.mod # styles, groups, computes and fixes -fix conp bot electrode/conp -1.0 1.805132 couple top 1.0 symm on ffield yes etypes 6*7 +fix conp bot electrode/conp -1.0 1.805132 couple top 1.0 symm on ffield yes etypes on thermo 50 thermo_style custom step temp c_ctemp epair etotal c_qtop c_qbot c_qztop c_qzbot diff --git a/examples/PACKAGES/electrode/au-aq/in.tf b/examples/PACKAGES/electrode/au-aq/in.tf index d73efd10fc..23beb357d8 100644 --- a/examples/PACKAGES/electrode/au-aq/in.tf +++ b/examples/PACKAGES/electrode/au-aq/in.tf @@ -6,7 +6,7 @@ boundary p p p # ffield uses periodic z-boundary and no slab include settings.mod # styles, groups, computes and fixes -fix conp bot electrode/conp -1.0 1.805132 couple top 1.0 symm on ffield yes etypes 6*7 +fix conp bot electrode/conp -1.0 1.805132 couple top 1.0 symm on ffield yes etypes on fix_modify conp tf 6 1.0 18.1715745 fix_modify conp tf 7 1.0 18.1715745 diff --git a/examples/PACKAGES/electrode/au-aq/log.26Apr2022.au-aq-ffield.g++.1 b/examples/PACKAGES/electrode/au-aq/log.1Dec2022.au-aq-ffield.g++.1 similarity index 52% rename from examples/PACKAGES/electrode/au-aq/log.26Apr2022.au-aq-ffield.g++.1 rename to examples/PACKAGES/electrode/au-aq/log.1Dec2022.au-aq-ffield.g++.1 index 76e15ebe53..2c43724875 100644 --- a/examples/PACKAGES/electrode/au-aq/log.26Apr2022.au-aq-ffield.g++.1 +++ b/examples/PACKAGES/electrode/au-aq/log.1Dec2022.au-aq-ffield.g++.1 @@ -1,4 +1,4 @@ -LAMMPS (24 Mar 2022) +LAMMPS (3 Nov 2022) # electrodes with constant potential using finite field # for z-periodic gold-saline electrochemical cell @@ -37,8 +37,8 @@ Finding 1-2 1-3 1-4 neighbors ... 1 = max # of 1-3 neighbors 1 = max # of 1-4 neighbors 2 = max # of special neighbors - special bonds CPU = 0.002 seconds - read_data CPU = 0.051 seconds + special bonds CPU = 0.006 seconds + read_data CPU = 0.097 seconds group bot type 6 1620 atoms in group bot @@ -52,11 +52,12 @@ group electrolyte type 1 2 3 4 5 fix nvt electrolyte nvt temp 298.0 298.0 241 fix shake SPC shake 1e-4 20 0 b 1 2 a 1 +Finding SHAKE clusters ... 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 2160 = # of frozen angles - find clusters CPU = 0.002 seconds + find clusters CPU = 0.006 seconds variable q atom q variable qz atom q*(z-lz/2) @@ -67,12 +68,41 @@ compute qzbot bot reduce sum v_qz compute ctemp electrolyte temp -fix conp bot electrode/conp -1.0 1.805132 couple top 1.0 symm on ffield yes etypes 6*7 +fix conp bot electrode/conp -1.0 1.805132 couple top 1.0 symm on ffield yes etypes on 3240 atoms in group conp_group thermo 50 thermo_style custom step temp c_ctemp epair etotal c_qtop c_qbot c_qztop c_qzbot run 500 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- kspace_style pppm/electrode command: + +@article{Ahrens2021, +author = {Ahrens-Iwers, Ludwig J.V. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0063381}, +title = {{Constant potential simulations on a mesh}}, +journal = {Journal of Chemical Physics}, +year = {2021} +volume = {155}, +pages = {104104}, +} +- fix electrode command: + +@article{Ahrens2022 +author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0099239}, +title = {{ELECTRODE: An electrochemistry package for LAMMPS}}, +journal = {The Journal of Chemical Physics}, +year = {2022} +volume = {157}, +pages = {084801}, +} +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + PPPM/electrode initialization ... using 12-bit tables for long-range coulomb (src/kspace.cpp:342) G vector (1/distance) = 0.24017705 @@ -82,9 +112,9 @@ PPPM/electrode initialization ... estimated relative force accuracy = 1.093542e-07 using double precision MKL FFT 3d grid and FFT values/proc = 472567 349920 - generated 21 of 21 mixed pair_coeff terms from geometric mixing rule +Generated 21 of 21 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... - update every 1 steps, delay 10 steps, check yes + update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 17 ghost atom cutoff = 17 @@ -105,35 +135,35 @@ Neighbor list info ... pair build: skip stencil: none bin: none -Per MPI rank memory allocation (min/avg/max) = 194.6 | 194.6 | 194.6 Mbytes +Per MPI rank memory allocation (min/avg/max) = 194.8 | 194.8 | 194.8 Mbytes Step Temp c_ctemp E_pair TotEng c_qtop c_qbot c_qztop c_qzbot - 0 171.61215 298.06731 -39212.819 -35306.164 4.1391573 -4.1391573 78.718381 131.56372 - 50 147.03139 255.37383 -39870.139 -36523.051 4.1312167 -4.1312167 78.563872 131.30255 - 100 149.89027 260.33932 -39878.859 -36466.689 4.0217834 -4.0217834 76.482548 127.82573 - 150 151.7382 263.54893 -39873.178 -36418.942 4.0469977 -4.0469977 76.967548 128.59855 - 200 151.7508 263.57081 -39827.015 -36372.492 4.1830375 -4.1830375 79.554159 132.93925 - 250 152.61146 265.06566 -39791.293 -36317.177 4.1835865 -4.1835865 79.56665 132.97185 - 300 153.51486 266.63475 -39751.841 -36257.16 4.1571861 -4.1571861 79.061431 132.12905 - 350 156.35115 271.561 -39754.955 -36195.708 4.3498059 -4.3498059 82.720202 138.28678 - 400 156.26118 271.40474 -39690.781 -36133.582 4.3444079 -4.3444079 82.619396 138.11873 - 450 158.54164 275.36558 -39681.083 -36071.97 4.2020488 -4.2020488 79.912674 133.55185 - 500 161.40138 280.33258 -39684.185 -36009.972 4.3021924 -4.3021924 81.807527 136.7464 -Loop time of 246.197 on 1 procs for 500 steps with 9798 atoms + 0 171.61215 298.06731 -39021.917 -35115.261 4.1391573 -4.1391573 78.718381 131.56372 + 50 147.03139 255.37383 -39679.603 -36332.515 4.1312167 -4.1312167 78.563872 131.30255 + 100 149.89027 260.33932 -39693.369 -36281.2 4.0217834 -4.0217834 76.482548 127.82573 + 150 151.7382 263.54893 -39686.526 -36232.29 4.0469977 -4.0469977 76.967548 128.59855 + 200 151.7508 263.57081 -39634.089 -36179.566 4.1830375 -4.1830375 79.554159 132.93925 + 250 152.61146 265.06566 -39598.341 -36124.226 4.1835865 -4.1835865 79.56665 132.97185 + 300 153.51486 266.63475 -39560.107 -36065.426 4.1571861 -4.1571861 79.06143 132.12905 + 350 156.35115 271.561 -39554.338 -35995.09 4.3498059 -4.3498059 82.720202 138.28678 + 400 156.26118 271.40474 -39490.412 -35933.213 4.344408 -4.344408 82.619398 138.11874 + 450 158.54163 275.36557 -39487.28 -35878.167 4.2020489 -4.2020489 79.912677 133.55186 + 500 161.40137 280.33257 -39485.763 -35811.55 4.3021927 -4.3021927 81.807532 136.74641 +Loop time of 146.959 on 1 procs for 500 steps with 9798 atoms -Performance: 0.175 ns/day, 136.776 hours/ns, 2.031 timesteps/s -356.3% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 0.294 ns/day, 81.644 hours/ns, 3.402 timesteps/s, 33.336 katom-step/s +100.0% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 105.64 | 105.64 | 105.64 | 0.0 | 42.91 -Bond | 0.0010592 | 0.0010592 | 0.0010592 | 0.0 | 0.00 -Kspace | 37.643 | 37.643 | 37.643 | 0.0 | 15.29 -Neigh | 5.8827 | 5.8827 | 5.8827 | 0.0 | 2.39 -Comm | 0.18181 | 0.18181 | 0.18181 | 0.0 | 0.07 -Output | 0.0055762 | 0.0055762 | 0.0055762 | 0.0 | 0.00 -Modify | 96.78 | 96.78 | 96.78 | 0.0 | 39.31 -Other | | 0.06346 | | | 0.03 +Pair | 69.832 | 69.832 | 69.832 | 0.0 | 47.52 +Bond | 0.00091634 | 0.00091634 | 0.00091634 | 0.0 | 0.00 +Kspace | 33.817 | 33.817 | 33.817 | 0.0 | 23.01 +Neigh | 4.2067 | 4.2067 | 4.2067 | 0.0 | 2.86 +Comm | 0.12212 | 0.12212 | 0.12212 | 0.0 | 0.08 +Output | 0.0031896 | 0.0031896 | 0.0031896 | 0.0 | 0.00 +Modify | 38.92 | 38.92 | 38.92 | 0.0 | 26.48 +Other | | 0.05687 | | | 0.04 Nlocal: 9798 ave 9798 max 9798 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -147,4 +177,4 @@ Ave neighs/atom = 842.63544 Ave special neighs/atom = 1.3227189 Neighbor list builds = 22 Dangerous builds = 0 -Total wall time: 0:19:39 +Total wall time: 0:05:33 diff --git a/examples/PACKAGES/electrode/au-aq/log.26Apr2022.au-aq-ffield.g++.4 b/examples/PACKAGES/electrode/au-aq/log.1Dec2022.au-aq-ffield.g++.4 similarity index 53% rename from examples/PACKAGES/electrode/au-aq/log.26Apr2022.au-aq-ffield.g++.4 rename to examples/PACKAGES/electrode/au-aq/log.1Dec2022.au-aq-ffield.g++.4 index 685a71eb74..5a18629cab 100644 --- a/examples/PACKAGES/electrode/au-aq/log.26Apr2022.au-aq-ffield.g++.4 +++ b/examples/PACKAGES/electrode/au-aq/log.1Dec2022.au-aq-ffield.g++.4 @@ -1,4 +1,4 @@ -LAMMPS (24 Mar 2022) +LAMMPS (3 Nov 2022) # electrodes with constant potential using finite field # for z-periodic gold-saline electrochemical cell @@ -39,7 +39,7 @@ Finding 1-2 1-3 1-4 neighbors ... 1 = max # of 1-4 neighbors 2 = max # of special neighbors special bonds CPU = 0.002 seconds - read_data CPU = 0.149 seconds + read_data CPU = 0.118 seconds group bot type 6 1620 atoms in group bot @@ -53,11 +53,12 @@ group electrolyte type 1 2 3 4 5 fix nvt electrolyte nvt temp 298.0 298.0 241 fix shake SPC shake 1e-4 20 0 b 1 2 a 1 +Finding SHAKE clusters ... 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 2160 = # of frozen angles - find clusters CPU = 0.003 seconds + find clusters CPU = 0.002 seconds variable q atom q variable qz atom q*(z-lz/2) @@ -68,12 +69,41 @@ compute qzbot bot reduce sum v_qz compute ctemp electrolyte temp -fix conp bot electrode/conp -1.0 1.805132 couple top 1.0 symm on ffield yes etypes 6*7 +fix conp bot electrode/conp -1.0 1.805132 couple top 1.0 symm on ffield yes etypes on 3240 atoms in group conp_group thermo 50 thermo_style custom step temp c_ctemp epair etotal c_qtop c_qbot c_qztop c_qzbot run 500 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- kspace_style pppm/electrode command: + +@article{Ahrens2021, +author = {Ahrens-Iwers, Ludwig J.V. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0063381}, +title = {{Constant potential simulations on a mesh}}, +journal = {Journal of Chemical Physics}, +year = {2021} +volume = {155}, +pages = {104104}, +} +- fix electrode command: + +@article{Ahrens2022 +author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0099239}, +title = {{ELECTRODE: An electrochemistry package for LAMMPS}}, +journal = {The Journal of Chemical Physics}, +year = {2022} +volume = {157}, +pages = {084801}, +} +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + PPPM/electrode initialization ... using 12-bit tables for long-range coulomb (src/kspace.cpp:342) G vector (1/distance) = 0.24017705 @@ -83,9 +113,9 @@ PPPM/electrode initialization ... estimated relative force accuracy = 1.093542e-07 using double precision MKL FFT 3d grid and FFT values/proc = 138958 87480 - generated 21 of 21 mixed pair_coeff terms from geometric mixing rule +Generated 21 of 21 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... - update every 1 steps, delay 10 steps, check yes + update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 17 ghost atom cutoff = 17 @@ -106,35 +136,35 @@ Neighbor list info ... pair build: skip stencil: none bin: none -Per MPI rank memory allocation (min/avg/max) = 118.1 | 120.6 | 123.1 Mbytes +Per MPI rank memory allocation (min/avg/max) = 118.2 | 120.7 | 123.2 Mbytes Step Temp c_ctemp E_pair TotEng c_qtop c_qbot c_qztop c_qzbot - 0 171.61215 298.06731 -39212.819 -35306.164 4.1391573 -4.1391573 78.718381 131.56372 - 50 147.03139 255.37383 -39870.139 -36523.051 4.1312167 -4.1312167 78.563872 131.30255 - 100 149.89027 260.33932 -39878.859 -36466.689 4.0217834 -4.0217834 76.482548 127.82573 - 150 151.7382 263.54893 -39873.178 -36418.942 4.0469977 -4.0469977 76.967548 128.59855 - 200 151.7508 263.57081 -39827.015 -36372.492 4.1830375 -4.1830375 79.554159 132.93925 - 250 152.61146 265.06566 -39791.293 -36317.177 4.1835865 -4.1835865 79.56665 132.97185 - 300 153.51486 266.63475 -39751.841 -36257.16 4.1571861 -4.1571861 79.061431 132.12905 - 350 156.35115 271.561 -39754.955 -36195.708 4.3498059 -4.3498059 82.7202 138.28678 - 400 156.26118 271.40474 -39690.781 -36133.582 4.3444079 -4.3444079 82.619398 138.11873 - 450 158.54163 275.36558 -39681.083 -36071.97 4.2020488 -4.2020488 79.912675 133.55185 - 500 161.40138 280.33257 -39684.185 -36009.972 4.3021924 -4.3021924 81.807527 136.7464 -Loop time of 111.902 on 4 procs for 500 steps with 9798 atoms + 0 171.61215 298.06731 -39021.917 -35115.261 4.1391573 -4.1391573 78.718381 131.56372 + 50 147.03139 255.37383 -39679.603 -36332.515 4.1312167 -4.1312167 78.563872 131.30255 + 100 149.89027 260.33932 -39693.369 -36281.2 4.0217834 -4.0217834 76.482548 127.82573 + 150 151.7382 263.54893 -39686.526 -36232.29 4.0469977 -4.0469977 76.967548 128.59855 + 200 151.7508 263.57081 -39634.089 -36179.566 4.1830375 -4.1830375 79.554159 132.93925 + 250 152.61146 265.06566 -39598.341 -36124.226 4.1835864 -4.1835864 79.56665 132.97185 + 300 153.51486 266.63475 -39560.107 -36065.426 4.1571861 -4.1571861 79.06143 132.12905 + 350 156.35115 271.561 -39554.338 -35995.09 4.3498059 -4.3498059 82.720201 138.28678 + 400 156.26118 271.40474 -39490.412 -35933.213 4.3444079 -4.3444079 82.619397 138.11873 + 450 158.54163 275.36558 -39487.279 -35878.167 4.202049 -4.202049 79.912678 133.55186 + 500 161.40137 280.33256 -39485.763 -35811.55 4.3021925 -4.3021925 81.807529 136.7464 +Loop time of 97.2399 on 4 procs for 500 steps with 9798 atoms -Performance: 0.386 ns/day, 62.168 hours/ns, 4.468 timesteps/s -97.2% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 0.444 ns/day, 54.022 hours/ns, 5.142 timesteps/s, 50.381 katom-step/s +87.0% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 21.816 | 31.136 | 40.866 | 166.5 | 27.82 -Bond | 0.00073413 | 0.00080346 | 0.00084203 | 0.0 | 0.00 -Kspace | 29.546 | 39.137 | 48.326 | 146.4 | 34.97 -Neigh | 2.5867 | 2.5872 | 2.5877 | 0.0 | 2.31 -Comm | 0.33289 | 0.33603 | 0.33791 | 0.3 | 0.30 -Output | 0.0022537 | 0.0030028 | 0.005192 | 2.3 | 0.00 -Modify | 38.498 | 38.635 | 38.77 | 2.2 | 34.53 -Other | | 0.06679 | | | 0.06 +Pair | 19.363 | 28.08 | 37.126 | 160.3 | 28.88 +Bond | 0.00094043 | 0.00096516 | 0.00098016 | 0.0 | 0.00 +Kspace | 31.655 | 40.554 | 49.143 | 131.3 | 41.71 +Neigh | 2.2289 | 2.2294 | 2.2297 | 0.0 | 2.29 +Comm | 0.5341 | 0.54079 | 0.5478 | 0.9 | 0.56 +Output | 0.0024141 | 0.0026943 | 0.0034176 | 0.8 | 0.00 +Modify | 25.6 | 25.755 | 25.908 | 2.8 | 26.49 +Other | | 0.07733 | | | 0.08 Nlocal: 2449.5 ave 2908 max 2012 min Histogram: 2 0 0 0 0 0 0 0 0 2 @@ -148,4 +178,4 @@ Ave neighs/atom = 842.63544 Ave special neighs/atom = 1.3227189 Neighbor list builds = 22 Dangerous builds = 0 -Total wall time: 0:07:48 +Total wall time: 0:03:03 diff --git a/examples/PACKAGES/electrode/au-aq/log.26Apr2022.au-aq-tf.g++.1 b/examples/PACKAGES/electrode/au-aq/log.1Dec2022.au-aq-tf.g++.1 similarity index 53% rename from examples/PACKAGES/electrode/au-aq/log.26Apr2022.au-aq-tf.g++.1 rename to examples/PACKAGES/electrode/au-aq/log.1Dec2022.au-aq-tf.g++.1 index 316e092c55..5ed60bc88a 100644 --- a/examples/PACKAGES/electrode/au-aq/log.26Apr2022.au-aq-tf.g++.1 +++ b/examples/PACKAGES/electrode/au-aq/log.1Dec2022.au-aq-tf.g++.1 @@ -1,4 +1,4 @@ -LAMMPS (24 Mar 2022) +LAMMPS (3 Nov 2022) # electrodes with constant potential using finite field # for z-periodic gold-saline electrochemical cell # using Thomas-Fermi metallicity model: electrode q and qz will be @@ -39,8 +39,8 @@ Finding 1-2 1-3 1-4 neighbors ... 1 = max # of 1-3 neighbors 1 = max # of 1-4 neighbors 2 = max # of special neighbors - special bonds CPU = 0.010 seconds - read_data CPU = 0.115 seconds + special bonds CPU = 0.003 seconds + read_data CPU = 0.065 seconds group bot type 6 1620 atoms in group bot @@ -54,11 +54,12 @@ group electrolyte type 1 2 3 4 5 fix nvt electrolyte nvt temp 298.0 298.0 241 fix shake SPC shake 1e-4 20 0 b 1 2 a 1 +Finding SHAKE clusters ... 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 2160 = # of frozen angles - find clusters CPU = 0.010 seconds + find clusters CPU = 0.002 seconds variable q atom q variable qz atom q*(z-lz/2) @@ -69,7 +70,7 @@ compute qzbot bot reduce sum v_qz compute ctemp electrolyte temp -fix conp bot electrode/conp -1.0 1.805132 couple top 1.0 symm on ffield yes etypes 6*7 +fix conp bot electrode/conp -1.0 1.805132 couple top 1.0 symm on ffield yes etypes on 3240 atoms in group conp_group fix_modify conp tf 6 1.0 18.1715745 fix_modify conp tf 7 1.0 18.1715745 @@ -77,6 +78,35 @@ fix_modify conp tf 7 1.0 18.1715745 thermo 50 thermo_style custom step temp c_ctemp epair etotal c_qtop c_qbot c_qztop c_qzbot run 500 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- kspace_style pppm/electrode command: + +@article{Ahrens2021, +author = {Ahrens-Iwers, Ludwig J.V. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0063381}, +title = {{Constant potential simulations on a mesh}}, +journal = {Journal of Chemical Physics}, +year = {2021} +volume = {155}, +pages = {104104}, +} +- fix electrode command: + +@article{Ahrens2022 +author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0099239}, +title = {{ELECTRODE: An electrochemistry package for LAMMPS}}, +journal = {The Journal of Chemical Physics}, +year = {2022} +volume = {157}, +pages = {084801}, +} +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + PPPM/electrode initialization ... using 12-bit tables for long-range coulomb (src/kspace.cpp:342) G vector (1/distance) = 0.24017705 @@ -86,9 +116,9 @@ PPPM/electrode initialization ... estimated relative force accuracy = 1.093542e-07 using double precision MKL FFT 3d grid and FFT values/proc = 472567 349920 - generated 21 of 21 mixed pair_coeff terms from geometric mixing rule +Generated 21 of 21 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... - update every 1 steps, delay 10 steps, check yes + update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 17 ghost atom cutoff = 17 @@ -109,35 +139,35 @@ Neighbor list info ... pair build: skip stencil: none bin: none -Per MPI rank memory allocation (min/avg/max) = 194.6 | 194.6 | 194.6 Mbytes +Per MPI rank memory allocation (min/avg/max) = 194.8 | 194.8 | 194.8 Mbytes Step Temp c_ctemp E_pair TotEng c_qtop c_qbot c_qztop c_qzbot - 0 171.61215 298.06731 -39190.106 -35283.45 4.0804484 -4.0804484 79.075127 131.20697 - 50 147.14308 255.56782 -39849.964 -36500.334 3.9990346 -3.9990346 77.497181 128.57759 - 100 149.94935 260.44194 -39857.533 -36444.019 3.8613914 -3.8613914 74.82985 124.15315 - 150 151.95924 263.93285 -39855.567 -36396.299 3.8677064 -3.8677064 74.957279 124.33201 - 200 151.66737 263.42591 -39802.585 -36349.961 3.99842 -3.99842 77.491015 128.54496 - 250 152.36874 264.64408 -39763.306 -36294.716 3.9925863 -3.9925863 77.379445 128.37226 - 300 153.83916 267.19802 -39737.075 -36235.012 3.94995 -3.94995 76.553896 127.00395 - 350 155.88897 270.75827 -39722.265 -36173.539 4.0598524 -4.0598524 78.679643 130.5394 - 400 156.51993 271.85415 -39674.759 -36111.669 4.1312899 -4.1312899 80.060369 132.83599 - 450 160.21339 278.26919 -39697.962 -36050.793 3.9068098 -3.9068098 75.713484 125.59216 - 500 161.63639 280.74075 -39669.412 -35989.849 3.9261656 -3.9261656 76.0806 126.22255 -Loop time of 280.183 on 1 procs for 500 steps with 9798 atoms + 0 171.61215 298.06731 -39001.911 -35095.255 4.0804484 -4.0804484 79.075127 131.20697 + 50 147.14308 255.56782 -39665.525 -36315.894 3.9990346 -3.9990346 77.497181 128.57759 + 100 149.94935 260.44194 -39679.441 -36265.927 3.8613914 -3.8613914 74.82985 124.15315 + 150 151.95924 263.93285 -39677.184 -36217.916 3.8677064 -3.8677064 74.957279 124.33201 + 200 151.66737 263.42591 -39618.173 -36165.549 3.99842 -3.99842 77.491015 128.54496 + 250 152.36874 264.64408 -39579.164 -36110.574 3.9925863 -3.9925863 77.379445 128.37226 + 300 153.83916 267.19802 -39554.899 -36052.836 3.94995 -3.94995 76.553896 127.00395 + 350 155.88897 270.75827 -39535.02 -35986.294 4.0598524 -4.0598524 78.679643 130.5394 + 400 156.51993 271.85415 -39484.219 -35921.13 4.1312898 -4.1312898 80.060368 132.83598 + 450 160.21339 278.26919 -39517.776 -35870.607 3.9068098 -3.9068098 75.713484 125.59216 + 500 161.63639 280.74075 -39488.333 -35808.771 3.9261656 -3.9261656 76.080599 126.22255 +Loop time of 185.804 on 1 procs for 500 steps with 9798 atoms -Performance: 0.154 ns/day, 155.657 hours/ns, 1.785 timesteps/s -341.9% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 0.233 ns/day, 103.225 hours/ns, 2.691 timesteps/s, 26.366 katom-step/s +100.0% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 119.69 | 119.69 | 119.69 | 0.0 | 42.72 -Bond | 0.0010952 | 0.0010952 | 0.0010952 | 0.0 | 0.00 -Kspace | 42.137 | 42.137 | 42.137 | 0.0 | 15.04 -Neigh | 6.5403 | 6.5403 | 6.5403 | 0.0 | 2.33 -Comm | 0.19411 | 0.19411 | 0.19411 | 0.0 | 0.07 -Output | 0.0053644 | 0.0053644 | 0.0053644 | 0.0 | 0.00 -Modify | 111.54 | 111.54 | 111.54 | 0.0 | 39.81 -Other | | 0.07244 | | | 0.03 +Pair | 91 | 91 | 91 | 0.0 | 48.98 +Bond | 0.0010315 | 0.0010315 | 0.0010315 | 0.0 | 0.00 +Kspace | 40.32 | 40.32 | 40.32 | 0.0 | 21.70 +Neigh | 5.6505 | 5.6505 | 5.6505 | 0.0 | 3.04 +Comm | 0.15304 | 0.15304 | 0.15304 | 0.0 | 0.08 +Output | 0.0041829 | 0.0041829 | 0.0041829 | 0.0 | 0.00 +Modify | 48.607 | 48.607 | 48.607 | 0.0 | 26.16 +Other | | 0.06807 | | | 0.04 Nlocal: 9798 ave 9798 max 9798 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -151,4 +181,4 @@ Ave neighs/atom = 842.7079 Ave special neighs/atom = 1.3227189 Neighbor list builds = 23 Dangerous builds = 0 -Total wall time: 0:21:11 +Total wall time: 0:06:18 diff --git a/examples/PACKAGES/electrode/au-aq/log.26Apr2022.au-aq-tf.g++.4 b/examples/PACKAGES/electrode/au-aq/log.1Dec2022.au-aq-tf.g++.4 similarity index 53% rename from examples/PACKAGES/electrode/au-aq/log.26Apr2022.au-aq-tf.g++.4 rename to examples/PACKAGES/electrode/au-aq/log.1Dec2022.au-aq-tf.g++.4 index 450a6c1fda..9791c35b43 100644 --- a/examples/PACKAGES/electrode/au-aq/log.26Apr2022.au-aq-tf.g++.4 +++ b/examples/PACKAGES/electrode/au-aq/log.1Dec2022.au-aq-tf.g++.4 @@ -1,4 +1,4 @@ -LAMMPS (24 Mar 2022) +LAMMPS (3 Nov 2022) # electrodes with constant potential using finite field # for z-periodic gold-saline electrochemical cell # using Thomas-Fermi metallicity model: electrode q and qz will be @@ -41,7 +41,7 @@ Finding 1-2 1-3 1-4 neighbors ... 1 = max # of 1-4 neighbors 2 = max # of special neighbors special bonds CPU = 0.002 seconds - read_data CPU = 0.091 seconds + read_data CPU = 0.114 seconds group bot type 6 1620 atoms in group bot @@ -55,11 +55,12 @@ group electrolyte type 1 2 3 4 5 fix nvt electrolyte nvt temp 298.0 298.0 241 fix shake SPC shake 1e-4 20 0 b 1 2 a 1 +Finding SHAKE clusters ... 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 2160 = # of frozen angles - find clusters CPU = 0.001 seconds + find clusters CPU = 0.002 seconds variable q atom q variable qz atom q*(z-lz/2) @@ -70,7 +71,7 @@ compute qzbot bot reduce sum v_qz compute ctemp electrolyte temp -fix conp bot electrode/conp -1.0 1.805132 couple top 1.0 symm on ffield yes etypes 6*7 +fix conp bot electrode/conp -1.0 1.805132 couple top 1.0 symm on ffield yes etypes on 3240 atoms in group conp_group fix_modify conp tf 6 1.0 18.1715745 fix_modify conp tf 7 1.0 18.1715745 @@ -78,6 +79,35 @@ fix_modify conp tf 7 1.0 18.1715745 thermo 50 thermo_style custom step temp c_ctemp epair etotal c_qtop c_qbot c_qztop c_qzbot run 500 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- kspace_style pppm/electrode command: + +@article{Ahrens2021, +author = {Ahrens-Iwers, Ludwig J.V. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0063381}, +title = {{Constant potential simulations on a mesh}}, +journal = {Journal of Chemical Physics}, +year = {2021} +volume = {155}, +pages = {104104}, +} +- fix electrode command: + +@article{Ahrens2022 +author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0099239}, +title = {{ELECTRODE: An electrochemistry package for LAMMPS}}, +journal = {The Journal of Chemical Physics}, +year = {2022} +volume = {157}, +pages = {084801}, +} +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + PPPM/electrode initialization ... using 12-bit tables for long-range coulomb (src/kspace.cpp:342) G vector (1/distance) = 0.24017705 @@ -87,9 +117,9 @@ PPPM/electrode initialization ... estimated relative force accuracy = 1.093542e-07 using double precision MKL FFT 3d grid and FFT values/proc = 138958 87480 - generated 21 of 21 mixed pair_coeff terms from geometric mixing rule +Generated 21 of 21 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... - update every 1 steps, delay 10 steps, check yes + update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 17 ghost atom cutoff = 17 @@ -110,35 +140,35 @@ Neighbor list info ... pair build: skip stencil: none bin: none -Per MPI rank memory allocation (min/avg/max) = 118.1 | 120.6 | 123.1 Mbytes +Per MPI rank memory allocation (min/avg/max) = 118.2 | 120.7 | 123.2 Mbytes Step Temp c_ctemp E_pair TotEng c_qtop c_qbot c_qztop c_qzbot - 0 171.61215 298.06731 -39190.106 -35283.45 4.0804484 -4.0804484 79.075127 131.20697 - 50 147.14308 255.56782 -39849.964 -36500.334 3.9990346 -3.9990346 77.497181 128.57759 - 100 149.94935 260.44194 -39857.533 -36444.019 3.8613914 -3.8613914 74.82985 124.15315 - 150 151.95924 263.93285 -39855.567 -36396.299 3.8677064 -3.8677064 74.957279 124.33201 - 200 151.66737 263.42591 -39802.585 -36349.961 3.99842 -3.99842 77.491015 128.54496 - 250 152.36874 264.64408 -39763.306 -36294.716 3.9925863 -3.9925863 77.379445 128.37226 - 300 153.83916 267.19802 -39737.075 -36235.012 3.94995 -3.94995 76.553896 127.00395 - 350 155.88897 270.75827 -39722.265 -36173.539 4.0598524 -4.0598524 78.679643 130.5394 - 400 156.51993 271.85415 -39674.759 -36111.669 4.1312899 -4.1312899 80.060369 132.83599 - 450 160.21339 278.26919 -39697.962 -36050.793 3.9068098 -3.9068098 75.713485 125.59216 - 500 161.63639 280.74075 -39669.412 -35989.849 3.9261654 -3.9261654 76.080597 126.22255 -Loop time of 110.716 on 4 procs for 500 steps with 9798 atoms + 0 171.61215 298.06731 -39001.911 -35095.255 4.0804484 -4.0804484 79.075127 131.20697 + 50 147.14308 255.56782 -39665.525 -36315.894 3.9990346 -3.9990346 77.497181 128.57759 + 100 149.94935 260.44194 -39679.441 -36265.927 3.8613914 -3.8613914 74.82985 124.15315 + 150 151.95924 263.93285 -39677.184 -36217.916 3.8677064 -3.8677064 74.957279 124.33201 + 200 151.66737 263.42591 -39618.173 -36165.549 3.99842 -3.99842 77.491015 128.54496 + 250 152.36874 264.64408 -39579.163 -36110.574 3.9925863 -3.9925863 77.379445 128.37226 + 300 153.83916 267.19802 -39554.899 -36052.835 3.94995 -3.94995 76.553896 127.00395 + 350 155.88897 270.75826 -39535.02 -35986.294 4.0598523 -4.0598523 78.679642 130.5394 + 400 156.51993 271.85415 -39484.219 -35921.13 4.1312897 -4.1312897 80.060366 132.83598 + 450 160.21339 278.26919 -39517.776 -35870.607 3.9068099 -3.9068099 75.713486 125.59216 + 500 161.63639 280.74075 -39488.333 -35808.771 3.9261657 -3.9261657 76.080602 126.22256 +Loop time of 104.099 on 4 procs for 500 steps with 9798 atoms -Performance: 0.390 ns/day, 61.509 hours/ns, 4.516 timesteps/s -97.2% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 0.415 ns/day, 57.833 hours/ns, 4.803 timesteps/s, 47.061 katom-step/s +87.7% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 21.17 | 30.449 | 39.65 | 164.9 | 27.50 -Bond | 0.0007313 | 0.00077537 | 0.00081477 | 0.0 | 0.00 -Kspace | 29.854 | 38.911 | 48.058 | 143.8 | 35.14 -Neigh | 2.7206 | 2.7213 | 2.722 | 0.0 | 2.46 -Comm | 0.33023 | 0.33225 | 0.33384 | 0.2 | 0.30 -Output | 0.0024528 | 0.0027565 | 0.0035754 | 0.9 | 0.00 -Modify | 38.091 | 38.233 | 38.365 | 2.1 | 34.53 -Other | | 0.06636 | | | 0.06 +Pair | 20.951 | 30.326 | 40.07 | 166.7 | 29.13 +Bond | 0.00098259 | 0.0010706 | 0.0011926 | 0.3 | 0.00 +Kspace | 33.465 | 43.037 | 52.268 | 137.5 | 41.34 +Neigh | 2.6007 | 2.6014 | 2.6021 | 0.0 | 2.50 +Comm | 0.57766 | 0.58318 | 0.58875 | 0.7 | 0.56 +Output | 0.0022277 | 0.0024765 | 0.0031841 | 0.8 | 0.00 +Modify | 27.292 | 27.47 | 27.647 | 3.1 | 26.39 +Other | | 0.0787 | | | 0.08 Nlocal: 2449.5 ave 2908 max 2017 min Histogram: 2 0 0 0 0 0 0 0 0 2 @@ -147,9 +177,9 @@ Histogram: 2 0 0 0 0 0 0 0 0 2 Neighs: 2.06421e+06 ave 2.7551e+06 max 1.40237e+06 min Histogram: 2 0 0 0 0 0 0 0 0 2 -Total # of neighbors = 8256853 -Ave neighs/atom = 842.708 +Total # of neighbors = 8256852 +Ave neighs/atom = 842.7079 Ave special neighs/atom = 1.3227189 Neighbor list builds = 23 Dangerous builds = 0 -Total wall time: 0:08:22 +Total wall time: 0:03:12 diff --git a/examples/PACKAGES/electrode/graph-il/.gitignore b/examples/PACKAGES/electrode/graph-il/.gitignore index 8ee8bfa0f2..592bb61996 100644 --- a/examples/PACKAGES/electrode/graph-il/.gitignore +++ b/examples/PACKAGES/electrode/graph-il/.gitignore @@ -1 +1,2 @@ log.lammps* +in.temp diff --git a/examples/PACKAGES/electrode/graph-il/algo_test.sh b/examples/PACKAGES/electrode/graph-il/algo_test.sh new file mode 100755 index 0000000000..6106fe02dc --- /dev/null +++ b/examples/PACKAGES/electrode/graph-il/algo_test.sh @@ -0,0 +1,28 @@ +#!/bin/bash + +LMP_BIN="$1" +NP="${2:-1}" +echo "MPI over $NP procs:" +for feat in conp etypes tf +do + echo "Using base input file in.$feat:" + echo "mat_inv, log excerpts:" + logfile="log.algo_test.$NP.$feat" + mpirun -np $NP $LMP_BIN -i in.$feat -l $logfile > /dev/null 2>&1 + grep -A2 'Per MPI rank' $logfile + grep -B1 'Loop time' $logfile + rm $logfile + for cgtype in mat_cg cg + do + for tol in 1e-4 1e-5 1e-6 + do + echo "$cgtype, tol = $tol, log excerpts:" + logfile="log.algo_test.$NP.$feat.$cgtype.$tol" + sed '/electrode/ s/$/ algo '"$cgtype"' '"$tol"'/' in.$feat > in.temp + mpirun -np $NP $LMP_BIN -i in.temp -l $logfile > /dev/null 2>&1 + grep -A2 'Per MPI rank' $logfile + grep -B1 'Loop time' $logfile + rm $logfile + done + done +done diff --git a/examples/PACKAGES/electrode/graph-il/data.graph-il b/examples/PACKAGES/electrode/graph-il/data.graph-il index 600adeb64f..597e3c21d8 100644 --- a/examples/PACKAGES/electrode/graph-il/data.graph-il +++ b/examples/PACKAGES/electrode/graph-il/data.graph-il @@ -3,7 +3,7 @@ LAMMPS data file. CGCMM style. atom_style full generated by VMD/TopoTools v1.7 o 3776 atoms 640 bonds 320 angles - 5 atom types + 6 atom types 2 bond types 1 angle types @@ -18,6 +18,7 @@ LAMMPS data file. 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31.973658 28.754999 61.574997 # 5 +3672 646 6 0.000000 30.743900 28.045000 61.574997 # 5 +3673 644 6 0.000000 1.229756 30.885000 58.225006 # 5 +3674 646 6 0.000000 1.229756 30.885000 61.574997 # 5 +3675 644 6 0.000000 2.459512 31.594999 58.225006 # 5 +3676 644 6 0.000000 3.689268 30.885000 58.225006 # 5 +3677 646 6 0.000000 3.689268 30.885000 61.574997 # 5 +3678 646 6 0.000000 2.459512 30.174999 61.574997 # 5 +3679 644 6 0.000000 4.919024 31.594999 58.225006 # 5 +3680 644 6 0.000000 6.148780 30.885000 58.225006 # 5 +3681 646 6 0.000000 6.148780 30.885000 61.574997 # 5 +3682 646 6 0.000000 4.919024 30.174999 61.574997 # 5 +3683 644 6 0.000000 7.378536 31.594999 58.225006 # 5 +3684 644 6 0.000000 8.608293 30.885000 58.225006 # 5 +3685 646 6 0.000000 8.608293 30.885000 61.574997 # 5 +3686 646 6 0.000000 7.378536 30.174999 61.574997 # 5 +3687 644 6 0.000000 9.838048 31.594999 58.225006 # 5 +3688 644 6 0.000000 11.067804 30.885000 58.225006 # 5 +3689 646 6 0.000000 11.067804 30.885000 61.574997 # 5 +3690 646 6 0.000000 9.838048 30.174999 61.574997 # 5 +3691 644 6 0.000000 12.297561 31.594999 58.225006 # 5 +3692 644 6 0.000000 13.527316 30.885000 58.225006 # 5 +3693 646 6 0.000000 13.527316 30.885000 61.574997 # 5 +3694 646 6 0.000000 12.297561 30.174999 61.574997 # 5 +3695 644 6 0.000000 14.757072 31.594999 58.225006 # 5 +3696 644 6 0.000000 15.986829 30.885000 58.225006 # 5 +3697 646 6 0.000000 15.986829 30.885000 61.574997 # 5 +3698 646 6 0.000000 14.757072 30.174999 61.574997 # 5 +3699 644 6 0.000000 17.216585 31.594999 58.225006 # 5 +3700 644 6 0.000000 18.446341 30.885000 58.225006 # 5 +3701 646 6 0.000000 18.446341 30.885000 61.574997 # 5 +3702 646 6 0.000000 17.216585 30.174999 61.574997 # 5 +3703 644 6 0.000000 19.676096 31.594999 58.225006 # 5 +3704 644 6 0.000000 20.905853 30.885000 58.225006 # 5 +3705 646 6 0.000000 20.905853 30.885000 61.574997 # 5 +3706 646 6 0.000000 19.676096 30.174999 61.574997 # 5 +3707 644 6 0.000000 22.135609 31.594999 58.225006 # 5 +3708 644 6 0.000000 23.365364 30.885000 58.225006 # 5 +3709 646 6 0.000000 23.365364 30.885000 61.574997 # 5 +3710 646 6 0.000000 22.135609 30.174999 61.574997 # 5 +3711 644 6 0.000000 24.595121 31.594999 58.225006 # 5 +3712 644 6 0.000000 25.824877 30.885000 58.225006 # 5 +3713 646 6 0.000000 25.824877 30.885000 61.574997 # 5 +3714 646 6 0.000000 24.595121 30.174999 61.574997 # 5 +3715 644 6 0.000000 27.054632 31.594999 58.225006 # 5 +3716 644 6 0.000000 28.284389 30.885000 58.225006 # 5 +3717 646 6 0.000000 28.284389 30.885000 61.574997 # 5 +3718 646 6 0.000000 27.054632 30.174999 61.574997 # 5 +3719 644 6 0.000000 29.514145 31.594999 58.225006 # 5 +3720 644 6 0.000000 30.743900 30.885000 58.225006 # 5 +3721 646 6 0.000000 30.743900 30.885000 61.574997 # 5 +3722 646 6 0.000000 29.514145 30.174999 61.574997 # 5 +3723 644 6 0.000000 31.973658 31.594999 58.225006 # 5 +3724 646 6 0.000000 31.973658 30.174999 61.574997 # 5 +3725 644 6 0.000000 1.229756 33.724998 58.225006 # 5 +3726 644 6 0.000000 2.459512 33.014999 58.225006 # 5 +3727 646 6 0.000000 2.459512 33.014999 61.574997 # 5 +3728 646 6 0.000000 1.229756 32.305000 61.574997 # 5 +3729 644 6 0.000000 3.689268 33.724998 58.225006 # 5 +3730 644 6 0.000000 4.919024 33.014999 58.225006 # 5 +3731 646 6 0.000000 4.919024 33.014999 61.574997 # 5 +3732 646 6 0.000000 3.689268 32.305000 61.574997 # 5 +3733 644 6 0.000000 6.148780 33.724998 58.225006 # 5 +3734 644 6 0.000000 7.378536 33.014999 58.225006 # 5 +3735 646 6 0.000000 7.378536 33.014999 61.574997 # 5 +3736 646 6 0.000000 6.148780 32.305000 61.574997 # 5 +3737 644 6 0.000000 8.608293 33.724998 58.225006 # 5 +3738 644 6 0.000000 9.838048 33.014999 58.225006 # 5 +3739 646 6 0.000000 9.838048 33.014999 61.574997 # 5 +3740 646 6 0.000000 8.608293 32.305000 61.574997 # 5 +3741 644 6 0.000000 11.067804 33.724998 58.225006 # 5 +3742 644 6 0.000000 12.297561 33.014999 58.225006 # 5 +3743 646 6 0.000000 12.297561 33.014999 61.574997 # 5 +3744 646 6 0.000000 11.067804 32.305000 61.574997 # 5 +3745 644 6 0.000000 13.527316 33.724998 58.225006 # 5 +3746 644 6 0.000000 14.757072 33.014999 58.225006 # 5 +3747 646 6 0.000000 14.757072 33.014999 61.574997 # 5 +3748 646 6 0.000000 13.527316 32.305000 61.574997 # 5 +3749 644 6 0.000000 15.986829 33.724998 58.225006 # 5 +3750 644 6 0.000000 17.216585 33.014999 58.225006 # 5 +3751 646 6 0.000000 17.216585 33.014999 61.574997 # 5 +3752 646 6 0.000000 15.986829 32.305000 61.574997 # 5 +3753 644 6 0.000000 18.446341 33.724998 58.225006 # 5 +3754 644 6 0.000000 19.676096 33.014999 58.225006 # 5 +3755 646 6 0.000000 19.676096 33.014999 61.574997 # 5 +3756 646 6 0.000000 18.446341 32.305000 61.574997 # 5 +3757 644 6 0.000000 20.905853 33.724998 58.225006 # 5 +3758 644 6 0.000000 22.135609 33.014999 58.225006 # 5 +3759 646 6 0.000000 22.135609 33.014999 61.574997 # 5 +3760 646 6 0.000000 20.905853 32.305000 61.574997 # 5 +3761 644 6 0.000000 23.365364 33.724998 58.225006 # 5 +3762 644 6 0.000000 24.595121 33.014999 58.225006 # 5 +3763 646 6 0.000000 24.595121 33.014999 61.574997 # 5 +3764 646 6 0.000000 23.365364 32.305000 61.574997 # 5 +3765 644 6 0.000000 25.824877 33.724998 58.225006 # 5 +3766 644 6 0.000000 27.054632 33.014999 58.225006 # 5 +3767 646 6 0.000000 27.054632 33.014999 61.574997 # 5 +3768 646 6 0.000000 25.824877 32.305000 61.574997 # 5 +3769 644 6 0.000000 28.284389 33.724998 58.225006 # 5 +3770 644 6 0.000000 29.514145 33.014999 58.225006 # 5 +3771 646 6 0.000000 29.514145 33.014999 61.574997 # 5 +3772 646 6 0.000000 28.284389 32.305000 61.574997 # 5 +3773 644 6 0.000000 30.743900 33.724998 58.225006 # 5 +3774 644 6 0.000000 31.973658 33.014999 58.225006 # 5 +3775 646 6 0.000000 31.973658 33.014999 61.574997 # 5 +3776 646 6 0.000000 30.743900 32.305000 61.574997 # 5 Bonds diff --git a/examples/PACKAGES/electrode/graph-il/in.conp b/examples/PACKAGES/electrode/graph-il/in.conp index 12fcd88541..e5eec24da3 100644 --- a/examples/PACKAGES/electrode/graph-il/in.conp +++ b/examples/PACKAGES/electrode/graph-il/in.conp @@ -3,9 +3,9 @@ boundary p p f # slab calculation include settings.mod # styles, groups, computes and fixes -kspace_modify slab 3.0 +kspace_modify slab 3.0 # amat twostep -fix conp bot electrode/conp -1.0 1.979 couple top 1.0 symm on +fix conp bot electrode/conp -1.0 1.979 couple top 1.0 symm on #algo mat_inv thermo 50 thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop diff --git a/examples/PACKAGES/electrode/graph-il/in.conq b/examples/PACKAGES/electrode/graph-il/in.conq index 08429924d4..7f315a4b12 100644 --- a/examples/PACKAGES/electrode/graph-il/in.conq +++ b/examples/PACKAGES/electrode/graph-il/in.conq @@ -5,14 +5,10 @@ boundary p p f # slab calculation include settings.mod # styles, groups, computes and fixes kspace_modify slab 3.0 -fix conq bot electrode/conq -1.0 1.979 couple top 1.0 etypes 5 # conq doesn't take symm option - -# ask fix conq to output electrode potentials to internal variables -variable vbot internal 0.0 -variable vtop internal 0.0 -fix_modify conq set v bot vbot -fix_modify conq set v top vtop +fix conq bot electrode/conq -1.0 1.979 couple top 1.0 etypes on # symm on +variable dv equal f_conq[2]-f_conq[1] +# symm on and off give different electrode potentials, but identical potential difference thermo 50 -thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop v_vbot v_vtop +thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop f_conq[1] f_conq[2] v_dv run 500 diff --git a/examples/PACKAGES/electrode/graph-il/in.conq2 b/examples/PACKAGES/electrode/graph-il/in.conq2 index 46c9ecbf99..d860bf6c1a 100644 --- a/examples/PACKAGES/electrode/graph-il/in.conq2 +++ b/examples/PACKAGES/electrode/graph-il/in.conq2 @@ -5,30 +5,16 @@ boundary p p f # slab calculation include settings.mod # styles, groups, computes and fixes kspace_modify slab 3.0 -fix conp bot electrode/conp v_vbot 1.979 couple top v_vtop etypes 5 +fix conp bot electrode/conp v_vbot 1.979 couple top v_vtop etypes on -# get the four entries of electrode elastance matrix -variable me00 internal 0.0 -variable me01 internal 0.0 -variable me10 internal 0.0 -variable me11 internal 0.0 -fix_modify conp set me bot bot me00 -fix_modify conp set me bot top me01 -fix_modify conp set me top bot me10 -fix_modify conp set me top top me11 - -# get the 0V charges (qsb), and excess charge required to reach preset total charges -variable qsb_bot internal 0.0 -variable qsb_top internal 0.0 -fix_modify conp set qsb bot qsb_bot -fix_modify conp set qsb top qsb_top -variable qex_bot equal -1.0-v_qsb_bot # difference between desired and 0V charge -variable qex_top equal 1.0-v_qsb_top # difference between desired and 0V charge +variable qex_bot equal -1.0-f_conp[1][1] # difference between desired and 0V charge +variable qex_top equal 1.0-f_conp[2][1] # difference between desired and 0V charge # calculate imposed potential as elastance * excess charge # note: fix will wait until the run setup to look for its potential variables -variable vbot equal v_me00*v_qex_bot+v_me01*v_qex_top -variable vtop equal v_me10*v_qex_bot+v_me11*v_qex_top +# which is why we can define variable names *after* fix conp without error +variable vbot equal f_conp[1][4]*v_qex_bot+f_conp[1][5]*v_qex_top +variable vtop equal f_conp[2][4]*v_qex_bot+f_conp[2][5]*v_qex_top thermo 50 thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop v_vbot v_vtop diff --git a/examples/PACKAGES/electrode/graph-il/in.etypes b/examples/PACKAGES/electrode/graph-il/in.etypes index 30edebdc77..990c8bb415 100644 --- a/examples/PACKAGES/electrode/graph-il/in.etypes +++ b/examples/PACKAGES/electrode/graph-il/in.etypes @@ -5,7 +5,7 @@ boundary p p f # slab calculation include settings.mod # styles, groups, computes and fixes kspace_modify slab 3.0 -fix conp bot electrode/conp -1.0 1.979 couple top 1.0 symm on etypes 5 +fix conp bot electrode/conp -1.0 1.979 couple top 1.0 symm on etypes on thermo 50 thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop diff --git a/examples/PACKAGES/electrode/graph-il/in.ffield b/examples/PACKAGES/electrode/graph-il/in.ffield index 3d07402ffd..0771e91e62 100644 --- a/examples/PACKAGES/electrode/graph-il/in.ffield +++ b/examples/PACKAGES/electrode/graph-il/in.ffield @@ -4,7 +4,7 @@ boundary p p p # ffield uses periodic z-boundary and no slab include settings.mod # styles, groups, computes and fixes -fix conp bot electrode/conp -1.0 1.979 couple top 1.0 symm on etypes 5 ffield yes +fix conp bot electrode/conp -1.0 1.979 couple top 1.0 symm on etypes on ffield yes thermo 50 thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop diff --git a/examples/PACKAGES/electrode/graph-il/in.ramp b/examples/PACKAGES/electrode/graph-il/in.ramp index da6053ff9d..e4b897937d 100644 --- a/examples/PACKAGES/electrode/graph-il/in.ramp +++ b/examples/PACKAGES/electrode/graph-il/in.ramp @@ -6,7 +6,7 @@ include settings.mod # styles, groups, computes and fixes kspace_modify slab 3.0 variable v equal ramp(2,4) -fix conp bot electrode/conp 0.0 1.979 couple top v_v symm on etypes 5 +fix conp bot electrode/conp 0.0 1.979 couple top v_v symm on etypes on thermo 50 thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop v_v diff --git a/examples/PACKAGES/electrode/graph-il/in.thermo b/examples/PACKAGES/electrode/graph-il/in.thermo index a1d75196c9..eed574bff6 100644 --- a/examples/PACKAGES/electrode/graph-il/in.thermo +++ b/examples/PACKAGES/electrode/graph-il/in.thermo @@ -6,9 +6,9 @@ include settings.mod # styles, groups, computes and fixes kspace_modify slab 3.0 unfix nvt # remove NVT thermostat included from "settings.mod" -fix conpthermo bot electrode/thermo -1.0 1.979 couple top 1.0 etypes 5 temp 500 100 7 # temp tau rng +fix conpthermo bot electrode/thermo -1.0 1.979 couple top 1.0 etypes on temp 500 100 7 symm on # temp tau rng # to compare to regular constant potential, switch previous line to this: -#fix conp bot electrode/conp -1.0 1.979 couple top 1.0 etypes 5 symm on +#fix conp bot electrode/conp -1.0 1.979 couple top 1.0 etypes on symm on fix nve electrolyte nve # note ionic liquid does not reach 500K immediately diff --git a/examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-conp.g++.1 b/examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-conp.g++.1 similarity index 51% rename from examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-conp.g++.1 rename to examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-conp.g++.1 index 086f109958..c5cd2579af 100644 --- a/examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-conp.g++.1 +++ b/examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-conp.g++.1 @@ -1,4 +1,4 @@ -LAMMPS (24 Mar 2022) +LAMMPS (3 Nov 2022) # electrodes with constant potential # for graphene-ionic liquid supercapacitor @@ -37,13 +37,20 @@ Finding 1-2 1-3 1-4 neighbors ... 1 = max # of 1-3 neighbors 1 = max # of 1-4 neighbors 2 = max # of special neighbors - special bonds CPU = 0.001 seconds - read_data CPU = 0.036 seconds + special bonds CPU = 0.004 seconds + read_data CPU = 0.027 seconds -group bot molecule 641 -416 atoms in group bot -group top molecule 642 +# replicate 4 4 1 # test different sys sizes + +variable zpos atom "z > 0" +group zpos variable zpos +1891 atoms in group zpos +group ele type 5 +832 atoms in group ele +group top intersect ele zpos 416 atoms in group top +group bot subtract ele top +416 atoms in group bot group bmi type 1 2 3 960 atoms in group bmi @@ -52,24 +59,54 @@ group electrolyte type 1 2 3 4 fix nvt electrolyte nvt temp 500.0 500.0 100 fix shake bmi shake 1e-4 20 0 b 1 2 a 1 +Finding SHAKE clusters ... 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 320 = # of frozen angles - find clusters CPU = 0.001 seconds + find clusters CPU = 0.005 seconds variable q atom q compute qtop top reduce sum v_q compute qbot bot reduce sum v_q compute ctemp electrolyte temp -kspace_modify slab 3.0 +kspace_modify slab 3.0 # amat twostep -fix conp bot electrode/conp -1.0 1.979 couple top 1.0 symm on +fix conp bot electrode/conp -1.0 1.979 couple top 1.0 symm on #algo mat_inv 832 atoms in group conp_group thermo 50 thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop run 500 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- kspace_style pppm/electrode command: + +@article{Ahrens2021, +author = {Ahrens-Iwers, Ludwig J.V. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0063381}, +title = {{Constant potential simulations on a mesh}}, +journal = {Journal of Chemical Physics}, +year = {2021} +volume = {155}, +pages = {104104}, +} +- fix electrode command: + +@article{Ahrens2022 +author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0099239}, +title = {{ELECTRODE: An electrochemistry package for LAMMPS}}, +journal = {The Journal of Chemical Physics}, +year = {2022} +volume = {157}, +pages = {084801}, +} +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + PPPM/electrode initialization ... using 12-bit tables for long-range coulomb (src/kspace.cpp:342) G vector (1/distance) = 0.20904498 @@ -79,9 +116,9 @@ PPPM/electrode initialization ... estimated relative force accuracy = 1.1149519e-07 using double precision MKL FFT 3d grid and FFT values/proc = 307242 204800 - generated 10 of 10 mixed pair_coeff terms from geometric mixing rule +Generated 15 of 15 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... - update every 1 steps, delay 10 steps, check yes + update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 18 ghost atom cutoff = 18 @@ -97,35 +134,35 @@ Neighbor list info ... pair build: copy stencil: none bin: none -Per MPI rank memory allocation (min/avg/max) = 57.15 | 57.15 | 57.15 Mbytes +Per MPI rank memory allocation (min/avg/max) = 57.19 | 57.19 | 57.19 Mbytes Step Temp c_ctemp E_pair TotEng c_qbot c_qtop - 0 0 0 25137191 25137191 0.0085142912 -0.0085142912 + 0 0 0 25137190 25137190 0.0085142912 -0.0085142912 50 17.83755 64.26354 25137031 25137214 0.0045923944 -0.0045923944 - 100 48.393682 174.34846 25136774 25137273 -0.009514517 0.009514517 - 150 70.421272 253.7075 25136655 25137380 -0.033017005 0.033017005 - 200 82.204844 296.16031 25136667 25137514 -0.063668175 0.063668175 - 250 87.54223 315.38937 25136757 25137659 -0.096776257 0.096776257 - 300 91.704746 330.38571 25136865 25137810 -0.1283784 0.1283784 - 350 100.36017 361.56871 25136934 25137968 -0.15649799 0.15649799 - 400 111.37575 401.25467 25136986 25138133 -0.18065435 0.18065435 - 450 121.79848 438.80476 25137043 25138298 -0.19979365 0.19979365 - 500 126.95916 457.39718 25137145 25138453 -0.21037535 0.21037535 -Loop time of 103.439 on 1 procs for 500 steps with 3776 atoms + 100 48.393682 174.34846 25136775 25137273 -0.009514517 0.009514517 + 150 70.421272 253.7075 25136657 25137382 -0.033017005 0.033017005 + 200 82.204844 296.16031 25136670 25137517 -0.063668175 0.063668175 + 250 87.54223 315.38937 25136762 25137663 -0.096776257 0.096776257 + 300 91.704746 330.38571 25136871 25137816 -0.1283784 0.1283784 + 350 100.36017 361.56871 25136941 25137975 -0.15649799 0.15649799 + 400 111.37575 401.25467 25136994 25138141 -0.18065435 0.18065435 + 450 121.79848 438.80476 25137052 25138307 -0.19979365 0.19979365 + 500 126.95916 457.39718 25137155 25138463 -0.21037535 0.21037535 +Loop time of 91.5523 on 1 procs for 500 steps with 3776 atoms -Performance: 0.418 ns/day, 57.466 hours/ns, 4.834 timesteps/s -393.6% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 0.472 ns/day, 50.862 hours/ns, 5.461 timesteps/s, 20.622 katom-step/s +100.0% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 19.309 | 19.309 | 19.309 | 0.0 | 18.67 -Bond | 0.0018867 | 0.0018867 | 0.0018867 | 0.0 | 0.00 -Kspace | 23.047 | 23.047 | 23.047 | 0.0 | 22.28 -Neigh | 0.25707 | 0.25707 | 0.25707 | 0.0 | 0.25 -Comm | 0.070734 | 0.070734 | 0.070734 | 0.0 | 0.07 -Output | 0.0023085 | 0.0023085 | 0.0023085 | 0.0 | 0.00 -Modify | 60.73 | 60.73 | 60.73 | 0.0 | 58.71 -Other | | 0.01994 | | | 0.02 +Pair | 18.906 | 18.906 | 18.906 | 0.0 | 20.65 +Bond | 0.0012922 | 0.0012922 | 0.0012922 | 0.0 | 0.00 +Kspace | 34.476 | 34.476 | 34.476 | 0.0 | 37.66 +Neigh | 0.26641 | 0.26641 | 0.26641 | 0.0 | 0.29 +Comm | 0.069067 | 0.069067 | 0.069067 | 0.0 | 0.08 +Output | 0.0021466 | 0.0021466 | 0.0021466 | 0.0 | 0.00 +Modify | 37.805 | 37.805 | 37.805 | 0.0 | 41.29 +Other | | 0.0271 | | | 0.03 Nlocal: 3776 ave 3776 max 3776 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -139,4 +176,4 @@ Ave neighs/atom = 457.18432 Ave special neighs/atom = 0.50847458 Neighbor list builds = 7 Dangerous builds = 0 -Total wall time: 0:03:10 +Total wall time: 0:01:48 diff --git a/examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-conp.g++.4 b/examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-conp.g++.4 similarity index 51% rename from examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-conp.g++.4 rename to examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-conp.g++.4 index f74768b08d..ba941705aa 100644 --- a/examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-conp.g++.4 +++ b/examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-conp.g++.4 @@ -1,4 +1,4 @@ -LAMMPS (24 Mar 2022) +LAMMPS (3 Nov 2022) # electrodes with constant potential # for graphene-ionic liquid supercapacitor @@ -38,13 +38,20 @@ Finding 1-2 1-3 1-4 neighbors ... 1 = max # of 1-3 neighbors 1 = max # of 1-4 neighbors 2 = max # of special neighbors - special bonds CPU = 0.001 seconds - read_data CPU = 0.014 seconds + special bonds CPU = 0.003 seconds + read_data CPU = 0.038 seconds -group bot molecule 641 -416 atoms in group bot -group top molecule 642 +# replicate 4 4 1 # test different sys sizes + +variable zpos atom "z > 0" +group zpos variable zpos +1891 atoms in group zpos +group ele type 5 +832 atoms in group ele +group top intersect ele zpos 416 atoms in group top +group bot subtract ele top +416 atoms in group bot group bmi type 1 2 3 960 atoms in group bmi @@ -53,24 +60,54 @@ group electrolyte type 1 2 3 4 fix nvt electrolyte nvt temp 500.0 500.0 100 fix shake bmi shake 1e-4 20 0 b 1 2 a 1 +Finding SHAKE clusters ... 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 320 = # of frozen angles - find clusters CPU = 0.001 seconds + find clusters CPU = 0.003 seconds variable q atom q compute qtop top reduce sum v_q compute qbot bot reduce sum v_q compute ctemp electrolyte temp -kspace_modify slab 3.0 +kspace_modify slab 3.0 # amat twostep -fix conp bot electrode/conp -1.0 1.979 couple top 1.0 symm on +fix conp bot electrode/conp -1.0 1.979 couple top 1.0 symm on #algo mat_inv 832 atoms in group conp_group thermo 50 thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop run 500 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- kspace_style pppm/electrode command: + +@article{Ahrens2021, +author = {Ahrens-Iwers, Ludwig J.V. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0063381}, +title = {{Constant potential simulations on a mesh}}, +journal = {Journal of Chemical Physics}, +year = {2021} +volume = {155}, +pages = {104104}, +} +- fix electrode command: + +@article{Ahrens2022 +author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0099239}, +title = {{ELECTRODE: An electrochemistry package for LAMMPS}}, +journal = {The Journal of Chemical Physics}, +year = {2022} +volume = {157}, +pages = {084801}, +} +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + PPPM/electrode initialization ... using 12-bit tables for long-range coulomb (src/kspace.cpp:342) G vector (1/distance) = 0.20904498 @@ -80,9 +117,9 @@ PPPM/electrode initialization ... estimated relative force accuracy = 1.1149519e-07 using double precision MKL FFT 3d grid and FFT values/proc = 151593 85504 - generated 10 of 10 mixed pair_coeff terms from geometric mixing rule +Generated 15 of 15 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... - update every 1 steps, delay 10 steps, check yes + update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 18 ghost atom cutoff = 18 @@ -98,35 +135,35 @@ Neighbor list info ... pair build: copy stencil: none bin: none -Per MPI rank memory allocation (min/avg/max) = 23.13 | 26.96 | 30.79 Mbytes +Per MPI rank memory allocation (min/avg/max) = 23.16 | 26.99 | 30.82 Mbytes Step Temp c_ctemp E_pair TotEng c_qbot c_qtop - 0 0 0 25137191 25137191 0.0085142912 -0.0085142912 + 0 0 0 25137190 25137190 0.0085142912 -0.0085142912 50 17.83755 64.26354 25137031 25137214 0.0045923944 -0.0045923944 - 100 48.393682 174.34846 25136774 25137273 -0.009514517 0.009514517 - 150 70.421272 253.7075 25136655 25137380 -0.033017005 0.033017005 - 200 82.204844 296.16031 25136667 25137514 -0.063668175 0.063668175 - 250 87.54223 315.38937 25136757 25137659 -0.096776257 0.096776257 - 300 91.704746 330.38571 25136865 25137810 -0.1283784 0.1283784 - 350 100.36017 361.56871 25136934 25137968 -0.15649799 0.15649799 - 400 111.37575 401.25467 25136986 25138133 -0.18065435 0.18065435 - 450 121.79848 438.80476 25137043 25138298 -0.19979365 0.19979365 - 500 126.95916 457.39718 25137145 25138453 -0.21037535 0.21037535 -Loop time of 49.6656 on 4 procs for 500 steps with 3776 atoms + 100 48.393682 174.34846 25136775 25137273 -0.009514517 0.009514517 + 150 70.421272 253.7075 25136657 25137382 -0.033017005 0.033017005 + 200 82.204844 296.16031 25136670 25137517 -0.063668175 0.063668175 + 250 87.54223 315.38937 25136762 25137663 -0.096776257 0.096776257 + 300 91.704746 330.38571 25136871 25137816 -0.1283784 0.1283784 + 350 100.36017 361.56871 25136941 25137975 -0.15649799 0.15649799 + 400 111.37575 401.25467 25136994 25138141 -0.18065435 0.18065435 + 450 121.79848 438.80476 25137052 25138307 -0.19979365 0.19979365 + 500 126.95916 457.39718 25137155 25138463 -0.21037535 0.21037535 +Loop time of 49.6413 on 4 procs for 500 steps with 3776 atoms -Performance: 0.870 ns/day, 27.592 hours/ns, 10.067 timesteps/s -95.1% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 0.870 ns/day, 27.578 hours/ns, 10.072 timesteps/s, 38.033 katom-step/s +76.3% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 5.968 | 6.1677 | 6.382 | 6.5 | 12.42 -Bond | 0.00071151 | 0.00078617 | 0.00090387 | 0.0 | 0.00 -Kspace | 17.345 | 17.558 | 17.755 | 3.8 | 35.35 -Neigh | 0.10939 | 0.10945 | 0.10948 | 0.0 | 0.22 -Comm | 0.15295 | 0.15474 | 0.15699 | 0.4 | 0.31 -Output | 0.00074458 | 0.0010336 | 0.0018799 | 1.5 | 0.00 -Modify | 25.634 | 25.641 | 25.645 | 0.1 | 51.63 -Other | | 0.03276 | | | 0.07 +Pair | 5.3666 | 5.4998 | 5.6946 | 5.4 | 11.08 +Bond | 0.0011638 | 0.0012711 | 0.0014555 | 0.3 | 0.00 +Kspace | 24.047 | 24.241 | 24.374 | 2.6 | 48.83 +Neigh | 0.088235 | 0.088328 | 0.088432 | 0.0 | 0.18 +Comm | 0.30907 | 0.31913 | 0.32916 | 1.7 | 0.64 +Output | 0.0010669 | 0.0014463 | 0.0024232 | 1.5 | 0.00 +Modify | 19.435 | 19.445 | 19.454 | 0.2 | 39.17 +Other | | 0.04549 | | | 0.09 Nlocal: 944 ave 951 max 941 min Histogram: 1 2 0 0 0 0 0 0 0 1 @@ -140,4 +177,4 @@ Ave neighs/atom = 457.18432 Ave special neighs/atom = 0.50847458 Neighbor list builds = 7 Dangerous builds = 0 -Total wall time: 0:01:11 +Total wall time: 0:00:55 diff --git a/examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-conq.g++.1 b/examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-conq.g++.1 new file mode 100644 index 0000000000..c75238dc36 --- /dev/null +++ b/examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-conq.g++.1 @@ -0,0 +1,186 @@ +LAMMPS (3 Nov 2022) +# electrodes with constrained total charges +# for graphene-ionic liquid supercapacitor + +boundary p p f # slab calculation +include settings.mod # styles, groups, computes and fixes +# set boundary in main script because ffield is periodic +units real +# distribute electrode atoms among all processors: +if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2" + +atom_style full +pair_style lj/cut/coul/long 16 +bond_style harmonic +angle_style harmonic +kspace_style pppm/electrode 1e-7 +# kspace_modify in main script because ffield is periodic + +read_data "data.graph-il" +Reading data file ... + orthogonal box = (0 0 -68) to (32.2 34.4 68) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 3776 atoms + scanning bonds ... + 2 = max bonds/atom + scanning angles ... + 1 = max angles/atom + reading bonds ... + 640 bonds + reading angles ... + 320 angles +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.002 seconds + read_data CPU = 0.023 seconds + +# replicate 4 4 1 # test different sys sizes + +variable zpos atom "z > 0" +group zpos variable zpos +1891 atoms in group zpos +group ele type 5 +832 atoms in group ele +group top intersect ele zpos +416 atoms in group top +group bot subtract ele top +416 atoms in group bot + +group bmi type 1 2 3 +960 atoms in group bmi +group electrolyte type 1 2 3 4 +1280 atoms in group electrolyte + +fix nvt electrolyte nvt temp 500.0 500.0 100 +fix shake bmi shake 1e-4 20 0 b 1 2 a 1 +Finding SHAKE clusters ... + 0 = # of size 2 clusters + 0 = # of size 3 clusters + 0 = # of size 4 clusters + 320 = # of frozen angles + find clusters CPU = 0.002 seconds + +variable q atom q +compute qtop top reduce sum v_q +compute qbot bot reduce sum v_q +compute ctemp electrolyte temp +kspace_modify slab 3.0 + +fix conq bot electrode/conq -1.0 1.979 couple top 1.0 etypes on # symm on +832 atoms in group conp_group +variable dv equal f_conq[2]-f_conq[1] +# symm on and off give different electrode potentials, but identical potential difference + +thermo 50 +thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop f_conq[1] f_conq[2] v_dv +run 500 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- kspace_style pppm/electrode command: + +@article{Ahrens2021, +author = {Ahrens-Iwers, Ludwig J.V. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0063381}, +title = {{Constant potential simulations on a mesh}}, +journal = {Journal of Chemical Physics}, +year = {2021} +volume = {155}, +pages = {104104}, +} +- fix electrode command: + +@article{Ahrens2022 +author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0099239}, +title = {{ELECTRODE: An electrochemistry package for LAMMPS}}, +journal = {The Journal of Chemical Physics}, +year = {2022} +volume = {157}, +pages = {084801}, +} +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +PPPM/electrode initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:342) + G vector (1/distance) = 0.20904498 + grid = 32 32 200 + stencil order = 5 + estimated absolute RMS force accuracy = 3.7023506e-05 + estimated relative force accuracy = 1.1149519e-07 + using double precision MKL FFT + 3d grid and FFT values/proc = 307242 204800 +Generated 15 of 15 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 18 + ghost atom cutoff = 18 + binsize = 9, bins = 4 4 16 + 3 neighbor lists, perpetual/occasional/extra = 2 1 0 + (1) pair lj/cut/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard + (2) fix electrode/conq, occasional, skip from (1) + attributes: half, newton on + pair build: skip + stencil: none + bin: none + (3) fix electrode/conq, perpetual, skip from (1) + attributes: half, newton on + pair build: skip + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 54.25 | 54.25 | 54.25 Mbytes + Step Temp c_ctemp E_pair TotEng c_qbot c_qtop f_conq[1] f_conq[2] v_dv + 0 0 0 25137446 25137446 -1 1 -9.931852 10.097344 20.029196 + 50 20.206425 72.797911 25137263 25137472 -1 1 -9.4359366 9.5964514 19.032388 + 100 55.931663 201.50563 25136961 25137537 -1 1 -8.0440112 8.1861787 16.23019 + 150 81.389273 293.22204 25136818 25137656 -1 1 -6.1113109 6.2267114 12.338022 + 200 92.867946 334.57639 25136841 25137798 -1 1 -4.1857807 4.2740694 8.4598501 + 250 97.518304 351.33028 25136942 25137946 -1 1 -2.8383703 2.9101475 5.7485179 + 300 102.36577 368.79431 25137045 25138099 -1 1 -2.3831643 2.4461115 4.8292759 + 350 113.66597 409.50566 25137086 25138256 -1 1 -2.7083563 2.7457811 5.4541374 + 400 122.8443 442.57252 25137148 25138413 -1 1 -3.4311003 3.3941657 6.825266 + 450 128.63713 463.44243 25137235 25138560 -1 1 -4.132871 3.9852959 8.1181669 + 500 131.18361 472.61665 25137344 25138695 -1 1 -4.5104095 4.2567261 8.7671355 +Loop time of 89.4461 on 1 procs for 500 steps with 3776 atoms + +Performance: 0.483 ns/day, 49.692 hours/ns, 5.590 timesteps/s, 21.108 katom-step/s +100.0% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 19.404 | 19.404 | 19.404 | 0.0 | 21.69 +Bond | 0.0014902 | 0.0014902 | 0.0014902 | 0.0 | 0.00 +Kspace | 35.449 | 35.449 | 35.449 | 0.0 | 39.63 +Neigh | 0.26499 | 0.26499 | 0.26499 | 0.0 | 0.30 +Comm | 0.068497 | 0.068497 | 0.068497 | 0.0 | 0.08 +Output | 0.0023974 | 0.0023974 | 0.0023974 | 0.0 | 0.00 +Modify | 34.225 | 34.225 | 34.225 | 0.0 | 38.26 +Other | | 0.03044 | | | 0.03 + +Nlocal: 3776 ave 3776 max 3776 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 12510 ave 12510 max 12510 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 1.72559e+06 ave 1.72559e+06 max 1.72559e+06 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 1725588 +Ave neighs/atom = 456.98835 +Ave special neighs/atom = 0.50847458 +Neighbor list builds = 6 +Dangerous builds = 0 +Total wall time: 0:01:48 diff --git a/examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-conq.g++.4 b/examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-conq.g++.4 new file mode 100644 index 0000000000..65a143ad13 --- /dev/null +++ b/examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-conq.g++.4 @@ -0,0 +1,187 @@ +LAMMPS (3 Nov 2022) +# electrodes with constrained total charges +# for graphene-ionic liquid supercapacitor + +boundary p p f # slab calculation +include settings.mod # styles, groups, computes and fixes +# set boundary in main script because ffield is periodic +units real +# distribute electrode atoms among all processors: +if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2" +processors * * 2 + +atom_style full +pair_style lj/cut/coul/long 16 +bond_style harmonic +angle_style harmonic +kspace_style pppm/electrode 1e-7 +# kspace_modify in main script because ffield is periodic + +read_data "data.graph-il" +Reading data file ... + orthogonal box = (0 0 -68) to (32.2 34.4 68) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 3776 atoms + scanning bonds ... + 2 = max bonds/atom + scanning angles ... + 1 = max angles/atom + reading bonds ... + 640 bonds + reading angles ... + 320 angles +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.002 seconds + read_data CPU = 0.034 seconds + +# replicate 4 4 1 # test different sys sizes + +variable zpos atom "z > 0" +group zpos variable zpos +1891 atoms in group zpos +group ele type 5 +832 atoms in group ele +group top intersect ele zpos +416 atoms in group top +group bot subtract ele top +416 atoms in group bot + +group bmi type 1 2 3 +960 atoms in group bmi +group electrolyte type 1 2 3 4 +1280 atoms in group electrolyte + +fix nvt electrolyte nvt temp 500.0 500.0 100 +fix shake bmi shake 1e-4 20 0 b 1 2 a 1 +Finding SHAKE clusters ... + 0 = # of size 2 clusters + 0 = # of size 3 clusters + 0 = # of size 4 clusters + 320 = # of frozen angles + find clusters CPU = 0.002 seconds + +variable q atom q +compute qtop top reduce sum v_q +compute qbot bot reduce sum v_q +compute ctemp electrolyte temp +kspace_modify slab 3.0 + +fix conq bot electrode/conq -1.0 1.979 couple top 1.0 etypes on # symm on +832 atoms in group conp_group +variable dv equal f_conq[2]-f_conq[1] +# symm on and off give different electrode potentials, but identical potential difference + +thermo 50 +thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop f_conq[1] f_conq[2] v_dv +run 500 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- kspace_style pppm/electrode command: + +@article{Ahrens2021, +author = {Ahrens-Iwers, Ludwig J.V. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0063381}, +title = {{Constant potential simulations on a mesh}}, +journal = {Journal of Chemical Physics}, +year = {2021} +volume = {155}, +pages = {104104}, +} +- fix electrode command: + +@article{Ahrens2022 +author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0099239}, +title = {{ELECTRODE: An electrochemistry package for LAMMPS}}, +journal = {The Journal of Chemical Physics}, +year = {2022} +volume = {157}, +pages = {084801}, +} +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +PPPM/electrode initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:342) + G vector (1/distance) = 0.20904498 + grid = 32 32 200 + stencil order = 5 + estimated absolute RMS force accuracy = 3.7023506e-05 + estimated relative force accuracy = 1.1149519e-07 + using double precision MKL FFT + 3d grid and FFT values/proc = 151593 85504 +Generated 15 of 15 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 18 + ghost atom cutoff = 18 + binsize = 9, bins = 4 4 16 + 3 neighbor lists, perpetual/occasional/extra = 2 1 0 + (1) pair lj/cut/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard + (2) fix electrode/conq, occasional, skip from (1) + attributes: half, newton on + pair build: skip + stencil: none + bin: none + (3) fix electrode/conq, perpetual, skip from (1) + attributes: half, newton on + pair build: skip + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 22.9 | 26.72 | 30.55 Mbytes + Step Temp c_ctemp E_pair TotEng c_qbot c_qtop f_conq[1] f_conq[2] v_dv + 0 0 0 25137446 25137446 -1 1 -9.931852 10.097344 20.029196 + 50 20.206425 72.797911 25137263 25137472 -1 1 -9.4359366 9.5964514 19.032388 + 100 55.931663 201.50563 25136961 25137537 -1 1 -8.0440112 8.1861787 16.23019 + 150 81.389273 293.22204 25136818 25137656 -1 1 -6.1113109 6.2267114 12.338022 + 200 92.867946 334.57639 25136841 25137798 -1 1 -4.1857807 4.2740694 8.4598501 + 250 97.518304 351.33028 25136942 25137946 -1 1 -2.8383703 2.9101475 5.7485179 + 300 102.36577 368.79431 25137045 25138099 -1 1 -2.3831643 2.4461115 4.8292759 + 350 113.66597 409.50566 25137086 25138256 -1 1 -2.7083563 2.7457811 5.4541374 + 400 122.8443 442.57252 25137148 25138413 -1 1 -3.4311003 3.3941657 6.825266 + 450 128.63713 463.44243 25137235 25138560 -1 1 -4.132871 3.9852959 8.1181669 + 500 131.18361 472.61665 25137344 25138695 -1 1 -4.5104095 4.2567261 8.7671355 +Loop time of 53.4299 on 4 procs for 500 steps with 3776 atoms + +Performance: 0.809 ns/day, 29.683 hours/ns, 9.358 timesteps/s, 35.336 katom-step/s +74.0% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 5.5806 | 5.8872 | 6.1547 | 8.8 | 11.02 +Bond | 0.0011404 | 0.0012245 | 0.0012898 | 0.2 | 0.00 +Kspace | 26.55 | 26.822 | 27.129 | 4.1 | 50.20 +Neigh | 0.098647 | 0.099673 | 0.10083 | 0.3 | 0.19 +Comm | 0.35493 | 0.37282 | 0.3909 | 2.1 | 0.70 +Output | 0.0012274 | 0.001617 | 0.0026374 | 1.5 | 0.00 +Modify | 20.172 | 20.188 | 20.203 | 0.3 | 37.78 +Other | | 0.05647 | | | 0.11 + +Nlocal: 944 ave 948 max 940 min +Histogram: 1 0 0 1 0 0 1 0 0 1 +Nghost: 5920.5 ave 5941 max 5899 min +Histogram: 1 0 0 0 1 1 0 0 0 1 +Neighs: 431397 ave 442329 max 421103 min +Histogram: 2 0 0 0 0 0 0 0 1 1 + +Total # of neighbors = 1725588 +Ave neighs/atom = 456.98835 +Ave special neighs/atom = 0.50847458 +Neighbor list builds = 6 +Dangerous builds = 0 +Total wall time: 0:00:59 diff --git a/examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-conq2.g++.1 b/examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-conq2.g++.1 new file mode 100644 index 0000000000..a3eedd22c7 --- /dev/null +++ b/examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-conq2.g++.1 @@ -0,0 +1,193 @@ +LAMMPS (3 Nov 2022) +# electrodes with constrained total charges imposed from dynamically computed potentials +# for graphene-ionic liquid supercapacitor + +boundary p p f # slab calculation +include settings.mod # styles, groups, computes and fixes +# set boundary in main script because ffield is periodic +units real +# distribute electrode atoms among all processors: +if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2" + +atom_style full +pair_style lj/cut/coul/long 16 +bond_style harmonic +angle_style harmonic +kspace_style pppm/electrode 1e-7 +# kspace_modify in main script because ffield is periodic + +read_data "data.graph-il" +Reading data file ... + orthogonal box = (0 0 -68) to (32.2 34.4 68) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 3776 atoms + scanning bonds ... + 2 = max bonds/atom + scanning angles ... + 1 = max angles/atom + reading bonds ... + 640 bonds + reading angles ... + 320 angles +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.002 seconds + read_data CPU = 0.022 seconds + +# replicate 4 4 1 # test different sys sizes + +variable zpos atom "z > 0" +group zpos variable zpos +1891 atoms in group zpos +group ele type 5 +832 atoms in group ele +group top intersect ele zpos +416 atoms in group top +group bot subtract ele top +416 atoms in group bot + +group bmi type 1 2 3 +960 atoms in group bmi +group electrolyte type 1 2 3 4 +1280 atoms in group electrolyte + +fix nvt electrolyte nvt temp 500.0 500.0 100 +fix shake bmi shake 1e-4 20 0 b 1 2 a 1 +Finding SHAKE clusters ... + 0 = # of size 2 clusters + 0 = # of size 3 clusters + 0 = # of size 4 clusters + 320 = # of frozen angles + find clusters CPU = 0.001 seconds + +variable q atom q +compute qtop top reduce sum v_q +compute qbot bot reduce sum v_q +compute ctemp electrolyte temp +kspace_modify slab 3.0 + +fix conp bot electrode/conp v_vbot 1.979 couple top v_vtop etypes on +832 atoms in group conp_group + +variable qex_bot equal -1.0-f_conp[1][1] # difference between desired and 0V charge +variable qex_top equal 1.0-f_conp[2][1] # difference between desired and 0V charge + +# calculate imposed potential as elastance * excess charge +# note: fix will wait until the run setup to look for its potential variables +# which is why we can define variable names *after* fix conp without error +variable vbot equal f_conp[1][4]*v_qex_bot+f_conp[1][5]*v_qex_top +variable vtop equal f_conp[2][4]*v_qex_bot+f_conp[2][5]*v_qex_top + +thermo 50 +thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop v_vbot v_vtop +run 500 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- kspace_style pppm/electrode command: + +@article{Ahrens2021, +author = {Ahrens-Iwers, Ludwig J.V. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0063381}, +title = {{Constant potential simulations on a mesh}}, +journal = {Journal of Chemical Physics}, +year = {2021} +volume = {155}, +pages = {104104}, +} +- fix electrode command: + +@article{Ahrens2022 +author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0099239}, +title = {{ELECTRODE: An electrochemistry package for LAMMPS}}, +journal = {The Journal of Chemical Physics}, +year = {2022} +volume = {157}, +pages = {084801}, +} +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +PPPM/electrode initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:342) + G vector (1/distance) = 0.20904498 + grid = 32 32 200 + stencil order = 5 + estimated absolute RMS force accuracy = 3.7023506e-05 + estimated relative force accuracy = 1.1149519e-07 + using double precision MKL FFT + 3d grid and FFT values/proc = 307242 204800 +Generated 15 of 15 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 18 + ghost atom cutoff = 18 + binsize = 9, bins = 4 4 16 + 3 neighbor lists, perpetual/occasional/extra = 2 1 0 + (1) pair lj/cut/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard + (2) fix electrode/conp, occasional, skip from (1) + attributes: half, newton on + pair build: skip + stencil: none + bin: none + (3) fix electrode/conp, perpetual, skip from (1) + attributes: half, newton on + pair build: skip + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 54.25 | 54.25 | 54.25 Mbytes + Step Temp c_ctemp E_pair TotEng c_qbot c_qtop v_vbot v_vtop + 0 0 0 25137446 25137446 -1 1 -9.931852 10.097344 + 50 20.206425 72.797911 25137263 25137472 -1 1 -9.4359366 9.5964514 + 100 55.931663 201.50563 25136961 25137537 -1 1 -8.0440112 8.1861787 + 150 81.389273 293.22204 25136818 25137656 -1 1 -6.1113109 6.2267114 + 200 92.867946 334.57639 25136841 25137798 -1 1 -4.1857807 4.2740694 + 250 97.518304 351.33028 25136942 25137946 -1 1 -2.8383703 2.9101475 + 300 102.36577 368.79431 25137045 25138099 -1 1 -2.3831643 2.4461115 + 350 113.66597 409.50566 25137086 25138256 -1 1 -2.7083563 2.7457811 + 400 122.8443 442.57252 25137148 25138413 -1 1 -3.4311003 3.3941657 + 450 128.63713 463.44243 25137235 25138560 -1 1 -4.132871 3.9852959 + 500 131.18361 472.61665 25137344 25138695 -1 1 -4.5104095 4.2567261 +Loop time of 85.5691 on 1 procs for 500 steps with 3776 atoms + +Performance: 0.505 ns/day, 47.538 hours/ns, 5.843 timesteps/s, 22.064 katom-step/s +100.0% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 18.558 | 18.558 | 18.558 | 0.0 | 21.69 +Bond | 0.001404 | 0.001404 | 0.001404 | 0.0 | 0.00 +Kspace | 33.78 | 33.78 | 33.78 | 0.0 | 39.48 +Neigh | 0.27017 | 0.27017 | 0.27017 | 0.0 | 0.32 +Comm | 0.067438 | 0.067438 | 0.067438 | 0.0 | 0.08 +Output | 0.0026656 | 0.0026656 | 0.0026656 | 0.0 | 0.00 +Modify | 32.86 | 32.86 | 32.86 | 0.0 | 38.40 +Other | | 0.02916 | | | 0.03 + +Nlocal: 3776 ave 3776 max 3776 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 12510 ave 12510 max 12510 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 1.72559e+06 ave 1.72559e+06 max 1.72559e+06 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 1725588 +Ave neighs/atom = 456.98835 +Ave special neighs/atom = 0.50847458 +Neighbor list builds = 6 +Dangerous builds = 0 +Total wall time: 0:01:42 diff --git a/examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-conq2.g++.4 b/examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-conq2.g++.4 new file mode 100644 index 0000000000..a0b182f3bb --- /dev/null +++ b/examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-conq2.g++.4 @@ -0,0 +1,194 @@ +LAMMPS (3 Nov 2022) +# electrodes with constrained total charges imposed from dynamically computed potentials +# for graphene-ionic liquid supercapacitor + +boundary p p f # slab calculation +include settings.mod # styles, groups, computes and fixes +# set boundary in main script because ffield is periodic +units real +# distribute electrode atoms among all processors: +if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2" +processors * * 2 + +atom_style full +pair_style lj/cut/coul/long 16 +bond_style harmonic +angle_style harmonic +kspace_style pppm/electrode 1e-7 +# kspace_modify in main script because ffield is periodic + +read_data "data.graph-il" +Reading data file ... + orthogonal box = (0 0 -68) to (32.2 34.4 68) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 3776 atoms + scanning bonds ... + 2 = max bonds/atom + scanning angles ... + 1 = max angles/atom + reading bonds ... + 640 bonds + reading angles ... + 320 angles +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.005 seconds + read_data CPU = 0.044 seconds + +# replicate 4 4 1 # test different sys sizes + +variable zpos atom "z > 0" +group zpos variable zpos +1891 atoms in group zpos +group ele type 5 +832 atoms in group ele +group top intersect ele zpos +416 atoms in group top +group bot subtract ele top +416 atoms in group bot + +group bmi type 1 2 3 +960 atoms in group bmi +group electrolyte type 1 2 3 4 +1280 atoms in group electrolyte + +fix nvt electrolyte nvt temp 500.0 500.0 100 +fix shake bmi shake 1e-4 20 0 b 1 2 a 1 +Finding SHAKE clusters ... + 0 = # of size 2 clusters + 0 = # of size 3 clusters + 0 = # of size 4 clusters + 320 = # of frozen angles + find clusters CPU = 0.002 seconds + +variable q atom q +compute qtop top reduce sum v_q +compute qbot bot reduce sum v_q +compute ctemp electrolyte temp +kspace_modify slab 3.0 + +fix conp bot electrode/conp v_vbot 1.979 couple top v_vtop etypes on +832 atoms in group conp_group + +variable qex_bot equal -1.0-f_conp[1][1] # difference between desired and 0V charge +variable qex_top equal 1.0-f_conp[2][1] # difference between desired and 0V charge + +# calculate imposed potential as elastance * excess charge +# note: fix will wait until the run setup to look for its potential variables +# which is why we can define variable names *after* fix conp without error +variable vbot equal f_conp[1][4]*v_qex_bot+f_conp[1][5]*v_qex_top +variable vtop equal f_conp[2][4]*v_qex_bot+f_conp[2][5]*v_qex_top + +thermo 50 +thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop v_vbot v_vtop +run 500 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- kspace_style pppm/electrode command: + +@article{Ahrens2021, +author = {Ahrens-Iwers, Ludwig J.V. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0063381}, +title = {{Constant potential simulations on a mesh}}, +journal = {Journal of Chemical Physics}, +year = {2021} +volume = {155}, +pages = {104104}, +} +- fix electrode command: + +@article{Ahrens2022 +author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0099239}, +title = {{ELECTRODE: An electrochemistry package for LAMMPS}}, +journal = {The Journal of Chemical Physics}, +year = {2022} +volume = {157}, +pages = {084801}, +} +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +PPPM/electrode initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:342) + G vector (1/distance) = 0.20904498 + grid = 32 32 200 + stencil order = 5 + estimated absolute RMS force accuracy = 3.7023506e-05 + estimated relative force accuracy = 1.1149519e-07 + using double precision MKL FFT + 3d grid and FFT values/proc = 151593 85504 +Generated 15 of 15 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 18 + ghost atom cutoff = 18 + binsize = 9, bins = 4 4 16 + 3 neighbor lists, perpetual/occasional/extra = 2 1 0 + (1) pair lj/cut/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard + (2) fix electrode/conp, occasional, skip from (1) + attributes: half, newton on + pair build: skip + stencil: none + bin: none + (3) fix electrode/conp, perpetual, skip from (1) + attributes: half, newton on + pair build: skip + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 22.9 | 26.72 | 30.55 Mbytes + Step Temp c_ctemp E_pair TotEng c_qbot c_qtop v_vbot v_vtop + 0 0 0 25137446 25137446 -1 1 -9.931852 10.097344 + 50 20.206425 72.797911 25137263 25137472 -1 1 -9.4359366 9.5964514 + 100 55.931663 201.50563 25136961 25137537 -1 1 -8.0440112 8.1861787 + 150 81.389273 293.22204 25136818 25137656 -1 1 -6.1113109 6.2267114 + 200 92.867946 334.57639 25136841 25137798 -1 1 -4.1857807 4.2740694 + 250 97.518304 351.33028 25136942 25137946 -1 1 -2.8383703 2.9101475 + 300 102.36577 368.79431 25137045 25138099 -1 1 -2.3831643 2.4461115 + 350 113.66597 409.50566 25137086 25138256 -1 1 -2.7083563 2.7457811 + 400 122.8443 442.57252 25137148 25138413 -1 1 -3.4311003 3.3941657 + 450 128.63713 463.44243 25137235 25138560 -1 1 -4.132871 3.9852959 + 500 131.18361 472.61665 25137344 25138695 -1 1 -4.5104095 4.2567261 +Loop time of 54.0351 on 4 procs for 500 steps with 3776 atoms + +Performance: 0.799 ns/day, 30.019 hours/ns, 9.253 timesteps/s, 34.940 katom-step/s +75.8% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 6.5878 | 6.8799 | 7.1455 | 8.0 | 12.73 +Bond | 0.0011081 | 0.0014187 | 0.0018792 | 0.8 | 0.00 +Kspace | 25.907 | 26.173 | 26.464 | 4.1 | 48.44 +Neigh | 0.16417 | 0.16425 | 0.16438 | 0.0 | 0.30 +Comm | 0.34948 | 0.36296 | 0.37524 | 1.9 | 0.67 +Output | 0.0017398 | 0.0021707 | 0.0033966 | 1.5 | 0.00 +Modify | 20.392 | 20.403 | 20.416 | 0.2 | 37.76 +Other | | 0.04783 | | | 0.09 + +Nlocal: 944 ave 948 max 940 min +Histogram: 1 0 0 1 0 0 1 0 0 1 +Nghost: 5920.5 ave 5941 max 5899 min +Histogram: 1 0 0 0 1 1 0 0 0 1 +Neighs: 431397 ave 442329 max 421103 min +Histogram: 2 0 0 0 0 0 0 0 1 1 + +Total # of neighbors = 1725588 +Ave neighs/atom = 456.98835 +Ave special neighs/atom = 0.50847458 +Neighbor list builds = 6 +Dangerous builds = 0 +Total wall time: 0:01:00 diff --git a/examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-etypes.g++.1 b/examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-etypes.g++.1 similarity index 54% rename from examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-etypes.g++.1 rename to examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-etypes.g++.1 index 3b2fe8b6a1..7fccf30e98 100644 --- a/examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-etypes.g++.1 +++ b/examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-etypes.g++.1 @@ -1,4 +1,4 @@ -LAMMPS (24 Mar 2022) +LAMMPS (3 Nov 2022) # electrodes with constant potential and smart neighborlists # for graphene-ionic liquid supercapacitor @@ -37,13 +37,20 @@ Finding 1-2 1-3 1-4 neighbors ... 1 = max # of 1-3 neighbors 1 = max # of 1-4 neighbors 2 = max # of special neighbors - special bonds CPU = 0.001 seconds - read_data CPU = 0.024 seconds + special bonds CPU = 0.002 seconds + read_data CPU = 0.021 seconds -group bot molecule 641 -416 atoms in group bot -group top molecule 642 +# replicate 4 4 1 # test different sys sizes + +variable zpos atom "z > 0" +group zpos variable zpos +1891 atoms in group zpos +group ele type 5 +832 atoms in group ele +group top intersect ele zpos 416 atoms in group top +group bot subtract ele top +416 atoms in group bot group bmi type 1 2 3 960 atoms in group bmi @@ -52,6 +59,7 @@ group electrolyte type 1 2 3 4 fix nvt electrolyte nvt temp 500.0 500.0 100 fix shake bmi shake 1e-4 20 0 b 1 2 a 1 +Finding SHAKE clusters ... 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters @@ -64,12 +72,41 @@ compute qbot bot reduce sum v_q compute ctemp electrolyte temp kspace_modify slab 3.0 -fix conp bot electrode/conp -1.0 1.979 couple top 1.0 symm on etypes 5 +fix conp bot electrode/conp -1.0 1.979 couple top 1.0 symm on etypes on 832 atoms in group conp_group thermo 50 thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop run 500 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- kspace_style pppm/electrode command: + +@article{Ahrens2021, +author = {Ahrens-Iwers, Ludwig J.V. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0063381}, +title = {{Constant potential simulations on a mesh}}, +journal = {Journal of Chemical Physics}, +year = {2021} +volume = {155}, +pages = {104104}, +} +- fix electrode command: + +@article{Ahrens2022 +author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0099239}, +title = {{ELECTRODE: An electrochemistry package for LAMMPS}}, +journal = {The Journal of Chemical Physics}, +year = {2022} +volume = {157}, +pages = {084801}, +} +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + PPPM/electrode initialization ... using 12-bit tables for long-range coulomb (src/kspace.cpp:342) G vector (1/distance) = 0.20904498 @@ -79,9 +116,9 @@ PPPM/electrode initialization ... estimated relative force accuracy = 1.1149519e-07 using double precision MKL FFT 3d grid and FFT values/proc = 307242 204800 - generated 10 of 10 mixed pair_coeff terms from geometric mixing rule +Generated 15 of 15 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... - update every 1 steps, delay 10 steps, check yes + update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 18 ghost atom cutoff = 18 @@ -102,35 +139,35 @@ Neighbor list info ... pair build: skip stencil: none bin: none -Per MPI rank memory allocation (min/avg/max) = 56.89 | 56.89 | 56.89 Mbytes +Per MPI rank memory allocation (min/avg/max) = 54.25 | 54.25 | 54.25 Mbytes Step Temp c_ctemp E_pair TotEng c_qbot c_qtop - 0 0 0 25137191 25137191 0.0085142912 -0.0085142912 + 0 0 0 25137190 25137190 0.0085142912 -0.0085142912 50 17.83755 64.26354 25137031 25137214 0.0045923944 -0.0045923944 - 100 48.393682 174.34846 25136774 25137273 -0.009514517 0.009514517 - 150 70.421272 253.7075 25136655 25137380 -0.033017005 0.033017005 - 200 82.204844 296.16031 25136667 25137514 -0.063668175 0.063668175 - 250 87.54223 315.38937 25136757 25137659 -0.096776257 0.096776257 - 300 91.704746 330.38571 25136865 25137810 -0.1283784 0.1283784 - 350 100.36017 361.56871 25136934 25137968 -0.15649799 0.15649799 - 400 111.37575 401.25467 25136986 25138133 -0.18065435 0.18065435 - 450 121.79848 438.80476 25137043 25138298 -0.19979365 0.19979365 - 500 126.95916 457.39718 25137145 25138453 -0.21037535 0.21037535 -Loop time of 63.497 on 1 procs for 500 steps with 3776 atoms + 100 48.393682 174.34846 25136775 25137273 -0.009514517 0.009514517 + 150 70.421272 253.7075 25136657 25137382 -0.033017005 0.033017005 + 200 82.204844 296.16031 25136670 25137517 -0.063668175 0.063668175 + 250 87.54223 315.38937 25136762 25137663 -0.096776257 0.096776257 + 300 91.704746 330.38571 25136871 25137816 -0.1283784 0.1283784 + 350 100.36017 361.56871 25136942 25137975 -0.15649799 0.15649799 + 400 111.37575 401.25467 25136994 25138141 -0.18065435 0.18065435 + 450 121.79848 438.80476 25137052 25138307 -0.19979365 0.19979365 + 500 126.95916 457.39718 25137155 25138463 -0.21037535 0.21037535 +Loop time of 87.0709 on 1 procs for 500 steps with 3776 atoms -Performance: 0.680 ns/day, 35.276 hours/ns, 7.874 timesteps/s -393.9% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 0.496 ns/day, 48.373 hours/ns, 5.742 timesteps/s, 21.683 katom-step/s +100.0% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 20.628 | 20.628 | 20.628 | 0.0 | 32.49 -Bond | 0.0019309 | 0.0019309 | 0.0019309 | 0.0 | 0.00 -Kspace | 23.61 | 23.61 | 23.61 | 0.0 | 37.18 -Neigh | 0.28156 | 0.28156 | 0.28156 | 0.0 | 0.44 -Comm | 0.061191 | 0.061191 | 0.061191 | 0.0 | 0.10 -Output | 0.0022666 | 0.0022666 | 0.0022666 | 0.0 | 0.00 -Modify | 18.891 | 18.891 | 18.891 | 0.0 | 29.75 -Other | | 0.02047 | | | 0.03 +Pair | 18.617 | 18.617 | 18.617 | 0.0 | 21.38 +Bond | 0.0014056 | 0.0014056 | 0.0014056 | 0.0 | 0.00 +Kspace | 34.856 | 34.856 | 34.856 | 0.0 | 40.03 +Neigh | 0.30015 | 0.30015 | 0.30015 | 0.0 | 0.34 +Comm | 0.065303 | 0.065303 | 0.065303 | 0.0 | 0.08 +Output | 0.0021663 | 0.0021663 | 0.0021663 | 0.0 | 0.00 +Modify | 33.201 | 33.201 | 33.201 | 0.0 | 38.13 +Other | | 0.0282 | | | 0.03 Nlocal: 3776 ave 3776 max 3776 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -144,4 +181,4 @@ Ave neighs/atom = 457.18432 Ave special neighs/atom = 0.50847458 Neighbor list builds = 7 Dangerous builds = 0 -Total wall time: 0:02:24 +Total wall time: 0:01:43 diff --git a/examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-etypes.g++.4 b/examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-etypes.g++.4 similarity index 54% rename from examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-etypes.g++.4 rename to examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-etypes.g++.4 index ed34a0c735..c0f4139689 100644 --- a/examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-etypes.g++.4 +++ b/examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-etypes.g++.4 @@ -1,4 +1,4 @@ -LAMMPS (24 Mar 2022) +LAMMPS (3 Nov 2022) # electrodes with constant potential and smart neighborlists # for graphene-ionic liquid supercapacitor @@ -38,13 +38,20 @@ Finding 1-2 1-3 1-4 neighbors ... 1 = max # of 1-3 neighbors 1 = max # of 1-4 neighbors 2 = max # of special neighbors - special bonds CPU = 0.001 seconds - read_data CPU = 0.016 seconds + special bonds CPU = 0.004 seconds + read_data CPU = 0.047 seconds -group bot molecule 641 -416 atoms in group bot -group top molecule 642 +# replicate 4 4 1 # test different sys sizes + +variable zpos atom "z > 0" +group zpos variable zpos +1891 atoms in group zpos +group ele type 5 +832 atoms in group ele +group top intersect ele zpos 416 atoms in group top +group bot subtract ele top +416 atoms in group bot group bmi type 1 2 3 960 atoms in group bmi @@ -53,11 +60,12 @@ group electrolyte type 1 2 3 4 fix nvt electrolyte nvt temp 500.0 500.0 100 fix shake bmi shake 1e-4 20 0 b 1 2 a 1 +Finding SHAKE clusters ... 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 320 = # of frozen angles - find clusters CPU = 0.001 seconds + find clusters CPU = 0.005 seconds variable q atom q compute qtop top reduce sum v_q @@ -65,12 +73,41 @@ compute qbot bot reduce sum v_q compute ctemp electrolyte temp kspace_modify slab 3.0 -fix conp bot electrode/conp -1.0 1.979 couple top 1.0 symm on etypes 5 +fix conp bot electrode/conp -1.0 1.979 couple top 1.0 symm on etypes on 832 atoms in group conp_group thermo 50 thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop run 500 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- kspace_style pppm/electrode command: + +@article{Ahrens2021, +author = {Ahrens-Iwers, Ludwig J.V. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0063381}, +title = {{Constant potential simulations on a mesh}}, +journal = {Journal of Chemical Physics}, +year = {2021} +volume = {155}, +pages = {104104}, +} +- fix electrode command: + +@article{Ahrens2022 +author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0099239}, +title = {{ELECTRODE: An electrochemistry package for LAMMPS}}, +journal = {The Journal of Chemical Physics}, +year = {2022} +volume = {157}, +pages = {084801}, +} +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + PPPM/electrode initialization ... using 12-bit tables for long-range coulomb (src/kspace.cpp:342) G vector (1/distance) = 0.20904498 @@ -80,9 +117,9 @@ PPPM/electrode initialization ... estimated relative force accuracy = 1.1149519e-07 using double precision MKL FFT 3d grid and FFT values/proc = 151593 85504 - generated 10 of 10 mixed pair_coeff terms from geometric mixing rule +Generated 15 of 15 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... - update every 1 steps, delay 10 steps, check yes + update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 18 ghost atom cutoff = 18 @@ -103,35 +140,35 @@ Neighbor list info ... pair build: skip stencil: none bin: none -Per MPI rank memory allocation (min/avg/max) = 23.63 | 27.46 | 31.29 Mbytes +Per MPI rank memory allocation (min/avg/max) = 22.9 | 26.72 | 30.55 Mbytes Step Temp c_ctemp E_pair TotEng c_qbot c_qtop - 0 0 0 25137191 25137191 0.0085142912 -0.0085142912 + 0 0 0 25137190 25137190 0.0085142912 -0.0085142912 50 17.83755 64.26354 25137031 25137214 0.0045923944 -0.0045923944 - 100 48.393682 174.34846 25136774 25137273 -0.009514517 0.009514517 - 150 70.421272 253.7075 25136655 25137380 -0.033017005 0.033017005 - 200 82.204844 296.16031 25136667 25137514 -0.063668175 0.063668175 - 250 87.54223 315.38937 25136757 25137659 -0.096776257 0.096776257 - 300 91.704746 330.38571 25136865 25137810 -0.1283784 0.1283784 - 350 100.36017 361.56871 25136934 25137968 -0.15649799 0.15649799 - 400 111.37575 401.25467 25136986 25138133 -0.18065435 0.18065435 - 450 121.79848 438.80476 25137043 25138298 -0.19979365 0.19979365 - 500 126.95916 457.39718 25137145 25138453 -0.21037535 0.21037535 -Loop time of 30.7883 on 4 procs for 500 steps with 3776 atoms + 100 48.393682 174.34846 25136775 25137273 -0.009514517 0.009514517 + 150 70.421272 253.7075 25136657 25137382 -0.033017005 0.033017005 + 200 82.204844 296.16031 25136670 25137517 -0.063668175 0.063668175 + 250 87.54223 315.38937 25136762 25137663 -0.096776257 0.096776257 + 300 91.704746 330.38571 25136871 25137816 -0.1283784 0.1283784 + 350 100.36017 361.56871 25136942 25137975 -0.15649799 0.15649799 + 400 111.37575 401.25467 25136994 25138141 -0.18065435 0.18065435 + 450 121.79848 438.80476 25137052 25138307 -0.19979365 0.19979365 + 500 126.95916 457.39718 25137155 25138463 -0.21037535 0.21037535 +Loop time of 48.4075 on 4 procs for 500 steps with 3776 atoms -Performance: 1.403 ns/day, 17.105 hours/ns, 16.240 timesteps/s -94.1% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 0.892 ns/day, 26.893 hours/ns, 10.329 timesteps/s, 39.002 katom-step/s +75.3% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 6.5102 | 6.7303 | 6.9362 | 7.6 | 21.86 -Bond | 0.00064504 | 0.00071061 | 0.000779 | 0.0 | 0.00 -Kspace | 14.081 | 14.287 | 14.507 | 5.2 | 46.40 -Neigh | 0.11831 | 0.11841 | 0.11851 | 0.0 | 0.38 -Comm | 0.12216 | 0.12434 | 0.12651 | 0.6 | 0.40 -Output | 0.00083347 | 0.0010533 | 0.0017069 | 1.2 | 0.00 -Modify | 9.5052 | 9.5071 | 9.5093 | 0.1 | 30.88 -Other | | 0.01927 | | | 0.06 +Pair | 5.3095 | 5.5504 | 5.7923 | 8.2 | 11.47 +Bond | 0.0011128 | 0.0012414 | 0.0014028 | 0.3 | 0.00 +Kspace | 24.084 | 24.322 | 24.559 | 3.9 | 50.24 +Neigh | 0.093557 | 0.09408 | 0.094377 | 0.1 | 0.19 +Comm | 0.30394 | 0.31319 | 0.3225 | 1.6 | 0.65 +Output | 0.0012719 | 0.0015908 | 0.0024592 | 1.3 | 0.00 +Modify | 18.066 | 18.079 | 18.091 | 0.2 | 37.35 +Other | | 0.04692 | | | 0.10 Nlocal: 944 ave 951 max 941 min Histogram: 1 2 0 0 0 0 0 0 0 1 @@ -145,4 +182,4 @@ Ave neighs/atom = 457.18432 Ave special neighs/atom = 0.50847458 Neighbor list builds = 7 Dangerous builds = 0 -Total wall time: 0:00:56 +Total wall time: 0:00:54 diff --git a/examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-ffield.g++.1 b/examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-ffield.g++.1 similarity index 54% rename from examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-ffield.g++.1 rename to examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-ffield.g++.1 index b7c2eea523..2103f43dfd 100644 --- a/examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-ffield.g++.1 +++ b/examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-ffield.g++.1 @@ -1,4 +1,4 @@ -LAMMPS (24 Mar 2022) +LAMMPS (3 Nov 2022) # electrodes with constant potential using finite field # for z-periodic graphene-ionic liquid supercapacitor @@ -37,13 +37,20 @@ Finding 1-2 1-3 1-4 neighbors ... 1 = max # of 1-3 neighbors 1 = max # of 1-4 neighbors 2 = max # of special neighbors - special bonds CPU = 0.001 seconds - read_data CPU = 0.022 seconds + special bonds CPU = 0.002 seconds + read_data CPU = 0.021 seconds -group bot molecule 641 -416 atoms in group bot -group top molecule 642 +# replicate 4 4 1 # test different sys sizes + +variable zpos atom "z > 0" +group zpos variable zpos +1891 atoms in group zpos +group ele type 5 +832 atoms in group ele +group top intersect ele zpos 416 atoms in group top +group bot subtract ele top +416 atoms in group bot group bmi type 1 2 3 960 atoms in group bmi @@ -52,6 +59,7 @@ group electrolyte type 1 2 3 4 fix nvt electrolyte nvt temp 500.0 500.0 100 fix shake bmi shake 1e-4 20 0 b 1 2 a 1 +Finding SHAKE clusters ... 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters @@ -63,12 +71,41 @@ compute qtop top reduce sum v_q compute qbot bot reduce sum v_q compute ctemp electrolyte temp -fix conp bot electrode/conp -1.0 1.979 couple top 1.0 symm on etypes 5 ffield yes +fix conp bot electrode/conp -1.0 1.979 couple top 1.0 symm on etypes on ffield yes 832 atoms in group conp_group thermo 50 thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop run 500 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- kspace_style pppm/electrode command: + +@article{Ahrens2021, +author = {Ahrens-Iwers, Ludwig J.V. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0063381}, +title = {{Constant potential simulations on a mesh}}, +journal = {Journal of Chemical Physics}, +year = {2021} +volume = {155}, +pages = {104104}, +} +- fix electrode command: + +@article{Ahrens2022 +author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0099239}, +title = {{ELECTRODE: An electrochemistry package for LAMMPS}}, +journal = {The Journal of Chemical Physics}, +year = {2022} +volume = {157}, +pages = {084801}, +} +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + PPPM/electrode initialization ... using 12-bit tables for long-range coulomb (src/kspace.cpp:342) G vector (1/distance) = 0.20949995 @@ -78,9 +115,9 @@ PPPM/electrode initialization ... estimated relative force accuracy = 1.0544465e-07 using double precision MKL FFT 3d grid and FFT values/proc = 147537 92160 - generated 10 of 10 mixed pair_coeff terms from geometric mixing rule +Generated 15 of 15 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... - update every 1 steps, delay 10 steps, check yes + update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 18 ghost atom cutoff = 18 @@ -101,35 +138,35 @@ Neighbor list info ... pair build: skip stencil: none bin: none -Per MPI rank memory allocation (min/avg/max) = 49.5 | 49.5 | 49.5 Mbytes +Per MPI rank memory allocation (min/avg/max) = 46.1 | 46.1 | 46.1 Mbytes Step Temp c_ctemp E_pair TotEng c_qbot c_qtop - 0 0 0 25137187 25137187 0.0085209384 -0.0085209384 - 50 17.837642 64.263873 25137027 25137211 0.0045513522 -0.0045513522 - 100 48.393984 174.34955 25136771 25137269 -0.0097291786 0.0097291786 - 150 70.421823 253.70949 25136651 25137377 -0.033522793 0.033522793 - 200 82.205535 296.1628 25136664 25137510 -0.064555648 0.064555648 - 250 87.542843 315.39158 25136754 25137655 -0.098075546 0.098075546 - 300 91.705733 330.38927 25136862 25137806 -0.13006751 0.13006751 - 350 100.36128 361.5727 25136930 25137964 -0.15852814 0.15852814 - 400 111.37586 401.25505 25136982 25138129 -0.18297207 0.18297207 - 450 121.79814 438.80351 25137039 25138294 -0.2023394 0.2023394 - 500 126.95882 457.39597 25137142 25138449 -0.21305221 0.21305221 -Loop time of 36.7618 on 1 procs for 500 steps with 3776 atoms + 0 0 0 25137186 25137186 0.0085209384 -0.0085209384 + 50 17.837642 64.263873 25137027 25137210 0.0045513522 -0.0045513522 + 100 48.393984 174.34955 25136771 25137270 -0.0097291786 0.0097291786 + 150 70.421823 253.70949 25136653 25137378 -0.033522793 0.033522793 + 200 82.205535 296.1628 25136667 25137513 -0.064555648 0.064555648 + 250 87.542843 315.39158 25136758 25137660 -0.098075546 0.098075546 + 300 91.705733 330.38927 25136868 25137812 -0.13006751 0.13006751 + 350 100.36128 361.5727 25136938 25137971 -0.15852814 0.15852814 + 400 111.37586 401.25505 25136990 25138137 -0.18297207 0.18297207 + 450 121.79814 438.80351 25137049 25138303 -0.2023394 0.2023394 + 500 126.95882 457.39597 25137151 25138459 -0.21305221 0.21305221 +Loop time of 53.8411 on 1 procs for 500 steps with 3776 atoms -Performance: 1.175 ns/day, 20.423 hours/ns, 13.601 timesteps/s -393.9% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 0.802 ns/day, 29.912 hours/ns, 9.287 timesteps/s, 35.066 katom-step/s +100.0% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 19.737 | 19.737 | 19.737 | 0.0 | 53.69 -Bond | 0.00092668 | 0.00092668 | 0.00092668 | 0.0 | 0.00 -Kspace | 6.5854 | 6.5854 | 6.5854 | 0.0 | 17.91 -Neigh | 0.33914 | 0.33914 | 0.33914 | 0.0 | 0.92 -Comm | 0.090124 | 0.090124 | 0.090124 | 0.0 | 0.25 -Output | 0.0013975 | 0.0013975 | 0.0013975 | 0.0 | 0.00 -Modify | 9.9834 | 9.9834 | 9.9834 | 0.0 | 27.16 -Other | | 0.02455 | | | 0.07 +Pair | 19.843 | 19.843 | 19.843 | 0.0 | 36.85 +Bond | 0.0016963 | 0.0016963 | 0.0016963 | 0.0 | 0.00 +Kspace | 11.232 | 11.232 | 11.232 | 0.0 | 20.86 +Neigh | 0.39189 | 0.39189 | 0.39189 | 0.0 | 0.73 +Comm | 0.12348 | 0.12348 | 0.12348 | 0.0 | 0.23 +Output | 0.0017904 | 0.0017904 | 0.0017904 | 0.0 | 0.00 +Modify | 22.207 | 22.207 | 22.207 | 0.0 | 41.25 +Other | | 0.04008 | | | 0.07 Nlocal: 3776 ave 3776 max 3776 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -143,4 +180,4 @@ Ave neighs/atom = 493.56224 Ave special neighs/atom = 0.50847458 Neighbor list builds = 7 Dangerous builds = 0 -Total wall time: 0:01:39 +Total wall time: 0:01:10 diff --git a/examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-ffield.g++.4 b/examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-ffield.g++.4 similarity index 54% rename from examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-ffield.g++.4 rename to examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-ffield.g++.4 index 205c08d88e..223530d493 100644 --- a/examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-ffield.g++.4 +++ b/examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-ffield.g++.4 @@ -1,4 +1,4 @@ -LAMMPS (24 Mar 2022) +LAMMPS (3 Nov 2022) # electrodes with constant potential using finite field # for z-periodic graphene-ionic liquid supercapacitor @@ -38,13 +38,20 @@ Finding 1-2 1-3 1-4 neighbors ... 1 = max # of 1-3 neighbors 1 = max # of 1-4 neighbors 2 = max # of special neighbors - special bonds CPU = 0.001 seconds - read_data CPU = 0.016 seconds + special bonds CPU = 0.002 seconds + read_data CPU = 0.033 seconds -group bot molecule 641 -416 atoms in group bot -group top molecule 642 +# replicate 4 4 1 # test different sys sizes + +variable zpos atom "z > 0" +group zpos variable zpos +1891 atoms in group zpos +group ele type 5 +832 atoms in group ele +group top intersect ele zpos 416 atoms in group top +group bot subtract ele top +416 atoms in group bot group bmi type 1 2 3 960 atoms in group bmi @@ -53,23 +60,53 @@ group electrolyte type 1 2 3 4 fix nvt electrolyte nvt temp 500.0 500.0 100 fix shake bmi shake 1e-4 20 0 b 1 2 a 1 +Finding SHAKE clusters ... 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 320 = # of frozen angles - find clusters CPU = 0.001 seconds + find clusters CPU = 0.002 seconds variable q atom q compute qtop top reduce sum v_q compute qbot bot reduce sum v_q compute ctemp electrolyte temp -fix conp bot electrode/conp -1.0 1.979 couple top 1.0 symm on etypes 5 ffield yes +fix conp bot electrode/conp -1.0 1.979 couple top 1.0 symm on etypes on ffield yes 832 atoms in group conp_group thermo 50 thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop run 500 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- kspace_style pppm/electrode command: + +@article{Ahrens2021, +author = {Ahrens-Iwers, Ludwig J.V. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0063381}, +title = {{Constant potential simulations on a mesh}}, +journal = {Journal of Chemical Physics}, +year = {2021} +volume = {155}, +pages = {104104}, +} +- fix electrode command: + +@article{Ahrens2022 +author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0099239}, +title = {{ELECTRODE: An electrochemistry package for LAMMPS}}, +journal = {The Journal of Chemical Physics}, +year = {2022} +volume = {157}, +pages = {084801}, +} +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + PPPM/electrode initialization ... using 12-bit tables for long-range coulomb (src/kspace.cpp:342) G vector (1/distance) = 0.20949995 @@ -79,9 +116,9 @@ PPPM/electrode initialization ... estimated relative force accuracy = 1.0544465e-07 using double precision MKL FFT 3d grid and FFT values/proc = 46644 23552 - generated 10 of 10 mixed pair_coeff terms from geometric mixing rule +Generated 15 of 15 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... - update every 1 steps, delay 10 steps, check yes + update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 18 ghost atom cutoff = 18 @@ -102,35 +139,35 @@ Neighbor list info ... pair build: skip stencil: none bin: none -Per MPI rank memory allocation (min/avg/max) = 21.96 | 22.27 | 22.77 Mbytes +Per MPI rank memory allocation (min/avg/max) = 21.23 | 21.34 | 21.65 Mbytes Step Temp c_ctemp E_pair TotEng c_qbot c_qtop - 0 0 0 25137187 25137187 0.0085209384 -0.0085209384 - 50 17.837642 64.263873 25137027 25137211 0.0045513522 -0.0045513522 - 100 48.393984 174.34955 25136771 25137269 -0.0097291786 0.0097291786 - 150 70.421823 253.70949 25136651 25137377 -0.033522793 0.033522793 - 200 82.205535 296.1628 25136664 25137510 -0.064555648 0.064555648 - 250 87.542843 315.39158 25136754 25137655 -0.098075546 0.098075546 - 300 91.705733 330.38927 25136862 25137806 -0.13006751 0.13006751 - 350 100.36128 361.5727 25136930 25137964 -0.15852814 0.15852814 - 400 111.37586 401.25505 25136982 25138129 -0.18297207 0.18297207 - 450 121.79814 438.80351 25137039 25138294 -0.2023394 0.2023394 - 500 126.95882 457.39597 25137142 25138449 -0.21305221 0.21305221 -Loop time of 19.3932 on 4 procs for 500 steps with 3776 atoms + 0 0 0 25137186 25137186 0.0085209384 -0.0085209384 + 50 17.837642 64.263873 25137027 25137210 0.0045513522 -0.0045513522 + 100 48.393984 174.34955 25136771 25137270 -0.0097291786 0.0097291786 + 150 70.421823 253.70949 25136653 25137378 -0.033522793 0.033522793 + 200 82.205535 296.1628 25136667 25137513 -0.064555648 0.064555648 + 250 87.542843 315.39158 25136758 25137660 -0.098075546 0.098075546 + 300 91.705733 330.38927 25136868 25137812 -0.13006751 0.13006751 + 350 100.36128 361.5727 25136938 25137971 -0.15852814 0.15852814 + 400 111.37586 401.25505 25136990 25138137 -0.18297207 0.18297207 + 450 121.79814 438.80351 25137049 25138303 -0.2023394 0.2023394 + 500 126.95882 457.39597 25137151 25138459 -0.21305221 0.21305221 +Loop time of 26.2807 on 4 procs for 500 steps with 3776 atoms -Performance: 2.228 ns/day, 10.774 hours/ns, 25.782 timesteps/s -96.3% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 1.644 ns/day, 14.600 hours/ns, 19.025 timesteps/s, 71.840 katom-step/s +83.1% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 7.1247 | 7.6399 | 8.1323 | 13.3 | 39.39 -Bond | 0.00072445 | 0.00077581 | 0.00085933 | 0.0 | 0.00 -Kspace | 5.098 | 5.5905 | 6.1036 | 15.6 | 28.83 -Neigh | 0.145 | 0.14517 | 0.14532 | 0.0 | 0.75 -Comm | 0.24683 | 0.25127 | 0.25907 | 1.0 | 1.30 -Output | 0.00084146 | 0.0011298 | 0.0019741 | 1.5 | 0.01 -Modify | 5.6957 | 5.7129 | 5.729 | 0.6 | 29.46 -Other | | 0.05153 | | | 0.27 +Pair | 5.8233 | 6.1941 | 6.6294 | 12.1 | 23.57 +Bond | 0.0010807 | 0.0011705 | 0.0013494 | 0.3 | 0.00 +Kspace | 8.0325 | 8.4703 | 8.8457 | 10.4 | 32.23 +Neigh | 0.14184 | 0.1421 | 0.14238 | 0.1 | 0.54 +Comm | 0.52248 | 0.54323 | 0.56352 | 2.7 | 2.07 +Output | 0.00079782 | 0.0011547 | 0.0021987 | 1.8 | 0.00 +Modify | 10.831 | 10.856 | 10.881 | 0.7 | 41.31 +Other | | 0.07293 | | | 0.28 Nlocal: 944 ave 951 max 941 min Histogram: 1 2 0 0 0 0 0 0 0 1 @@ -144,4 +181,4 @@ Ave neighs/atom = 493.56224 Ave special neighs/atom = 0.50847458 Neighbor list builds = 7 Dangerous builds = 0 -Total wall time: 0:00:44 +Total wall time: 0:00:32 diff --git a/examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-ramp.g++.1 b/examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-ramp.g++.1 similarity index 52% rename from examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-ramp.g++.1 rename to examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-ramp.g++.1 index 1dfcbac360..819a605f35 100644 --- a/examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-ramp.g++.1 +++ b/examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-ramp.g++.1 @@ -1,4 +1,4 @@ -LAMMPS (24 Mar 2022) +LAMMPS (3 Nov 2022) # electrodes with equal-style ramped (electrode-)constant potential # for graphene-ionic liquid supercapacitor @@ -37,13 +37,20 @@ Finding 1-2 1-3 1-4 neighbors ... 1 = max # of 1-3 neighbors 1 = max # of 1-4 neighbors 2 = max # of special neighbors - special bonds CPU = 0.001 seconds - read_data CPU = 0.014 seconds + special bonds CPU = 0.002 seconds + read_data CPU = 0.021 seconds -group bot molecule 641 -416 atoms in group bot -group top molecule 642 +# replicate 4 4 1 # test different sys sizes + +variable zpos atom "z > 0" +group zpos variable zpos +1891 atoms in group zpos +group ele type 5 +832 atoms in group ele +group top intersect ele zpos 416 atoms in group top +group bot subtract ele top +416 atoms in group bot group bmi type 1 2 3 960 atoms in group bmi @@ -52,6 +59,7 @@ group electrolyte type 1 2 3 4 fix nvt electrolyte nvt temp 500.0 500.0 100 fix shake bmi shake 1e-4 20 0 b 1 2 a 1 +Finding SHAKE clusters ... 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters @@ -65,12 +73,41 @@ compute ctemp electrolyte temp kspace_modify slab 3.0 variable v equal ramp(2,4) -fix conp bot electrode/conp 0.0 1.979 couple top v_v symm on etypes 5 +fix conp bot electrode/conp 0.0 1.979 couple top v_v symm on etypes on 832 atoms in group conp_group thermo 50 thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop v_v run 500 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- kspace_style pppm/electrode command: + +@article{Ahrens2021, +author = {Ahrens-Iwers, Ludwig J.V. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0063381}, +title = {{Constant potential simulations on a mesh}}, +journal = {Journal of Chemical Physics}, +year = {2021} +volume = {155}, +pages = {104104}, +} +- fix electrode command: + +@article{Ahrens2022 +author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0099239}, +title = {{ELECTRODE: An electrochemistry package for LAMMPS}}, +journal = {The Journal of Chemical Physics}, +year = {2022} +volume = {157}, +pages = {084801}, +} +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + PPPM/electrode initialization ... using 12-bit tables for long-range coulomb (src/kspace.cpp:342) G vector (1/distance) = 0.20904498 @@ -80,9 +117,9 @@ PPPM/electrode initialization ... estimated relative force accuracy = 1.1149519e-07 using double precision MKL FFT 3d grid and FFT values/proc = 307242 204800 - generated 10 of 10 mixed pair_coeff terms from geometric mixing rule +Generated 15 of 15 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... - update every 1 steps, delay 10 steps, check yes + update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 18 ghost atom cutoff = 18 @@ -103,35 +140,35 @@ Neighbor list info ... pair build: skip stencil: none bin: none -Per MPI rank memory allocation (min/avg/max) = 56.89 | 56.89 | 56.89 Mbytes +Per MPI rank memory allocation (min/avg/max) = 54.25 | 54.25 | 54.25 Mbytes Step Temp c_ctemp E_pair TotEng c_qbot c_qtop v_v - 0 0 0 25137191 25137191 0.0085142912 -0.0085142912 2 - 50 17.839699 64.271283 25137031 25137214 -0.0067894391 0.0067894391 2.2 - 100 48.411618 174.41308 25136774 25137273 -0.033422174 0.033422174 2.4 - 150 70.478909 253.91515 25136654 25137380 -0.071583953 0.071583953 2.6 - 200 82.322716 296.58497 25136666 25137513 -0.11962095 0.11962095 2.8 - 250 87.739905 316.10153 25136754 25137658 -0.17281469 0.17281469 3 - 300 91.974584 331.35786 25136861 25137808 -0.22657123 0.22657123 3.2 - 350 100.73048 362.90284 25136928 25137965 -0.27817429 0.27817429 3.4 - 400 111.78597 402.73256 25136977 25138129 -0.32659395 0.32659395 3.6 - 450 122.14181 440.04167 25137033 25138291 -0.37054363 0.37054363 3.8 - 500 127.32331 458.70912 25137133 25138444 -0.40653009 0.40653009 4 -Loop time of 50.8569 on 1 procs for 500 steps with 3776 atoms + 0 0 0 25137190 25137190 0.0085142912 -0.0085142912 2 + 50 17.839699 64.271283 25137031 25137215 -0.0067894391 0.0067894391 2.2 + 100 48.411618 174.41308 25136776 25137275 -0.033422174 0.033422174 2.4 + 150 70.478909 253.91515 25136658 25137384 -0.071583953 0.071583953 2.6 + 200 82.322716 296.58497 25136673 25137521 -0.11962095 0.11962095 2.8 + 250 87.739905 316.10153 25136766 25137670 -0.17281469 0.17281469 3 + 300 91.974584 331.35786 25136877 25137825 -0.22657123 0.22657123 3.2 + 350 100.73048 362.90284 25136949 25137987 -0.27817429 0.27817429 3.4 + 400 111.78597 402.73256 25137004 25138156 -0.32659395 0.32659395 3.6 + 450 122.14181 440.04167 25137066 25138324 -0.37054363 0.37054363 3.8 + 500 127.32331 458.70912 25137171 25138482 -0.40653009 0.40653009 4 +Loop time of 87.6405 on 1 procs for 500 steps with 3776 atoms -Performance: 0.849 ns/day, 28.254 hours/ns, 9.831 timesteps/s -393.5% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 0.493 ns/day, 48.689 hours/ns, 5.705 timesteps/s, 21.543 katom-step/s +100.0% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 18.166 | 18.166 | 18.166 | 0.0 | 35.72 -Bond | 0.00091918 | 0.00091918 | 0.00091918 | 0.0 | 0.00 -Kspace | 17.267 | 17.267 | 17.267 | 0.0 | 33.95 -Neigh | 0.27635 | 0.27635 | 0.27635 | 0.0 | 0.54 -Comm | 0.044714 | 0.044714 | 0.044714 | 0.0 | 0.09 -Output | 0.0018345 | 0.0018345 | 0.0018345 | 0.0 | 0.00 -Modify | 15.086 | 15.086 | 15.086 | 0.0 | 29.66 -Other | | 0.01409 | | | 0.03 +Pair | 18.484 | 18.484 | 18.484 | 0.0 | 21.09 +Bond | 0.0016824 | 0.0016824 | 0.0016824 | 0.0 | 0.00 +Kspace | 35.426 | 35.426 | 35.426 | 0.0 | 40.42 +Neigh | 0.30201 | 0.30201 | 0.30201 | 0.0 | 0.34 +Comm | 0.066546 | 0.066546 | 0.066546 | 0.0 | 0.08 +Output | 0.0022768 | 0.0022768 | 0.0022768 | 0.0 | 0.00 +Modify | 33.33 | 33.33 | 33.33 | 0.0 | 38.03 +Other | | 0.0286 | | | 0.03 Nlocal: 3776 ave 3776 max 3776 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -145,4 +182,4 @@ Ave neighs/atom = 457.17161 Ave special neighs/atom = 0.50847458 Neighbor list builds = 7 Dangerous builds = 0 -Total wall time: 0:01:50 +Total wall time: 0:01:44 diff --git a/examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-ramp.g++.4 b/examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-ramp.g++.4 similarity index 52% rename from examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-ramp.g++.4 rename to examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-ramp.g++.4 index ca7625acd6..9287a669db 100644 --- a/examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-ramp.g++.4 +++ b/examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-ramp.g++.4 @@ -1,4 +1,4 @@ -LAMMPS (24 Mar 2022) +LAMMPS (3 Nov 2022) # electrodes with equal-style ramped (electrode-)constant potential # for graphene-ionic liquid supercapacitor @@ -38,13 +38,20 @@ Finding 1-2 1-3 1-4 neighbors ... 1 = max # of 1-3 neighbors 1 = max # of 1-4 neighbors 2 = max # of special neighbors - special bonds CPU = 0.001 seconds - read_data CPU = 0.024 seconds + special bonds CPU = 0.003 seconds + read_data CPU = 0.034 seconds -group bot molecule 641 -416 atoms in group bot -group top molecule 642 +# replicate 4 4 1 # test different sys sizes + +variable zpos atom "z > 0" +group zpos variable zpos +1891 atoms in group zpos +group ele type 5 +832 atoms in group ele +group top intersect ele zpos 416 atoms in group top +group bot subtract ele top +416 atoms in group bot group bmi type 1 2 3 960 atoms in group bmi @@ -53,11 +60,12 @@ group electrolyte type 1 2 3 4 fix nvt electrolyte nvt temp 500.0 500.0 100 fix shake bmi shake 1e-4 20 0 b 1 2 a 1 +Finding SHAKE clusters ... 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 320 = # of frozen angles - find clusters CPU = 0.001 seconds + find clusters CPU = 0.002 seconds variable q atom q compute qtop top reduce sum v_q @@ -66,12 +74,41 @@ compute ctemp electrolyte temp kspace_modify slab 3.0 variable v equal ramp(2,4) -fix conp bot electrode/conp 0.0 1.979 couple top v_v symm on etypes 5 +fix conp bot electrode/conp 0.0 1.979 couple top v_v symm on etypes on 832 atoms in group conp_group thermo 50 thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop v_v run 500 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- kspace_style pppm/electrode command: + +@article{Ahrens2021, +author = {Ahrens-Iwers, Ludwig J.V. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0063381}, +title = {{Constant potential simulations on a mesh}}, +journal = {Journal of Chemical Physics}, +year = {2021} +volume = {155}, +pages = {104104}, +} +- fix electrode command: + +@article{Ahrens2022 +author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0099239}, +title = {{ELECTRODE: An electrochemistry package for LAMMPS}}, +journal = {The Journal of Chemical Physics}, +year = {2022} +volume = {157}, +pages = {084801}, +} +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + PPPM/electrode initialization ... using 12-bit tables for long-range coulomb (src/kspace.cpp:342) G vector (1/distance) = 0.20904498 @@ -81,9 +118,9 @@ PPPM/electrode initialization ... estimated relative force accuracy = 1.1149519e-07 using double precision MKL FFT 3d grid and FFT values/proc = 151593 85504 - generated 10 of 10 mixed pair_coeff terms from geometric mixing rule +Generated 15 of 15 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... - update every 1 steps, delay 10 steps, check yes + update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 18 ghost atom cutoff = 18 @@ -104,35 +141,35 @@ Neighbor list info ... pair build: skip stencil: none bin: none -Per MPI rank memory allocation (min/avg/max) = 23.63 | 27.46 | 31.29 Mbytes +Per MPI rank memory allocation (min/avg/max) = 22.9 | 26.72 | 30.55 Mbytes Step Temp c_ctemp E_pair TotEng c_qbot c_qtop v_v - 0 0 0 25137191 25137191 0.0085142912 -0.0085142912 2 - 50 17.839699 64.271283 25137031 25137214 -0.0067894391 0.0067894391 2.2 - 100 48.411618 174.41308 25136774 25137273 -0.033422174 0.033422174 2.4 - 150 70.478909 253.91515 25136654 25137380 -0.071583953 0.071583953 2.6 - 200 82.322716 296.58497 25136666 25137513 -0.11962095 0.11962095 2.8 - 250 87.739905 316.10153 25136754 25137658 -0.17281469 0.17281469 3 - 300 91.974584 331.35786 25136861 25137808 -0.22657123 0.22657123 3.2 - 350 100.73048 362.90284 25136928 25137965 -0.27817429 0.27817429 3.4 - 400 111.78597 402.73256 25136977 25138129 -0.32659395 0.32659395 3.6 - 450 122.14181 440.04167 25137033 25138291 -0.37054363 0.37054363 3.8 - 500 127.32331 458.70912 25137133 25138444 -0.40653009 0.40653009 4 -Loop time of 31.7642 on 4 procs for 500 steps with 3776 atoms + 0 0 0 25137190 25137190 0.0085142912 -0.0085142912 2 + 50 17.839699 64.271283 25137031 25137215 -0.0067894391 0.0067894391 2.2 + 100 48.411618 174.41308 25136776 25137275 -0.033422174 0.033422174 2.4 + 150 70.478909 253.91515 25136658 25137384 -0.071583953 0.071583953 2.6 + 200 82.322716 296.58497 25136673 25137521 -0.11962095 0.11962095 2.8 + 250 87.739905 316.10153 25136766 25137670 -0.17281469 0.17281469 3 + 300 91.974584 331.35786 25136877 25137825 -0.22657123 0.22657123 3.2 + 350 100.73048 362.90284 25136949 25137987 -0.27817429 0.27817429 3.4 + 400 111.78597 402.73256 25137004 25138156 -0.32659395 0.32659395 3.6 + 450 122.14181 440.04167 25137066 25138324 -0.37054363 0.37054363 3.8 + 500 127.32331 458.70912 25137171 25138482 -0.40653009 0.40653009 4 +Loop time of 49.2075 on 4 procs for 500 steps with 3776 atoms -Performance: 1.360 ns/day, 17.647 hours/ns, 15.741 timesteps/s -94.1% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 0.878 ns/day, 27.337 hours/ns, 10.161 timesteps/s, 38.368 katom-step/s +75.7% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 6.7949 | 7.0359 | 7.3092 | 7.9 | 22.15 -Bond | 0.00069874 | 0.00073747 | 0.00077928 | 0.0 | 0.00 -Kspace | 14.375 | 14.648 | 14.89 | 5.5 | 46.12 -Neigh | 0.12057 | 0.1206 | 0.12062 | 0.0 | 0.38 -Comm | 0.13412 | 0.13439 | 0.13483 | 0.1 | 0.42 -Output | 0.0010019 | 0.0013088 | 0.0020937 | 1.3 | 0.00 -Modify | 9.8017 | 9.8025 | 9.8031 | 0.0 | 30.86 -Other | | 0.02036 | | | 0.06 +Pair | 5.7517 | 5.9151 | 6.0961 | 6.6 | 12.02 +Bond | 0.0011959 | 0.0013362 | 0.0014512 | 0.2 | 0.00 +Kspace | 24.223 | 24.404 | 24.566 | 3.2 | 49.59 +Neigh | 0.10283 | 0.10288 | 0.10301 | 0.0 | 0.21 +Comm | 0.30801 | 0.31944 | 0.33141 | 2.0 | 0.65 +Output | 0.0010416 | 0.0014127 | 0.0024086 | 1.5 | 0.00 +Modify | 18.405 | 18.418 | 18.432 | 0.3 | 37.43 +Other | | 0.04459 | | | 0.09 Nlocal: 944 ave 951 max 941 min Histogram: 1 2 0 0 0 0 0 0 0 1 @@ -146,4 +183,4 @@ Ave neighs/atom = 457.17161 Ave special neighs/atom = 0.50847458 Neighbor list builds = 7 Dangerous builds = 0 -Total wall time: 0:00:58 +Total wall time: 0:00:55 diff --git a/examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-thermo.g++.1 b/examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-thermo.g++.1 similarity index 55% rename from examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-thermo.g++.1 rename to examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-thermo.g++.1 index e6fe963222..42eeb1f97e 100644 --- a/examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-thermo.g++.1 +++ b/examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-thermo.g++.1 @@ -1,4 +1,4 @@ -LAMMPS (24 Mar 2022) +LAMMPS (3 Nov 2022) # electrodes with thermopotentiostat # for graphene-ionic liquid supercapacitor @@ -38,12 +38,19 @@ Finding 1-2 1-3 1-4 neighbors ... 1 = max # of 1-4 neighbors 2 = max # of special neighbors special bonds CPU = 0.002 seconds - read_data CPU = 0.024 seconds + read_data CPU = 0.021 seconds -group bot molecule 641 -416 atoms in group bot -group top molecule 642 +# replicate 4 4 1 # test different sys sizes + +variable zpos atom "z > 0" +group zpos variable zpos +1891 atoms in group zpos +group ele type 5 +832 atoms in group ele +group top intersect ele zpos 416 atoms in group top +group bot subtract ele top +416 atoms in group bot group bmi type 1 2 3 960 atoms in group bmi @@ -52,11 +59,12 @@ group electrolyte type 1 2 3 4 fix nvt electrolyte nvt temp 500.0 500.0 100 fix shake bmi shake 1e-4 20 0 b 1 2 a 1 +Finding SHAKE clusters ... 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 320 = # of frozen angles - find clusters CPU = 0.000 seconds + find clusters CPU = 0.001 seconds variable q atom q compute qtop top reduce sum v_q @@ -65,10 +73,10 @@ compute ctemp electrolyte temp kspace_modify slab 3.0 unfix nvt # remove NVT thermostat included from "settings.mod" -fix conpthermo bot electrode/thermo -1.0 1.979 couple top 1.0 etypes 5 temp 500 100 7 # temp tau rng +fix conpthermo bot electrode/thermo -1.0 1.979 couple top 1.0 etypes on temp 500 100 7 symm on # temp tau rng 832 atoms in group conp_group # to compare to regular constant potential, switch previous line to this: -#fix conp bot electrode/conp -1.0 1.979 couple top 1.0 etypes 5 symm on +#fix conp bot electrode/conp -1.0 1.979 couple top 1.0 etypes on symm on fix nve electrolyte nve # note ionic liquid does not reach 500K immediately @@ -77,6 +85,35 @@ fix nve electrolyte nve thermo 50 thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop run 500 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- kspace_style pppm/electrode command: + +@article{Ahrens2021, +author = {Ahrens-Iwers, Ludwig J.V. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0063381}, +title = {{Constant potential simulations on a mesh}}, +journal = {Journal of Chemical Physics}, +year = {2021} +volume = {155}, +pages = {104104}, +} +- fix electrode command: + +@article{Ahrens2022 +author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0099239}, +title = {{ELECTRODE: An electrochemistry package for LAMMPS}}, +journal = {The Journal of Chemical Physics}, +year = {2022} +volume = {157}, +pages = {084801}, +} +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + PPPM/electrode initialization ... using 12-bit tables for long-range coulomb (src/kspace.cpp:342) G vector (1/distance) = 0.20904498 @@ -86,9 +123,9 @@ PPPM/electrode initialization ... estimated relative force accuracy = 1.1149519e-07 using double precision MKL FFT 3d grid and FFT values/proc = 307242 204800 - generated 10 of 10 mixed pair_coeff terms from geometric mixing rule +Generated 15 of 15 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... - update every 1 steps, delay 10 steps, check yes + update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 18 ghost atom cutoff = 18 @@ -109,35 +146,35 @@ Neighbor list info ... pair build: skip stencil: none bin: none -Per MPI rank memory allocation (min/avg/max) = 56.89 | 56.89 | 56.89 Mbytes +Per MPI rank memory allocation (min/avg/max) = 54.25 | 54.25 | 54.25 Mbytes Step Temp c_ctemp E_pair TotEng c_qbot c_qtop - 0 0 0 25137187 25137187 0.12767613 -0.12767613 - 50 16.63971 59.94807 25137031 25137203 0.11714714 -0.11714714 - 100 40.785523 146.93846 25136782 25137202 0.1278358 -0.1278358 - 150 53.394067 192.3634 25136654 25137204 0.080257143 -0.080257143 - 200 56.419019 203.26143 25136624 25137205 0.024756489 -0.024756489 - 250 54.922935 197.87147 25136640 25137205 -0.024533719 0.024533719 - 300 52.884861 190.52888 25136660 25137205 -0.066341094 0.066341094 - 350 52.41676 188.84244 25136666 25137206 -0.089546252 0.089546252 - 400 54.366979 195.86852 25136646 25137206 -0.10239753 0.10239753 - 450 54.906542 197.81241 25136642 25137208 -0.099987401 0.099987401 - 500 54.33841 195.7656 25136642 25137201 -0.21295942 0.21295942 -Loop time of 49.9831 on 1 procs for 500 steps with 3776 atoms + 0 0 0 25137188 25137188 0.12767608 -0.12767608 + 50 16.63971 59.94807 25137031 25137202 0.11714711 -0.11714711 + 100 40.785523 146.93846 25136782 25137202 0.12783578 -0.12783578 + 150 53.394067 192.3634 25136653 25137203 0.080257127 -0.080257127 + 200 56.419019 203.26143 25136623 25137204 0.024756474 -0.024756474 + 250 54.922935 197.87147 25136641 25137206 -0.024533734 0.024533734 + 300 52.884861 190.52888 25136664 25137209 -0.066341109 0.066341109 + 350 52.41676 188.84244 25136670 25137210 -0.089546266 0.089546266 + 400 54.366979 195.86852 25136651 25137211 -0.10239755 0.10239755 + 450 54.906542 197.81241 25136645 25137210 -0.099987411 0.099987411 + 500 54.33841 195.7656 25136656 25137216 -0.21295943 0.21295943 +Loop time of 87.5281 on 1 procs for 500 steps with 3776 atoms -Performance: 0.864 ns/day, 27.768 hours/ns, 10.003 timesteps/s -393.3% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 0.494 ns/day, 48.627 hours/ns, 5.712 timesteps/s, 21.570 katom-step/s +100.0% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 17.01 | 17.01 | 17.01 | 0.0 | 34.03 -Bond | 0.0010374 | 0.0010374 | 0.0010374 | 0.0 | 0.00 -Kspace | 18.096 | 18.096 | 18.096 | 0.0 | 36.20 -Neigh | 0.1828 | 0.1828 | 0.1828 | 0.0 | 0.37 -Comm | 0.043856 | 0.043856 | 0.043856 | 0.0 | 0.09 -Output | 0.0018373 | 0.0018373 | 0.0018373 | 0.0 | 0.00 -Modify | 14.632 | 14.632 | 14.632 | 0.0 | 29.27 -Other | | 0.01548 | | | 0.03 +Pair | 18.819 | 18.819 | 18.819 | 0.0 | 21.50 +Bond | 0.0014336 | 0.0014336 | 0.0014336 | 0.0 | 0.00 +Kspace | 34.891 | 34.891 | 34.891 | 0.0 | 39.86 +Neigh | 0.21542 | 0.21542 | 0.21542 | 0.0 | 0.25 +Comm | 0.063383 | 0.063383 | 0.063383 | 0.0 | 0.07 +Output | 0.0020476 | 0.0020476 | 0.0020476 | 0.0 | 0.00 +Modify | 33.507 | 33.507 | 33.507 | 0.0 | 38.28 +Other | | 0.0281 | | | 0.03 Nlocal: 3776 ave 3776 max 3776 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -151,4 +188,4 @@ Ave neighs/atom = 457.08845 Ave special neighs/atom = 0.50847458 Neighbor list builds = 5 Dangerous builds = 0 -Total wall time: 0:01:50 +Total wall time: 0:01:44 diff --git a/examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-thermo.g++.4 b/examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-thermo.g++.4 similarity index 55% rename from examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-thermo.g++.4 rename to examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-thermo.g++.4 index 006fe4d31b..200dc681df 100644 --- a/examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-thermo.g++.4 +++ b/examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-thermo.g++.4 @@ -1,4 +1,4 @@ -LAMMPS (24 Mar 2022) +LAMMPS (3 Nov 2022) # electrodes with thermopotentiostat # for graphene-ionic liquid supercapacitor @@ -39,12 +39,19 @@ Finding 1-2 1-3 1-4 neighbors ... 1 = max # of 1-4 neighbors 2 = max # of special neighbors special bonds CPU = 0.002 seconds - read_data CPU = 0.025 seconds + read_data CPU = 0.036 seconds -group bot molecule 641 -416 atoms in group bot -group top molecule 642 +# replicate 4 4 1 # test different sys sizes + +variable zpos atom "z > 0" +group zpos variable zpos +1891 atoms in group zpos +group ele type 5 +832 atoms in group ele +group top intersect ele zpos 416 atoms in group top +group bot subtract ele top +416 atoms in group bot group bmi type 1 2 3 960 atoms in group bmi @@ -53,11 +60,12 @@ group electrolyte type 1 2 3 4 fix nvt electrolyte nvt temp 500.0 500.0 100 fix shake bmi shake 1e-4 20 0 b 1 2 a 1 +Finding SHAKE clusters ... 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 320 = # of frozen angles - find clusters CPU = 0.001 seconds + find clusters CPU = 0.005 seconds variable q atom q compute qtop top reduce sum v_q @@ -66,10 +74,10 @@ compute ctemp electrolyte temp kspace_modify slab 3.0 unfix nvt # remove NVT thermostat included from "settings.mod" -fix conpthermo bot electrode/thermo -1.0 1.979 couple top 1.0 etypes 5 temp 500 100 7 # temp tau rng +fix conpthermo bot electrode/thermo -1.0 1.979 couple top 1.0 etypes on temp 500 100 7 symm on # temp tau rng 832 atoms in group conp_group # to compare to regular constant potential, switch previous line to this: -#fix conp bot electrode/conp -1.0 1.979 couple top 1.0 etypes 5 symm on +#fix conp bot electrode/conp -1.0 1.979 couple top 1.0 etypes on symm on fix nve electrolyte nve # note ionic liquid does not reach 500K immediately @@ -78,6 +86,35 @@ fix nve electrolyte nve thermo 50 thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop run 500 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- kspace_style pppm/electrode command: + +@article{Ahrens2021, +author = {Ahrens-Iwers, Ludwig J.V. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0063381}, +title = {{Constant potential simulations on a mesh}}, +journal = {Journal of Chemical Physics}, +year = {2021} +volume = {155}, +pages = {104104}, +} +- fix electrode command: + +@article{Ahrens2022 +author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0099239}, +title = {{ELECTRODE: An electrochemistry package for LAMMPS}}, +journal = {The Journal of Chemical Physics}, +year = {2022} +volume = {157}, +pages = {084801}, +} +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + PPPM/electrode initialization ... using 12-bit tables for long-range coulomb (src/kspace.cpp:342) G vector (1/distance) = 0.20904498 @@ -87,9 +124,9 @@ PPPM/electrode initialization ... estimated relative force accuracy = 1.1149519e-07 using double precision MKL FFT 3d grid and FFT values/proc = 151593 85504 - generated 10 of 10 mixed pair_coeff terms from geometric mixing rule +Generated 15 of 15 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... - update every 1 steps, delay 10 steps, check yes + update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 18 ghost atom cutoff = 18 @@ -110,35 +147,35 @@ Neighbor list info ... pair build: skip stencil: none bin: none -Per MPI rank memory allocation (min/avg/max) = 23.63 | 27.46 | 31.29 Mbytes +Per MPI rank memory allocation (min/avg/max) = 22.9 | 26.72 | 30.55 Mbytes Step Temp c_ctemp E_pair TotEng c_qbot c_qtop - 0 0 0 25137187 25137187 0.12767613 -0.12767613 - 50 16.63971 59.94807 25137031 25137203 0.11714714 -0.11714714 - 100 40.785523 146.93846 25136782 25137202 0.1278358 -0.1278358 - 150 53.394067 192.3634 25136654 25137204 0.080257143 -0.080257143 - 200 56.419019 203.26143 25136624 25137205 0.024756489 -0.024756489 - 250 54.922935 197.87147 25136640 25137205 -0.024533719 0.024533719 - 300 52.884861 190.52888 25136660 25137205 -0.066341094 0.066341094 - 350 52.41676 188.84244 25136666 25137206 -0.089546252 0.089546252 - 400 54.366979 195.86852 25136646 25137206 -0.10239753 0.10239753 - 450 54.906542 197.81241 25136642 25137208 -0.099987401 0.099987401 - 500 54.33841 195.7656 25136642 25137201 -0.21295942 0.21295942 -Loop time of 27.6772 on 4 procs for 500 steps with 3776 atoms + 0 0 0 25137188 25137188 0.12767608 -0.12767608 + 50 16.63971 59.94807 25137031 25137202 0.11714711 -0.11714711 + 100 40.785523 146.93846 25136782 25137202 0.12783578 -0.12783578 + 150 53.394067 192.3634 25136653 25137203 0.080257127 -0.080257127 + 200 56.419019 203.26143 25136623 25137204 0.024756474 -0.024756474 + 250 54.922935 197.87147 25136641 25137206 -0.024533734 0.024533734 + 300 52.884861 190.52888 25136664 25137209 -0.066341109 0.066341109 + 350 52.41676 188.84244 25136670 25137210 -0.089546266 0.089546266 + 400 54.366979 195.86852 25136651 25137211 -0.10239755 0.10239755 + 450 54.906542 197.81241 25136645 25137210 -0.099987411 0.099987411 + 500 54.33841 195.7656 25136656 25137216 -0.21295943 0.21295943 +Loop time of 49.2564 on 4 procs for 500 steps with 3776 atoms -Performance: 1.561 ns/day, 15.376 hours/ns, 18.065 timesteps/s -91.7% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 0.877 ns/day, 27.365 hours/ns, 10.151 timesteps/s, 38.330 katom-step/s +76.1% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 4.6214 | 4.8032 | 4.9546 | 6.5 | 17.35 -Bond | 0.0005324 | 0.00060509 | 0.00069468 | 0.0 | 0.00 -Kspace | 13.883 | 14.034 | 14.216 | 3.8 | 50.71 -Neigh | 0.061704 | 0.061727 | 0.06176 | 0.0 | 0.22 -Comm | 0.10101 | 0.10374 | 0.10645 | 0.8 | 0.37 -Output | 0.00086818 | 0.0010909 | 0.001715 | 1.1 | 0.00 -Modify | 8.65 | 8.6524 | 8.6545 | 0.1 | 31.26 -Other | | 0.02055 | | | 0.07 +Pair | 5.6984 | 5.9083 | 6.1177 | 6.4 | 12.00 +Bond | 0.0011785 | 0.0012201 | 0.0013055 | 0.1 | 0.00 +Kspace | 24.311 | 24.519 | 24.729 | 3.1 | 49.78 +Neigh | 0.075406 | 0.075487 | 0.07556 | 0.0 | 0.15 +Comm | 0.29972 | 0.30943 | 0.31881 | 1.7 | 0.63 +Output | 0.0012474 | 0.001684 | 0.0027062 | 1.5 | 0.00 +Modify | 18.377 | 18.384 | 18.391 | 0.2 | 37.32 +Other | | 0.05679 | | | 0.12 Nlocal: 944 ave 951 max 940 min Histogram: 1 1 1 0 0 0 0 0 0 1 @@ -152,4 +189,4 @@ Ave neighs/atom = 457.08845 Ave special neighs/atom = 0.50847458 Neighbor list builds = 5 Dangerous builds = 0 -Total wall time: 0:00:50 +Total wall time: 0:00:55 diff --git a/examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-conq.g++.1 b/examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-conq.g++.1 deleted file mode 100644 index 5722e357ec..0000000000 --- a/examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-conq.g++.1 +++ /dev/null @@ -1,153 +0,0 @@ -LAMMPS (24 Mar 2022) -# electrodes with constrained total charges -# for graphene-ionic liquid supercapacitor - -boundary p p f # slab calculation -include settings.mod # styles, groups, computes and fixes -# set boundary in main script because ffield is periodic -units real -# distribute electrode atoms among all processors: -if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2" - -atom_style full -pair_style lj/cut/coul/long 16 -bond_style harmonic -angle_style harmonic -kspace_style pppm/electrode 1e-7 -# kspace_modify in main script because ffield is periodic - -read_data "data.graph-il" -Reading data file ... - orthogonal box = (0 0 -68) to (32.2 34.4 68) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 3776 atoms - scanning bonds ... - 2 = max bonds/atom - scanning angles ... - 1 = max angles/atom - reading bonds ... - 640 bonds - reading angles ... - 320 angles -Finding 1-2 1-3 1-4 neighbors ... - special bond factors lj: 0 0 0 - special bond factors coul: 0 0 0 - 2 = max # of 1-2 neighbors - 1 = max # of 1-3 neighbors - 1 = max # of 1-4 neighbors - 2 = max # of special neighbors - special bonds CPU = 0.001 seconds - read_data CPU = 0.012 seconds - -group bot molecule 641 -416 atoms in group bot -group top molecule 642 -416 atoms in group top - -group bmi type 1 2 3 -960 atoms in group bmi -group electrolyte type 1 2 3 4 -1280 atoms in group electrolyte - -fix nvt electrolyte nvt temp 500.0 500.0 100 -fix shake bmi shake 1e-4 20 0 b 1 2 a 1 - 0 = # of size 2 clusters - 0 = # of size 3 clusters - 0 = # of size 4 clusters - 320 = # of frozen angles - find clusters CPU = 0.000 seconds - -variable q atom q -compute qtop top reduce sum v_q -compute qbot bot reduce sum v_q -compute ctemp electrolyte temp -kspace_modify slab 3.0 - -fix conq bot electrode/conq -1.0 1.979 couple top 1.0 etypes 5 # conq doesn't take symm option -832 atoms in group conp_group - -# ask fix conq to output electrode potentials to internal variables -variable vbot internal 0.0 -variable vtop internal 0.0 -fix_modify conq set v bot vbot -fix_modify conq set v top vtop - -thermo 50 -thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop v_vbot v_vtop -run 500 -PPPM/electrode initialization ... - using 12-bit tables for long-range coulomb (src/kspace.cpp:342) - G vector (1/distance) = 0.20904498 - grid = 32 32 200 - stencil order = 5 - estimated absolute RMS force accuracy = 3.7023506e-05 - estimated relative force accuracy = 1.1149519e-07 - using double precision MKL FFT - 3d grid and FFT values/proc = 307242 204800 - generated 10 of 10 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 18 - ghost atom cutoff = 18 - binsize = 9, bins = 4 4 16 - 3 neighbor lists, perpetual/occasional/extra = 2 1 0 - (1) pair lj/cut/coul/long, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/3d - bin: standard - (2) fix electrode/conq, occasional, skip from (1) - attributes: half, newton on - pair build: skip - stencil: none - bin: none - (3) fix electrode/conq, perpetual, skip from (1) - attributes: half, newton on - pair build: skip - stencil: none - bin: none -Per MPI rank memory allocation (min/avg/max) = 56.89 | 56.89 | 56.89 Mbytes - Step Temp c_ctemp E_pair TotEng c_qbot c_qtop v_vbot v_vtop - 0 0 0 25136984 25136984 -1 1 -9.931852 10.097344 - 50 20.206425 72.797911 25136825 25137033 -1 1 -9.4359366 9.5964514 - 100 55.931663 201.50563 25136587 25137163 -1 1 -8.0440112 8.1861787 - 150 81.389273 293.22204 25136533 25137371 -1 1 -6.1113109 6.2267114 - 200 92.867946 334.57639 25136646 25137603 -1 1 -4.1857807 4.2740694 - 250 97.518304 351.33028 25136809 25137814 -1 1 -2.8383703 2.9101475 - 300 102.36577 368.79431 25136933 25137987 -1 1 -2.3831643 2.4461115 - 350 113.66597 409.50566 25136960 25138131 -1 1 -2.7083563 2.7457811 - 400 122.8443 442.57252 25136991 25138256 -1 1 -3.4311003 3.3941657 - 450 128.63713 463.44243 25137048 25138373 -1 1 -4.132871 3.9852959 - 500 131.18361 472.61665 25137142 25138493 -1 1 -4.5104095 4.2567261 -Loop time of 48.9361 on 1 procs for 500 steps with 3776 atoms - -Performance: 0.883 ns/day, 27.187 hours/ns, 10.217 timesteps/s -393.9% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 17.652 | 17.652 | 17.652 | 0.0 | 36.07 -Bond | 0.0010418 | 0.0010418 | 0.0010418 | 0.0 | 0.00 -Kspace | 16.566 | 16.566 | 16.566 | 0.0 | 33.85 -Neigh | 0.21584 | 0.21584 | 0.21584 | 0.0 | 0.44 -Comm | 0.04167 | 0.04167 | 0.04167 | 0.0 | 0.09 -Output | 0.0014585 | 0.0014585 | 0.0014585 | 0.0 | 0.00 -Modify | 14.445 | 14.445 | 14.445 | 0.0 | 29.52 -Other | | 0.0134 | | | 0.03 - -Nlocal: 3776 ave 3776 max 3776 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 12510 ave 12510 max 12510 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 1.72559e+06 ave 1.72559e+06 max 1.72559e+06 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 1725588 -Ave neighs/atom = 456.98835 -Ave special neighs/atom = 0.50847458 -Neighbor list builds = 6 -Dangerous builds = 0 -Total wall time: 0:01:43 diff --git a/examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-conq.g++.4 b/examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-conq.g++.4 deleted file mode 100644 index 96343114e6..0000000000 --- a/examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-conq.g++.4 +++ /dev/null @@ -1,154 +0,0 @@ -LAMMPS (24 Mar 2022) -# electrodes with constrained total charges -# for graphene-ionic liquid supercapacitor - -boundary p p f # slab calculation -include settings.mod # styles, groups, computes and fixes -# set boundary in main script because ffield is periodic -units real -# distribute electrode atoms among all processors: -if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2" -processors * * 2 - -atom_style full -pair_style lj/cut/coul/long 16 -bond_style harmonic -angle_style harmonic -kspace_style pppm/electrode 1e-7 -# kspace_modify in main script because ffield is periodic - -read_data "data.graph-il" -Reading data file ... - orthogonal box = (0 0 -68) to (32.2 34.4 68) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 3776 atoms - scanning bonds ... - 2 = max bonds/atom - scanning angles ... - 1 = max angles/atom - reading bonds ... - 640 bonds - reading angles ... - 320 angles -Finding 1-2 1-3 1-4 neighbors ... - special bond factors lj: 0 0 0 - special bond factors coul: 0 0 0 - 2 = max # of 1-2 neighbors - 1 = max # of 1-3 neighbors - 1 = max # of 1-4 neighbors - 2 = max # of special neighbors - special bonds CPU = 0.001 seconds - read_data CPU = 0.020 seconds - -group bot molecule 641 -416 atoms in group bot -group top molecule 642 -416 atoms in group top - -group bmi type 1 2 3 -960 atoms in group bmi -group electrolyte type 1 2 3 4 -1280 atoms in group electrolyte - -fix nvt electrolyte nvt temp 500.0 500.0 100 -fix shake bmi shake 1e-4 20 0 b 1 2 a 1 - 0 = # of size 2 clusters - 0 = # of size 3 clusters - 0 = # of size 4 clusters - 320 = # of frozen angles - find clusters CPU = 0.001 seconds - -variable q atom q -compute qtop top reduce sum v_q -compute qbot bot reduce sum v_q -compute ctemp electrolyte temp -kspace_modify slab 3.0 - -fix conq bot electrode/conq -1.0 1.979 couple top 1.0 etypes 5 # conq doesn't take symm option -832 atoms in group conp_group - -# ask fix conq to output electrode potentials to internal variables -variable vbot internal 0.0 -variable vtop internal 0.0 -fix_modify conq set v bot vbot -fix_modify conq set v top vtop - -thermo 50 -thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop v_vbot v_vtop -run 500 -PPPM/electrode initialization ... - using 12-bit tables for long-range coulomb (src/kspace.cpp:342) - G vector (1/distance) = 0.20904498 - grid = 32 32 200 - stencil order = 5 - estimated absolute RMS force accuracy = 3.7023506e-05 - estimated relative force accuracy = 1.1149519e-07 - using double precision MKL FFT - 3d grid and FFT values/proc = 151593 85504 - generated 10 of 10 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 18 - ghost atom cutoff = 18 - binsize = 9, bins = 4 4 16 - 3 neighbor lists, perpetual/occasional/extra = 2 1 0 - (1) pair lj/cut/coul/long, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/3d - bin: standard - (2) fix electrode/conq, occasional, skip from (1) - attributes: half, newton on - pair build: skip - stencil: none - bin: none - (3) fix electrode/conq, perpetual, skip from (1) - attributes: half, newton on - pair build: skip - stencil: none - bin: none -Per MPI rank memory allocation (min/avg/max) = 23.63 | 27.46 | 31.29 Mbytes - Step Temp c_ctemp E_pair TotEng c_qbot c_qtop v_vbot v_vtop - 0 0 0 25136984 25136984 -1 1 -9.931852 10.097344 - 50 20.206425 72.797911 25136825 25137033 -1 1 -9.4359366 9.5964514 - 100 55.931663 201.50563 25136587 25137163 -1 1 -8.0440112 8.1861787 - 150 81.389273 293.22204 25136533 25137371 -1 1 -6.1113109 6.2267114 - 200 92.867946 334.57639 25136646 25137603 -1 1 -4.1857807 4.2740694 - 250 97.518304 351.33028 25136809 25137814 -1 1 -2.8383703 2.9101475 - 300 102.36577 368.79431 25136933 25137987 -1 1 -2.3831643 2.4461115 - 350 113.66597 409.50566 25136960 25138131 -1 1 -2.7083563 2.7457811 - 400 122.8443 442.57252 25136991 25138256 -1 1 -3.4311003 3.3941657 - 450 128.63713 463.44243 25137048 25138373 -1 1 -4.132871 3.9852959 - 500 131.18361 472.61665 25137142 25138493 -1 1 -4.5104095 4.2567261 -Loop time of 28.8336 on 4 procs for 500 steps with 3776 atoms - -Performance: 1.498 ns/day, 16.019 hours/ns, 17.341 timesteps/s -94.1% CPU use with 4 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 5.7721 | 5.9353 | 6.144 | 6.0 | 20.58 -Bond | 0.00057855 | 0.00067043 | 0.00074793 | 0.0 | 0.00 -Kspace | 13.485 | 13.694 | 13.857 | 4.0 | 47.49 -Neigh | 0.092021 | 0.092044 | 0.092068 | 0.0 | 0.32 -Comm | 0.11486 | 0.11638 | 0.11801 | 0.4 | 0.40 -Output | 0.00090452 | 0.001109 | 0.0017097 | 1.0 | 0.00 -Modify | 8.974 | 8.9761 | 8.978 | 0.1 | 31.13 -Other | | 0.01837 | | | 0.06 - -Nlocal: 944 ave 948 max 940 min -Histogram: 1 0 0 1 0 0 1 0 0 1 -Nghost: 5920.5 ave 5941 max 5899 min -Histogram: 1 0 0 0 1 1 0 0 0 1 -Neighs: 431397 ave 442329 max 421103 min -Histogram: 2 0 0 0 0 0 0 0 1 1 - -Total # of neighbors = 1725588 -Ave neighs/atom = 456.98835 -Ave special neighs/atom = 0.50847458 -Neighbor list builds = 6 -Dangerous builds = 0 -Total wall time: 0:00:51 diff --git a/examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-conq2.g++.1 b/examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-conq2.g++.1 deleted file mode 100644 index 4465ed311d..0000000000 --- a/examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-conq2.g++.1 +++ /dev/null @@ -1,170 +0,0 @@ -LAMMPS (24 Mar 2022) -# electrodes with constrained total charges imposed from dynamically computed potentials -# for graphene-ionic liquid supercapacitor - -boundary p p f # slab calculation -include settings.mod # styles, groups, computes and fixes -# set boundary in main script because ffield is periodic -units real -# distribute electrode atoms among all processors: -if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2" - -atom_style full -pair_style lj/cut/coul/long 16 -bond_style harmonic -angle_style harmonic -kspace_style pppm/electrode 1e-7 -# kspace_modify in main script because ffield is periodic - -read_data "data.graph-il" -Reading data file ... - orthogonal box = (0 0 -68) to (32.2 34.4 68) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 3776 atoms - scanning bonds ... - 2 = max bonds/atom - scanning angles ... - 1 = max angles/atom - reading bonds ... - 640 bonds - reading angles ... - 320 angles -Finding 1-2 1-3 1-4 neighbors ... - special bond factors lj: 0 0 0 - special bond factors coul: 0 0 0 - 2 = max # of 1-2 neighbors - 1 = max # of 1-3 neighbors - 1 = max # of 1-4 neighbors - 2 = max # of special neighbors - special bonds CPU = 0.001 seconds - read_data CPU = 0.031 seconds - -group bot molecule 641 -416 atoms in group bot -group top molecule 642 -416 atoms in group top - -group bmi type 1 2 3 -960 atoms in group bmi -group electrolyte type 1 2 3 4 -1280 atoms in group electrolyte - -fix nvt electrolyte nvt temp 500.0 500.0 100 -fix shake bmi shake 1e-4 20 0 b 1 2 a 1 - 0 = # of size 2 clusters - 0 = # of size 3 clusters - 0 = # of size 4 clusters - 320 = # of frozen angles - find clusters CPU = 0.001 seconds - -variable q atom q -compute qtop top reduce sum v_q -compute qbot bot reduce sum v_q -compute ctemp electrolyte temp -kspace_modify slab 3.0 - -fix conp bot electrode/conp v_vbot 1.979 couple top v_vtop etypes 5 -832 atoms in group conp_group - -# get the four entries of electrode elastance matrix -variable me00 internal 0.0 -variable me01 internal 0.0 -variable me10 internal 0.0 -variable me11 internal 0.0 -fix_modify conp set me bot bot me00 -fix_modify conp set me bot top me01 -fix_modify conp set me top bot me10 -fix_modify conp set me top top me11 - -# get the 0V charges (qsb), and excess charge required to reach preset total charges -variable qsb_bot internal 0.0 -variable qsb_top internal 0.0 -fix_modify conp set qsb bot qsb_bot -fix_modify conp set qsb top qsb_top -variable qex_bot equal -1.0-v_qsb_bot # difference between desired and 0V charge -variable qex_top equal 1.0-v_qsb_top # difference between desired and 0V charge - -# calculate imposed potential as elastance * excess charge -# note: fix will wait until the run setup to look for its potential variables -variable vbot equal v_me00*v_qex_bot+v_me01*v_qex_top -variable vtop equal v_me10*v_qex_bot+v_me11*v_qex_top - -thermo 50 -thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop v_vbot v_vtop -run 500 -PPPM/electrode initialization ... - using 12-bit tables for long-range coulomb (src/kspace.cpp:342) - G vector (1/distance) = 0.20904498 - grid = 32 32 200 - stencil order = 5 - estimated absolute RMS force accuracy = 3.7023506e-05 - estimated relative force accuracy = 1.1149519e-07 - using double precision MKL FFT - 3d grid and FFT values/proc = 307242 204800 - generated 10 of 10 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 18 - ghost atom cutoff = 18 - binsize = 9, bins = 4 4 16 - 3 neighbor lists, perpetual/occasional/extra = 2 1 0 - (1) pair lj/cut/coul/long, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/3d - bin: standard - (2) fix electrode/conp, occasional, skip from (1) - attributes: half, newton on - pair build: skip - stencil: none - bin: none - (3) fix electrode/conp, perpetual, skip from (1) - attributes: half, newton on - pair build: skip - stencil: none - bin: none -Per MPI rank memory allocation (min/avg/max) = 56.89 | 56.89 | 56.89 Mbytes - Step Temp c_ctemp E_pair TotEng c_qbot c_qtop v_vbot v_vtop - 0 0 0 25136984 25136984 -1 1 -9.931852 10.097344 - 50 20.206425 72.797911 25136825 25137033 -1 1 -9.4359366 9.5964514 - 100 55.931663 201.50563 25136587 25137163 -1 1 -8.0440112 8.1861787 - 150 81.389273 293.22204 25136533 25137371 -1 1 -6.1113109 6.2267114 - 200 92.867946 334.57639 25136646 25137603 -1 1 -4.1857807 4.2740694 - 250 97.518304 351.33028 25136809 25137814 -1 1 -2.8383703 2.9101475 - 300 102.36577 368.79431 25136933 25137987 -1 1 -2.3831643 2.4461115 - 350 113.66597 409.50566 25136960 25138131 -1 1 -2.7083563 2.7457811 - 400 122.8443 442.57252 25136991 25138256 -1 1 -3.4311003 3.3941657 - 450 128.63713 463.44243 25137048 25138373 -1 1 -4.132871 3.9852959 - 500 131.18361 472.61665 25137142 25138493 -1 1 -4.5104095 4.2567261 -Loop time of 62.9692 on 1 procs for 500 steps with 3776 atoms - -Performance: 0.686 ns/day, 34.983 hours/ns, 7.940 timesteps/s -393.7% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 20.307 | 20.307 | 20.307 | 0.0 | 32.25 -Bond | 0.0020074 | 0.0020074 | 0.0020074 | 0.0 | 0.00 -Kspace | 23.562 | 23.562 | 23.562 | 0.0 | 37.42 -Neigh | 0.26149 | 0.26149 | 0.26149 | 0.0 | 0.42 -Comm | 0.059436 | 0.059436 | 0.059436 | 0.0 | 0.09 -Output | 0.0023888 | 0.0023888 | 0.0023888 | 0.0 | 0.00 -Modify | 18.756 | 18.756 | 18.756 | 0.0 | 29.79 -Other | | 0.01897 | | | 0.03 - -Nlocal: 3776 ave 3776 max 3776 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 12510 ave 12510 max 12510 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 1.72559e+06 ave 1.72559e+06 max 1.72559e+06 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 1725588 -Ave neighs/atom = 456.98835 -Ave special neighs/atom = 0.50847458 -Neighbor list builds = 6 -Dangerous builds = 0 -Total wall time: 0:02:26 diff --git a/examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-conq2.g++.4 b/examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-conq2.g++.4 deleted file mode 100644 index cf8ddf60a3..0000000000 --- a/examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-conq2.g++.4 +++ /dev/null @@ -1,171 +0,0 @@ -LAMMPS (24 Mar 2022) -# electrodes with constrained total charges imposed from dynamically computed potentials -# for graphene-ionic liquid supercapacitor - -boundary p p f # slab calculation -include settings.mod # styles, groups, computes and fixes -# set boundary in main script because ffield is periodic -units real -# distribute electrode atoms among all processors: -if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2" -processors * * 2 - -atom_style full -pair_style lj/cut/coul/long 16 -bond_style harmonic -angle_style harmonic -kspace_style pppm/electrode 1e-7 -# kspace_modify in main script because ffield is periodic - -read_data "data.graph-il" -Reading data file ... - orthogonal box = (0 0 -68) to (32.2 34.4 68) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 3776 atoms - scanning bonds ... - 2 = max bonds/atom - scanning angles ... - 1 = max angles/atom - reading bonds ... - 640 bonds - reading angles ... - 320 angles -Finding 1-2 1-3 1-4 neighbors ... - special bond factors lj: 0 0 0 - special bond factors coul: 0 0 0 - 2 = max # of 1-2 neighbors - 1 = max # of 1-3 neighbors - 1 = max # of 1-4 neighbors - 2 = max # of special neighbors - special bonds CPU = 0.001 seconds - read_data CPU = 0.019 seconds - -group bot molecule 641 -416 atoms in group bot -group top molecule 642 -416 atoms in group top - -group bmi type 1 2 3 -960 atoms in group bmi -group electrolyte type 1 2 3 4 -1280 atoms in group electrolyte - -fix nvt electrolyte nvt temp 500.0 500.0 100 -fix shake bmi shake 1e-4 20 0 b 1 2 a 1 - 0 = # of size 2 clusters - 0 = # of size 3 clusters - 0 = # of size 4 clusters - 320 = # of frozen angles - find clusters CPU = 0.001 seconds - -variable q atom q -compute qtop top reduce sum v_q -compute qbot bot reduce sum v_q -compute ctemp electrolyte temp -kspace_modify slab 3.0 - -fix conp bot electrode/conp v_vbot 1.979 couple top v_vtop etypes 5 -832 atoms in group conp_group - -# get the four entries of electrode elastance matrix -variable me00 internal 0.0 -variable me01 internal 0.0 -variable me10 internal 0.0 -variable me11 internal 0.0 -fix_modify conp set me bot bot me00 -fix_modify conp set me bot top me01 -fix_modify conp set me top bot me10 -fix_modify conp set me top top me11 - -# get the 0V charges (qsb), and excess charge required to reach preset total charges -variable qsb_bot internal 0.0 -variable qsb_top internal 0.0 -fix_modify conp set qsb bot qsb_bot -fix_modify conp set qsb top qsb_top -variable qex_bot equal -1.0-v_qsb_bot # difference between desired and 0V charge -variable qex_top equal 1.0-v_qsb_top # difference between desired and 0V charge - -# calculate imposed potential as elastance * excess charge -# note: fix will wait until the run setup to look for its potential variables -variable vbot equal v_me00*v_qex_bot+v_me01*v_qex_top -variable vtop equal v_me10*v_qex_bot+v_me11*v_qex_top - -thermo 50 -thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop v_vbot v_vtop -run 500 -PPPM/electrode initialization ... - using 12-bit tables for long-range coulomb (src/kspace.cpp:342) - G vector (1/distance) = 0.20904498 - grid = 32 32 200 - stencil order = 5 - estimated absolute RMS force accuracy = 3.7023506e-05 - estimated relative force accuracy = 1.1149519e-07 - using double precision MKL FFT - 3d grid and FFT values/proc = 151593 85504 - generated 10 of 10 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 18 - ghost atom cutoff = 18 - binsize = 9, bins = 4 4 16 - 3 neighbor lists, perpetual/occasional/extra = 2 1 0 - (1) pair lj/cut/coul/long, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/3d - bin: standard - (2) fix electrode/conp, occasional, skip from (1) - attributes: half, newton on - pair build: skip - stencil: none - bin: none - (3) fix electrode/conp, perpetual, skip from (1) - attributes: half, newton on - pair build: skip - stencil: none - bin: none -Per MPI rank memory allocation (min/avg/max) = 23.63 | 27.46 | 31.29 Mbytes - Step Temp c_ctemp E_pair TotEng c_qbot c_qtop v_vbot v_vtop - 0 0 0 25136984 25136984 -1 1 -9.931852 10.097344 - 50 20.206425 72.797911 25136825 25137033 -1 1 -9.4359366 9.5964514 - 100 55.931663 201.50563 25136587 25137163 -1 1 -8.0440112 8.1861787 - 150 81.389273 293.22204 25136533 25137371 -1 1 -6.1113109 6.2267114 - 200 92.867946 334.57639 25136646 25137603 -1 1 -4.1857807 4.2740694 - 250 97.518304 351.33028 25136809 25137814 -1 1 -2.8383703 2.9101475 - 300 102.36577 368.79431 25136933 25137987 -1 1 -2.3831643 2.4461115 - 350 113.66597 409.50566 25136960 25138131 -1 1 -2.7083563 2.7457811 - 400 122.8443 442.57252 25136991 25138256 -1 1 -3.4311003 3.3941657 - 450 128.63713 463.44243 25137048 25138373 -1 1 -4.132871 3.9852959 - 500 131.18361 472.61665 25137142 25138493 -1 1 -4.5104095 4.2567261 -Loop time of 33.4031 on 4 procs for 500 steps with 3776 atoms - -Performance: 1.293 ns/day, 18.557 hours/ns, 14.969 timesteps/s -94.3% CPU use with 4 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 7.1262 | 7.3913 | 7.611 | 6.8 | 22.13 -Bond | 0.0007191 | 0.00079089 | 0.00087005 | 0.0 | 0.00 -Kspace | 15.139 | 15.358 | 15.623 | 4.7 | 45.98 -Neigh | 0.10374 | 0.10377 | 0.10383 | 0.0 | 0.31 -Comm | 0.14245 | 0.14353 | 0.14563 | 0.3 | 0.43 -Output | 0.0012987 | 0.0015671 | 0.0022434 | 1.0 | 0.00 -Modify | 10.381 | 10.383 | 10.384 | 0.0 | 31.08 -Other | | 0.02134 | | | 0.06 - -Nlocal: 944 ave 948 max 940 min -Histogram: 1 0 0 1 0 0 1 0 0 1 -Nghost: 5920.5 ave 5941 max 5899 min -Histogram: 1 0 0 0 1 1 0 0 0 1 -Neighs: 431397 ave 442329 max 421103 min -Histogram: 2 0 0 0 0 0 0 0 1 1 - -Total # of neighbors = 1725588 -Ave neighs/atom = 456.98835 -Ave special neighs/atom = 0.50847458 -Neighbor list builds = 6 -Dangerous builds = 0 -Total wall time: 0:01:01 diff --git a/examples/PACKAGES/electrode/graph-il/settings.mod b/examples/PACKAGES/electrode/graph-il/settings.mod index dcdaf7bfcd..ffbbfb1cc4 100644 --- a/examples/PACKAGES/electrode/graph-il/settings.mod +++ b/examples/PACKAGES/electrode/graph-il/settings.mod @@ -12,8 +12,13 @@ kspace_style pppm/electrode 1e-7 read_data "data.graph-il" -group bot molecule 641 -group top molecule 642 +# replicate 4 4 1 # test different sys sizes + +variable zpos atom "z > 0" +group zpos variable zpos +group ele type 5 +group top intersect ele zpos +group bot subtract ele top group bmi type 1 2 3 group electrolyte type 1 2 3 4 diff --git a/examples/PACKAGES/electrode/madelung/.gitignore b/examples/PACKAGES/electrode/madelung/.gitignore new file mode 100644 index 0000000000..89d8d1a065 --- /dev/null +++ b/examples/PACKAGES/electrode/madelung/.gitignore @@ -0,0 +1,2 @@ +*.csv +*.txt diff --git a/examples/PACKAGES/electrode/madelung/data.au-elyt b/examples/PACKAGES/electrode/madelung/data.au-elyt new file mode 100644 index 0000000000..366e317378 --- /dev/null +++ b/examples/PACKAGES/electrode/madelung/data.au-elyt @@ -0,0 +1,27 @@ +LAMMPS data file via write_data, version 24 Dec 2020, timestep = 0 + +4 atoms +3 atom types + +0 1 xlo xhi +0 1 ylo yhi +-10 10 zlo zhi + +Masses + +1 196.966553 +2 196.966553 +3 1.0 + +Pair Coeffs # lj/cut/coul/long + +1 0 0 +2 0 0 +3 0 0 + +Atoms # full + +1 1 1 0.00 0.00 0.00 -2.00 # bottom electrode +2 2 2 0.00 0.00 0.00 2.00 # top electrode +3 3 3 0.50 0.00 0.00 -1.00 # bottom electrolyte +4 3 3 -0.50 0.00 0.00 1.00 # top electrolyte diff --git a/examples/PACKAGES/electrode/madelung/eval.py b/examples/PACKAGES/electrode/madelung/eval.py new file mode 100644 index 0000000000..2f5a355d9b --- /dev/null +++ b/examples/PACKAGES/electrode/madelung/eval.py @@ -0,0 +1,53 @@ +#!/usr/env/python3 + +import sys +import os.path as op + + +def rel_error(out, ref): + return 100 * abs((ref - out) / out) + + +assert len(sys.argv) == 5 + +with open(sys.argv[1]) as f: + ref_line = f.readlines()[-1].split(", ") +e_ref = float(ref_line[1]) +q_ref = float(ref_line[3]) +inv11_ref = float(ref_line[4]) +inv12_ref = float(ref_line[5]) +b1_ref = float(ref_line[6]) + +# out.csv +with open(sys.argv[2]) as f: + out_line = f.readlines()[-1].split(", ") +e_out = float(out_line[0]) +q_out = float(out_line[1]) + +out_lines = [("energy", e_ref, e_out), ("charge", q_ref, q_out)] + +# vec.csv +vec_file = "vec.csv" +if op.isfile(vec_file): + with open(sys.argv[4]) as f: + vec_line = f.readlines()[1:] + b1_out = float(vec_line[0]) + b2_out = float(vec_line[1]) + out_lines.append(("b1", b1_ref, b1_out)) + +# inv.csv +inv_file = "inv.csv" +if op.isfile(inv_file): + with open(inv_file) as f: + inv_line = f.readlines()[1].split() + inv11_out = float(inv_line[0]) + inv12_out = float(inv_line[1]) + out_lines.append(("inv11", inv11_ref, inv11_out)) + +lines = [] +for label, ref, out in out_lines: + error = rel_error(out, ref) + lines.append(f"{label}: {out:.5f}, {error:.5f}\n") + +with open("madelung.txt", 'a') as f: + f.writelines(lines) diff --git a/examples/PACKAGES/electrode/madelung/in.cg b/examples/PACKAGES/electrode/madelung/in.cg new file mode 100644 index 0000000000..39a90a1f29 --- /dev/null +++ b/examples/PACKAGES/electrode/madelung/in.cg @@ -0,0 +1,11 @@ +boundary p p f +kspace_style ewald/electrode 1.0e-8 +kspace_modify slab 8.0 # ew3dc + +include "settings.mod" # styles, computes, groups and fixes + +thermo_style custom step pe c_qbot c_qtop +fix conp bot electrode/conp 0 2 couple top 1 symm on algo cg 1e-6 + +run 0 + diff --git a/examples/PACKAGES/electrode/madelung/in.ewald-ew2d b/examples/PACKAGES/electrode/madelung/in.ewald-ew2d new file mode 100644 index 0000000000..2f54e747d1 --- /dev/null +++ b/examples/PACKAGES/electrode/madelung/in.ewald-ew2d @@ -0,0 +1,11 @@ +boundary p p f +kspace_style ewald/electrode 1.0e-8 +kspace_modify slab ew2d + +include "settings.mod" # styles, computes, groups and fixes + +thermo_style custom step pe c_qbot c_qtop +fix conp bot electrode/conp 0 2 couple top 1 symm on write_inv inv.csv write_vec vec.csv + +run 0 + diff --git a/examples/PACKAGES/electrode/madelung/in.ewald-ew3dc b/examples/PACKAGES/electrode/madelung/in.ewald-ew3dc new file mode 100644 index 0000000000..c89804ef11 --- /dev/null +++ b/examples/PACKAGES/electrode/madelung/in.ewald-ew3dc @@ -0,0 +1,11 @@ +boundary p p f +kspace_style ewald/electrode 1.0e-8 +kspace_modify slab 8.0 # ew3dc + +include "settings.mod" # styles, computes, groups and fixes + +thermo_style custom step pe c_qbot c_qtop +fix conp bot electrode/conp 0 2 couple top 1 symm on write_inv inv.csv write_vec vec.csv + +run 0 + diff --git a/examples/PACKAGES/electrode/madelung/in.ewald-ffield b/examples/PACKAGES/electrode/madelung/in.ewald-ffield new file mode 100644 index 0000000000..c30f82159b --- /dev/null +++ b/examples/PACKAGES/electrode/madelung/in.ewald-ffield @@ -0,0 +1,10 @@ +boundary p p p +kspace_style ewald/electrode 1.0e-8 + +include "settings.mod" # styles, computes, groups and fixes + +thermo_style custom step pe c_qbot c_qtop +fix conp bot electrode/conp 0 2 couple top 1 symm on ffield yes write_inv inv.csv write_vec vec.csv + +run 0 + diff --git a/examples/PACKAGES/electrode/madelung/in.pppm-ew3dc b/examples/PACKAGES/electrode/madelung/in.pppm-ew3dc new file mode 100644 index 0000000000..c36587af08 --- /dev/null +++ b/examples/PACKAGES/electrode/madelung/in.pppm-ew3dc @@ -0,0 +1,11 @@ +boundary p p f +kspace_style pppm/electrode 1.0e-10 +kspace_modify slab 8.0 # ew3dc + +include "settings.mod" # styles, computes, groups and fixes + +thermo_style custom step pe c_qbot c_qtop +fix conp bot electrode/conp 0 2 couple top 1 symm on write_inv inv.csv write_vec vec.csv + +run 0 + diff --git a/examples/PACKAGES/electrode/madelung/in.pppm-ffield b/examples/PACKAGES/electrode/madelung/in.pppm-ffield new file mode 100644 index 0000000000..e161485e6f --- /dev/null +++ b/examples/PACKAGES/electrode/madelung/in.pppm-ffield @@ -0,0 +1,10 @@ +boundary p p p +kspace_style pppm/electrode 1.0e-10 + +include "settings.mod" # styles, computes, groups and fixes + +thermo_style custom step pe c_qbot c_qtop +fix conp bot electrode/conp 0 2 couple top 1 symm on ffield yes write_inv inv.csv write_vec vec.csv + +run 0 + diff --git a/examples/PACKAGES/electrode/madelung/log.1Dec2022.madelung-cg.g++.1 b/examples/PACKAGES/electrode/madelung/log.1Dec2022.madelung-cg.g++.1 new file mode 100644 index 0000000000..a0cd4d959c --- /dev/null +++ b/examples/PACKAGES/electrode/madelung/log.1Dec2022.madelung-cg.g++.1 @@ -0,0 +1,131 @@ +LAMMPS (3 Nov 2022) +boundary p p f +kspace_style ewald/electrode 1.0e-8 +kspace_modify slab 8.0 # ew3dc + +include "settings.mod" # styles, computes, groups and fixes +# set boundary in main script because ffield is periodic +units real +# distribute electrode atoms among all processors: +if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2" + +atom_style full +pair_style lj/cut/coul/long 12 + +read_data "data.au-elyt" +Reading data file ... + orthogonal box = (0 0 -10) to (1 1 10) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 4 atoms +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + special bonds CPU = 0.001 seconds + read_data CPU = 0.003 seconds + +group bot type 1 +1 atoms in group bot +group top type 2 +1 atoms in group top + +# get electrode charges +variable q atom q +compute qbot bot reduce sum v_q +compute qtop top reduce sum v_q + +compute compute_pe all pe +variable vpe equal c_compute_pe +variable charge equal c_qtop +fix fxprint all print 1 "${vpe}, ${charge}" file "out.csv" + +thermo_style custom step pe c_qbot c_qtop +fix conp bot electrode/conp 0 2 couple top 1 symm on algo cg 1e-6 +2 atoms in group conp_group + +run 0 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- fix electrode command: + +@article{Ahrens2022 +author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0099239}, +title = {{ELECTRODE: An electrochemistry package for LAMMPS}}, +journal = {The Journal of Chemical Physics}, +year = {2022} +volume = {157}, +pages = {084801}, +} +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +Ewald/electrode initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:342) +WARNING: For better accuracy use 'pair_modify table 0' (src/kspace.cpp:365) + G vector (1/distance) = 0.32261103 + estimated absolute RMS force accuracy = 3.8272011e-06 + estimated relative force accuracy = 1.1525502e-08 + KSpace vectors: actual max1d max3d = 52 50 515150 + kxmax kymax kzmax = 1 1 50 +Generated 3 of 3 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 1 1 3 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair lj/cut/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard + (2) fix electrode/conp, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/domain.cpp:966) +139.943964815502, 0.279214485147241 +Per MPI rank memory allocation (min/avg/max) = 144.1 | 144.1 | 144.1 Mbytes + Step PotEng c_qbot c_qtop + 0 139.94396 -0.27921449 0.27921449 +Loop time of 1.092e-06 on 1 procs for 0 steps with 4 atoms + +91.6% 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 | 0 | 0 | 0.0 | 0.00 +Bond | 0 | 0 | 0 | 0.0 | 0.00 +Kspace | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 1.092e-06 | | |100.00 + +Nlocal: 4 ave 4 max 4 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 3596 ave 3596 max 3596 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 4790 ave 4790 max 4790 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 4790 +Ave neighs/atom = 1197.5 +Ave special neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds = 0 + +Average conjugate gradient steps: 1 +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/electrode/madelung/log.1Dec2022.madelung-ewald-ew2d.g++.1 b/examples/PACKAGES/electrode/madelung/log.1Dec2022.madelung-ewald-ew2d.g++.1 new file mode 100644 index 0000000000..ff0a8550cd --- /dev/null +++ b/examples/PACKAGES/electrode/madelung/log.1Dec2022.madelung-ewald-ew2d.g++.1 @@ -0,0 +1,130 @@ +LAMMPS (3 Nov 2022) +boundary p p f +kspace_style ewald/electrode 1.0e-8 +kspace_modify slab ew2d + +include "settings.mod" # styles, computes, groups and fixes +# set boundary in main script because ffield is periodic +units real +# distribute electrode atoms among all processors: +if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2" + +atom_style full +pair_style lj/cut/coul/long 12 + +read_data "data.au-elyt" +Reading data file ... + orthogonal box = (0 0 -10) to (1 1 10) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 4 atoms +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + special bonds CPU = 0.001 seconds + read_data CPU = 0.002 seconds + +group bot type 1 +1 atoms in group bot +group top type 2 +1 atoms in group top + +# get electrode charges +variable q atom q +compute qbot bot reduce sum v_q +compute qtop top reduce sum v_q + +compute compute_pe all pe +variable vpe equal c_compute_pe +variable charge equal c_qtop +fix fxprint all print 1 "${vpe}, ${charge}" file "out.csv" + +thermo_style custom step pe c_qbot c_qtop +fix conp bot electrode/conp 0 2 couple top 1 symm on write_inv inv.csv write_vec vec.csv +2 atoms in group conp_group + +run 0 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- fix electrode command: + +@article{Ahrens2022 +author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0099239}, +title = {{ELECTRODE: An electrochemistry package for LAMMPS}}, +journal = {The Journal of Chemical Physics}, +year = {2022} +volume = {157}, +pages = {084801}, +} +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +Ewald/electrode initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:342) +WARNING: For better accuracy use 'pair_modify table 0' (src/kspace.cpp:365) + G vector (1/distance) = 0.32261103 + estimated absolute RMS force accuracy = 9.9990544e-06 + estimated relative force accuracy = 3.0111855e-08 + KSpace vectors: actual max1d max3d = 2 8 2456 + kxmax kymax kzmax = 1 1 8 +Generated 3 of 3 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 1 1 3 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair lj/cut/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard + (2) fix electrode/conp, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/domain.cpp:966) +139.946125020193, 0.279214126709814 +Per MPI rank memory allocation (min/avg/max) = 20.42 | 20.42 | 20.42 Mbytes + Step PotEng c_qbot c_qtop + 0 139.94613 -0.27921413 0.27921413 +Loop time of 1.082e-06 on 1 procs for 0 steps with 4 atoms + +0.0% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Bond | 0 | 0 | 0 | 0.0 | 0.00 +Kspace | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 1.082e-06 | | |100.00 + +Nlocal: 4 ave 4 max 4 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 3596 ave 3596 max 3596 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 4790 ave 4790 max 4790 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 4790 +Ave neighs/atom = 1197.5 +Ave special neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds = 0 + +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/electrode/madelung/log.1Dec2022.madelung-ewald-ew3dc.g++.1 b/examples/PACKAGES/electrode/madelung/log.1Dec2022.madelung-ewald-ew3dc.g++.1 new file mode 100644 index 0000000000..5374b09ff1 --- /dev/null +++ b/examples/PACKAGES/electrode/madelung/log.1Dec2022.madelung-ewald-ew3dc.g++.1 @@ -0,0 +1,130 @@ +LAMMPS (3 Nov 2022) +boundary p p f +kspace_style ewald/electrode 1.0e-8 +kspace_modify slab 8.0 # ew3dc + +include "settings.mod" # styles, computes, groups and fixes +# set boundary in main script because ffield is periodic +units real +# distribute electrode atoms among all processors: +if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2" + +atom_style full +pair_style lj/cut/coul/long 12 + +read_data "data.au-elyt" +Reading data file ... + orthogonal box = (0 0 -10) to (1 1 10) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 4 atoms +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + special bonds CPU = 0.001 seconds + read_data CPU = 0.003 seconds + +group bot type 1 +1 atoms in group bot +group top type 2 +1 atoms in group top + +# get electrode charges +variable q atom q +compute qbot bot reduce sum v_q +compute qtop top reduce sum v_q + +compute compute_pe all pe +variable vpe equal c_compute_pe +variable charge equal c_qtop +fix fxprint all print 1 "${vpe}, ${charge}" file "out.csv" + +thermo_style custom step pe c_qbot c_qtop +fix conp bot electrode/conp 0 2 couple top 1 symm on write_inv inv.csv write_vec vec.csv +2 atoms in group conp_group + +run 0 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- fix electrode command: + +@article{Ahrens2022 +author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0099239}, +title = {{ELECTRODE: An electrochemistry package for LAMMPS}}, +journal = {The Journal of Chemical Physics}, +year = {2022} +volume = {157}, +pages = {084801}, +} +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +Ewald/electrode initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:342) +WARNING: For better accuracy use 'pair_modify table 0' (src/kspace.cpp:365) + G vector (1/distance) = 0.32261103 + estimated absolute RMS force accuracy = 3.8272011e-06 + estimated relative force accuracy = 1.1525502e-08 + KSpace vectors: actual max1d max3d = 52 50 515150 + kxmax kymax kzmax = 1 1 50 +Generated 3 of 3 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 1 1 3 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair lj/cut/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard + (2) fix electrode/conp, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/domain.cpp:966) +139.943964815502, 0.279214485147238 +Per MPI rank memory allocation (min/avg/max) = 144.1 | 144.1 | 144.1 Mbytes + Step PotEng c_qbot c_qtop + 0 139.94396 -0.27921449 0.27921449 +Loop time of 7.31e-07 on 1 procs for 0 steps with 4 atoms + +0.0% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Bond | 0 | 0 | 0 | 0.0 | 0.00 +Kspace | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 7.31e-07 | | |100.00 + +Nlocal: 4 ave 4 max 4 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 3596 ave 3596 max 3596 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 4790 ave 4790 max 4790 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 4790 +Ave neighs/atom = 1197.5 +Ave special neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds = 0 + +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/electrode/madelung/log.1Dec2022.madelung-ewald-ffield.g++.1 b/examples/PACKAGES/electrode/madelung/log.1Dec2022.madelung-ewald-ffield.g++.1 new file mode 100644 index 0000000000..ea3799809d --- /dev/null +++ b/examples/PACKAGES/electrode/madelung/log.1Dec2022.madelung-ewald-ffield.g++.1 @@ -0,0 +1,129 @@ +LAMMPS (3 Nov 2022) +boundary p p p +kspace_style ewald/electrode 1.0e-8 + +include "settings.mod" # styles, computes, groups and fixes +# set boundary in main script because ffield is periodic +units real +# distribute electrode atoms among all processors: +if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2" + +atom_style full +pair_style lj/cut/coul/long 12 + +read_data "data.au-elyt" +Reading data file ... + orthogonal box = (0 0 -10) to (1 1 10) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 4 atoms +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + special bonds CPU = 0.001 seconds + read_data CPU = 0.002 seconds + +group bot type 1 +1 atoms in group bot +group top type 2 +1 atoms in group top + +# get electrode charges +variable q atom q +compute qbot bot reduce sum v_q +compute qtop top reduce sum v_q + +compute compute_pe all pe +variable vpe equal c_compute_pe +variable charge equal c_qtop +fix fxprint all print 1 "${vpe}, ${charge}" file "out.csv" + +thermo_style custom step pe c_qbot c_qtop +fix conp bot electrode/conp 0 2 couple top 1 symm on ffield yes write_inv inv.csv write_vec vec.csv +2 atoms in group conp_group + +run 0 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- fix electrode command: + +@article{Ahrens2022 +author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0099239}, +title = {{ELECTRODE: An electrochemistry package for LAMMPS}}, +journal = {The Journal of Chemical Physics}, +year = {2022} +volume = {157}, +pages = {084801}, +} +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +Ewald/electrode initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:342) +WARNING: For better accuracy use 'pair_modify table 0' (src/kspace.cpp:365) + G vector (1/distance) = 0.32261103 + estimated absolute RMS force accuracy = 9.9990544e-06 + estimated relative force accuracy = 3.0111855e-08 + KSpace vectors: actual max1d max3d = 10 8 2456 + kxmax kymax kzmax = 1 1 8 +Generated 3 of 3 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 1 1 3 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair lj/cut/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard + (2) fix electrode/conp, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/domain.cpp:966) +138.299024320284, 0.287160231879378 +Per MPI rank memory allocation (min/avg/max) = 21.19 | 21.19 | 21.19 Mbytes + Step PotEng c_qbot c_qtop + 0 138.29902 -0.28716023 0.28716023 +Loop time of 1.804e-06 on 1 procs for 0 steps with 4 atoms + +55.4% 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 | 0 | 0 | 0.0 | 0.00 +Bond | 0 | 0 | 0 | 0.0 | 0.00 +Kspace | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 1.804e-06 | | |100.00 + +Nlocal: 4 ave 4 max 4 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 10796 ave 10796 max 10796 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 4790 ave 4790 max 4790 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 4790 +Ave neighs/atom = 1197.5 +Ave special neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds = 0 + +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/electrode/madelung/log.1Dec2022.madelung-pppm-ew3dc.g++.1 b/examples/PACKAGES/electrode/madelung/log.1Dec2022.madelung-pppm-ew3dc.g++.1 new file mode 100644 index 0000000000..a3961bd3cb --- /dev/null +++ b/examples/PACKAGES/electrode/madelung/log.1Dec2022.madelung-pppm-ew3dc.g++.1 @@ -0,0 +1,143 @@ +LAMMPS (3 Nov 2022) +boundary p p f +kspace_style pppm/electrode 1.0e-10 +kspace_modify slab 8.0 # ew3dc + +include "settings.mod" # styles, computes, groups and fixes +# set boundary in main script because ffield is periodic +units real +# distribute electrode atoms among all processors: +if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2" + +atom_style full +pair_style lj/cut/coul/long 12 + +read_data "data.au-elyt" +Reading data file ... + orthogonal box = (0 0 -10) to (1 1 10) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 4 atoms +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + special bonds CPU = 0.001 seconds + read_data CPU = 0.003 seconds + +group bot type 1 +1 atoms in group bot +group top type 2 +1 atoms in group top + +# get electrode charges +variable q atom q +compute qbot bot reduce sum v_q +compute qtop top reduce sum v_q + +compute compute_pe all pe +variable vpe equal c_compute_pe +variable charge equal c_qtop +fix fxprint all print 1 "${vpe}, ${charge}" file "out.csv" + +thermo_style custom step pe c_qbot c_qtop +fix conp bot electrode/conp 0 2 couple top 1 symm on write_inv inv.csv write_vec vec.csv +2 atoms in group conp_group + +run 0 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- kspace_style pppm/electrode command: + +@article{Ahrens2021, +author = {Ahrens-Iwers, Ludwig J.V. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0063381}, +title = {{Constant potential simulations on a mesh}}, +journal = {Journal of Chemical Physics}, +year = {2021} +volume = {155}, +pages = {104104}, +} +- fix electrode command: + +@article{Ahrens2022 +author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0099239}, +title = {{ELECTRODE: An electrochemistry package for LAMMPS}}, +journal = {The Journal of Chemical Physics}, +year = {2022} +volume = {157}, +pages = {084801}, +} +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +PPPM/electrode initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:342) +WARNING: For better accuracy use 'pair_modify table 0' (src/kspace.cpp:365) + G vector (1/distance) = 0.37216302 + grid = 12 12 375 + stencil order = 5 + estimated absolute RMS force accuracy = 9.4312865e-06 + estimated relative force accuracy = 2.8402039e-08 + using double precision MKL FFT + 3d grid and FFT values/proc = 637099 54000 +Generated 3 of 3 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 1 1 3 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair lj/cut/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard + (2) fix electrode/conp, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/domain.cpp:966) +139.946107219358, 0.279214187928028 +Per MPI rank memory allocation (min/avg/max) = 40.22 | 40.22 | 40.22 Mbytes + Step PotEng c_qbot c_qtop + 0 139.94611 -0.27921419 0.27921419 +Loop time of 8.32e-07 on 1 procs for 0 steps with 4 atoms + +0.0% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Bond | 0 | 0 | 0 | 0.0 | 0.00 +Kspace | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 8.32e-07 | | |100.00 + +Nlocal: 4 ave 4 max 4 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 3596 ave 3596 max 3596 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 4790 ave 4790 max 4790 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 4790 +Ave neighs/atom = 1197.5 +Ave special neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds = 0 + +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/electrode/madelung/log.1Dec2022.madelung-pppm-ffield.g++.1 b/examples/PACKAGES/electrode/madelung/log.1Dec2022.madelung-pppm-ffield.g++.1 new file mode 100644 index 0000000000..64664e7443 --- /dev/null +++ b/examples/PACKAGES/electrode/madelung/log.1Dec2022.madelung-pppm-ffield.g++.1 @@ -0,0 +1,142 @@ +LAMMPS (3 Nov 2022) +boundary p p p +kspace_style pppm/electrode 1.0e-10 + +include "settings.mod" # styles, computes, groups and fixes +# set boundary in main script because ffield is periodic +units real +# distribute electrode atoms among all processors: +if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2" + +atom_style full +pair_style lj/cut/coul/long 12 + +read_data "data.au-elyt" +Reading data file ... + orthogonal box = (0 0 -10) to (1 1 10) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 4 atoms +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + special bonds CPU = 0.001 seconds + read_data CPU = 0.002 seconds + +group bot type 1 +1 atoms in group bot +group top type 2 +1 atoms in group top + +# get electrode charges +variable q atom q +compute qbot bot reduce sum v_q +compute qtop top reduce sum v_q + +compute compute_pe all pe +variable vpe equal c_compute_pe +variable charge equal c_qtop +fix fxprint all print 1 "${vpe}, ${charge}" file "out.csv" + +thermo_style custom step pe c_qbot c_qtop +fix conp bot electrode/conp 0 2 couple top 1 symm on ffield yes write_inv inv.csv write_vec vec.csv +2 atoms in group conp_group + +run 0 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- kspace_style pppm/electrode command: + +@article{Ahrens2021, +author = {Ahrens-Iwers, Ludwig J.V. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0063381}, +title = {{Constant potential simulations on a mesh}}, +journal = {Journal of Chemical Physics}, +year = {2021} +volume = {155}, +pages = {104104}, +} +- fix electrode command: + +@article{Ahrens2022 +author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0099239}, +title = {{ELECTRODE: An electrochemistry package for LAMMPS}}, +journal = {The Journal of Chemical Physics}, +year = {2022} +volume = {157}, +pages = {084801}, +} +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +PPPM/electrode initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:342) +WARNING: For better accuracy use 'pair_modify table 0' (src/kspace.cpp:365) + G vector (1/distance) = 0.37297537 + grid = 12 12 90 + stencil order = 5 + estimated absolute RMS force accuracy = 9.4312758e-06 + estimated relative force accuracy = 2.8402007e-08 + using double precision MKL FFT + 3d grid and FFT values/proc = 174824 12960 +Generated 3 of 3 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 1 1 3 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair lj/cut/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard + (2) fix electrode/conp, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/domain.cpp:966) +138.298994634846, 0.287160247352281 +Per MPI rank memory allocation (min/avg/max) = 16.7 | 16.7 | 16.7 Mbytes + Step PotEng c_qbot c_qtop + 0 138.29899 -0.28716025 0.28716025 +Loop time of 1.022e-06 on 1 procs for 0 steps with 4 atoms + +0.0% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Bond | 0 | 0 | 0 | 0.0 | 0.00 +Kspace | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 1.022e-06 | | |100.00 + +Nlocal: 4 ave 4 max 4 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 10796 ave 10796 max 10796 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 4790 ave 4790 max 4790 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 4790 +Ave neighs/atom = 1197.5 +Ave special neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds = 0 + +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/electrode/madelung/plate_cap.py b/examples/PACKAGES/electrode/madelung/plate_cap.py new file mode 100755 index 0000000000..62d52fe102 --- /dev/null +++ b/examples/PACKAGES/electrode/madelung/plate_cap.py @@ -0,0 +1,94 @@ +#!/usr/bin/env python3 + +import numpy as np +from scipy.special import erf + +ETA = 2 +SQRT2 = np.sqrt(2) +COULOMB = 332.06371 # Coulomb constant in Lammps 'real' units +QE2F = 23.060549 +LENGTH = 10000 # convergence parameter + + +def lattice(length): + """indices combinations of images in one quadrant""" + x = np.arange(length) # range(length) + y = np.arange(1, length) + return np.array(np.meshgrid(x, y)).T.reshape(-1, 2) + + +def a_element(r): + """Coulomb contribution of two Gaussians""" + return erf(ETA / SQRT2 * r) / r + + +def b_element(r, q): + """Coulomb contribution of a Gaussian with a point charge""" + return q * erf(ETA * r) / r + + +a = 1 # nearest neighbor distance i.e. lattice constant / sqrt(2) +x_elec = [-2, 2] +x_elyt = [-1, 1] +q_elyt = [0.5, -0.5] +distance_plates = x_elec[1] - x_elec[0] # distance between plates +v = np.array([-0.5, 0.5]) * (QE2F / COULOMB) + +# distances to images within electrode and to opposite electrode +distances = a * np.linalg.norm(lattice(LENGTH), axis=1) +opposite_distances = np.sqrt(np.square(distances) + distance_plates ** 2) + +# self interaction and within original box +A_11 = np.sqrt(2 / np.pi) * ETA +A_12 = erf(ETA * distance_plates / SQRT2) / distance_plates + +# interaction with periodic images +A_11 += 4 * np.sum(a_element(distances)) +A_12 += 4 * np.sum(a_element(opposite_distances)) +A = np.array([[A_11, A_12], [A_12, A_11]]) +inv = np.linalg.inv(A) +e = np.array([1, 1]) +inv -= np.matmul(inv, np.matmul(np.outer(e, e), inv)) / np.dot(e, np.dot(inv, e)) + +# electrode-electrolyte interaction +b = [] +for x in x_elec: + bi = 0 + for y, q in zip(x_elyt, q_elyt): + d = abs(y - x) + bi += b_element(d, q) + image_distances = np.sqrt(np.square(distances) + d ** 2) + bi += 4 * np.sum(b_element(image_distances, q)) + b.append(bi) +b = np.array(b) + +# electrolyte-electrolyte energy +elyt_11 = 4 * np.sum(1 / distances) +distance_elyt = x_elyt[1] - x_elyt[0] +elyt_12 = 1 / distance_elyt + 4 * np.sum( + 1 / np.sqrt(np.square(distances) + distance_elyt ** 2) +) +elyt = np.array([[elyt_11, elyt_12], [elyt_12, elyt_11]]) +energy_elyt = 0.5 * np.dot(q_elyt, np.dot(elyt, q_elyt)) + +# electrode charges and energy +q = np.dot(inv, v - b) +energy = COULOMB * (0.5 * np.dot(q, np.dot(A, q)) + np.dot(b, q) + energy_elyt) + +print( + "length, energy / kcal/mol, q1 / e, q2 / e, inv11 / A, inv12 / A, b1 / e/A, b2 / e/A" +) +print( + ", ".join( + [ + str(LENGTH), + f"{energy:.8f}", + f"{q[0]:.10f}", + f"{q[1]:.10f}", + f"{inv[0, 0]:.10f}", + f"{inv[0, 1]:.10f}", + f"{b[0]:.8f}", + f"{b[1]:.8f}", + ] + ) +) diff --git a/examples/PACKAGES/electrode/madelung/settings.mod b/examples/PACKAGES/electrode/madelung/settings.mod new file mode 100644 index 0000000000..aa1096ea81 --- /dev/null +++ b/examples/PACKAGES/electrode/madelung/settings.mod @@ -0,0 +1,22 @@ +# set boundary in main script because ffield is periodic +units real +# distribute electrode atoms among all processors: +if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2" + +atom_style full +pair_style lj/cut/coul/long 12 + +read_data "data.au-elyt" + +group bot type 1 +group top type 2 + +# get electrode charges +variable q atom q +compute qbot bot reduce sum v_q +compute qtop top reduce sum v_q + +compute compute_pe all pe +variable vpe equal c_compute_pe +variable charge equal c_qtop +fix fxprint all print 1 "${vpe}, ${charge}" file "out.csv" diff --git a/examples/PACKAGES/electrode/madelung/test.sh b/examples/PACKAGES/electrode/madelung/test.sh new file mode 100644 index 0000000000..edac04f5b1 --- /dev/null +++ b/examples/PACKAGES/electrode/madelung/test.sh @@ -0,0 +1,23 @@ +#!/bin/bash -e + +lmpbin=$1 +if [ ! -f $lmpbin ]; then + echo "LAMMPS binary '$lmpbin' is not a file" + exit 1 +fi + +ref_out="plate_cap.csv" +if [ ! -f $ref_out ]; then + echo "Generating reference data" + python3 plate_cap.py > $ref_out +fi + +echo "Running Lammps inputs" +rm -rf madelung.txt && touch madelung.txt +for file in in.*; do + printf "\n$file\n" >> madelung.txt + rm -f out.csv inv.csv vec.csv + $lmpbin -i $file &> /dev/null + python3 eval.py $ref_out out.csv inv.csv vec.csv +done +cat madelung.txt diff --git a/examples/PACKAGES/electrode/piston/.gitignore b/examples/PACKAGES/electrode/piston/.gitignore new file mode 100644 index 0000000000..9336c29266 --- /dev/null +++ b/examples/PACKAGES/electrode/piston/.gitignore @@ -0,0 +1,2 @@ +top_wall.csv +data.pistoned diff --git a/examples/PACKAGES/electrode/piston/data.piston b/examples/PACKAGES/electrode/piston/data.piston new file mode 100644 index 0000000000..815edff7ba --- /dev/null +++ b/examples/PACKAGES/electrode/piston/data.piston @@ -0,0 +1,2128 @@ +LAMMPS data file via write_data, version 23 Jun 2022, timestep = 5000 + +726 atoms +4 atom types +420 bonds +1 bond types +210 angles +1 angle types + +0 17.6494 xlo xhi +0 20.3798 ylo yhi +0 26.0000 zlo zhi + +Masses + +1 500 +2 196.97 +3 15.9994 +4 1.008 + +Pair Coeffs # lj/cut/coul/long + +1 0.069 2.78 +2 5.29 2.951 +3 0.1553 3.166 +4 0 0 + +Bond Coeffs # harmonic + +1 600 1 + +Angle Coeffs # harmonic + +1 75 109.47 + +Atoms # full + +49 25 2 0 0 0 2.4018 0 0 0 +50 25 2 0 1.4708 2.5475 2.4018 0 0 0 +51 26 2 0 0 5.0949 2.4018 0 0 0 +57 29 2 0 2.9416 0 2.4018 0 0 0 +58 29 2 0 4.4124 2.5475 2.4018 0 0 0 +59 30 2 0 2.9416 5.0949 2.4018 0 0 0 +65 33 2 0 5.8832 0 2.4018 0 0 0 +66 33 2 0 7.354000000000001 2.5475 2.4018 0 0 0 +67 34 2 0 5.8832 5.0949 2.4018 0 0 0 +243 97 4 0.4238 4.215372213007002 2.2225202484567896 5.2803935587652235 0 0 0 +52 26 2 0 1.4708 7.6424 2.4018 0 0 0 +53 27 2 0 0 10.1898 2.4018 0 0 0 +60 30 2 0 4.4124 7.6424 2.4018 0 0 0 +61 31 2 0 2.9416 10.1898 2.4018 0 0 0 +68 34 2 0 7.354000000000001 7.6424 2.4018 0 0 0 +69 35 2 0 5.8832 10.1898 2.4018 0 0 0 +387 145 4 0.4238 5.821325736406644 4.80211316415021 5.03726935778638 0 0 0 +260 103 4 0.4238 4.266650899557808 6.124697675258705 6.600494419311919 0 0 0 +277 109 3 -0.8476 1.1595300211865478 9.226136831721583 5.6374387660682395 0 0 0 +422 157 4 0.4238 5.186379561937092 9.246331162340214 5.010378323358909 0 0 0 +278 109 4 0.4238 0.16509455550271238 9.324889581001292 5.600728087976438 0 0 0 +421 157 3 -0.8476 4.267061402816361 8.96456307950511 5.285080645137098 0 0 0 +372 140 4 0.4238 7.72049151444727 3.1081049977971733 5.624439615628745 0 0 0 +241 97 3 -0.8476 4.979583082691343 1.5807071976248444 5.344102790419773 0 0 0 +367 139 3 -0.8476 3.3292653199701174 3.842283776550616 5.301650818590438 0 0 0 +368 139 4 0.4238 3.684070197838302 4.776085383558861 5.2555059732229505 0 0 0 +369 139 4 0.4238 2.4614244393932903 3.790665660238261 4.807496843609001 0 0 0 +237 95 4 0.4238 0.8688372424570395 0.5637480725652825 15.837861037745109 0 0 0 +242 97 4 0.4238 5.838317925620407 2.08972820515595 5.4030316190296865 0 0 0 +244 98 3 -0.8476 3.06007349186706 3.3156446548102743 7.800821206312822 0 0 0 +245 98 4 0.4238 3.292495500569735 3.349267797972537 6.828787504752208 0 0 0 +246 98 4 0.4238 3.244639762451247 4.205236417313474 8.21862706780732 0 0 0 +357 135 4 0.4238 5.599931101613284 2.8266561120576155 8.823939192896898 0 0 0 +248 99 4 0.4238 4.69094628305157 1.7475560287256833 10.940028326694172 0 0 0 +355 135 3 -0.8476 6.1056692668831944 3.4565727858406277 8.234503978839392 0 0 0 +370 140 3 -0.8476 8.260944365686607 2.344956325089386 5.9787203639370485 0 0 0 +5 3 1 0 0 10.1898 21.4018 0 0 0 +115 55 3 -0.8476 0.6685955791423209 1.1406007302132561 5.285707584884053 0 0 0 +117 55 4 0.4238 0.8471253049325846 2.1223521279380155 5.351215251536808 0 0 0 +337 129 3 -0.8476 3.5673781090835357 0.1584650058169618 11.855592597757308 0 1 0 +423 157 4 0.4238 3.5925256519953384 9.568512539363969 4.86052578384893 0 0 0 +388 146 3 -0.8476 4.577545906676629 5.911730949363624 8.247639703277793 0 0 0 +371 140 4 0.4238 8.763880514062548 2.641297854555424 6.790654426306619 0 0 0 +389 146 4 0.4238 5.229395912055183 5.212412787511029 8.540975963214175 0 0 0 +498 182 4 0.4238 8.708572501204229 1.6439616819374039 8.893386862511662 0 0 0 +499 183 3 -0.8476 8.788151456935827 1.747387315190607 11.831408961401284 0 0 0 +356 135 4 0.4238 7.087379176847249 3.3036660348840203 8.347928594928105 0 0 0 +235 95 3 -0.8476 1.101376037954613 0.60797910815167 14.866280241985807 0 0 0 +338 129 4 0.4238 3.086322043066555 0.17977406211341077 10.979161321324465 0 1 0 +101 50 4 0.4238 2.3452088829773485 1.679109649521978 7.998572278214729 0 0 0 +102 50 4 0.4238 1.7396190746664724 0.7815651122817325 6.776156174616777 0 0 0 +264 104 4 0.4238 1.314649046187711 7.151850339115251 5.356458350291402 0 0 0 +261 103 4 0.4238 4.344863408391302 7.229373831864509 5.400411210770298 0 0 0 +385 145 3 -0.8476 6.530003789922046 4.200582924498773 5.405965238572253 0 0 0 +386 145 4 0.4238 6.338765403718886 4.011523164034656 6.369128936305808 0 0 0 +390 146 4 0.4238 4.287287022740962 6.4497527910965 9.039019879824611 0 0 0 +259 103 3 -0.8476 4.571078813074718 6.29125568333872 5.662634084209634 0 0 0 +289 113 3 -0.8476 4.563599041145234 10.086229905664549 15.478505257325894 0 0 0 +262 104 3 -0.8476 0.9505514460098017 6.233602776791171 5.200720279695964 0 0 0 +234 94 4 0.4238 4.252305918517927 1.5104772744979198 15.776671832358746 0 0 0 +280 110 3 -0.8476 1.4649156019387215 8.625787955794543 8.210124183091255 0 0 0 +282 110 4 0.4238 1.2707547191832915 8.813324944957127 7.247247535393375 0 0 0 +404 151 4 0.4238 7.729904936627753 8.547350043185194 4.926160208837444 0 0 0 +405 151 4 0.4238 7.2770516978143425 8.988822091523867 6.431700948049315 0 0 0 +406 152 3 -0.8476 6.948766849242647 7.673937623994841 7.644671158708728 0 0 0 +407 152 4 0.4238 6.525795796205249 7.732575312342498 8.54891509101289 0 0 0 +408 152 4 0.4238 6.276846030142793 7.340427836539666 6.983389418751862 0 0 0 +281 110 4 0.4238 2.4144110839464337 8.86628530860492 8.41166651398434 0 0 0 +20 10 1 0 7.354000000000001 7.6424 21.4018 0 0 0 +403 151 3 -0.8476 7.1864312239576424 9.196956401727144 5.457807169763902 0 0 0 +140 63 4 0.4238 0.4912611771674119 5.483308431151843 7.32949919291062 0 0 0 +285 111 4 0.4238 2.222990438980817 7.758768979093943 9.602927616521612 0 0 0 +409 153 3 -0.8476 5.935160755403179 7.784141671985828 10.24740953450964 0 0 0 +410 153 4 0.4238 4.93909044392348 7.872166125675881 10.23761068803176 0 0 0 +283 111 3 -0.8476 2.9298247024233324 7.37829634209124 10.199271578404066 0 0 0 +284 111 4 0.4238 2.726159641339314 7.613476216764882 11.149646102042892 0 0 0 +300 116 4 0.4238 4.275274919124041 9.222842133138407 7.0364892960604974 0 0 0 +512 187 4 0.4238 8.159095215967982 5.212728585270325 5.862691743711303 0 0 0 +298 116 3 -0.8476 4.190494283036901 9.481049160440392 7.998852108176557 0 0 0 +13 7 1 0 2.9416 10.1898 21.4018 0 0 0 +167 72 4 0.4238 0.6888402225915744 9.490941300073734 17.687956507725275 0 0 0 +429 159 4 0.4238 6.704370008541906 9.570813638495862 9.75268746894169 0 0 0 +108 52 4 0.4238 0.4307356664021716 1.1201849372165382 13.39567680690473 0 0 0 +12 6 1 0 4.4124 7.6424 21.4018 0 0 0 +247 99 3 -0.8476 4.798369931390891 2.717477731578589 10.72159669011324 0 0 0 +249 99 4 0.4238 5.569724797087956 3.0916316888033455 11.236399566632782 0 0 0 +267 105 4 0.4238 3.62546649656917 4.334166934495396 11.516982003845238 0 0 0 +150 66 4 0.4238 0.3228287181315222 5.899276873013697 16.725238911862725 0 0 0 +232 94 3 -0.8476 4.980041500359598 0.8346261397826029 15.659938276309026 0 0 0 +103 51 3 -0.8476 1.3815948057839214 1.9892393072986618 10.960941799077768 0 0 0 +105 51 4 0.4238 2.0221030524072807 2.7460833084547516 11.091083546320654 0 0 0 +250 100 3 -0.8476 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1 146 145 147 +174 1 704 703 705 +175 1 560 559 561 +176 1 599 598 600 +177 1 311 310 312 +178 1 140 139 141 +179 1 398 397 399 +180 1 320 319 321 +181 1 491 490 492 +182 1 371 370 372 +183 1 611 610 612 +184 1 155 154 156 +185 1 182 181 183 +186 1 629 628 630 +187 1 488 487 489 +188 1 527 526 528 +189 1 152 151 153 +190 1 161 160 162 +191 1 221 220 222 +192 1 350 349 351 +193 1 473 472 474 +194 1 287 286 288 +195 1 668 667 669 +196 1 233 232 234 +197 1 557 556 558 +198 1 614 613 615 +199 1 452 451 453 +200 1 428 427 429 +201 1 410 409 411 +202 1 674 673 675 +203 1 617 616 618 +204 1 530 529 531 +205 1 380 379 381 +206 1 659 658 660 +207 1 455 454 456 +208 1 176 175 177 +209 1 506 505 507 +210 1 164 163 165 diff --git a/examples/PACKAGES/electrode/piston/in.piston b/examples/PACKAGES/electrode/piston/in.piston new file mode 100644 index 0000000000..35b4790935 --- /dev/null +++ b/examples/PACKAGES/electrode/piston/in.piston @@ -0,0 +1,65 @@ +# The intention is to find the average position of one wall at atmospheric +# pressure. The output is the wall position over time which can be used to +# find the average position for a run with fixed wall position. +# +# ----------------- Init Section ----------------- + +atom_style full +units real +boundary p p f +kspace_style pppm/electrode 1e-4 +kspace_modify slab 3.0 +pair_style lj/cut/coul/long 8 8 +bond_style harmonic +angle_style harmonic +if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2" + +# ----------------- Atom Definition Section ----------------- + +read_data "data.piston" + +# ----------------- Settings Section ----------------- + +pair_coeff 1 1 0.069 2.78 +pair_coeff 2 2 5.29 2.951 +pair_coeff 3 3 0.1553 3.166 +pair_coeff 4 4 0.0 0.0 +bond_coeff 1 600.0 1.0 +angle_coeff 1 75.0 109.47 +group wall type 1 +group gold type 2 +group spce type 3:4 +group ele union wall gold +fix fRattleSPCE spce shake 0.0001 10 0 b 1 a 1 +pair_modify mix arithmetic + +# ----------------- Run Section ----------------- + +neigh_modify every 1 delay 0 +timestep 2 +fix fxnvt spce nvt temp 300 300 500 +fix fxforce_au gold setforce 0.0 0.0 0.0 + +# equilibrate z-coordinate of upper electrode while keeping the electrode rigid +fix fxforce_wa wall setforce 0.0 0.0 NULL +fix fxpressure wall aveforce 0 0 -0.005246 # atomspheric pressure: area/force->nktv2p +fix fxdrag wall viscous 100 +fix fxrigid wall rigid/nve single + +# maintain constant potential during equilibration +# 'algo cg' allows for moving electrodes +fix fxele ele electrode/conp 0.0 1.805 symm on algo cg 1e-4 + +# setup output and run +variable q atom q +compute qwa wall reduce sum v_q +compute qau gold reduce sum v_q +variable top_wall equal (bound(wall,zmin)) +compute temp_mobile spce temp +variable s equal step +fix fxprint all print 1000 "${s} ${top_wall}" file top_wall.csv screen no +thermo_style custom step c_temp_mobile c_qwa c_qau v_top_wall +thermo 5000 +run 100000 +write_data "data.piston.final" + diff --git a/examples/PACKAGES/electrode/piston/log.1Dec2022.piston.g++.1 b/examples/PACKAGES/electrode/piston/log.1Dec2022.piston.g++.1 new file mode 100644 index 0000000000..a5b6d4cd4f --- /dev/null +++ b/examples/PACKAGES/electrode/piston/log.1Dec2022.piston.g++.1 @@ -0,0 +1,223 @@ +LAMMPS (3 Nov 2022) +# The intention is to find the average position of one wall at atmospheric +# pressure. The output is the wall position over time which can be used to +# find the average position for a run with fixed wall position. +# +# ----------------- Init Section ----------------- + +atom_style full +units real +boundary p p f +kspace_style pppm/electrode 1e-4 +kspace_modify slab 3.0 +pair_style lj/cut/coul/long 8 8 +bond_style harmonic +angle_style harmonic +if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2" + +# ----------------- Atom Definition Section ----------------- + +read_data "data.piston" +Reading data file ... + orthogonal box = (0 0 0) to (17.6494 20.3798 26) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 726 atoms + reading velocities ... + 726 velocities + scanning bonds ... + 2 = max bonds/atom + scanning angles ... + 1 = max angles/atom + reading bonds ... + 420 bonds + reading angles ... + 210 angles +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.001 seconds + read_data CPU = 0.011 seconds + +# ----------------- Settings Section ----------------- + +pair_coeff 1 1 0.069 2.78 +pair_coeff 2 2 5.29 2.951 +pair_coeff 3 3 0.1553 3.166 +pair_coeff 4 4 0.0 0.0 +bond_coeff 1 600.0 1.0 +angle_coeff 1 75.0 109.47 +group wall type 1 +48 atoms in group wall +group gold type 2 +48 atoms in group gold +group spce type 3:4 +630 atoms in group spce +group ele union wall gold +96 atoms in group ele +fix fRattleSPCE spce shake 0.0001 10 0 b 1 a 1 +Finding SHAKE clusters ... + 0 = # of size 2 clusters + 0 = # of size 3 clusters + 0 = # of size 4 clusters + 210 = # of frozen angles + find clusters CPU = 0.000 seconds +pair_modify mix arithmetic + +# ----------------- Run Section ----------------- + +neigh_modify every 1 delay 0 +timestep 2 +fix fxnvt spce nvt temp 300 300 500 +fix fxforce_au gold setforce 0.0 0.0 0.0 + +# equilibrate z-coordinate of upper electrode while keeping the electrode rigid +fix fxforce_wa wall setforce 0.0 0.0 NULL +fix fxpressure wall aveforce 0 0 -0.005246 # atomspheric pressure: area/force->nktv2p +fix fxdrag wall viscous 100 +fix fxrigid wall rigid/nve single + 1 rigid bodies with 48 atoms + +# maintain constant potential during equilibration +# 'algo cg' allows for moving electrodes +fix fxele ele electrode/conp 0.0 1.805 symm on algo cg 1e-4 +96 atoms in group conp_group + +# setup output and run +variable q atom q +compute qwa wall reduce sum v_q +compute qau gold reduce sum v_q +variable top_wall equal (bound(wall,zmin)) +compute temp_mobile spce temp +variable s equal step +fix fxprint all print 1000 "${s} ${top_wall}" file top_wall.csv screen no +thermo_style custom step c_temp_mobile c_qwa c_qau v_top_wall +thermo 5000 +run 100000 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- kspace_style pppm/electrode command: + +@article{Ahrens2021, +author = {Ahrens-Iwers, Ludwig J.V. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0063381}, +title = {{Constant potential simulations on a mesh}}, +journal = {Journal of Chemical Physics}, +year = {2021} +volume = {155}, +pages = {104104}, +} +- fix electrode command: + +@article{Ahrens2022 +author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0099239}, +title = {{ELECTRODE: An electrochemistry package for LAMMPS}}, +journal = {The Journal of Chemical Physics}, +year = {2022} +volume = {157}, +pages = {084801}, +} +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +PPPM/electrode initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:342) + G vector (1/distance) = 0.32814871 + grid = 12 15 36 + stencil order = 5 + estimated absolute RMS force accuracy = 0.02930901 + estimated relative force accuracy = 8.8263214e-05 + using double precision MKL FFT + 3d grid and FFT values/proc = 15884 6480 +Generated 6 of 6 mixed pair_coeff terms from arithmetic mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 10 + ghost atom cutoff = 10 + binsize = 5, bins = 4 5 6 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair lj/cut/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard + (2) fix electrode/conp, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 11.7 | 11.7 | 11.7 Mbytes + Step c_temp_mobile c_qwa c_qau v_top_wall + 0 303.38967 -0.042963484 0.042963484 21.4018 + 5000 285.08828 -0.26105255 0.26105255 25.155629 + 10000 323.19176 -0.26264003 0.26264003 24.541676 + 15000 310.479 -0.27318148 0.27318148 23.141522 + 20000 295.18544 -0.11313444 0.11313444 23.828735 + 25000 295.38607 -0.25433086 0.25433086 23.673314 + 30000 288.0613 -0.30099901 0.30099901 23.438086 + 35000 278.5591 -0.15823576 0.15823576 24.311915 + 40000 303.95751 -0.19941381 0.19941381 23.69594 + 45000 279.026 -0.1659962 0.1659962 23.588604 + 50000 298.79278 -0.28866703 0.28866703 23.372508 + 55000 301.03353 -0.078370381 0.078370381 23.192985 + 60000 306.77965 -0.12807205 0.12807205 23.968574 + 65000 309.86008 -0.27162663 0.27162663 23.616704 + 70000 287.31116 -0.029751882 0.029751882 23.667495 + 75000 312.48654 -0.10759866 0.10759866 23.504105 + 80000 309.94267 -0.2558548 0.2558548 23.810576 + 85000 328.04389 -0.1575471 0.1575471 24.013437 + 90000 302.9806 -0.032002164 0.032002164 24.264432 + 95000 294.20804 -0.27797238 0.27797238 23.291758 + 100000 307.63019 -0.19047448 0.19047448 23.632147 +Loop time of 530.844 on 1 procs for 100000 steps with 726 atoms + +Performance: 32.552 ns/day, 0.737 hours/ns, 188.379 timesteps/s, 136.763 katom-step/s +100.0% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 190.47 | 190.47 | 190.47 | 0.0 | 35.88 +Bond | 0.10754 | 0.10754 | 0.10754 | 0.0 | 0.02 +Kspace | 73.179 | 73.179 | 73.179 | 0.0 | 13.79 +Neigh | 24.209 | 24.209 | 24.209 | 0.0 | 4.56 +Comm | 1.6857 | 1.6857 | 1.6857 | 0.0 | 0.32 +Output | 0.0016861 | 0.0016861 | 0.0016861 | 0.0 | 0.00 +Modify | 240.23 | 240.23 | 240.23 | 0.0 | 45.26 +Other | | 0.9595 | | | 0.18 + +Nlocal: 726 ave 726 max 726 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 2335 ave 2335 max 2335 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 120271 ave 120271 max 120271 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 120271 +Ave neighs/atom = 165.66253 +Ave special neighs/atom = 1.7355372 +Neighbor list builds = 7722 +Dangerous builds = 0 +write_data "data.piston.final" +System init for write_data ... +PPPM/electrode initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:342) + G vector (1/distance) = 0.32814871 + grid = 12 15 36 + stencil order = 5 + estimated absolute RMS force accuracy = 0.029311365 + estimated relative force accuracy = 8.8270304e-05 + using double precision MKL FFT + 3d grid and FFT values/proc = 15884 6480 +Generated 6 of 6 mixed pair_coeff terms from arithmetic mixing rule + +Average conjugate gradient steps: 1.981 +Total wall time: 0:08:50 diff --git a/examples/PACKAGES/electrode/piston/log.1Dec2022.piston.g++.4 b/examples/PACKAGES/electrode/piston/log.1Dec2022.piston.g++.4 new file mode 100644 index 0000000000..ffb6bcc61c --- /dev/null +++ b/examples/PACKAGES/electrode/piston/log.1Dec2022.piston.g++.4 @@ -0,0 +1,224 @@ +LAMMPS (3 Nov 2022) +# The intention is to find the average position of one wall at atmospheric +# pressure. The output is the wall position over time which can be used to +# find the average position for a run with fixed wall position. +# +# ----------------- Init Section ----------------- + +atom_style full +units real +boundary p p f +kspace_style pppm/electrode 1e-4 +kspace_modify slab 3.0 +pair_style lj/cut/coul/long 8 8 +bond_style harmonic +angle_style harmonic +if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2" +processors * * 2 + +# ----------------- Atom Definition Section ----------------- + +read_data "data.piston" +Reading data file ... + orthogonal box = (0 0 0) to (17.6494 20.3798 26) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 726 atoms + reading velocities ... + 726 velocities + scanning bonds ... + 2 = max bonds/atom + scanning angles ... + 1 = max angles/atom + reading bonds ... + 420 bonds + reading angles ... + 210 angles +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.001 seconds + read_data CPU = 0.017 seconds + +# ----------------- Settings Section ----------------- + +pair_coeff 1 1 0.069 2.78 +pair_coeff 2 2 5.29 2.951 +pair_coeff 3 3 0.1553 3.166 +pair_coeff 4 4 0.0 0.0 +bond_coeff 1 600.0 1.0 +angle_coeff 1 75.0 109.47 +group wall type 1 +48 atoms in group wall +group gold type 2 +48 atoms in group gold +group spce type 3:4 +630 atoms in group spce +group ele union wall gold +96 atoms in group ele +fix fRattleSPCE spce shake 0.0001 10 0 b 1 a 1 +Finding SHAKE clusters ... + 0 = # of size 2 clusters + 0 = # of size 3 clusters + 0 = # of size 4 clusters + 210 = # of frozen angles + find clusters CPU = 0.002 seconds +pair_modify mix arithmetic + +# ----------------- Run Section ----------------- + +neigh_modify every 1 delay 0 +timestep 2 +fix fxnvt spce nvt temp 300 300 500 +fix fxforce_au gold setforce 0.0 0.0 0.0 + +# equilibrate z-coordinate of upper electrode while keeping the electrode rigid +fix fxforce_wa wall setforce 0.0 0.0 NULL +fix fxpressure wall aveforce 0 0 -0.005246 # atomspheric pressure: area/force->nktv2p +fix fxdrag wall viscous 100 +fix fxrigid wall rigid/nve single + 1 rigid bodies with 48 atoms + +# maintain constant potential during equilibration +# 'algo cg' allows for moving electrodes +fix fxele ele electrode/conp 0.0 1.805 symm on algo cg 1e-4 +96 atoms in group conp_group + +# setup output and run +variable q atom q +compute qwa wall reduce sum v_q +compute qau gold reduce sum v_q +variable top_wall equal (bound(wall,zmin)) +compute temp_mobile spce temp +variable s equal step +fix fxprint all print 1000 "${s} ${top_wall}" file top_wall.csv screen no +thermo_style custom step c_temp_mobile c_qwa c_qau v_top_wall +thermo 5000 +run 100000 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- kspace_style pppm/electrode command: + +@article{Ahrens2021, +author = {Ahrens-Iwers, Ludwig J.V. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0063381}, +title = {{Constant potential simulations on a mesh}}, +journal = {Journal of Chemical Physics}, +year = {2021} +volume = {155}, +pages = {104104}, +} +- fix electrode command: + +@article{Ahrens2022 +author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0099239}, +title = {{ELECTRODE: An electrochemistry package for LAMMPS}}, +journal = {The Journal of Chemical Physics}, +year = {2022} +volume = {157}, +pages = {084801}, +} +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +PPPM/electrode initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:342) + G vector (1/distance) = 0.32814871 + grid = 12 15 36 + stencil order = 5 + estimated absolute RMS force accuracy = 0.02930901 + estimated relative force accuracy = 8.8263214e-05 + using double precision MKL FFT + 3d grid and FFT values/proc = 8512 2880 +Generated 6 of 6 mixed pair_coeff terms from arithmetic mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 10 + ghost atom cutoff = 10 + binsize = 5, bins = 4 5 6 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair lj/cut/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard + (2) fix electrode/conp, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 10.06 | 10.22 | 10.41 Mbytes + Step c_temp_mobile c_qwa c_qau v_top_wall + 0 303.38967 -0.042963484 0.042963484 21.4018 + 5000 292.03027 -0.19040435 0.19040435 24.581338 + 10000 309.52764 -0.48308301 0.48308301 23.776985 + 15000 295.00243 -0.16591109 0.16591109 23.672038 + 20000 293.5536 -0.086669084 0.086669084 23.426455 + 25000 303.0079 -0.16488112 0.16488112 23.862966 + 30000 306.31463 -0.23192653 0.23192653 23.819882 + 35000 303.66268 -0.2317907 0.2317907 23.495344 + 40000 301.39435 -0.34661329 0.34661329 23.657835 + 45000 291.61205 -0.30539427 0.30539427 23.437303 + 50000 298.65319 -0.096107034 0.096107034 23.57809 + 55000 282.65069 -0.14943539 0.14943539 23.823728 + 60000 310.64182 -0.17418813 0.17418813 23.286959 + 65000 308.47141 -0.02075662 0.02075662 23.91313 + 70000 292.5186 -0.080163162 0.080163162 23.96283 + 75000 270.13928 -0.029528648 0.029528648 23.488972 + 80000 322.10914 0.030761045 -0.030761045 23.47592 + 85000 310.60347 -0.24069996 0.24069996 23.987091 + 90000 294.35695 -0.070458235 0.070458235 23.397929 + 95000 308.69043 -0.2652581 0.2652581 23.473813 + 100000 318.71883 0.024035956 -0.024035956 23.449863 +Loop time of 590.232 on 4 procs for 100000 steps with 726 atoms + +Performance: 29.277 ns/day, 0.820 hours/ns, 169.425 timesteps/s, 123.003 katom-step/s +72.5% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 57.391 | 75.867 | 96.292 | 212.1 | 12.85 +Bond | 0.10177 | 0.11042 | 0.12415 | 2.7 | 0.02 +Kspace | 102.79 | 123.16 | 141.5 | 165.7 | 20.87 +Neigh | 12.808 | 12.895 | 12.982 | 2.3 | 2.18 +Comm | 18.885 | 19.973 | 21.064 | 24.0 | 3.38 +Output | 0.0022573 | 0.0022749 | 0.0023225 | 0.1 | 0.00 +Modify | 355.89 | 356.74 | 357.61 | 4.2 | 60.44 +Other | | 1.478 | | | 0.25 + +Nlocal: 181.5 ave 207 max 169 min +Histogram: 2 0 1 0 0 0 0 0 0 1 +Nghost: 1961.5 ave 1984 max 1926 min +Histogram: 1 0 0 0 0 0 1 0 1 1 +Neighs: 30051 ave 41646 max 20775 min +Histogram: 1 1 0 0 0 0 1 0 0 1 + +Total # of neighbors = 120204 +Ave neighs/atom = 165.57025 +Ave special neighs/atom = 1.7355372 +Neighbor list builds = 7663 +Dangerous builds = 0 +write_data "data.piston.final" +System init for write_data ... +PPPM/electrode initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:342) + G vector (1/distance) = 0.32814871 + grid = 12 15 36 + stencil order = 5 + estimated absolute RMS force accuracy = 0.029311028 + estimated relative force accuracy = 8.8269289e-05 + using double precision MKL FFT + 3d grid and FFT values/proc = 8512 2880 +Generated 6 of 6 mixed pair_coeff terms from arithmetic mixing rule + +Average conjugate gradient steps: 1.982 +Total wall time: 0:09:50 diff --git a/examples/PACKAGES/electrode/planar/log.26Apr2022.planar-ewald-ew2d.g++.1 b/examples/PACKAGES/electrode/planar/log.1Dec2022.planar-ewald-ew2d.g++.1 similarity index 76% rename from examples/PACKAGES/electrode/planar/log.26Apr2022.planar-ewald-ew2d.g++.1 rename to examples/PACKAGES/electrode/planar/log.1Dec2022.planar-ewald-ew2d.g++.1 index b01114e64c..bc2cf5b1e3 100644 --- a/examples/PACKAGES/electrode/planar/log.26Apr2022.planar-ewald-ew2d.g++.1 +++ b/examples/PACKAGES/electrode/planar/log.1Dec2022.planar-ewald-ew2d.g++.1 @@ -1,4 +1,4 @@ -LAMMPS (24 Mar 2022) +LAMMPS (3 Nov 2022) boundary p p f kspace_style ewald/electrode 1.0e-7 kspace_modify slab ew2d @@ -28,8 +28,8 @@ Finding 1-2 1-3 1-4 neighbors ... 0 = max # of 1-3 neighbors 0 = max # of 1-4 neighbors 1 = max # of special neighbors - special bonds CPU = 0.000 seconds - read_data CPU = 0.006 seconds + special bonds CPU = 0.001 seconds + read_data CPU = 0.005 seconds group bot molecule 1 144 atoms in group bot @@ -67,6 +67,24 @@ thermo 1 thermo_style custom step v_v c_qbot c_qtop v_qtheory v_percdev run 10 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- fix electrode command: + +@article{Ahrens2022 +author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0099239}, +title = {{ELECTRODE: An electrochemistry package for LAMMPS}}, +journal = {The Journal of Chemical Physics}, +year = {2022} +volume = {157}, +pages = {084801}, +} +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) Ewald/electrode initialization ... WARNING: System is not charge neutral, net charge = 0.000219 (src/kspace.cpp:327) @@ -76,9 +94,9 @@ WARNING: System is not charge neutral, net charge = 0.000219 (src/kspace.cpp:327 estimated relative force accuracy = 1.2145309e-07 KSpace vectors: actual max1d max3d = 90 5 665 kxmax kymax kzmax = 3 3 5 - generated 1 of 1 mixed pair_coeff terms from geometric mixing rule +Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... - update every 1 steps, delay 10 steps, check yes + update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 16 ghost atom cutoff = 16 @@ -94,7 +112,7 @@ Neighbor list info ... pair build: copy stencil: none bin: none -Per MPI rank memory allocation (min/avg/max) = 15.93 | 15.93 | 15.93 Mbytes +Per MPI rank memory allocation (min/avg/max) = 15.94 | 15.94 | 15.94 Mbytes Step v_v c_qbot c_qtop v_qtheory v_percdev 0 0 0 0 0 0 1 0.2 -0.030920491 0.030920491 0.031376826 -1.4543703 @@ -107,22 +125,22 @@ Per MPI rank memory allocation (min/avg/max) = 15.93 | 15.93 | 15.93 Mbytes 8 1.6 -0.24736393 0.24736393 0.25101461 -1.4543704 9 1.8 -0.27828442 0.27828442 0.28239144 -1.4543704 10 2 -0.30920491 0.30920491 0.31376826 -1.4543704 -Loop time of 0.0912872 on 1 procs for 10 steps with 288 atoms +Loop time of 0.0451804 on 1 procs for 10 steps with 288 atoms -Performance: 9.465 ns/day, 2.536 hours/ns, 109.544 timesteps/s -400.1% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 19.123 ns/day, 1.255 hours/ns, 221.335 timesteps/s, 63.744 katom-step/s +100.0% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.0086713 | 0.0086713 | 0.0086713 | 0.0 | 9.50 -Bond | 3.759e-06 | 3.759e-06 | 3.759e-06 | 0.0 | 0.00 -Kspace | 0.04575 | 0.04575 | 0.04575 | 0.0 | 50.12 +Pair | 0.0046814 | 0.0046814 | 0.0046814 | 0.0 | 10.36 +Bond | 1.293e-06 | 1.293e-06 | 1.293e-06 | 0.0 | 0.00 +Kspace | 0.028302 | 0.028302 | 0.028302 | 0.0 | 62.64 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.00018224 | 0.00018224 | 0.00018224 | 0.0 | 0.20 -Output | 0.0027569 | 0.0027569 | 0.0027569 | 0.0 | 3.02 -Modify | 0.03386 | 0.03386 | 0.03386 | 0.0 | 37.09 -Other | | 6.314e-05 | | | 0.07 +Comm | 7.3611e-05 | 7.3611e-05 | 7.3611e-05 | 0.0 | 0.16 +Output | 0.001128 | 0.001128 | 0.001128 | 0.0 | 2.50 +Modify | 0.010919 | 0.010919 | 0.010919 | 0.0 | 24.17 +Other | | 7.567e-05 | | | 0.17 Nlocal: 288 ave 288 max 288 min Histogram: 1 0 0 0 0 0 0 0 0 0 diff --git a/examples/PACKAGES/electrode/planar/log.26Apr2022.planar-ewald-ew2d.g++.4 b/examples/PACKAGES/electrode/planar/log.1Dec2022.planar-ewald-ew2d.g++.4 similarity index 76% rename from examples/PACKAGES/electrode/planar/log.26Apr2022.planar-ewald-ew2d.g++.4 rename to examples/PACKAGES/electrode/planar/log.1Dec2022.planar-ewald-ew2d.g++.4 index 29a0d660a1..b5243e747c 100644 --- a/examples/PACKAGES/electrode/planar/log.26Apr2022.planar-ewald-ew2d.g++.4 +++ b/examples/PACKAGES/electrode/planar/log.1Dec2022.planar-ewald-ew2d.g++.4 @@ -1,4 +1,4 @@ -LAMMPS (24 Mar 2022) +LAMMPS (3 Nov 2022) boundary p p f kspace_style ewald/electrode 1.0e-7 kspace_modify slab ew2d @@ -29,8 +29,8 @@ Finding 1-2 1-3 1-4 neighbors ... 0 = max # of 1-3 neighbors 0 = max # of 1-4 neighbors 1 = max # of special neighbors - special bonds CPU = 0.001 seconds - read_data CPU = 0.008 seconds + special bonds CPU = 0.003 seconds + read_data CPU = 0.009 seconds group bot molecule 1 144 atoms in group bot @@ -68,6 +68,24 @@ thermo 1 thermo_style custom step v_v c_qbot c_qtop v_qtheory v_percdev run 10 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- fix electrode command: + +@article{Ahrens2022 +author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0099239}, +title = {{ELECTRODE: An electrochemistry package for LAMMPS}}, +journal = {The Journal of Chemical Physics}, +year = {2022} +volume = {157}, +pages = {084801}, +} +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) Ewald/electrode initialization ... WARNING: System is not charge neutral, net charge = 0.000219 (src/kspace.cpp:327) @@ -77,9 +95,9 @@ WARNING: System is not charge neutral, net charge = 0.000219 (src/kspace.cpp:327 estimated relative force accuracy = 1.2145309e-07 KSpace vectors: actual max1d max3d = 90 5 665 kxmax kymax kzmax = 3 3 5 - generated 1 of 1 mixed pair_coeff terms from geometric mixing rule +Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... - update every 1 steps, delay 10 steps, check yes + update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 16 ghost atom cutoff = 16 @@ -95,7 +113,7 @@ Neighbor list info ... pair build: copy stencil: none bin: none -Per MPI rank memory allocation (min/avg/max) = 15.96 | 15.96 | 15.96 Mbytes +Per MPI rank memory allocation (min/avg/max) = 15.97 | 15.97 | 15.97 Mbytes Step v_v c_qbot c_qtop v_qtheory v_percdev 0 0 0 0 0 0 1 0.2 -0.030920491 0.030920491 0.031376826 -1.4543703 @@ -108,22 +126,22 @@ Per MPI rank memory allocation (min/avg/max) = 15.96 | 15.96 | 15.96 Mbytes 8 1.6 -0.24736393 0.24736393 0.25101461 -1.4543704 9 1.8 -0.27828442 0.27828442 0.28239144 -1.4543704 10 2 -0.30920491 0.30920491 0.31376826 -1.4543704 -Loop time of 0.0456609 on 4 procs for 10 steps with 288 atoms +Loop time of 0.022489 on 4 procs for 10 steps with 288 atoms -Performance: 18.922 ns/day, 1.268 hours/ns, 219.006 timesteps/s -86.7% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 38.419 ns/day, 0.625 hours/ns, 444.661 timesteps/s, 128.062 katom-step/s +91.6% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.0019389 | 0.0024013 | 0.0030807 | 0.9 | 5.26 -Bond | 1.493e-06 | 1.7132e-06 | 1.935e-06 | 0.0 | 0.00 -Kspace | 0.016165 | 0.016695 | 0.017072 | 0.3 | 36.56 +Pair | 0.0011688 | 0.0013694 | 0.0016077 | 0.4 | 6.09 +Bond | 6.72e-07 | 7.59e-07 | 9.02e-07 | 0.0 | 0.00 +Kspace | 0.0077542 | 0.0093901 | 0.010384 | 1.0 | 41.75 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.0030891 | 0.0037595 | 0.0040145 | 0.6 | 8.23 -Output | 0.0024177 | 0.0027885 | 0.0037099 | 1.0 | 6.11 -Modify | 0.01944 | 0.019746 | 0.020327 | 0.2 | 43.24 -Other | | 0.0002691 | | | 0.59 +Comm | 0.0015392 | 0.0016945 | 0.00183 | 0.3 | 7.53 +Output | 0.00084374 | 0.0010929 | 0.0015437 | 0.8 | 4.86 +Modify | 0.007495 | 0.0084669 | 0.010081 | 1.1 | 37.65 +Other | | 0.0004745 | | | 2.11 Nlocal: 72 ave 72 max 72 min Histogram: 4 0 0 0 0 0 0 0 0 0 diff --git a/examples/PACKAGES/electrode/planar/log.26Apr2022.planar-ewald-ew3dc.g++.1 b/examples/PACKAGES/electrode/planar/log.1Dec2022.planar-ewald-ew3dc.g++.1 similarity index 76% rename from examples/PACKAGES/electrode/planar/log.26Apr2022.planar-ewald-ew3dc.g++.1 rename to examples/PACKAGES/electrode/planar/log.1Dec2022.planar-ewald-ew3dc.g++.1 index d5292ad6ef..bebd5aed4a 100644 --- a/examples/PACKAGES/electrode/planar/log.26Apr2022.planar-ewald-ew3dc.g++.1 +++ b/examples/PACKAGES/electrode/planar/log.1Dec2022.planar-ewald-ew3dc.g++.1 @@ -1,4 +1,4 @@ -LAMMPS (24 Mar 2022) +LAMMPS (3 Nov 2022) boundary p p f kspace_style ewald/electrode 1.0e-7 kspace_modify slab 3.0 # ew3dc @@ -28,8 +28,8 @@ Finding 1-2 1-3 1-4 neighbors ... 0 = max # of 1-3 neighbors 0 = max # of 1-4 neighbors 1 = max # of special neighbors - special bonds CPU = 0.000 seconds - read_data CPU = 0.007 seconds + special bonds CPU = 0.001 seconds + read_data CPU = 0.004 seconds group bot molecule 1 144 atoms in group bot @@ -67,6 +67,24 @@ thermo 1 thermo_style custom step v_v c_qbot c_qtop v_qtheory v_percdev run 10 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- fix electrode command: + +@article{Ahrens2022 +author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0099239}, +title = {{ELECTRODE: An electrochemistry package for LAMMPS}}, +journal = {The Journal of Chemical Physics}, +year = {2022} +volume = {157}, +pages = {084801}, +} +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) Ewald/electrode initialization ... WARNING: System is not charge neutral, net charge = 0.000219 (src/kspace.cpp:327) @@ -76,9 +94,9 @@ WARNING: System is not charge neutral, net charge = 0.000219 (src/kspace.cpp:327 estimated relative force accuracy = 9.3919471e-08 KSpace vectors: actual max1d max3d = 266 12 7812 kxmax kymax kzmax = 3 3 12 - generated 1 of 1 mixed pair_coeff terms from geometric mixing rule +Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... - update every 1 steps, delay 10 steps, check yes + update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 16 ghost atom cutoff = 16 @@ -94,7 +112,7 @@ Neighbor list info ... pair build: copy stencil: none bin: none -Per MPI rank memory allocation (min/avg/max) = 27.27 | 27.27 | 27.27 Mbytes +Per MPI rank memory allocation (min/avg/max) = 27.29 | 27.29 | 27.29 Mbytes Step v_v c_qbot c_qtop v_qtheory v_percdev 0 0 0 0 0 0 1 0.2 -0.030925182 0.030925182 0.031376826 -1.4394194 @@ -107,22 +125,22 @@ Per MPI rank memory allocation (min/avg/max) = 27.27 | 27.27 | 27.27 Mbytes 8 1.6 -0.24740146 0.24740146 0.25101461 -1.4394195 9 1.8 -0.27832664 0.27832664 0.28239144 -1.4394195 10 2 -0.30925182 0.30925182 0.31376826 -1.4394195 -Loop time of 0.0672288 on 1 procs for 10 steps with 288 atoms +Loop time of 0.0243868 on 1 procs for 10 steps with 288 atoms -Performance: 12.852 ns/day, 1.867 hours/ns, 148.746 timesteps/s -400.4% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 35.429 ns/day, 0.677 hours/ns, 410.058 timesteps/s, 118.097 katom-step/s +100.0% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.0071442 | 0.0071442 | 0.0071442 | 0.0 | 10.63 -Bond | 2.976e-06 | 2.976e-06 | 2.976e-06 | 0.0 | 0.00 -Kspace | 0.0097903 | 0.0097903 | 0.0097903 | 0.0 | 14.56 +Pair | 0.0041504 | 0.0041504 | 0.0041504 | 0.0 | 17.02 +Bond | 8.92e-07 | 8.92e-07 | 8.92e-07 | 0.0 | 0.00 +Kspace | 0.0046942 | 0.0046942 | 0.0046942 | 0.0 | 19.25 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.00023514 | 0.00023514 | 0.00023514 | 0.0 | 0.35 -Output | 0.0029795 | 0.0029795 | 0.0029795 | 0.0 | 4.43 -Modify | 0.047009 | 0.047009 | 0.047009 | 0.0 | 69.92 -Other | | 6.809e-05 | | | 0.10 +Comm | 6.7942e-05 | 6.7942e-05 | 6.7942e-05 | 0.0 | 0.28 +Output | 0.0010799 | 0.0010799 | 0.0010799 | 0.0 | 4.43 +Modify | 0.014311 | 0.014311 | 0.014311 | 0.0 | 58.69 +Other | | 8.199e-05 | | | 0.34 Nlocal: 288 ave 288 max 288 min Histogram: 1 0 0 0 0 0 0 0 0 0 diff --git a/examples/PACKAGES/electrode/planar/log.26Apr2022.planar-ewald-ew3dc.g++.4 b/examples/PACKAGES/electrode/planar/log.1Dec2022.planar-ewald-ew3dc.g++.4 similarity index 76% rename from examples/PACKAGES/electrode/planar/log.26Apr2022.planar-ewald-ew3dc.g++.4 rename to examples/PACKAGES/electrode/planar/log.1Dec2022.planar-ewald-ew3dc.g++.4 index 92c5bf3cea..9899edc256 100644 --- a/examples/PACKAGES/electrode/planar/log.26Apr2022.planar-ewald-ew3dc.g++.4 +++ b/examples/PACKAGES/electrode/planar/log.1Dec2022.planar-ewald-ew3dc.g++.4 @@ -1,4 +1,4 @@ -LAMMPS (24 Mar 2022) +LAMMPS (3 Nov 2022) boundary p p f kspace_style ewald/electrode 1.0e-7 kspace_modify slab 3.0 # ew3dc @@ -29,8 +29,8 @@ Finding 1-2 1-3 1-4 neighbors ... 0 = max # of 1-3 neighbors 0 = max # of 1-4 neighbors 1 = max # of special neighbors - special bonds CPU = 0.008 seconds - read_data CPU = 0.123 seconds + special bonds CPU = 0.003 seconds + read_data CPU = 0.007 seconds group bot molecule 1 144 atoms in group bot @@ -68,6 +68,24 @@ thermo 1 thermo_style custom step v_v c_qbot c_qtop v_qtheory v_percdev run 10 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- fix electrode command: + +@article{Ahrens2022 +author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0099239}, +title = {{ELECTRODE: An electrochemistry package for LAMMPS}}, +journal = {The Journal of Chemical Physics}, +year = {2022} +volume = {157}, +pages = {084801}, +} +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) Ewald/electrode initialization ... WARNING: System is not charge neutral, net charge = 0.000219 (src/kspace.cpp:327) @@ -77,9 +95,9 @@ WARNING: System is not charge neutral, net charge = 0.000219 (src/kspace.cpp:327 estimated relative force accuracy = 9.3919471e-08 KSpace vectors: actual max1d max3d = 266 12 7812 kxmax kymax kzmax = 3 3 12 - generated 1 of 1 mixed pair_coeff terms from geometric mixing rule +Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... - update every 1 steps, delay 10 steps, check yes + update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 16 ghost atom cutoff = 16 @@ -95,7 +113,7 @@ Neighbor list info ... pair build: copy stencil: none bin: none -Per MPI rank memory allocation (min/avg/max) = 27.31 | 27.31 | 27.31 Mbytes +Per MPI rank memory allocation (min/avg/max) = 27.32 | 27.32 | 27.32 Mbytes Step v_v c_qbot c_qtop v_qtheory v_percdev 0 0 0 0 0 0 1 0.2 -0.030925182 0.030925182 0.031376826 -1.4394194 @@ -108,22 +126,22 @@ Per MPI rank memory allocation (min/avg/max) = 27.31 | 27.31 | 27.31 Mbytes 8 1.6 -0.24740146 0.24740146 0.25101461 -1.4394195 9 1.8 -0.27832664 0.27832664 0.28239144 -1.4394195 10 2 -0.30925182 0.30925182 0.31376826 -1.4394195 -Loop time of 0.0459561 on 4 procs for 10 steps with 288 atoms +Loop time of 0.0200123 on 4 procs for 10 steps with 288 atoms -Performance: 18.801 ns/day, 1.277 hours/ns, 217.599 timesteps/s -95.8% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 43.173 ns/day, 0.556 hours/ns, 499.692 timesteps/s, 143.911 katom-step/s +90.2% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.0021527 | 0.0026891 | 0.0037845 | 1.3 | 5.85 -Bond | 1.303e-06 | 1.9462e-06 | 3.206e-06 | 0.0 | 0.00 -Kspace | 0.0066254 | 0.0077509 | 0.0083577 | 0.8 | 16.87 +Pair | 0.0014059 | 0.0015013 | 0.0015856 | 0.2 | 7.50 +Bond | 7.12e-07 | 8.9675e-07 | 1.19e-06 | 0.0 | 0.00 +Kspace | 0.0036091 | 0.0037586 | 0.0039024 | 0.2 | 18.78 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.00285 | 0.0057275 | 0.0067088 | 2.2 | 12.46 -Output | 0.0024325 | 0.0034682 | 0.0065316 | 3.0 | 7.55 -Modify | 0.025911 | 0.025969 | 0.026007 | 0.0 | 56.51 -Other | | 0.0003494 | | | 0.76 +Comm | 0.0017095 | 0.0017404 | 0.001775 | 0.1 | 8.70 +Output | 0.00092975 | 0.0010846 | 0.0015398 | 0.8 | 5.42 +Modify | 0.011292 | 0.011375 | 0.011438 | 0.1 | 56.84 +Other | | 0.0005509 | | | 2.75 Nlocal: 72 ave 72 max 72 min Histogram: 4 0 0 0 0 0 0 0 0 0 diff --git a/examples/PACKAGES/electrode/planar/log.26Apr2022.planar-ewald-ffield.g++.1 b/examples/PACKAGES/electrode/planar/log.1Dec2022.planar-ewald-ffield.g++.1 similarity index 77% rename from examples/PACKAGES/electrode/planar/log.26Apr2022.planar-ewald-ffield.g++.1 rename to examples/PACKAGES/electrode/planar/log.1Dec2022.planar-ewald-ffield.g++.1 index b0172323a3..3ea9920c7c 100644 --- a/examples/PACKAGES/electrode/planar/log.26Apr2022.planar-ewald-ffield.g++.1 +++ b/examples/PACKAGES/electrode/planar/log.1Dec2022.planar-ewald-ffield.g++.1 @@ -1,4 +1,4 @@ -LAMMPS (24 Mar 2022) +LAMMPS (3 Nov 2022) boundary p p p # finite field, fully periodic kspace_style ewald/electrode 1.0e-7 @@ -28,7 +28,7 @@ Finding 1-2 1-3 1-4 neighbors ... 0 = max # of 1-4 neighbors 1 = max # of special neighbors special bonds CPU = 0.001 seconds - read_data CPU = 0.010 seconds + read_data CPU = 0.004 seconds group bot molecule 1 144 atoms in group bot @@ -66,6 +66,24 @@ thermo 1 thermo_style custom step v_v c_qbot c_qtop v_qtheory v_percdev run 10 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- fix electrode command: + +@article{Ahrens2022 +author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0099239}, +title = {{ELECTRODE: An electrochemistry package for LAMMPS}}, +journal = {The Journal of Chemical Physics}, +year = {2022} +volume = {157}, +pages = {084801}, +} +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) Ewald/electrode initialization ... WARNING: System is not charge neutral, net charge = 0.000219 (src/kspace.cpp:327) @@ -75,9 +93,9 @@ WARNING: System is not charge neutral, net charge = 0.000219 (src/kspace.cpp:327 estimated relative force accuracy = 1.2145309e-07 KSpace vectors: actual max1d max3d = 95 5 665 kxmax kymax kzmax = 3 3 5 - generated 1 of 1 mixed pair_coeff terms from geometric mixing rule +Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... - update every 1 steps, delay 10 steps, check yes + update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 16 ghost atom cutoff = 16 @@ -93,7 +111,7 @@ Neighbor list info ... pair build: copy stencil: none bin: none -Per MPI rank memory allocation (min/avg/max) = 16.01 | 16.01 | 16.01 Mbytes +Per MPI rank memory allocation (min/avg/max) = 16.02 | 16.02 | 16.02 Mbytes Step v_v c_qbot c_qtop v_qtheory v_percdev 0 0 0 0 0 0 1 0.2 -0.030908718 0.030908718 0.031376826 -1.491893 @@ -106,22 +124,22 @@ Per MPI rank memory allocation (min/avg/max) = 16.01 | 16.01 | 16.01 Mbytes 8 1.6 -0.24726974 0.24726974 0.25101461 -1.491893 9 1.8 -0.27817846 0.27817846 0.28239144 -1.491893 10 2 -0.30908718 0.30908718 0.31376826 -1.491893 -Loop time of 0.0481838 on 1 procs for 10 steps with 288 atoms +Loop time of 0.0147727 on 1 procs for 10 steps with 288 atoms -Performance: 17.931 ns/day, 1.338 hours/ns, 207.539 timesteps/s -390.7% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 58.486 ns/day, 0.410 hours/ns, 676.926 timesteps/s, 194.955 katom-step/s +75.1% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.0071719 | 0.0071719 | 0.0071719 | 0.0 | 14.88 -Bond | 2.946e-06 | 2.946e-06 | 2.946e-06 | 0.0 | 0.01 -Kspace | 0.0038758 | 0.0038758 | 0.0038758 | 0.0 | 8.04 +Pair | 0.0035163 | 0.0035163 | 0.0035163 | 0.0 | 23.80 +Bond | 9.61e-07 | 9.61e-07 | 9.61e-07 | 0.0 | 0.01 +Kspace | 0.0018156 | 0.0018156 | 0.0018156 | 0.0 | 12.29 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.00053561 | 0.00053561 | 0.00053561 | 0.0 | 1.11 -Output | 0.0025385 | 0.0025385 | 0.0025385 | 0.0 | 5.27 -Modify | 0.033951 | 0.033951 | 0.033951 | 0.0 | 70.46 -Other | | 0.0001075 | | | 0.22 +Comm | 0.00012717 | 0.00012717 | 0.00012717 | 0.0 | 0.86 +Output | 0.00083495 | 0.00083495 | 0.00083495 | 0.0 | 5.65 +Modify | 0.0083949 | 0.0083949 | 0.0083949 | 0.0 | 56.83 +Other | | 8.273e-05 | | | 0.56 Nlocal: 288 ave 288 max 288 min Histogram: 1 0 0 0 0 0 0 0 0 0 diff --git a/examples/PACKAGES/electrode/planar/log.26Apr2022.planar-ewald-ffield.g++.4 b/examples/PACKAGES/electrode/planar/log.1Dec2022.planar-ewald-ffield.g++.4 similarity index 76% rename from examples/PACKAGES/electrode/planar/log.26Apr2022.planar-ewald-ffield.g++.4 rename to examples/PACKAGES/electrode/planar/log.1Dec2022.planar-ewald-ffield.g++.4 index b1ee1bec45..ef9c212755 100644 --- a/examples/PACKAGES/electrode/planar/log.26Apr2022.planar-ewald-ffield.g++.4 +++ b/examples/PACKAGES/electrode/planar/log.1Dec2022.planar-ewald-ffield.g++.4 @@ -1,4 +1,4 @@ -LAMMPS (24 Mar 2022) +LAMMPS (3 Nov 2022) boundary p p p # finite field, fully periodic kspace_style ewald/electrode 1.0e-7 @@ -28,8 +28,8 @@ Finding 1-2 1-3 1-4 neighbors ... 0 = max # of 1-3 neighbors 0 = max # of 1-4 neighbors 1 = max # of special neighbors - special bonds CPU = 0.001 seconds - read_data CPU = 0.026 seconds + special bonds CPU = 0.002 seconds + read_data CPU = 0.006 seconds group bot molecule 1 144 atoms in group bot @@ -67,6 +67,24 @@ thermo 1 thermo_style custom step v_v c_qbot c_qtop v_qtheory v_percdev run 10 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- fix electrode command: + +@article{Ahrens2022 +author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0099239}, +title = {{ELECTRODE: An electrochemistry package for LAMMPS}}, +journal = {The Journal of Chemical Physics}, +year = {2022} +volume = {157}, +pages = {084801}, +} +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) Ewald/electrode initialization ... WARNING: System is not charge neutral, net charge = 0.000219 (src/kspace.cpp:327) @@ -76,9 +94,9 @@ WARNING: System is not charge neutral, net charge = 0.000219 (src/kspace.cpp:327 estimated relative force accuracy = 1.2145309e-07 KSpace vectors: actual max1d max3d = 95 5 665 kxmax kymax kzmax = 3 3 5 - generated 1 of 1 mixed pair_coeff terms from geometric mixing rule +Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... - update every 1 steps, delay 10 steps, check yes + update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 16 ghost atom cutoff = 16 @@ -94,7 +112,7 @@ Neighbor list info ... pair build: copy stencil: none bin: none -Per MPI rank memory allocation (min/avg/max) = 15.97 | 15.97 | 15.97 Mbytes +Per MPI rank memory allocation (min/avg/max) = 15.98 | 15.98 | 15.98 Mbytes Step v_v c_qbot c_qtop v_qtheory v_percdev 0 0 0 0 0 0 1 0.2 -0.030908718 0.030908718 0.031376826 -1.491893 @@ -107,22 +125,22 @@ Per MPI rank memory allocation (min/avg/max) = 15.97 | 15.97 | 15.97 Mbytes 8 1.6 -0.24726974 0.24726974 0.25101461 -1.491893 9 1.8 -0.27817846 0.27817846 0.28239144 -1.491893 10 2 -0.30908718 0.30908718 0.31376826 -1.491893 -Loop time of 0.0294825 on 4 procs for 10 steps with 288 atoms +Loop time of 0.0151333 on 4 procs for 10 steps with 288 atoms -Performance: 29.306 ns/day, 0.819 hours/ns, 339.184 timesteps/s -99.8% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 57.093 ns/day, 0.420 hours/ns, 660.794 timesteps/s, 190.309 katom-step/s +41.1% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.0020718 | 0.0025674 | 0.0029431 | 0.7 | 8.71 -Bond | 1.423e-06 | 2.0293e-06 | 2.615e-06 | 0.0 | 0.01 -Kspace | 0.0028016 | 0.0031772 | 0.0035529 | 0.5 | 10.78 +Pair | 0.0014606 | 0.0015586 | 0.0016093 | 0.1 | 10.30 +Bond | 9.31e-07 | 1.0197e-06 | 1.084e-06 | 0.0 | 0.01 +Kspace | 0.0014157 | 0.0015231 | 0.0016295 | 0.2 | 10.06 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.0023552 | 0.0032209 | 0.0035502 | 0.9 | 10.92 -Output | 0.0011969 | 0.0016057 | 0.002676 | 1.5 | 5.45 -Modify | 0.018358 | 0.018553 | 0.018654 | 0.1 | 62.93 -Other | | 0.0003563 | | | 1.21 +Comm | 0.0019994 | 0.0020111 | 0.0020282 | 0.0 | 13.29 +Output | 0.00072893 | 0.00095378 | 0.0015177 | 0.0 | 6.30 +Modify | 0.0081934 | 0.0082729 | 0.0083794 | 0.1 | 54.67 +Other | | 0.0008128 | | | 5.37 Nlocal: 72 ave 72 max 72 min Histogram: 4 0 0 0 0 0 0 0 0 0 diff --git a/examples/PACKAGES/electrode/planar/log.26Apr2022.planar-pppm-ew3dc.g++.1 b/examples/PACKAGES/electrode/planar/log.1Dec2022.planar-pppm-ew3dc.g++.1 similarity index 73% rename from examples/PACKAGES/electrode/planar/log.26Apr2022.planar-pppm-ew3dc.g++.1 rename to examples/PACKAGES/electrode/planar/log.1Dec2022.planar-pppm-ew3dc.g++.1 index ff0ae7698a..2e5d18d09c 100644 --- a/examples/PACKAGES/electrode/planar/log.26Apr2022.planar-pppm-ew3dc.g++.1 +++ b/examples/PACKAGES/electrode/planar/log.1Dec2022.planar-pppm-ew3dc.g++.1 @@ -1,4 +1,4 @@ -LAMMPS (24 Mar 2022) +LAMMPS (3 Nov 2022) boundary p p f kspace_style pppm/electrode 1.0e-7 kspace_modify slab 3.0 @@ -28,8 +28,8 @@ Finding 1-2 1-3 1-4 neighbors ... 0 = max # of 1-3 neighbors 0 = max # of 1-4 neighbors 1 = max # of special neighbors - special bonds CPU = 0.000 seconds - read_data CPU = 0.007 seconds + special bonds CPU = 0.001 seconds + read_data CPU = 0.004 seconds group bot molecule 1 144 atoms in group bot @@ -67,6 +67,35 @@ thermo 1 thermo_style custom step v_v c_qbot c_qtop v_qtheory v_percdev run 10 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- kspace_style pppm/electrode command: + +@article{Ahrens2021, +author = {Ahrens-Iwers, Ludwig J.V. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0063381}, +title = {{Constant potential simulations on a mesh}}, +journal = {Journal of Chemical Physics}, +year = {2021} +volume = {155}, +pages = {104104}, +} +- fix electrode command: + +@article{Ahrens2022 +author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0099239}, +title = {{ELECTRODE: An electrochemistry package for LAMMPS}}, +journal = {The Journal of Chemical Physics}, +year = {2022} +volume = {157}, +pages = {084801}, +} +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) PPPM/electrode initialization ... WARNING: System is not charge neutral, net charge = 0.000219 (src/kspace.cpp:327) @@ -78,9 +107,9 @@ WARNING: System is not charge neutral, net charge = 0.000219 (src/kspace.cpp:327 estimated relative force accuracy = 8.4221827e-08 using double precision MKL FFT 3d grid and FFT values/proc = 4563 1600 - generated 1 of 1 mixed pair_coeff terms from geometric mixing rule +Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... - update every 1 steps, delay 10 steps, check yes + update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 16 ghost atom cutoff = 16 @@ -97,7 +126,7 @@ Neighbor list info ... stencil: none bin: none WARNING: Using kspace solver on system with no charge (src/kspace.cpp:314) -Per MPI rank memory allocation (min/avg/max) = 7.93 | 7.93 | 7.93 Mbytes +Per MPI rank memory allocation (min/avg/max) = 7.942 | 7.942 | 7.942 Mbytes Step v_v c_qbot c_qtop v_qtheory v_percdev 0 0 0 0 0 0 1 0.2 -0.030912769 0.030912769 0.031376826 -1.4789807 @@ -110,22 +139,22 @@ Per MPI rank memory allocation (min/avg/max) = 7.93 | 7.93 | 7.93 Mbytes 8 1.6 -0.24730215 0.24730215 0.25101461 -1.4789807 9 1.8 -0.27821492 0.27821492 0.28239144 -1.4789807 10 2 -0.30912769 0.30912769 0.31376826 -1.4789807 -Loop time of 0.0784857 on 1 procs for 10 steps with 288 atoms +Loop time of 0.0176221 on 1 procs for 10 steps with 288 atoms -Performance: 11.008 ns/day, 2.180 hours/ns, 127.412 timesteps/s -400.0% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 49.029 ns/day, 0.490 hours/ns, 567.471 timesteps/s, 163.432 katom-step/s +100.0% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.0075859 | 0.0075859 | 0.0075859 | 0.0 | 9.67 -Bond | 2.817e-06 | 2.817e-06 | 2.817e-06 | 0.0 | 0.00 -Kspace | 0.020841 | 0.020841 | 0.020841 | 0.0 | 26.55 +Pair | 0.0051407 | 0.0051407 | 0.0051407 | 0.0 | 29.17 +Bond | 9.92e-07 | 9.92e-07 | 9.92e-07 | 0.0 | 0.01 +Kspace | 0.0029456 | 0.0029456 | 0.0029456 | 0.0 | 16.72 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.00019415 | 0.00019415 | 0.00019415 | 0.0 | 0.25 -Output | 0.0032534 | 0.0032534 | 0.0032534 | 0.0 | 4.15 -Modify | 0.046545 | 0.046545 | 0.046545 | 0.0 | 59.30 -Other | | 6.246e-05 | | | 0.08 +Comm | 8.3497e-05 | 8.3497e-05 | 8.3497e-05 | 0.0 | 0.47 +Output | 0.0012832 | 0.0012832 | 0.0012832 | 0.0 | 7.28 +Modify | 0.0080737 | 0.0080737 | 0.0080737 | 0.0 | 45.82 +Other | | 9.442e-05 | | | 0.54 Nlocal: 288 ave 288 max 288 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -140,4 +169,4 @@ Ave special neighs/atom = 0 Neighbor list builds = 0 Dangerous builds = 0 -Total wall time: 0:00:10 +Total wall time: 0:00:01 diff --git a/examples/PACKAGES/electrode/planar/log.26Apr2022.planar-pppm-ew3dc.g++.4 b/examples/PACKAGES/electrode/planar/log.1Dec2022.planar-pppm-ew3dc.g++.4 similarity index 73% rename from examples/PACKAGES/electrode/planar/log.26Apr2022.planar-pppm-ew3dc.g++.4 rename to examples/PACKAGES/electrode/planar/log.1Dec2022.planar-pppm-ew3dc.g++.4 index 4fcb219a89..69950a5859 100644 --- a/examples/PACKAGES/electrode/planar/log.26Apr2022.planar-pppm-ew3dc.g++.4 +++ b/examples/PACKAGES/electrode/planar/log.1Dec2022.planar-pppm-ew3dc.g++.4 @@ -1,4 +1,4 @@ -LAMMPS (24 Mar 2022) +LAMMPS (3 Nov 2022) boundary p p f kspace_style pppm/electrode 1.0e-7 kspace_modify slab 3.0 @@ -29,8 +29,8 @@ Finding 1-2 1-3 1-4 neighbors ... 0 = max # of 1-3 neighbors 0 = max # of 1-4 neighbors 1 = max # of special neighbors - special bonds CPU = 0.000 seconds - read_data CPU = 0.014 seconds + special bonds CPU = 0.003 seconds + read_data CPU = 0.007 seconds group bot molecule 1 144 atoms in group bot @@ -68,6 +68,35 @@ thermo 1 thermo_style custom step v_v c_qbot c_qtop v_qtheory v_percdev run 10 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- kspace_style pppm/electrode command: + +@article{Ahrens2021, +author = {Ahrens-Iwers, Ludwig J.V. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0063381}, +title = {{Constant potential simulations on a mesh}}, +journal = {Journal of Chemical Physics}, +year = {2021} +volume = {155}, +pages = {104104}, +} +- fix electrode command: + +@article{Ahrens2022 +author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0099239}, +title = {{ELECTRODE: An electrochemistry package for LAMMPS}}, +journal = {The Journal of Chemical Physics}, +year = {2022} +volume = {157}, +pages = {084801}, +} +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) PPPM/electrode initialization ... WARNING: System is not charge neutral, net charge = 0.000219 (src/kspace.cpp:327) @@ -79,9 +108,9 @@ WARNING: System is not charge neutral, net charge = 0.000219 (src/kspace.cpp:327 estimated relative force accuracy = 8.4221827e-08 using double precision MKL FFT 3d grid and FFT values/proc = 2691 672 - generated 1 of 1 mixed pair_coeff terms from geometric mixing rule +Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... - update every 1 steps, delay 10 steps, check yes + update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 16 ghost atom cutoff = 16 @@ -98,7 +127,7 @@ Neighbor list info ... stencil: none bin: none WARNING: Using kspace solver on system with no charge (src/kspace.cpp:314) -Per MPI rank memory allocation (min/avg/max) = 7.716 | 7.765 | 7.814 Mbytes +Per MPI rank memory allocation (min/avg/max) = 7.725 | 7.774 | 7.823 Mbytes Step v_v c_qbot c_qtop v_qtheory v_percdev 0 0 0 0 0 0 1 0.2 -0.030912769 0.030912769 0.031376826 -1.4789807 @@ -111,22 +140,22 @@ Per MPI rank memory allocation (min/avg/max) = 7.716 | 7.765 | 7.814 Mbytes 8 1.6 -0.24730215 0.24730215 0.25101461 -1.4789807 9 1.8 -0.27821492 0.27821492 0.28239144 -1.4789807 10 2 -0.30912769 0.30912769 0.31376826 -1.4789807 -Loop time of 0.0296999 on 4 procs for 10 steps with 288 atoms +Loop time of 0.0162257 on 4 procs for 10 steps with 288 atoms -Performance: 29.091 ns/day, 0.825 hours/ns, 336.701 timesteps/s -91.5% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 53.249 ns/day, 0.451 hours/ns, 616.306 timesteps/s, 177.496 katom-step/s +50.4% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.0021578 | 0.0022153 | 0.0022978 | 0.1 | 7.46 -Bond | 1.161e-06 | 1.435e-06 | 1.943e-06 | 0.0 | 0.00 -Kspace | 0.0054884 | 0.0057437 | 0.0059072 | 0.2 | 19.34 +Pair | 0.0010955 | 0.0013022 | 0.0014351 | 0.3 | 8.03 +Bond | 6.13e-07 | 7.795e-07 | 1.031e-06 | 0.0 | 0.00 +Kspace | 0.0034606 | 0.003541 | 0.0036869 | 0.2 | 21.82 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.0015424 | 0.0025686 | 0.0031306 | 1.2 | 8.65 -Output | 0.0019229 | 0.0023315 | 0.0033526 | 1.2 | 7.85 -Modify | 0.016192 | 0.016494 | 0.016902 | 0.2 | 55.54 -Other | | 0.0003449 | | | 1.16 +Comm | 0.0015915 | 0.0017672 | 0.0019298 | 0.3 | 10.89 +Output | 0.00071528 | 0.00095256 | 0.001506 | 0.0 | 5.87 +Modify | 0.0080243 | 0.0080738 | 0.0081204 | 0.0 | 49.76 +Other | | 0.0005881 | | | 3.62 Nlocal: 72 ave 72 max 72 min Histogram: 4 0 0 0 0 0 0 0 0 0 @@ -141,4 +170,4 @@ Ave special neighs/atom = 0 Neighbor list builds = 0 Dangerous builds = 0 -Total wall time: 0:00:03 +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/electrode/planar/log.26Apr2022.planar-pppm-ffield.g++.1 b/examples/PACKAGES/electrode/planar/log.1Dec2022.planar-pppm-ffield.g++.1 similarity index 73% rename from examples/PACKAGES/electrode/planar/log.26Apr2022.planar-pppm-ffield.g++.1 rename to examples/PACKAGES/electrode/planar/log.1Dec2022.planar-pppm-ffield.g++.1 index be13b1ca10..eb8d857fbe 100644 --- a/examples/PACKAGES/electrode/planar/log.26Apr2022.planar-pppm-ffield.g++.1 +++ b/examples/PACKAGES/electrode/planar/log.1Dec2022.planar-pppm-ffield.g++.1 @@ -1,4 +1,4 @@ -LAMMPS (24 Mar 2022) +LAMMPS (3 Nov 2022) boundary p p p # finite field, fully periodic kspace_style pppm/electrode 1.0e-7 @@ -28,7 +28,7 @@ Finding 1-2 1-3 1-4 neighbors ... 0 = max # of 1-4 neighbors 1 = max # of special neighbors special bonds CPU = 0.001 seconds - read_data CPU = 0.006 seconds + read_data CPU = 0.004 seconds group bot molecule 1 144 atoms in group bot @@ -66,6 +66,35 @@ thermo 1 thermo_style custom step v_v c_qbot c_qtop v_qtheory v_percdev run 10 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- kspace_style pppm/electrode command: + +@article{Ahrens2021, +author = {Ahrens-Iwers, Ludwig J.V. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0063381}, +title = {{Constant potential simulations on a mesh}}, +journal = {Journal of Chemical Physics}, +year = {2021} +volume = {155}, +pages = {104104}, +} +- fix electrode command: + +@article{Ahrens2022 +author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0099239}, +title = {{ELECTRODE: An electrochemistry package for LAMMPS}}, +journal = {The Journal of Chemical Physics}, +year = {2022} +volume = {157}, +pages = {084801}, +} +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) PPPM/electrode initialization ... WARNING: System is not charge neutral, net charge = 0.000219 (src/kspace.cpp:327) @@ -77,9 +106,9 @@ WARNING: System is not charge neutral, net charge = 0.000219 (src/kspace.cpp:327 estimated relative force accuracy = 5.4638319e-08 using double precision MKL FFT 3d grid and FFT values/proc = 2873 768 - generated 1 of 1 mixed pair_coeff terms from geometric mixing rule +Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... - update every 1 steps, delay 10 steps, check yes + update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 16 ghost atom cutoff = 16 @@ -96,7 +125,7 @@ Neighbor list info ... stencil: none bin: none WARNING: Using kspace solver on system with no charge (src/kspace.cpp:314) -Per MPI rank memory allocation (min/avg/max) = 7.86 | 7.86 | 7.86 Mbytes +Per MPI rank memory allocation (min/avg/max) = 7.871 | 7.871 | 7.871 Mbytes Step v_v c_qbot c_qtop v_qtheory v_percdev 0 0 0 0 0 0 1 0.2 -0.030902 0.030902 0.031376826 -1.5133027 @@ -109,22 +138,22 @@ Per MPI rank memory allocation (min/avg/max) = 7.86 | 7.86 | 7.86 Mbytes 8 1.6 -0.247216 0.247216 0.25101461 -1.5133028 9 1.8 -0.278118 0.278118 0.28239144 -1.5133028 10 2 -0.30902 0.30902 0.31376826 -1.5133028 -Loop time of 0.054016 on 1 procs for 10 steps with 288 atoms +Loop time of 0.0150845 on 1 procs for 10 steps with 288 atoms -Performance: 15.995 ns/day, 1.500 hours/ns, 185.130 timesteps/s -400.3% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 57.277 ns/day, 0.419 hours/ns, 662.933 timesteps/s, 190.925 katom-step/s +90.5% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.0081119 | 0.0081119 | 0.0081119 | 0.0 | 15.02 -Bond | 4.802e-06 | 4.802e-06 | 4.802e-06 | 0.0 | 0.01 -Kspace | 0.0053539 | 0.0053539 | 0.0053539 | 0.0 | 9.91 +Pair | 0.0052281 | 0.0052281 | 0.0052281 | 0.0 | 34.66 +Bond | 9.72e-07 | 9.72e-07 | 9.72e-07 | 0.0 | 0.01 +Kspace | 0.0017267 | 0.0017267 | 0.0017267 | 0.0 | 11.45 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.00052577 | 0.00052577 | 0.00052577 | 0.0 | 0.97 -Output | 0.0033476 | 0.0033476 | 0.0033476 | 0.0 | 6.20 -Modify | 0.036562 | 0.036562 | 0.036562 | 0.0 | 67.69 -Other | | 0.0001102 | | | 0.20 +Comm | 0.00016423 | 0.00016423 | 0.00016423 | 0.0 | 1.09 +Output | 0.0010211 | 0.0010211 | 0.0010211 | 0.0 | 6.77 +Modify | 0.0068532 | 0.0068532 | 0.0068532 | 0.0 | 45.43 +Other | | 9.022e-05 | | | 0.60 Nlocal: 288 ave 288 max 288 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -138,4 +167,4 @@ Ave neighs/atom = 92 Ave special neighs/atom = 0 Neighbor list builds = 0 Dangerous builds = 0 -Total wall time: 0:00:09 +Total wall time: 0:00:01 diff --git a/examples/PACKAGES/electrode/planar/log.26Apr2022.planar-pppm-ffield.g++.4 b/examples/PACKAGES/electrode/planar/log.1Dec2022.planar-pppm-ffield.g++.4 similarity index 73% rename from examples/PACKAGES/electrode/planar/log.26Apr2022.planar-pppm-ffield.g++.4 rename to examples/PACKAGES/electrode/planar/log.1Dec2022.planar-pppm-ffield.g++.4 index 619ed2bc48..75b20bb7f2 100644 --- a/examples/PACKAGES/electrode/planar/log.26Apr2022.planar-pppm-ffield.g++.4 +++ b/examples/PACKAGES/electrode/planar/log.1Dec2022.planar-pppm-ffield.g++.4 @@ -1,4 +1,4 @@ -LAMMPS (24 Mar 2022) +LAMMPS (3 Nov 2022) boundary p p p # finite field, fully periodic kspace_style pppm/electrode 1.0e-7 @@ -28,8 +28,8 @@ Finding 1-2 1-3 1-4 neighbors ... 0 = max # of 1-3 neighbors 0 = max # of 1-4 neighbors 1 = max # of special neighbors - special bonds CPU = 0.001 seconds - read_data CPU = 0.022 seconds + special bonds CPU = 0.002 seconds + read_data CPU = 0.006 seconds group bot molecule 1 144 atoms in group bot @@ -67,6 +67,35 @@ thermo 1 thermo_style custom step v_v c_qbot c_qtop v_qtheory v_percdev run 10 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- kspace_style pppm/electrode command: + +@article{Ahrens2021, +author = {Ahrens-Iwers, Ludwig J.V. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0063381}, +title = {{Constant potential simulations on a mesh}}, +journal = {Journal of Chemical Physics}, +year = {2021} +volume = {155}, +pages = {104104}, +} +- fix electrode command: + +@article{Ahrens2022 +author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0099239}, +title = {{ELECTRODE: An electrochemistry package for LAMMPS}}, +journal = {The Journal of Chemical Physics}, +year = {2022} +volume = {157}, +pages = {084801}, +} +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) PPPM/electrode initialization ... WARNING: System is not charge neutral, net charge = 0.000219 (src/kspace.cpp:327) @@ -78,9 +107,9 @@ WARNING: System is not charge neutral, net charge = 0.000219 (src/kspace.cpp:327 estimated relative force accuracy = 5.4638319e-08 using double precision MKL FFT 3d grid and FFT values/proc = 1287 192 - generated 1 of 1 mixed pair_coeff terms from geometric mixing rule +Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... - update every 1 steps, delay 10 steps, check yes + update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 16 ghost atom cutoff = 16 @@ -97,7 +126,7 @@ Neighbor list info ... stencil: none bin: none WARNING: Using kspace solver on system with no charge (src/kspace.cpp:314) -Per MPI rank memory allocation (min/avg/max) = 7.712 | 7.712 | 7.712 Mbytes +Per MPI rank memory allocation (min/avg/max) = 7.721 | 7.721 | 7.721 Mbytes Step v_v c_qbot c_qtop v_qtheory v_percdev 0 0 0 0 0 0 1 0.2 -0.030902 0.030902 0.031376826 -1.5133027 @@ -110,22 +139,22 @@ Per MPI rank memory allocation (min/avg/max) = 7.712 | 7.712 | 7.712 Mbytes 8 1.6 -0.247216 0.247216 0.25101461 -1.5133028 9 1.8 -0.278118 0.278118 0.28239144 -1.5133028 10 2 -0.30902 0.30902 0.31376826 -1.5133028 -Loop time of 0.0301351 on 4 procs for 10 steps with 288 atoms +Loop time of 0.0169132 on 4 procs for 10 steps with 288 atoms -Performance: 28.671 ns/day, 0.837 hours/ns, 331.839 timesteps/s -99.8% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 51.084 ns/day, 0.470 hours/ns, 591.252 timesteps/s, 170.281 katom-step/s +49.8% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.0020768 | 0.0022701 | 0.0024074 | 0.3 | 7.53 -Bond | 1.271e-06 | 2.2107e-06 | 4.237e-06 | 0.0 | 0.01 -Kspace | 0.0039171 | 0.0040631 | 0.0042468 | 0.2 | 13.48 +Pair | 0.00098343 | 0.0013515 | 0.0015461 | 0.6 | 7.99 +Bond | 6.21e-07 | 6.81e-07 | 7.3e-07 | 0.0 | 0.00 +Kspace | 0.0036673 | 0.0038144 | 0.004106 | 0.3 | 22.55 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.0020711 | 0.0032953 | 0.0038884 | 1.3 | 10.93 -Output | 0.0013425 | 0.001877 | 0.0031692 | 1.7 | 6.23 -Modify | 0.018076 | 0.018252 | 0.018479 | 0.1 | 60.57 -Other | | 0.0003755 | | | 1.25 +Comm | 0.0015601 | 0.0016528 | 0.0017294 | 0.2 | 9.77 +Output | 0.00072013 | 0.00087465 | 0.0012429 | 0.0 | 5.17 +Modify | 0.0086712 | 0.0087641 | 0.0089049 | 0.1 | 51.82 +Other | | 0.0004551 | | | 2.69 Nlocal: 72 ave 72 max 72 min Histogram: 4 0 0 0 0 0 0 0 0 0 @@ -139,4 +168,4 @@ Ave neighs/atom = 92 Ave special neighs/atom = 0 Neighbor list builds = 0 Dangerous builds = 0 -Total wall time: 0:00:03 +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/pod/README.md b/examples/PACKAGES/pod/README.md new file mode 100644 index 0000000000..2c6db69200 --- /dev/null +++ b/examples/PACKAGES/pod/README.md @@ -0,0 +1,21 @@ +### Compile LAMMPS/POD + +Go to `lammps` directory and build with the POD package: + + cd path/to/lammps + mkdir build-pod + cd build-pod + cmake -C ../cmake/presets/basic.cmake -D PKG_ML-POD=on ../cmake + cmake --build . + +### Fit a POD potential for tantalum + +Go to `lammps/examples/PACKAGES/pod/Ta` directory and run + + lmp -in in.podfit + +See the README in `lammps/examples/PACKAGES/pod/Ta` for instructions on how to run MD with the potential. + +### Examples for other materials + +See [https://github.com/cesmix-mit/pod-examples](https://github.com/cesmix-mit/pod-examples) diff --git a/examples/PACKAGES/pod/Ta/README.md b/examples/PACKAGES/pod/Ta/README.md new file mode 100644 index 0000000000..031698550c --- /dev/null +++ b/examples/PACKAGES/pod/Ta/README.md @@ -0,0 +1,15 @@ +### POD example for Ta + +We will fit a potential to the `Ta` training data in the `XYZ` directory, which houses `.xyz` files +of the training data taken from [the FitSNAP repo](https://github.com/FitSNAP/FitSNAP/tree/master/examples/Ta_XYZ/XYZ) + +Fit POD with + + lmp -in in.fitpod + +This creates `Ta_coefficients.pod` for the linear model, which we can use to run MD with + + lmp -in in.pod + + + diff --git a/examples/PACKAGES/pod/Ta/Ta_coeff.pod b/examples/PACKAGES/pod/Ta/Ta_coeff.pod new file mode 120000 index 0000000000..ddf9c1426d --- /dev/null +++ b/examples/PACKAGES/pod/Ta/Ta_coeff.pod @@ -0,0 +1 @@ +../../../../potentials/Ta_coeff.pod \ No newline at end of file diff --git a/examples/PACKAGES/pod/Ta/Ta_coefficients.pod b/examples/PACKAGES/pod/Ta/Ta_coefficients.pod new file mode 100644 index 0000000000..c8943bb889 --- /dev/null +++ b/examples/PACKAGES/pod/Ta/Ta_coefficients.pod @@ -0,0 +1,33 @@ +POD_coefficients: 32 +-4.44242 +4.10219 +-2.36987 +-3.92184 +0.83796 +-0.79457 +0.26230 +-21.24294 +-15.38460 +-38.44056 +8.29872 +-42.54514 +2.79976 +3.76109 +5.23499 +0.04878 +2.96006 +0.09101 +-0.19257 +-0.24326 +-0.16735 +0.53738 +0.02236 +-0.00154 +0.02488 +-0.00565 +0.07672 +-0.05894 +-0.05604 +-0.12664 +0.11723 +0.00262 diff --git a/examples/PACKAGES/pod/Ta/Ta_data.pod b/examples/PACKAGES/pod/Ta/Ta_data.pod new file mode 100644 index 0000000000..0933f3e79a --- /dev/null +++ b/examples/PACKAGES/pod/Ta/Ta_data.pod @@ -0,0 +1,20 @@ +file_format extxyz +file_extension xyz + +path_to_training_data_set "XYZ" +path_to_test_data_set "XYZ" + +fitting_weight_energy 100.0 +fitting_weight_force 1.0 +fitting_regularization_parameter 1e-10 + +error_analysis_for_training_data_set 1 +error_analysis_for_test_data_set 0 + +# Add the following basename to the name of output files +basename_for_output_files Ta + +# number of digits after the decimal point for pod coefficients +precision_for_pod_coefficients 5 + + diff --git a/examples/PACKAGES/pod/Ta/Ta_param.pod b/examples/PACKAGES/pod/Ta/Ta_param.pod new file mode 100644 index 0000000000..00c01b01a6 --- /dev/null +++ b/examples/PACKAGES/pod/Ta/Ta_param.pod @@ -0,0 +1,32 @@ +# DATE: 2022-11-30 UNITS: metal CONTRIBUTOR: Ngoc Cuong Nguyen, exapde@gmail.com CITATION: https://arxiv.org/abs/2209.02362 +# chemical element symbols +species Ta + +# periodic boundary conditions +pbc 1 1 1 + +# inner cut-off radius +rin 1.0 + +# outer cut-off radius +rcut 5.0 + +# polynomial degrees for radial basis functions +bessel_polynomial_degree 3 +inverse_polynomial_degree 6 + +# one-body potential +onebody 1 + +# two-body linear POD potential +twobody_number_radial_basis_functions 6 + +# three-body linear POD potential +threebody_number_radial_basis_functions 5 +threebody_number_angular_basis_functions 5 + +# four-body linear SNAP potential +fourbody_snap_twojmax 0 + +# quadratic POD potential +quadratic_pod_potential 0 diff --git a/examples/PACKAGES/pod/Ta/Ta_training_analysis.pod b/examples/PACKAGES/pod/Ta/Ta_training_analysis.pod new file mode 100644 index 0000000000..d5bbec1cb8 --- /dev/null +++ b/examples/PACKAGES/pod/Ta/Ta_training_analysis.pod @@ -0,0 +1,387 @@ +# Displaced_A15.xyz + config # atoms energy DFT energy energy error force DFT force force error + 1 64 -753.4412087 -754.220443 0.01217553565 7.734608752 8.398670477 0.1147177501 + 2 64 -752.99206 -753.865255 0.01364367179 8.845831302 9.134430545 0.128875643 + 3 64 -753.3230789 -754.0221 0.01092220404 8.320493902 9.017261102 0.1155421197 + 4 64 -753.5972757 -754.279613 0.01066151964 7.709417685 8.381725092 0.1058659753 + 5 64 -753.0554721 -753.777209 0.01127713895 8.89827564 9.478314477 0.1191609049 + 6 64 -753.3515905 -754.048643 0.01089144564 7.808950564 8.465317938 0.1128142237 + 7 64 -753.6515992 -754.317603 0.01040630929 7.441773668 8.127690491 0.1024025645 + 8 64 -753.3305668 -753.969161 0.009978033993 8.524333384 9.425464952 0.1066300011 + 9 64 -753.3982699 -754.141988 0.01162059587 8.165654685 8.821346913 0.1141641875 +# Displaced_BCC.xyz + config # atoms energy DFT energy energy error force DFT force force error + 10 54 -631.72742 -631.019667 0.01310653789 15.42892812 16.625876 0.264811012 + 11 54 -632.2725892 -631.719595 0.01024063328 14.51788198 15.58666626 0.2236637006 + 12 54 -631.9431698 -631.386255 0.01031323642 15.21539049 15.92378883 0.2259171686 + 13 54 -633.0728554 -632.575826 0.009204247811 13.38472946 14.55977162 0.2050161952 + 14 54 -630.8933737 -630.450212 0.008206698429 16.5539163 16.96340726 0.2366453149 + 15 54 -632.0739208 -631.669379 0.007491515673 15.23887638 16.05757315 0.2280333831 + 16 54 -632.8030856 -632.431277 0.006885343815 14.21127984 14.69810718 0.2026063598 + 17 54 -631.6814096 -630.960068 0.01335817778 14.70924474 15.99073148 0.2283605143 + 18 54 -625.0410285 -623.378198 0.03079315656 23.39224423 24.67640432 0.3504654115 +# Displaced_FCC.xyz + config # atoms energy DFT energy energy error force DFT force force error + 19 48 -555.9696753 -555.899463 0.001462755232 6.079460735 6.084617063 0.07083484607 + 20 48 -555.9506355 -555.922478 0.0005866147697 6.28112122 6.297071211 0.09285822038 + 21 48 -555.8344979 -555.800269 0.0007131011841 6.153574445 6.021098636 0.08137696888 + 22 48 -556.2639568 -556.196151 0.001412620461 5.066504178 5.127955094 0.08649299664 + 23 48 -555.6269121 -555.488929 0.002874647697 6.848109842 7.050223459 0.08116202322 + 24 48 -556.1089332 -556.027926 0.001687649405 5.662035842 5.611881174 0.07953916327 + 25 48 -556.0580873 -555.968399 0.001868505799 5.879931332 5.979217189 0.07470196866 + 26 48 -556.0083267 -556.047132 0.0008084440258 5.752828608 5.544452585 0.08224848502 + 27 48 -555.82441 -555.747848 0.001595040721 6.367423657 6.47892568 0.09497869851 +# Elastic_BCC.xyz + config # atoms energy DFT energy energy error force DFT force force error + 28 2 -23.68353253 -23.689367 0.002917237243 0.0006486347527 0.0006222748589 7.696560647e-06 + 29 2 -23.68281295 -23.689888 0.003537526523 0.0006442481331 0.0006166052222 7.353613433e-06 + 30 2 -23.68293438 -23.689996 0.00353080996 0.0009115876426 0.0008810425642 1.183334558e-05 + 31 2 -23.68108003 -23.690957 0.004938485589 1.044193546e-06 0 4.166083011e-07 + 32 2 -23.67919793 -23.690521 0.005661535829 0.0006261455712 0.0005982273815 7.573309962e-06 + 33 2 -23.67785535 -23.69038 0.006262326378 0.0006219476538 0.0005925723585 8.098703345e-06 + 34 2 -23.68415292 -23.689202 0.00252453823 0.0006520193214 0.0006279363025 7.128171198e-06 + 35 2 -23.68169552 -23.690482 0.004393238412 0.0009021557258 0.0008640138888 1.329061297e-05 + 36 2 -23.68301023 -23.689902 0.003445886213 0.0006432418939 0.0006152154094 8.589463686e-06 + 37 2 -23.68063814 -23.690563 0.004962429905 0.0006318669831 0.0006038725031 7.463726891e-06 + 38 2 -23.68337588 -23.690207 0.003415557958 0.001118071502 0.00107369735 1.811741272e-05 + 39 2 -23.68369233 -23.689285 0.00279633424 0.0009215683923 0.000890013483 1.127366011e-05 + 40 2 -23.68344234 -23.689768 0.003162828655 0.001120158205 0.001080249045 1.630224161e-05 + 41 2 -23.68224173 -23.68968 0.003719136062 0.0009070521506 0.0008680034562 1.339908745e-05 + 42 2 -23.68259685 -23.690074 0.003738573623 0.00143649564 0.001373818765 2.432187597e-05 + 43 2 -23.68469428 -23.688108 0.001706858485 0.0006587619148 0.0006336134468 7.932733886e-06 + 44 2 -23.68405177 -23.689241 0.002594615211 0.0009223784492 0.0008880101351 1.189350098e-05 + 45 2 -23.68384626 -23.68952 0.002836868987 0.0009181252225 0.0008860011287 1.116431522e-05 + 46 2 -23.68524763 -23.686278 0.0005151850612 0.0006668258323 0.0006406777661 8.585622872e-06 + 47 2 -23.67629396 -23.690097 0.006901518594 0.0008737523828 0.0008410160522 1.125104926e-05 + 48 2 -23.67835169 -23.690811 0.006229654604 0.0008814028122 0.0008500070588 1.103963422e-05 + 49 2 -23.67981574 -23.690266 0.005225130991 0.001091936388 0.001044322747 1.944706281e-05 + 50 2 -23.68209703 -23.690597 0.004249983197 0.001105769275 0.001050833003 2.242828166e-05 + 51 2 -23.68050418 -23.690673 0.005084408246 0.000631172526 0.0006038907186 7.85857762e-06 + 52 2 -23.68185505 -23.690551 0.00434797299 0.0009022813915 0.0008590064028 1.486707593e-05 + 53 2 -23.68191508 -23.690693 0.004388958442 0.0009013677777 0.0008590110593 1.516503239e-05 + 54 2 -23.68097184 -23.69021 0.004619081961 0.0009000307855 0.0008730051546 9.670733045e-06 + 55 2 -23.68426495 -23.688943 0.002339025274 0.0009232115961 0.0008800306813 1.619629586e-05 + 56 2 -23.67842316 -23.690136 0.00585641942 0.0006239138245 0.000593996633 8.394193459e-06 + 57 2 -23.6849427 -23.687444 0.001250651312 0.0009347957747 0.000903059245 1.290489522e-05 + 58 2 -23.6836322 -23.689801 0.003084401813 0.0009160470298 0.0008740011442 1.424271291e-05 + 59 2 -23.6814842 -23.690408 0.00446190038 8.690218922e-07 0 3.245696982e-07 + 60 2 -23.68115817 -23.690362 0.004601914896 0.0006345480975 0.0006067503605 9.377221837e-06 + 61 2 -23.67229452 -23.688881 0.008293240443 0.0008566684404 0.0008250054545 1.108928728e-05 + 62 2 -23.6791352 -23.690515 0.005689901939 0.001534883496 0.001475779794 2.12469595e-05 + 63 2 -23.67786743 -23.690551 0.006341785918 0.0006228264143 0.0005996599036 7.295416678e-06 + 64 2 -23.68316372 -23.689487 0.003161641446 0.0006469755816 0.0006194384554 7.530154689e-06 + 65 2 -23.6834063 -23.68986 0.003226849907 0.0009142334935 0.0008860124153 1.052672488e-05 + 66 2 -23.68377813 -23.689288 0.002754934411 0.00145229412 0.001396479144 1.7028268e-05 + 67 2 -23.67700773 -23.690457 0.006724637324 0.0006187196638 0.0005939831647 7.080762894e-06 + 68 2 -23.67552804 -23.689792 0.007131981721 0.0008698720997 0.0008340587509 1.418233126e-05 + 69 2 -23.67583966 -23.690006 0.007083167889 0.0006146073806 0.0005897694465 8.070657469e-06 + 70 2 -23.6777397 -23.690571 0.006415648131 0.0006207500925 0.0005939781141 7.401996527e-06 + 71 2 -23.68270064 -23.690213 0.003756180649 0.001112284016 0.001084315452 1.142137177e-05 + 72 2 -23.67870666 -23.690617 0.005955171449 0.0006250314539 0.0006024682564 6.623275773e-06 + 73 2 -23.68231586 -23.689761 0.00372256923 0.0009095463313 0.0008790688255 1.222939687e-05 + 74 2 -23.67673328 -23.69027 0.006768359835 7.188704984e-07 0 2.129270719e-07 + 75 2 -23.68164707 -23.690599 0.004475963334 0.0006376044826 0.0006137752031 6.574310078e-06 + 76 2 -23.67997815 -23.69061 0.00531592353 9.698202065e-07 0 3.958704534e-07 + 77 2 -23.68008634 -23.690603 0.005258328411 0.0008923489326 0.0008590331775 1.256831367e-05 + 78 2 -23.68488966 -23.687908 0.001509170978 0.0009340324028 0.0009010105438 1.204104822e-05 + 79 2 -23.6795094 -23.690688 0.005589299031 0.0008890828456 0.0008470064935 1.419626566e-05 + 80 2 -23.68316126 -23.689988 0.003413372454 0.0006451612224 0.0006194465272 7.422528504e-06 + 81 2 -23.68321956 -23.689613 0.003196718897 0.000912899593 0.0008740732235 1.539555522e-05 + 82 2 -23.68181374 -23.690678 0.004432127652 0.0006373963006 0.0006123757017 7.454253264e-06 + 83 2 -23.68196226 -23.69017 0.004103870298 0.0009041773842 0.0008750051428 9.854119735e-06 + 84 2 -23.68483517 -23.687892 0.001528413806 0.001142179928 0.001112070142 1.229243027e-05 + 85 2 -23.68271169 -23.690132 0.003710155487 0.0009085291666 0.000868018433 1.49999647e-05 + 86 2 -23.68018066 -23.690843 0.005331170668 0.0006305009468 0.0006081134763 5.908815719e-06 + 87 2 -23.67957976 -23.690598 0.005509118787 0.001259431767 0.001217674833 1.243374729e-05 + 88 2 -23.67869549 -23.690656 0.005980257091 0.0006251939788 0.0006024765556 7.130239281e-06 + 89 2 -23.67884961 -23.690254 0.005702197143 0.001084797449 0.001043496047 1.68662339e-05 + 90 2 -23.67961701 -23.690694 0.005538492834 0.0006273834422 0.0006010740387 8.134278748e-06 + 91 2 -23.68202458 -23.690097 0.004036211359 0.0009041492449 0.0008730234819 1.169617364e-05 + 92 2 -23.68476212 -23.688402 0.001819942156 0.0006575509652 0.000632180354 7.746949898e-06 + 93 2 -23.68425036 -23.688669 0.002209320265 0.001133553123 0.001092474256 1.677033392e-05 + 94 2 -23.68017683 -23.690538 0.005180583191 0.0008923392716 0.0008610145179 1.053989885e-05 + 95 2 -23.68290142 -23.689722 0.003410287964 0.0006465597037 0.0006251287867 7.275875005e-06 + 96 2 -23.6789537 -23.690581 0.005813649829 7.452601434e-07 0 2.355432866e-07 + 97 2 -23.6840847 -23.688755 0.002335150427 0.0006519723076 0.0006251143895 8.250788079e-06 + 98 2 -23.67367881 -23.689312 0.007816596299 0.0008618264365 0.0008290597083 1.323477647e-05 + 99 2 -23.68489152 -23.687388 0.001248238956 0.001145929445 0.001120237475 1.049029355e-05 + 100 2 -23.68174648 -23.690664 0.004458761579 0.0006367386055 0.0006109402589 6.270984334e-06 + 101 2 -23.67450636 -23.68941 0.007451817634 0.0006119997091 0.0005883553348 7.715800123e-06 + 102 2 -23.68321442 -23.690035 0.003410290658 0.0009128748923 0.0008810062429 1.106310227e-05 + 103 2 -23.67584952 -23.690015 0.007082738579 0.0008706222251 0.0008450195264 9.898495893e-06 + 104 2 -23.67856154 -23.690752 0.006095232174 0.0006245583967 0.0005996415596 7.0338752e-06 + 105 2 -23.68297614 -23.689825 0.00342442945 0.0009134966073 0.0008800215906 1.147892484e-05 + 106 2 -23.67876135 -23.690562 0.00590032283 0.0008849512172 0.0008560011682 1.005528708e-05 + 107 2 -23.67874342 -23.690622 0.005939288687 0.0008835043772 0.0008390017878 1.530603189e-05 + 108 2 -23.6843441 -23.688764 0.002209950671 0.0009250850126 0.0008910185183 1.254407066e-05 + 109 2 -23.68340608 -23.690011 0.003302460748 0.0006464901241 0.0006194287691 7.216590251e-06 + 110 2 -23.68476306 -23.687696 0.001466471271 0.001143422035 0.001087589996 2.279977174e-05 + 111 2 -23.67977853 -23.691019 0.005620235289 0.000888876189 0.0008540035129 1.1779733e-05 + 112 2 -23.68440001 -23.689025 0.002312496017 6.723949117e-07 0 2.64867667e-07 + 113 2 -23.68208689 -23.689952 0.003932553163 7.386834034e-07 0 2.881506548e-07 + 114 2 -23.67935439 -23.69061 0.005627806505 0.0008872685213 0.0008580011655 1.019979918e-05 + 115 2 -23.68099138 -23.690595 0.004801812376 0.0008956193373 0.0008680069124 9.843191999e-06 + 116 2 -23.67743565 -23.690231 0.006397673953 0.0006194343635 0.0005925892338 8.542917156e-06 + 117 2 -23.67809541 -23.690469 0.006186797078 0.0008802359765 0.0008500294113 1.182654414e-05 + 118 2 -23.68279142 -23.690482 0.003845288647 0.0009078436148 0.0008740102974 1.225600095e-05 + 119 2 -23.67443144 -23.689613 0.007590778784 0.0008650318724 0.0008320192305 1.23538989e-05 + 120 2 -23.68501591 -23.687426 0.001205043668 0.001145633567 0.00109577735 2.03694619e-05 + 121 2 -23.68302307 -23.689562 0.003269464306 0.0006474095532 0.0006265237426 6.532536014e-06 + 122 2 -23.68134549 -23.6904 0.004527256823 4.272990719e-07 0 1.732352794e-07 + 123 2 -23.67843015 -23.690561 0.006065426647 0.0006235069318 0.0005982273815 6.816496585e-06 + 124 2 -23.67292129 -23.689107 0.008092853971 0.0008589766346 0.0008180073349 1.439377155e-05 + 125 2 -23.68123551 -23.690145 0.004454742608 0.0009009679944 0.0008740766557 1.132072203e-05 + 126 2 -23.67777646 -23.690482 0.006352769316 0.0006215821083 0.0005939983165 8.362048689e-06 + 127 2 -23.68318209 -23.689864 0.003340952886 0.0009142894487 0.0008860124153 1.044271435e-05 +# Elastic_FCC.xyz + config # atoms energy DFT energy energy error force DFT force force error + 128 4 -46.449456 -46.437936 0.002880000611 0.0007088173441 0.001265949446 0.0001573706237 + 129 4 -46.45317307 -46.438504 0.003667267825 0.0007210982328 0.001492549497 0.0002032393675 + 130 4 -46.44686167 -46.436378 0.002620918523 0.0004870837365 0.000810592376 0.0001107544174 + 131 4 -46.45357979 -46.441551 0.003007196305 0.0008634182131 0.001283675193 0.0001231453909 + 132 4 -46.42409677 -46.416957 0.001784942313 0.0007481922079 0.001186145859 0.0001205918882 + 133 4 -46.45078882 -46.440495 0.002573455911 0.0007289008721 0.001212440514 0.0001119490174 + 134 4 -46.4501363 -46.437972 0.003041076136 0.001116532125 0.002358226452 0.0003166808771 + 135 4 -46.46241981 -46.44586 0.004139951293 0.001077737689 0.002033949852 0.0002702964015 + 136 4 -46.44743429 -46.435744 0.002922571394 0.0008383971706 0.001690849491 0.0002711013554 + 137 4 -46.45237555 -46.438209 0.003541637787 0.0007039962535 0.001160049999 0.0001096430557 + 138 4 -46.43645451 -46.42629 0.002541127472 0.0004839683449 0.0005297018029 1.480491546e-05 + 139 4 -46.45466199 -46.443301 0.002840247268 0.0008590849412 0.001818421568 0.0002395191538 + 140 4 -46.4513559 -46.439002 0.003088474484 0.000980675092 0.001416973535 0.0001142710898 + 141 4 -46.44224357 -46.432438 0.00245139227 0.0008958100898 0.001010469198 5.862303988e-05 + 142 4 -46.41846428 -46.412654 0.001452568802 0.001104791425 0.001801959766 0.0001900084105 + 143 4 -46.45594552 -46.443231 0.003178629143 0.0006959928784 0.001691590967 0.0002104366356 + 144 4 -46.44141177 -46.431513 0.00247469212 0.001149659372 0.001680544852 0.0001329997122 + 145 4 -46.44458344 -46.435608 0.00224385943 0.0007110215089 0.0009593039143 5.831382606e-05 + 146 4 -46.45129649 -46.437689 0.003401871689 0.0007271142738 0.001217708504 0.0001414871092 + 147 4 -46.43755262 -46.428447 0.002276404472 0.0008708378565 0.002060081552 0.0003082033743 + 148 4 -46.44295113 -46.432255 0.00267403188 0.0005315813764 0.0006274201144 5.596270268e-05 + 149 4 -46.45482154 -46.442315 0.003126635324 0.0008653689406 0.002424436842 0.0004107290683 + 150 4 -46.44918467 -46.436613 0.003142918309 0.0004839663128 0.0005321240457 3.890880543e-05 + 151 4 -46.44094809 -46.430825 0.002530772174 0.0007559646277 0.001399987143 0.0001669802678 + 152 4 -46.44335614 -46.43312 0.002559035587 0.0004859700309 0.0007272771136 6.315695513e-05 + 153 4 -46.44518607 -46.434347 0.002709767129 0.0007148497795 0.001284451634 0.0001580665901 + 154 4 -46.43969219 -46.430573 0.002279798333 0.00072875179 0.001315746176 0.000142372977 + 155 4 -46.46201856 -46.445665 0.004088390852 0.0008369246217 0.00180789159 0.0002715757049 + 156 4 -46.44738266 -46.435898 0.002871166201 0.0007118215897 0.001869300939 0.0002650888178 + 157 4 -46.45279209 -46.442107 0.00267127163 0.0005099355574 0.0006020930161 3.155335447e-05 + 158 4 -46.44687446 -46.434432 0.003110615714 0.0008364031703 0.001092982159 9.484366005e-05 + 159 4 -46.45033825 -46.436308 0.003507562522 0.000995428139 0.001839150891 0.0002479613631 + 160 4 -46.43248168 -46.423938 0.002135919949 0.0007772193879 0.001463463016 0.0001986681069 + 161 4 -46.43702199 -46.428115 0.002226747981 0.0005418219957 0.0008584497656 9.283863381e-05 + 162 4 -46.43553597 -46.4269 0.002158992752 0.001008467413 0.001845719914 0.00024455962 + 163 4 -46.43191737 -46.421142 0.002693841371 0.0009169914298 0.001309150106 9.335100097e-05 + 164 4 -46.44107961 -46.432233 0.002211651338 0.0006944670911 0.0007253109678 2.446203898e-05 + 165 4 -46.44097784 -46.429408 0.002892459649 0.0007189999753 0.001068327665 9.331287519e-05 + 166 4 -46.45970672 -46.445145 0.003640430606 0.0008323398895 0.001776038288 0.000241778013 + 167 4 -46.44583143 -46.435868 0.002490857628 0.001007239475 0.002376074704 0.0003893124404 + 168 4 -46.4515773 -46.439663 0.002978574612 0.0004764710524 0.001119403413 0.0001156692402 + 169 4 -46.43612447 -46.428287 0.00195936642 0.001036891264 0.001277000392 6.942055774e-05 + 170 4 -46.4323966 -46.424584 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0.002794325435 0.0007102028538 0.001505586265 0.000179529909 + 203 4 -46.43168209 -46.422628 0.002263521917 0.0007374332623 0.001601713458 0.0002609325883 + 204 4 -46.45732644 -46.443535 0.00344786022 0.0009811025521 0.001590304373 0.0001690672254 + 205 4 -46.45144079 -46.439922 0.002879696366 0.0008698700101 0.001530493385 0.0001528171002 + 206 4 -46.44960522 -46.437675 0.002982555611 0.00112440729 0.002440246094 0.0004061057502 + 207 4 -46.45839808 -46.445558 0.003210018941 0.0006780842253 0.00113392416 0.0001196075532 + 208 4 -46.45130112 -46.439106 0.003048781046 0.0009934671927 0.001830731002 0.000245168776 + 209 4 -46.45826105 -46.443073 0.003797013279 0.0004759445984 0.0005766870902 2.863834812e-05 + 210 4 -46.4536082 -46.4397 0.003477049491 0.0006982622456 0.001204174406 0.0001154782847 + 211 4 -46.44819434 -46.436374 0.002955085327 0.0007363684621 0.001461656594 0.0002277550157 + 212 4 -46.43668282 -46.426557 0.00253145389 0.0007326220467 0.001359624213 0.0001251472548 + 213 4 -46.44485583 -46.434009 0.002711707903 0.000870647096 0.001391131194 0.0001541542453 + 214 4 -46.44732696 -46.436262 0.002766239028 0.001116549362 0.002503347159 0.0003211377445 + 215 4 -46.44414241 -46.434505 0.002409352177 0.0008685662223 0.001041637173 4.942106462e-05 + 216 4 -46.45095913 -46.438768 0.003047783488 0.0008482298138 0.001098285027 8.657909629e-05 + 217 4 -46.45111242 -46.440254 0.002714605501 0.0004892442432 0.0006069892915 5.824568303e-05 + 218 4 -46.43463407 -46.42286 0.002943517186 0.0004976409931 0.0007365242698 7.564906264e-05 + 219 4 -46.42611144 -46.418078 0.002008360417 0.001053243552 0.002028412187 0.0002473380313 + 220 4 -46.45344976 -46.440513 0.003234189608 0.0007024129954 0.001158189967 0.0001371889048 + 221 4 -46.41584187 -46.409824 0.001504467167 0.0007558580012 0.001759573812 0.0002386003087 + 222 4 -46.45494987 -46.440329 0.003655216631 0.0005034620022 0.0009534044263 0.0001064495091 + 223 4 -46.45000759 -46.43773 0.003069396495 0.0006831478015 0.000926180328 7.390298375e-05 + 224 4 -46.42538863 -46.416525 0.002215907169 0.0005605993692 0.0007573664899 5.946405938e-05 + 225 4 -46.45386072 -46.440293 0.003391930454 0.0006980795454 0.0007725386722 1.864508071e-05 + 226 4 -46.4527969 -46.43839 0.003601726069 0.0005103417187 0.0005612022808 1.656002337e-05 + 227 4 -46.45374294 -46.438916 0.00370673382 0.0006956794369 0.001650878554 0.0002154167998 +# GSF_110.xyz + config # atoms energy DFT energy energy error force DFT force force error + 228 24 -278.7403996 -279.068761 0.01368172569 2.282668754 1.756353161 0.04745635589 + 229 24 -279.902595 -279.784296 0.004929123883 0.9479314831 0.9057668891 0.02403120774 + 230 24 -279.9942014 -279.901657 0.003856015841 0.2795933118 0.001565946359 0.01120665859 + 231 24 -279.6335344 -279.584238 0.002054016532 1.573004204 1.035572248 0.05514377891 + 232 24 -279.9025974 -279.784283 0.004929767703 0.947921084 0.9056396189 0.02406018404 + 233 24 -279.1817177 -279.302158 0.005018345952 2.388096516 1.771965137 0.06275542538 + 234 24 -279.5900705 -279.55564 0.001434605813 1.950503627 1.405626506 0.05370441115 + 235 24 -279.0106063 -279.246939 0.00984719392 1.577003357 0.4813964151 0.08190583543 + 236 24 -279.1817217 -279.302157 0.005018138375 2.388094324 1.771953347 0.06275588675 + 237 24 -279.0107548 -279.246935 0.009840841347 1.576191869 0.4809484798 0.0819682416 + 238 24 -279.9941671 -279.896025 0.004089255845 0.2809227604 0.01060549839 0.01118927817 + 239 24 -279.6337951 -279.584237 0.002064919631 1.571895405 1.035836121 0.05510997377 + 240 24 -278.8616595 -279.124427 0.0109486445 2.383512182 1.809545887 0.06232801199 + 241 24 -279.2927133 -279.379366 0.003610531084 1.779238829 0.8982692706 0.07658702105 + 242 24 -279.292656 -279.37937 0.003613082676 1.779203263 0.898081355 0.0765940488 + 243 24 -278.8616573 -279.124427 0.01094873842 2.383511745 1.809523374 0.06232387507 + 244 24 -279.9942014 -279.901657 0.003856015842 0.27959331 0.001570374478 0.01120603916 + 245 24 -279.9072278 -279.79264 0.004774491325 0.8361247356 0.8392614852 0.02418251879 + 246 24 -279.9941671 -279.896025 0.004089255843 0.2809227622 0.01060243293 0.01118973247 + 247 24 -278.8973689 -279.206496 0.01288029691 1.390234609 0.005326518563 0.06648378416 + 248 24 -279.590075 -279.55564 0.001434791018 1.950495712 1.4056319 0.05370353355 + 249 24 -279.9072386 -279.79264 0.004774943229 0.8361385582 0.8392625708 0.02418484015 +# GSF_112.xyz + config # atoms energy DFT energy energy error force DFT force force error + 250 30 -345.1428414 -345.175835 0.001099787279 2.717783384 1.057395322 0.1393371019 + 251 30 -346.8213325 -346.361714 0.01532061701 1.6320981 1.220284939 0.1010819808 + 252 30 -346.3061373 -345.795524 0.01702044399 2.435031121 2.112860875 0.1171529224 + 253 30 -344.8834516 -345.164602 0.009371679669 3.314987489 1.765832199 0.1576958872 + 254 30 -346.9668291 -346.593523 0.01244353764 1.327935537 0.01148867129 0.08670065177 + 255 30 -346.7938009 -346.396186 0.01325383111 1.743989434 0.9954683928 0.09783463277 + 256 30 -345.0939055 -345.319406 0.007516682785 3.756566851 1.772040852 0.1806000978 + 257 30 -345.6468551 -345.594794 0.00173536844 3.432645857 1.516014157 0.1670589876 + 258 30 -346.2843474 -345.98566 0.00995624537 2.709563559 1.406252265 0.1356658489 + 259 30 -345.7058793 -345.383994 0.01072951129 2.464665654 0.963574308 0.13389942 + 260 30 -346.9664564 -346.582564 0.01279641284 1.32870642 0.0126740587 0.08670344939 + 261 30 -345.3305431 -345.452139 0.004053195139 4.515828739 2.787719406 0.1519418929 + 262 30 -346.966836 -346.593523 0.01244376534 1.327919807 0.01148834 0.08669988209 + 263 30 -345.5935851 -345.281949 0.01038786965 2.922665543 1.873142686 0.1300383724 + 264 30 -346.157169 -345.928661 0.007616932828 3.42803556 2.100874472 0.1330089569 + 265 30 -344.6836135 -345.111657 0.01426811685 4.87813643 3.358068319 0.1517605655 + 266 30 -346.8140968 -346.367123 0.01489912587 1.700448289 1.335797131 0.1014030448 + 267 30 -346.9664062 -346.582565 0.0127947081 1.328695393 0.01254743735 0.08670444025 + 268 30 -344.5284456 -344.91356 0.012837147 4.30679737 3.441834403 0.1293440404 + 269 30 -346.3471173 -345.836703 0.01701381162 2.177883948 1.608769148 0.1178087924 + 270 30 -344.9135302 -344.984307 0.002359225817 3.517317775 2.542628782 0.122092966 + 271 30 -346.7846048 -346.393931 0.01302245877 1.941770224 1.211680725 0.09898842713 +# Liquid.xyz + config # atoms energy DFT energy energy error force DFT force force error + 272 100 -1104.74829 -1105.601723 0.008534329546 31.13590643 31.39853886 0.5826598142 + 273 100 -1099.007356 -1099.673012 0.006656557481 34.30763539 32.03167218 0.6355970492 + 274 100 -1123.744375 -1121.31506 0.0242931528 23.69463257 20.81076453 0.4843518851 +# Surface.xyz + config # atoms energy DFT energy energy error force DFT force force error + 275 24 -279.9941674 -279.911828 0.003430809358 0.2809230273 0.002753093533 0.01155715982 + 276 48 -551.0953781 -555.359452 0.08883487284 6.541312712 0.003020630398 0.1949601982 + 277 40 -458.209131 -459.216162 0.02517577443 5.605061426 5.0461364 0.1098503638 + 278 40 -459.8554229 -461.144076 0.03221632783 2.691145822 0.005582740008 0.08174930001 + 279 24 -279.8970746 -279.635146 0.01091369091 1.238573481 1.288799837 0.008644383713 + 280 30 -346.9668295 -346.592525 0.01247681774 1.32793475 0.008446203407 0.08664452133 + 281 30 -345.8871537 -345.744506 0.004754921864 3.992236552 3.124961367 0.08594721633 +# Volume_A15.xyz + config # atoms energy DFT energy energy error force DFT force force error + 282 8 -66.46788051 -66.990732 0.06535643627 9.752469663e-15 0 1.665479097e-15 + 283 8 -72.67646146 -72.957807 0.03516819273 2.586146435e-14 0 4.592824963e-15 + 284 8 -94.20621366 -94.145745 0.00755858243 1.888003685e-14 0 2.536262854e-15 + 285 8 -94.43981933 -94.554682 0.01435783313 5.386472433e-15 0 7.930900378e-16 + 286 8 -79.39814886 -79.438363 0.005026767697 2.732255702e-14 0 4.777139332e-15 + 287 8 -69.38946962 -69.627817 0.02979342197 4.097415198e-15 0 6.093939011e-16 + 288 8 -83.05531805 -82.604907 0.05630138147 5.707505975e-15 0 9.444123724e-16 + 289 8 14.36690687 14.89048 0.0654466408 4.4225873e-14 0 6.966360359e-15 + 290 8 -94.13472519 -94.367599 0.02910922586 1.366361161e-14 0 1.887762444e-15 + 291 8 -89.38757156 -89.248227 0.01741807051 7.77370779e-15 0 1.130389185e-15 + 292 8 -87.49741165 -87.211997 0.03567683079 6.822093797e-15 0 9.11308066e-16 + 293 8 -93.42285179 -93.66897 0.03076477666 2.411445427e-15 0 4.058488494e-16 + 294 8 -8.05187323 -7.989166 0.007838403786 7.012640574e-14 0 1.102472786e-14 + 295 8 -85.3779751 -84.982834 0.04939263793 2.716993442e-15 0 4.647613313e-16 + 296 8 -92.37490481 -92.536373 0.0201835236 1.315958485e-14 0 1.882608652e-15 + 297 8 -26.56925158 -26.77612 0.02585855302 5.079538464e-14 0 8.697279448e-15 + 298 8 -77.90929192 -77.544107 0.04564811452 4.172342826e-15 0 7.131159089e-16 + 299 8 -80.55632181 -80.114217 0.05526310126 7.985686614e-15 0 1.195874996e-15 + 300 8 -41.83202596 -42.143041 0.03887688062 4.657987766e-14 0 8.540891409e-15 + 301 8 -91.02235339 -91.040671 0.002289700674 5.29233855e-15 0 8.086702604e-16 + 302 8 -84.76781055 -84.499231 0.03357244376 3.520461367e-14 0 6.70250169e-15 + 303 8 -60.71236154 -61.825173 0.1391014324 7.011275997e-15 0 1.104512893e-15 + 304 8 -91.5794594 -91.156873 0.05282330009 3.722647197e-15 0 6.096739866e-16 + 305 8 -54.28408457 -54.658744 0.04683242815 1.027218023e-13 0 1.699815447e-14 + 306 8 -72.29317827 -72.277255 0.00199040924 2.147214247e-15 0 3.631173776e-16 + 307 8 -75.14428628 -74.923334 0.02761903549 4.875315485e-15 0 8.058016421e-16 + 308 8 -64.41647714 -64.798066 0.04769860741 8.515566542e-15 0 1.300175245e-15 + 309 8 -93.29905733 -93.048342 0.03133941583 1.392455458e-14 0 1.75636545e-15 + 310 8 -63.56375833 -64.38702 0.1029077093 3.169925692e-15 0 4.425351867e-16 + 311 8 -88.81067445 -88.352871 0.05722543104 1.824573667e-14 0 3.223116218e-15 +# Volume_BCC.xyz + config # atoms energy DFT energy energy error force DFT force force error + 312 2 -16.38936242 -16.763625 0.1871312901 8.438105833e-16 0 3.261280135e-16 + 313 2 16.19675433 16.314145 0.05869533665 6.012211515e-14 0 2.140301825e-14 + 314 2 -21.24238574 -21.209071 0.01665736942 3.105315998e-15 0 1.031580172e-15 + 315 2 -15.80560502 -15.780524 0.01254051028 3.075772419e-14 0 1.04682611e-14 + 316 2 -19.05526774 -19.002205 0.02653137193 5.049484454e-15 0 1.840167643e-15 + 317 2 -22.67434567 -22.620568 0.02688883674 8.42211374e-16 0 2.844946501e-16 + 318 2 4.04311049 4.096885 0.02688725502 1.697721462e-14 0 5.111651843e-15 + 319 2 56.2105911 56.26276 0.02608445186 2.167345189e-13 0 8.162180947e-14 + 320 2 -22.55797904 -22.585113 0.01356697915 1.62710774e-15 0 5.666763355e-16 + 321 2 -21.75972417 -21.795501 0.0178884163 1.403784713e-15 0 3.978299172e-16 + 322 2 33.30678917 33.110078 0.09835558332 4.389819223e-14 0 1.229051583e-14 + 323 2 -20.82125169 -20.885998 0.0323731563 1.078546098e-15 0 2.960594732e-16 + 324 2 -23.55239721 -23.601336 0.02446939304 1.098352585e-15 0 3.53350523e-16 + 325 2 -23.17147126 -23.207313 0.01792086946 1.690886327e-15 0 6.164070796e-16 + 326 2 -19.78146338 -19.898089 0.05831281177 3.071791199e-15 0 1.188863822e-15 + 327 2 -23.45038238 -23.405474 0.02245418985 1.35097431e-15 0 4.949744318e-16 + 328 2 -4.653232293 -4.781324 0.06404585371 8.217105136e-15 0 2.951342874e-15 + 329 2 -18.67517238 -18.864936 0.09488180756 5.14040454e-16 0 1.896631e-16 + 330 2 -17.53439276 -17.813086 0.1393466189 6.912475817e-16 0 2.521131452e-16 + 331 2 -11.04889659 -11.197201 0.07415220345 1.082601284e-14 0 4.046820749e-15 + 332 2 -23.68489671 -23.696705 0.00590414498 1.843452652e-15 0 5.315481851e-16 +# Volume_FCC.xyz + config # atoms energy DFT energy energy error force DFT force force error + 333 4 -19.13390887 -19.075994 0.01447871809 1.517335469e-14 0 3.900232098e-15 + 334 4 -35.26038882 -34.873619 0.0966924543 3.754176171e-16 0 8.829019691e-17 + 335 4 -43.93272346 -43.950003 0.004319884817 1.957527644e-15 0 4.836987292e-16 + 336 4 -41.03733831 -40.991909 0.01135732773 2.229474894e-15 0 5.093220406e-16 + 337 4 -43.4228254 -43.453929 0.00777589967 2.787997321e-14 0 8.011425939e-15 + 338 4 -42.67289278 -42.686077 0.003296054 9.84568285e-16 0 2.229119667e-16 + 339 4 -33.58842759 -33.224653 0.09094364633 5.773580884e-16 0 1.303933813e-16 + 340 4 -27.01189372 -26.862709 0.03729618105 5.151726288e-15 0 1.109453787e-15 + 341 4 -25.59030438 -25.519883 0.01760534598 2.863765244e-16 0 7.531591092e-17 + 342 4 3.441093749 3.463071 0.005494312716 2.696629063e-14 0 6.828072631e-15 + 343 4 -31.9073245 -31.59595 0.07784362479 8.890859753e-16 0 1.682681772e-16 + 344 4 -45.06068744 -45.100466 0.009944641012 1.71159984e-15 0 3.996665291e-16 + 345 4 -46.03981427 -46.052258 0.0031109323 1.705627547e-15 0 4.273202162e-16 + 346 4 -30.24326213 -30.001189 0.06051828302 8.403226845e-16 0 2.104797818e-16 + 347 4 -22.957351 -22.8504 0.02673775024 6.125121657e-16 0 1.416690839e-16 + 348 4 -9.130654755 -9.164691 0.008509061334 1.894766019e-14 0 4.742914684e-15 + 349 4 -24.21746226 -24.150343 0.01677981454 1.777054657e-16 0 4.452456922e-17 + 350 4 -46.44761241 -46.426795 0.005204351765 2.043289244e-15 0 5.31981866e-16 + 351 4 -28.62111495 -28.451145 0.04249248833 8.802221276e-15 0 2.537755885e-15 + 352 4 40.31615798 40.341566 0.006352005141 2.120221165e-14 0 5.59689556e-15 + 353 4 19.51151427 19.617912 0.02659943252 6.461385682e-14 0 1.647388493e-14 + 354 4 -27.06356399 -26.954384 0.02729499736 3.089999778e-16 0 7.849623729e-17 + 355 4 -46.3678929 -46.323696 0.01104922394 2.195905041e-15 0 5.105869431e-16 + 356 4 -45.87221055 -45.828947 0.01081588677 1.843344298e-15 0 4.174901166e-16 + 357 4 -38.47076405 -38.16029 0.0776185126 2.683812325e-15 0 6.998163623e-16 + 358 4 -33.06813795 -32.919741 0.03709923634 1.577584492e-14 0 4.412991963e-15 + 359 4 -41.34431995 -41.272675 0.01791123821 2.234618078e-15 0 5.98499928e-16 + 360 4 -39.95757678 -39.753322 0.05106369446 1.172665551e-15 0 2.900618248e-16 + 361 4 -37.66252943 -37.547435 0.02877360828 6.430065721e-15 0 1.652468671e-15 + 362 4 -36.89659259 -36.52595 0.09266064636 3.213653781e-15 0 8.769027171e-16 + 363 4 -45.03250721 -45.016087 0.004105053074 1.112789617e-15 0 2.434395278e-16 diff --git a/examples/PACKAGES/pod/Ta/Ta_training_errors.pod b/examples/PACKAGES/pod/Ta/Ta_training_errors.pod new file mode 100644 index 0000000000..39b7af3723 --- /dev/null +++ b/examples/PACKAGES/pod/Ta/Ta_training_errors.pod @@ -0,0 +1,20 @@ +**************** Begin of Error Analysis for the Training Data Set **************** +--------------------------------------------------------------------------------------------------- + File | # configs | # atoms | MAE energy | RMSE energy | MAE force | RMSE force +--------------------------------------------------------------------------------------------------- +Displaced_A15.xyz 9 576 0.011286 0.011334 0.113353 0.141650 +Displaced_BCC.xyz 9 486 0.012178 0.014005 0.240613 0.312191 +Displaced_FCC.xyz 9 432 0.001445 0.001591 0.082688 0.103800 +Elastic_BCC.xyz 100 200 0.004452 0.004783 0.000010 0.000013 +Elastic_FCC.xyz 100 400 0.002865 0.002923 0.000146 0.000207 +GSF_110.xyz 22 528 0.005804 0.006853 0.047276 0.097819 +GSF_112.xyz 22 660 0.010588 0.011555 0.123342 0.191090 +Liquid.xyz 3 300 0.013161 0.015355 0.567536 0.757847 +Surface.xyz 7 236 0.025400 0.037555 0.096121 0.295623 +Volume_A15.xyz 30 240 0.039281 0.048678 0.000000 0.000000 +Volume_BCC.xyz 21 42 0.049766 0.067554 0.000000 0.000000 +Volume_FCC.xyz 31 124 0.030056 0.041738 0.000000 0.000000 +--------------------------------------------------------------------------------------------------- +All files 363 4224 0.012917 0.025797 0.122473 0.260052 +--------------------------------------------------------------------------------------------------- +**************** End of Error Analysis for the Training Data Set **************** diff --git a/examples/PACKAGES/pod/Ta/XYZ/Displaced_A15.xyz b/examples/PACKAGES/pod/Ta/XYZ/Displaced_A15.xyz new file mode 100644 index 0000000000..b144703144 --- /dev/null +++ b/examples/PACKAGES/pod/Ta/XYZ/Displaced_A15.xyz @@ -0,0 +1,594 @@ +64 +Lattice="10.6000003815 0.0 0.0 0.0 10.6000003815 0.0 0.0 0.0 10.6000003815" Properties=species:S:1:pos:R:3:forces:R:3 energy=-754.220443 stress="23963.03 -518.08 331.99 -518.08 26158.899999999998 289.93 331.99 289.93 26014.94" +Ta 10.54497 10.54551 10.5956 0.738379 0.48581 0.018519 +Ta 2.6058 2.59577 2.66276 0.983004 0.695353 -0.423917 +Ta 1.29338 2.62737 0.06659 0.967488 0.116743 -0.589823 +Ta 3.97859 2.60074 0.05226 -0.084389 0.137046 -0.423367 +Ta 0.06826 1.26322 2.67108 -0.470328 1.296441 -0.423078 +Ta 0.03489 4.006 2.58088 -0.263493 -1.182047 0.521328 +Ta 2.60404 0.03209 1.27573 0.332524 -0.382338 0.466834 +Ta 2.61384 0.03978 4.00017 0.19652 -0.552756 -0.617059 +Ta 5.26731 10.53909 0.0525 0.340753 0.932737 -1.082711 +Ta 8.00375 2.64902 2.69207 -0.352834 -0.034069 -0.546853 +Ta 6.64426 2.6613 10.54 0.209447 -0.170553 0.255905 +Ta 9.33824 2.64457 0.03106 -1.248523 0.1324 -0.277314 +Ta 5.3522 1.2665 2.5671 -0.296298 1.327488 0.591352 +Ta 5.27655 4.04903 2.65011 0.225842 -1.705193 -0.220596 +Ta 7.9997 10.54384 1.3323 -0.602859 0.598417 0.360383 +Ta 7.97961 10.59814 4.02363 -0.487819 0.018537 -0.681676 +Ta 0.07703 5.36114 0.02699 -0.850702 -0.481463 -0.618219 +Ta 2.6646 7.93725 2.60955 -0.375888 0.3131 0.609637 +Ta 1.40379 7.96668 10.52251 -1.425719 -0.081346 0.714056 +Ta 3.99035 7.99423 10.59771 -0.152265 -0.539619 0.318009 +Ta 0.04355 6.56889 2.62727 -0.178473 1.482119 0.427439 +Ta 0.00703 9.28757 2.68364 0.269104 -1.208309 -0.327712 +Ta 2.56957 5.34141 1.33893 0.850349 -0.517951 0.275559 +Ta 2.72447 5.25375 4.04037 -0.588363 0.226576 -0.96233 +Ta 10.53684 10.5759 5.2221 0.629328 0.101208 1.170955 +Ta 2.66913 2.7096 7.94723 0.175608 -0.725726 0.018084 +Ta 1.35438 2.68364 5.23358 -0.672848 -0.376194 0.690747 +Ta 3.92914 2.57652 5.21831 1.314233 0.49323 0.453261 +Ta 0.08152 1.31737 7.90103 -0.403463 -0.248525 0.230807 +Ta 0.01596 3.94268 7.99393 -0.081478 0.863863 -0.071733 +Ta 2.6785 10.52779 6.63557 -0.387653 0.744336 -0.69563 +Ta 2.57563 10.5398 9.20066 0.204661 1.016501 1.272453 +Ta 5.28026 5.2908 10.53874 0.210489 -0.369673 0.610136 +Ta 8.02116 8.00301 2.56791 -0.618631 -0.801014 1.16881 +Ta 6.56126 7.9104 0.04457 1.247918 -0.045758 -0.325354 +Ta 9.26485 7.95508 10.58594 0.342738 -0.215167 -0.069832 +Ta 5.26103 6.62842 2.63265 0.441032 0.314676 -0.03073 +Ta 5.28955 9.23968 2.5673 0.215784 0.14419 0.976532 +Ta 8.00221 5.33276 1.34132 -0.277749 -0.258368 -0.418189 +Ta 7.91864 5.28423 3.97891 0.132647 0.303744 -0.143621 +Ta 5.27037 0.01177 5.31967 0.293403 0.10204 -0.586267 +Ta 7.97577 2.58846 7.90284 -0.0766 0.318418 0.741565 +Ta 6.67111 2.70945 5.31433 -1.193866 -0.235149 -0.180348 +Ta 9.29025 2.58105 5.29066 0.286858 0.294859 0.204099 +Ta 5.2532 1.26795 7.91799 0.289819 0.925706 0.429944 +Ta 5.32703 4.04747 7.87622 0.177769 -1.251772 0.201923 +Ta 7.8991 10.56576 6.68405 0.011121 0.010154 -0.513286 +Ta 8.01539 10.54873 9.32177 -0.770371 0.244167 -0.539961 +Ta 10.59055 5.23373 5.29112 -0.122463 0.783939 0.309844 +Ta 2.7178 8.02017 8.01996 -0.833015 -1.143659 -1.244648 +Ta 1.28755 7.95382 5.35947 0.318174 -0.327947 -0.137883 +Ta 3.98149 8.00712 5.27935 -0.672169 -0.306686 0.158866 +Ta 0.04771 6.7013 8.02541 0.000928 -1.568952 -0.556323 +Ta 10.53454 9.27538 7.94586 0.490919 0.513788 -0.187133 +Ta 2.60384 5.37826 6.65237 0.107427 -0.010953 -0.135414 +Ta 2.65026 5.25782 9.27591 0.0403 0.521312 0.035425 +Ta 5.30975 5.33548 5.25863 -0.196083 -0.020488 0.519869 +Ta 7.98152 7.93147 7.94727 -0.52423 -0.25306 0.358801 +Ta 6.58336 7.99956 5.3353 0.546995 -0.296434 -0.355434 +Ta 9.20518 8.00165 5.34211 0.753656 -0.424927 -0.364529 +Ta 5.28813 6.67781 8.01704 0.382562 -1.149823 -0.614214 +Ta 5.2968 9.20687 7.96818 0.395589 1.452637 -0.053896 +Ta 7.90382 5.25794 6.62358 0.295654 0.152651 -0.023568 +Ta 8.00072 5.28621 9.26356 -0.210447 -0.178269 0.331507 +64 +Lattice = "10.6000003815 0.0 0.0 0.0 10.6000003815 0.0 0.0 0.0 10.6000003815" Properties=species:S:1:pos:R:3:forces:R:3 energy=-753.865255 stress="25885.719999999998 -817.02 -36.62 -817.02 23024.370000000003 -107.14 -36.62 -107.14 29257.940000000002" +Ta 0.04908 0.00115 10.57826 -0.437757 -0.090743 0.15803 +Ta 2.61654 2.71455 2.72901 0.449605 -0.435267 -0.828991 +Ta 1.39595 2.61446 10.52477 -2.072616 -0.051825 0.877711 +Ta 3.90381 2.6756 0.06766 2.144694 -0.090086 0.075882 +Ta 0.05742 1.31249 2.58872 -0.607352 0.532786 0.378598 +Ta 0.05697 4.05163 2.67585 -0.777264 -1.885963 -0.048956 +Ta 2.58852 10.55529 1.39238 0.39704 0.642203 -1.068312 +Ta 2.6599 0.00552 4.01733 0.064098 0.179003 -0.177005 +Ta 5.26427 10.58342 10.56227 -0.033574 0.346172 0.680676 +Ta 7.89236 2.6016 2.71779 0.82825 0.497825 -0.656618 +Ta 6.6321 2.63976 10.53024 -0.906833 -0.010611 0.365963 +Ta 9.21243 2.59505 0.06665 1.376958 0.080901 -0.441221 +Ta 5.30011 1.36599 2.71012 -0.451121 -0.806818 -0.284864 +Ta 5.34341 4.00547 2.68181 -0.579497 -0.053233 -0.287661 +Ta 8.03029 10.56076 1.30843 -0.336212 0.217222 0.347111 +Ta 7.92561 0.06228 3.97753 0.289092 -0.611239 0.468926 +Ta 0.03512 5.22736 0.04735 -0.453067 0.31946 -0.683277 +Ta 2.66581 7.98939 2.66641 -0.662165 -0.149468 -0.087742 +Ta 1.29579 7.92632 10.58792 0.533672 -0.070014 0.096584 +Ta 3.93283 7.88849 0.0809 -0.020345 0.48243 -0.397113 +Ta 10.5959 6.57196 2.63734 -0.21413 1.634343 -0.170283 +Ta 10.56437 9.25635 2.72679 0.039077 -0.10791 -0.719333 +Ta 2.72037 5.31366 1.24606 -0.29128 0.032642 2.069655 +Ta 2.69611 5.37769 3.9661 0.124193 -0.201649 -0.71097 +Ta 0.07372 10.52817 5.29093 -0.789865 0.878036 0.020208 +Ta 2.61857 2.70351 8.02211 0.56874 -0.164877 -0.950145 +Ta 1.31355 2.72095 5.3785 -0.076491 -0.288 -0.243411 +Ta 3.89644 2.57087 5.2537 1.240837 0.47266 0.656808 +Ta 10.58888 1.30214 7.86943 0.255233 0.272119 0.455833 +Ta 0.04887 4.01408 7.90126 -0.289007 -0.346757 0.12366 +Ta 2.72928 0.06945 6.66193 -0.685761 -0.244829 -0.502888 +Ta 2.58101 0.04872 9.23137 0.339459 -0.233213 1.335765 +Ta 5.34108 5.36912 0.05283 -0.013471 -0.867347 -0.774099 +Ta 7.88186 7.9551 2.72317 0.734048 0.105961 -1.272735 +Ta 6.55598 7.99717 10.53185 1.370203 -0.182535 0.648941 +Ta 9.31791 7.96193 0.00269 -1.127055 -0.301221 0.303103 +Ta 5.24453 6.70165 2.62389 0.229886 -1.204827 0.172016 +Ta 5.32205 9.27675 2.72023 -0.32778 1.003783 -0.614408 +Ta 7.86861 5.30945 1.31803 0.764624 -0.183537 -0.038771 +Ta 7.92333 5.29865 3.91698 0.625441 0.03111 0.856974 +Ta 5.25271 10.51825 5.34383 0.561912 0.756882 -0.236387 +Ta 8.0222 2.60801 7.87152 -0.458387 0.66717 1.04408 +Ta 6.60212 2.59356 5.37931 0.070225 0.10084 -0.482484 +Ta 9.30602 2.68963 5.26783 -0.344876 -0.18676 -0.015312 +Ta 5.34458 1.3199 7.96406 -0.207209 0.12974 -0.023385 +Ta 5.27345 3.97769 7.88365 0.225407 0.210336 0.49958 +Ta 7.90209 0.06243 6.6921 0.296301 -0.597326 -1.321812 +Ta 7.9791 10.56722 9.28911 -0.274024 0.193096 0.130562 +Ta 0.08155 5.37803 5.24262 -1.153238 -0.394578 0.405264 +Ta 2.69772 8.006 7.99419 -0.445287 -0.699603 -0.114074 +Ta 1.38725 7.96453 5.37281 -1.117986 -0.159911 -0.252436 +Ta 3.9138 7.92522 5.25427 1.483723 -0.15328 0.336593 +Ta 10.54558 6.64409 7.90011 0.381189 -0.437364 0.391497 +Ta 0.0414 9.23222 7.94529 -0.069632 0.550601 0.135542 +Ta 2.6176 5.26509 6.55154 0.497368 0.356473 1.817883 +Ta 2.67779 5.27183 9.34564 -0.09738 0.356697 -2.092389 +Ta 5.37167 5.22358 5.28383 -1.082933 0.58337 0.189313 +Ta 7.97831 7.95033 7.98746 -0.334998 -0.148464 -0.752988 +Ta 6.58772 7.97118 5.22845 0.250508 -0.279802 0.963668 +Ta 9.29703 7.96398 5.22074 -0.269342 -0.065478 0.796032 +Ta 5.35894 6.66603 8.02645 -0.160453 -0.945482 -0.543903 +Ta 5.25491 9.2658 7.91135 0.540075 0.33829 0.275545 +Ta 7.86723 5.29649 6.61035 0.852005 0.19428 0.109663 +Ta 8.01927 5.21862 9.29005 -0.365475 0.483588 -0.393695 +64 +Lattice = "10.6000003815 0.0 0.0 0.0 10.6000003815 0.0 0.0 0.0 10.6000003815" Properties=species:S:1:pos:R:3:forces:R:3 energy=-754.0221 stress="26594.42 1368.85 19.48 1368.85 26417.43 -1442.27 19.48 -1442.27 23937.75" +Ta 10.59872 10.5966 0.05505 -0.231571 0.031614 -0.560153 +Ta 2.72054 2.66769 2.56793 -0.779697 -0.12909 0.784258 +Ta 1.2783 2.60895 0.03547 0.744629 0.548126 -0.214124 +Ta 3.95508 2.65628 10.5551 -0.165396 0.001128 0.026529 +Ta 0.03293 1.39934 2.6967 0.072305 -0.873594 -0.208971 +Ta 10.5651 4.05678 2.65596 0.527021 -1.331302 0.031311 +Ta 2.60171 10.52714 1.285 0.350354 0.537482 0.600499 +Ta 2.68709 10.58122 3.91851 -0.372039 0.361715 0.809071 +Ta 5.31795 0.08026 0.03906 -0.106989 -0.635521 -0.720814 +Ta 8.02486 2.64122 2.59891 -0.739467 0.359337 0.641206 +Ta 6.60369 2.73118 0.06843 0.678906 -0.310297 -0.697991 +Ta 9.30745 2.57138 10.58055 -1.01243 0.693756 -0.108245 +Ta 5.35248 1.38217 2.58572 -0.13929 -0.071214 0.685498 +Ta 5.27678 4.05493 2.58839 0.361124 -1.418968 0.248615 +Ta 7.97704 10.56983 1.33943 -0.226745 0.137547 0.385956 +Ta 7.9205 10.58925 4.02197 -0.097537 0.228845 -1.559747 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0.710669 -0.438506 +Ta 0.04337 6.69689 8.01066 -0.426712 -1.619512 -0.55647 +Ta 10.54014 9.26136 7.89857 0.447195 1.282555 0.234867 +Ta 2.68344 5.29148 6.55058 -0.713159 0.045261 0.661323 +Ta 2.61535 5.26646 9.22004 -0.124682 0.621019 0.504493 +Ta 5.22677 5.33996 5.32711 1.047955 -1.01859 -0.083156 +Ta 7.93781 8.02504 7.94133 -0.089305 -0.92943 0.174588 +Ta 6.58943 7.89688 5.28857 1.109411 0.43459 0.232028 +Ta 9.26138 8.02661 5.25779 -0.279333 -0.594174 0.435718 +Ta 5.27411 6.62462 8.02195 0.25952 0.675178 -0.659935 +Ta 5.30985 9.30627 7.88256 -0.174466 -0.148032 0.732729 +Ta 7.99384 5.30652 6.67382 -0.405756 0.105152 -0.448951 +Ta 7.89346 5.23521 9.29012 0.232414 0.496659 0.293761 +64 +Lattice = "10.6000003815 0.0 0.0 0.0 10.6000003815 0.0 0.0 0.0 10.6000003815" Properties=species:S:1:pos:R:3:forces:R:3 energy=-754.279613 stress="23907.050000000003 444.79 -765.15 444.79 24515.940000000002 375.59 -765.15 375.59 27487.829999999998" +Ta 0.00046 10.54735 10.58932 0.114704 0.911029 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2.60926 0.349202 0.295946 0.196375 +Ta 5.365 9.35513 2.65232 -0.276908 -1.072093 0.33487 +Ta 7.99421 5.27285 1.26512 -0.338816 0.417402 0.989409 +Ta 7.93677 5.32858 3.96514 -0.064889 -0.126317 0.026895 +Ta 5.29831 0.06384 5.34991 -0.237157 -0.294846 -0.502816 +Ta 7.98101 2.63404 7.9256 -0.201557 -0.256297 0.618786 +Ta 6.68687 2.58375 5.27465 -0.880538 0.491034 0.225753 +Ta 9.31724 2.59345 5.36746 -0.514197 0.139552 -0.594594 +Ta 5.30469 1.39236 7.90055 -0.241299 -1.127636 0.542064 +Ta 5.36637 3.96474 7.94588 -0.457508 0.623304 -0.045721 +Ta 7.96852 10.54416 6.59542 0.045419 0.456297 0.883036 +Ta 8.01553 0.03504 9.33832 -0.703646 -0.11872 -0.79377 +Ta 10.53751 5.2766 5.33019 0.186467 0.354842 -0.464356 +Ta 2.67185 7.99879 7.94992 -0.462825 -0.70472 -0.660751 +Ta 1.32425 7.97625 5.27971 -0.162279 -0.301471 0.211964 +Ta 3.99685 7.99185 5.33585 0.128267 -0.133747 -0.138891 +Ta 0.00789 6.57979 7.98241 0.224508 0.703879 -0.465686 +Ta 10.56258 9.24146 7.92821 0.298346 0.405066 0.164699 +Ta 2.62183 5.25654 6.57113 0.142704 0.580891 0.073062 +Ta 2.62673 5.24695 9.20881 0.295489 0.626384 1.099379 +Ta 5.2818 5.28462 5.32566 0.254473 0.449594 -0.359163 +Ta 7.95127 7.97098 7.89566 -0.109482 -0.099213 1.128432 +Ta 6.69889 8.00506 5.30113 -1.722141 -0.416627 -0.484246 +Ta 9.22006 8.02217 5.33119 1.590079 -0.664694 -0.530738 +Ta 5.3507 6.64908 7.93434 -0.272774 -0.59058 -0.047159 +Ta 5.22906 9.26778 7.99824 0.577132 0.931079 -0.408552 +Ta 7.96263 5.26515 6.66322 -0.184291 0.081851 -0.89845 +Ta 8.00683 5.33642 9.24793 -0.405275 -0.01231 0.25158 +64 +Lattice = "10.6000003815 0.0 0.0 0.0 10.6000003815 0.0 0.0 0.0 10.6000003815" Properties=species:S:1:pos:R:3:forces:R:3 energy=-753.777209 stress="31083.73 984.91 488.79 984.91 26853.05 -530.71 488.79 -530.71 21811.85" +Ta 0.03525 10.52946 0.01429 -0.625379 0.911584 -0.075876 +Ta 2.67988 2.6352 2.61064 -0.661 -0.104938 -0.074584 +Ta 1.30583 2.57403 10.55611 0.849169 0.350685 0.363742 +Ta 4.00357 2.65046 10.56488 -0.371611 0.087052 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5.27023 4.0071 0.348505 0.46978 0.347783 +Ta 5.35908 0.08115 5.27632 -0.722672 -0.863673 0.500885 +Ta 8.00681 2.60911 7.87611 -0.950848 0.649728 1.17634 +Ta 6.63107 2.65234 5.3649 -0.782252 0.346241 -0.630632 +Ta 9.21464 2.71799 5.26365 0.65968 -0.244425 -0.123044 +Ta 5.22432 1.25125 8.02611 0.739331 1.510791 -0.273571 +Ta 5.22168 3.92029 7.91312 0.722496 0.766488 0.226631 +Ta 8.01588 0.04144 6.68445 -0.372854 -0.445221 -0.493611 +Ta 7.96204 10.55369 9.32548 -0.03274 0.375548 -0.623519 +Ta 0.01039 5.30368 5.2336 -0.715394 0.046629 0.901905 +Ta 2.5862 7.96502 7.96459 0.830832 -0.094714 -0.350325 +Ta 1.28578 7.88946 5.26227 1.126795 0.658952 0.004566 +Ta 3.96511 7.98863 5.30323 -0.273909 0.013132 -0.023712 +Ta 0.00505 6.67243 8.01234 -0.065254 -1.564213 -0.39785 +Ta 10.5258 9.23159 7.95484 0.714286 1.608236 -0.153688 +Ta 2.60834 5.24378 6.55963 0.476601 0.174876 0.899274 +Ta 2.60865 5.35101 9.24068 0.460063 -0.232332 0.21727 +Ta 5.34566 5.33553 5.26912 -1.0005 -0.062573 0.768202 +Ta 8.01116 7.98477 7.98864 -0.941009 -0.538031 -0.670857 +Ta 6.61332 7.98663 5.33587 0.694566 -0.00045 -0.06064 +Ta 9.34421 7.88519 5.33887 -1.50427 0.871847 -0.00909 +Ta 5.30405 6.66664 7.973 -0.127756 -0.408974 -0.168376 +Ta 5.3561 9.34104 7.93015 -0.198165 -1.429389 0.216524 +Ta 7.87231 5.36354 6.69962 0.402284 -0.367694 -0.602329 +Ta 7.98446 5.25368 9.3376 -0.122238 0.277788 -0.243182 +64 +Lattice = "10.6000003815 0.0 0.0 0.0 10.6000003815 0.0 0.0 0.0 10.6000003815" Properties=species:S:1:pos:R:3:forces:R:3 energy=-754.048643 stress="27656.57 549.87 1164.0900000000001 549.87 24561.93 -1132.43 1164.0900000000001 -1132.43 25335.96" +Ta 10.58466 10.52281 10.54428 0.51911 1.030769 0.289199 +Ta 2.58906 2.62515 2.58331 0.980313 0.465455 0.986329 +Ta 1.33407 2.72467 0.03386 -0.636192 -0.969554 -0.333663 +Ta 3.90797 2.72086 10.53991 1.707244 -0.292948 0.571866 +Ta 0.07897 1.2643 2.65645 -0.600839 0.915626 -0.026383 +Ta 0.02729 3.96468 2.62566 -0.026464 0.178205 0.595013 +Ta 2.71828 0.03582 1.37493 -0.503659 -0.164847 -1.238234 +Ta 2.71013 0.01388 3.94029 -0.26741 0.122146 0.391015 +Ta 5.24382 0.05221 10.59611 0.985051 -0.524959 -0.239796 +Ta 8.00676 2.68277 2.72931 -0.040705 0.112169 -1.076862 +Ta 6.67012 2.581 0.05294 -0.795944 0.604015 0.013416 +Ta 9.2906 2.70214 10.5277 0.106867 -0.725536 0.830297 +Ta 5.31566 1.36303 2.63231 0.204579 -0.39964 0.160289 +Ta 5.36545 3.97557 2.63811 -0.35758 0.374857 -0.341338 +Ta 7.9635 0.07881 1.30941 -0.122693 -0.323484 0.045005 +Ta 8.01171 0.06526 3.99574 -0.213713 -0.382574 -0.612077 +Ta 10.5812 5.22205 0.06058 0.340369 1.238874 -0.422064 +Ta 2.58751 8.02506 2.67969 0.836087 -0.974582 -0.640712 +Ta 1.32816 7.92066 10.55287 0.3286 -0.149546 0.174414 +Ta 3.98668 7.91992 10.56445 -0.068023 0.343984 0.387619 +Ta 0.00065 6.67904 2.65936 -0.006212 -0.780593 0.078132 +Ta 0.05141 9.2904 2.64974 -0.390999 -0.009998 -0.048165 +Ta 2.65941 5.21716 1.36289 0.011633 0.757694 -0.318475 +Ta 2.67774 5.34503 4.02694 -0.206769 -0.188612 -0.829644 +Ta 0.07746 0.06322 5.35824 -0.166456 -0.826729 -0.728653 +Ta 2.67942 2.71807 8.01719 -0.311027 -0.729342 -0.903137 +Ta 1.37014 2.70616 5.31634 0.189855 -0.02996 -0.111687 +Ta 4.04242 2.65384 5.28532 -0.699395 0.065315 0.059883 +Ta 10.59566 1.39908 7.95465 0.507488 -1.93197 -0.080117 +Ta 10.51853 3.8922 7.91939 1.002489 2.435127 0.268143 +Ta 2.65129 0.0155 6.54214 0.056264 0.079221 1.857275 +Ta 2.68757 10.53742 9.30663 -0.393454 0.179293 -0.909888 +Ta 5.29366 5.33327 10.53757 0.377812 -0.518568 1.064217 +Ta 7.98799 8.02663 2.73107 -0.740413 -0.111466 -0.791724 +Ta 6.6836 7.95804 10.58871 -0.388073 0.234483 0.294061 +Ta 9.35116 7.96667 0.00673 -1.079729 -0.437475 -0.039029 +Ta 5.25103 6.63708 2.69902 0.341543 0.027342 -0.389479 +Ta 5.25134 9.28648 2.56753 0.545209 0.148316 0.627297 +Ta 7.99616 5.36815 1.3789 -0.304224 -0.13761 -0.04399 +Ta 8.00478 5.33099 4.04177 -0.265505 0.058703 -0.773223 +Ta 5.22309 0.05914 5.36259 1.064104 -0.650463 -0.956514 +Ta 8.03289 2.6841 7.99696 -1.569866 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-0.427437 0.491553 0.583332 +Ta 5.29905 6.5928 8.01852 -0.005096 0.425504 -0.692783 +Ta 5.2848 9.23686 8.0324 0.055915 0.11712 -0.271961 +Ta 7.94377 5.22663 6.66616 -0.103255 0.624955 0.0228 +Ta 8.02399 5.3012 9.33589 -0.539595 0.360082 -0.504485 +64 +Lattice = "10.6000003815 0.0 0.0 0.0 10.6000003815 0.0 0.0 0.0 10.6000003815" Properties=species:S:1:pos:R:3:forces:R:3 energy=-754.317603 stress="19468.33 -58.66 -1082.3899999999999 -58.66 27430.38 -1004.03 -1082.3899999999999 -1004.03 27246.98" +Ta 10.59125 10.59066 0.01705 -0.118141 -0.145557 -0.396942 +Ta 2.66355 2.56976 2.70172 0.219448 0.641719 -0.568891 +Ta 1.28225 2.66379 0.00075 0.804753 -0.213095 0.055931 +Ta 3.97426 2.68113 0.01584 -0.5516 -0.108225 0.097343 +Ta 0.04505 1.26937 2.60223 -0.282662 0.758456 0.398993 +Ta 0.00712 3.91022 2.683 -0.114677 0.106269 -0.518987 +Ta 2.72684 10.52432 1.35392 -0.726917 0.472688 -0.797823 +Ta 2.65771 10.58165 3.96524 -0.077037 0.011007 0.534617 +Ta 5.24942 0.01366 0.0772 0.258031 -0.214153 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0.772419 0.170547 0.489784 +Ta 4.01712 2.69857 5.29807 -0.593672 -0.373102 0.08628 +Ta 0.0291 1.26201 7.95665 -0.228249 1.225911 0.153224 +Ta 0.01323 4.01408 7.91542 -0.130807 -1.640213 -0.047405 +Ta 2.6335 0.07389 6.60337 -0.001447 -0.190083 0.039412 +Ta 2.62747 0.02086 9.22021 -0.039118 0.087686 0.983273 +Ta 5.37311 5.37921 0.00104 -0.959972 -0.838327 0.018335 +Ta 7.9566 8.01813 2.65235 0.04766 -0.892332 -0.496011 +Ta 6.57317 7.93825 10.57796 0.775293 0.395418 -0.12899 +Ta 9.2694 7.88151 10.53712 -0.581566 0.421257 0.44285 +Ta 5.22009 6.55334 2.65222 0.48966 1.629995 -0.065174 +Ta 5.33963 9.271 2.62989 0.037846 -0.612714 0.384536 +Ta 8.02119 5.29672 1.35359 -0.362251 0.224738 -0.893573 +Ta 7.94827 5.36972 3.97268 0.104266 -0.263664 0.222094 +Ta 5.3297 10.56835 5.37217 -0.099087 0.370321 -0.98499 +Ta 7.91532 2.64246 8.00295 0.680096 -0.069447 -0.387023 +Ta 6.62199 2.68295 5.3771 0.284007 -0.162815 -0.500346 +Ta 9.2514 2.68433 5.35239 -0.118786 -0.470272 -0.408554 +Ta 5.32938 1.27255 7.97134 -0.303978 0.286044 0.13783 +Ta 5.30418 3.93812 7.93568 0.040155 0.762457 0.076378 +Ta 7.95987 10.54938 6.61642 -0.218528 0.46405 0.105442 +Ta 7.87538 0.02651 9.23341 0.304713 -0.390603 0.650333 +Ta 0.01871 5.23215 5.21873 -0.275057 0.30265 1.189576 +Ta 2.58005 8.01801 8.00091 0.903103 -0.811538 -0.942974 +Ta 1.35622 7.90716 5.21911 -0.69223 0.095275 0.734107 +Ta 3.91664 8.00527 5.23273 1.355059 -0.299637 0.764864 +Ta 0.05597 6.54262 7.99991 -0.53468 1.450745 -0.817521 +Ta 0.05678 9.22328 7.97883 -0.723123 0.147795 -0.085492 +Ta 2.66025 5.35371 6.64491 0.12943 -0.14096 -0.631864 +Ta 2.64384 5.23012 9.2296 0.184014 0.70864 1.326423 +Ta 5.34418 5.35604 5.295 -0.670333 -0.337693 0.183358 +Ta 7.96554 7.96325 7.88581 0.240713 -0.060137 0.461609 +Ta 6.67445 7.93954 5.26624 -0.870954 0.115388 0.099246 +Ta 9.32253 7.94305 5.27672 -0.121051 -0.177459 -0.101598 +Ta 5.37998 6.62136 8.01604 -0.697928 -0.125018 -0.551236 +Ta 5.23732 9.22012 7.8725 0.142822 0.596726 0.634521 +Ta 7.90914 5.35867 6.63564 0.470037 -0.554497 -0.783277 +Ta 7.8945 5.29107 9.20052 0.619005 0.147575 1.411797 +64 +Lattice = "10.6000003815 0.0 0.0 0.0 10.6000003815 0.0 0.0 0.0 10.6000003815" Properties=species:S:1:pos:R:3:forces:R:3 energy=-753.969161 stress="24114.940000000002 317.58 426.17 317.58 28035.48 -838.5899999999999 426.17 -838.5899999999999 25020.420000000002" +Ta 10.59947 10.59661 10.52413 -0.226907 -0.080536 0.902052 +Ta 2.59454 2.65092 2.68446 0.776819 0.171288 -0.551025 +Ta 1.33041 2.674 10.58143 0.176394 -0.183256 0.204614 +Ta 3.95295 2.58315 10.54506 0.854273 0.68598 0.610189 +Ta 10.59883 1.31774 2.66978 -0.091936 0.35913 -0.579748 +Ta 10.57967 3.96662 2.60593 0.084104 0.473431 0.095227 +Ta 2.59254 0.00678 1.31972 0.598698 0.099657 -0.823976 +Ta 2.59169 0.03133 3.90382 0.425043 -0.081448 1.419933 +Ta 5.37939 0.04023 0.07113 -1.005574 -0.469543 -0.545443 +Ta 7.94984 2.73234 2.65636 0.080843 -0.503649 -0.229292 +Ta 6.7035 2.71875 10.57105 -1.075835 -0.284081 0.217795 +Ta 9.33869 2.66536 10.5534 -0.645726 -0.07901 0.309219 +Ta 5.38144 1.37363 2.59678 -0.660687 -0.7539 0.448111 +Ta 5.27263 3.99656 2.66272 0.021249 -0.323657 0.146107 +Ta 7.96657 0.06435 1.30009 0.116005 -0.264227 0.267969 +Ta 7.99235 0.04847 3.89505 -0.241556 -0.152596 0.888561 +Ta 0.0218 5.29659 10.5698 0.190539 -0.014165 0.267054 +Ta 2.73175 8.00138 2.71285 -1.053594 -0.284418 -0.953258 +Ta 1.31806 7.96372 10.54256 -0.136246 -0.133944 0.366015 +Ta 3.91844 7.96217 10.56452 0.996651 0.062808 0.124581 +Ta 0.03602 6.66478 2.64422 0.197253 -0.463833 -0.145331 +Ta 10.5258 9.31439 2.65344 0.724814 -0.437657 -0.379722 +Ta 2.66149 5.31748 1.25965 -0.022671 0.017877 1.049002 +Ta 2.71043 5.3142 3.96356 -0.229855 -0.004722 -0.591605 +Ta 0.01714 0.02895 5.25397 -0.154714 -0.160145 0.666203 +Ta 2.64597 2.62331 8.00147 0.380032 0.718636 -0.704725 +Ta 1.34375 2.63266 5.31467 0.392862 -0.03449 -0.003614 +Ta 4.01969 2.72066 5.33483 -1.339879 -0.221236 -0.290386 +Ta 0.05334 1.28072 7.94153 -0.439149 1.033607 -0.306897 +Ta 10.56225 3.9163 7.87893 0.077647 0.175986 0.172003 +Ta 2.67491 10.58095 6.65598 -0.034472 0.357047 -1.370013 +Ta 2.61935 0.04143 9.225 0.449865 -0.403463 1.302128 +Ta 5.37858 5.37062 0.02738 -0.971327 -1.005554 -0.649326 +Ta 8.01211 7.93604 2.73 -0.650844 -0.187724 -0.927616 +Ta 6.6093 7.90613 0.06492 0.276128 0.710737 -0.478142 +Ta 9.28311 7.87808 10.53355 -0.273083 0.488493 0.413712 +Ta 5.22651 6.57935 2.58919 0.641086 0.512876 0.520235 +Ta 5.36331 9.19414 2.65024 0.022943 1.480425 0.177898 +Ta 7.9726 5.27207 1.2508 0.18907 0.389324 1.308572 +Ta 7.89187 5.26738 3.98139 0.703866 0.272666 -0.675214 +Ta 5.30786 0.02387 5.37311 -0.441452 -0.182156 -1.394336 +Ta 7.90554 2.64139 7.96721 0.778455 0.069504 -0.485925 +Ta 6.54626 2.62801 5.34703 1.838904 0.098736 -0.497372 +Ta 9.30386 2.63489 5.25676 -1.018893 -0.04522 0.187076 +Ta 5.34196 1.30641 7.91047 -0.440112 1.103483 0.738039 +Ta 5.33435 4.01755 7.93742 -0.433146 -1.463369 0.322362 +Ta 7.87923 10.59827 6.57191 0.570104 -0.011791 0.650285 +Ta 7.91667 0.07787 9.29291 0.417554 -0.726222 -0.85977 +Ta 0.00407 5.21804 5.29085 -0.306761 0.830359 -0.270748 +Ta 2.64244 8.01096 7.89122 -0.154505 -0.65194 -0.071913 +Ta 1.27073 7.96757 5.24059 1.78038 -0.289728 0.312266 +Ta 4.05652 7.94422 5.24628 -1.766243 -0.059655 0.397705 +Ta 10.55504 6.5449 8.02866 0.326135 1.292787 -0.813062 +Ta 10.54757 9.32356 7.97367 0.218025 -1.545104 -0.663048 +Ta 2.57132 5.31124 6.54943 0.638753 -0.09298 1.309355 +Ta 2.70552 5.36844 9.25923 -0.31279 -0.257789 -0.758911 +Ta 5.37917 5.32156 5.36422 -1.051024 0.088554 -0.982928 +Ta 7.96636 7.91391 7.89315 -0.365514 0.575159 0.279003 +Ta 6.60266 8.02328 5.30029 1.44818 -0.312672 -0.021217 +Ta 9.34959 7.99431 5.26212 -1.787702 -0.359966 0.327963 +Ta 5.27917 6.54337 7.93235 -0.08343 2.464228 0.472227 +Ta 5.31647 9.3383 7.99422 -0.013579 -1.711441 -0.018178 +Ta 7.90244 5.24771 6.59897 0.734729 0.047141 0.508435 +Ta 7.93795 5.34891 9.25032 0.301803 -0.342634 -0.33915 +64 +Lattice = "10.6000003815 0.0 0.0 0.0 10.6000003815 0.0 0.0 0.0 10.6000003815" Properties=species:S:1:pos:R:3:forces:R:3 energy=-754.141988 stress="22301.33 -285.37 -20.8 -285.37 25600.899999999998 162.91 -20.8 162.91 28086.86" +Ta 10.53107 10.5509 0.0015 0.70485 0.845648 -0.070019 +Ta 2.70215 2.61155 2.65638 -0.286099 0.325604 -0.074327 +Ta 1.39743 2.61545 0.05847 -1.474313 -0.095142 -0.280113 +Ta 3.97713 2.68268 10.5346 0.156378 -0.098493 0.356179 +Ta 0.03222 1.38317 2.60891 -0.081506 -1.587414 0.159126 +Ta 10.56764 3.92107 2.7266 0.259373 1.331992 -0.73363 +Ta 2.59022 10.55975 1.32456 0.049236 0.371753 0.102809 +Ta 2.70858 0.00916 4.05153 -0.701193 -0.070601 -1.695173 +Ta 5.26413 10.53793 0.03804 0.195324 0.197551 -0.279303 +Ta 7.92699 2.58218 2.67357 -0.196352 0.687631 -0.299411 +Ta 6.56938 2.58335 0.00915 0.481385 0.355506 0.054864 +Ta 9.21553 2.70158 0.00339 1.079668 -0.370583 0.25622 +Ta 5.29644 1.25773 2.66315 0.219113 1.844104 -0.251113 +Ta 5.25049 4.05699 2.72857 0.405022 -1.35655 -0.365109 +Ta 7.95797 0.00795 1.26652 -0.349291 -0.012386 0.95892 +Ta 7.95876 0.0029 3.97425 -0.085176 -0.246415 0.146522 +Ta 0.00111 5.29169 0.0101 0.244936 -0.074089 0.083447 +Ta 2.62824 7.99165 2.57985 0.090964 -0.453594 0.8187 +Ta 1.27056 8.03072 0.02474 0.413629 -0.598829 -0.229027 +Ta 3.95298 7.86756 0.04116 0.152752 0.468204 -0.422925 +Ta 10.52695 6.6817 2.6853 0.300417 -1.266839 -0.375852 +Ta 0.02498 9.27815 2.68712 -0.304899 0.803536 -0.158136 +Ta 2.65962 5.24127 1.35865 -0.043804 0.363366 -0.570782 +Ta 2.68315 5.34774 4.00482 -0.286335 -0.186484 -0.056142 +Ta 10.59249 0.03152 5.33264 0.313027 -0.429223 -0.38406 +Ta 2.58832 2.58393 7.94631 0.844596 0.451826 -0.031232 +Ta 1.37297 2.61641 5.29619 -0.990905 0.328928 -0.096763 +Ta 3.95207 2.62642 5.27401 1.187182 0.414363 0.303667 +Ta 0.01362 1.29568 7.93105 -0.217583 0.454567 0.400647 +Ta 0.06717 3.99538 7.88147 -0.472589 -0.121955 0.480331 +Ta 2.72677 10.57217 6.60708 -0.58854 0.058778 0.860541 +Ta 2.713 10.58575 9.24417 -0.506506 0.039032 0.567002 +Ta 5.30308 5.35945 0.05831 -0.152176 -0.937176 -0.30934 +Ta 7.87019 7.94183 2.57359 1.036899 0.327117 1.33664 +Ta 6.65928 7.9017 0.0785 -1.124811 0.536497 -0.907975 +Ta 9.22504 7.86881 10.58464 0.924083 0.364728 -0.065373 +Ta 5.29923 6.68288 2.66667 -0.266393 -0.338893 0.356213 +Ta 5.34057 9.3156 2.71909 -0.369711 -1.091863 -0.151577 +Ta 7.9974 5.33778 1.31662 -0.337005 -0.510079 -0.103385 +Ta 8.0053 5.25623 3.92597 -0.472408 0.14717 1.386647 +Ta 5.25104 0.03317 5.26596 1.390735 -0.14389 0.946126 +Ta 7.98045 2.60832 7.99115 0.289511 0.923595 -0.088863 +Ta 6.70353 2.60779 5.33602 -1.549564 0.47403 -0.141706 +Ta 9.2746 2.58651 5.33229 0.918837 0.547058 -0.191653 +Ta 5.38008 1.39809 7.98274 -0.530078 -0.860802 -0.130916 +Ta 5.33862 3.99447 7.94033 -0.428322 -0.31397 0.179289 +Ta 7.95961 0.05884 6.68706 -0.114391 -0.600564 -1.150373 +Ta 7.95876 0.02794 9.26141 -0.363392 -0.320188 0.423549 +Ta 0.06343 5.2606 5.22321 -0.328214 0.242764 0.905362 +Ta 2.68463 7.97169 7.9776 -0.420291 -0.285961 -0.011666 +Ta 1.29864 7.91228 5.24043 0.869986 0.358854 0.269282 +Ta 3.95071 8.01668 5.34254 0.539614 -0.279841 -0.051604 +Ta 10.52651 6.66919 7.95196 0.773319 -0.746678 -0.127338 +Ta 10.55688 9.28857 7.96148 0.62099 -0.258731 -0.038343 +Ta 2.70803 5.32339 6.70382 -0.389582 -0.121461 -1.219023 +Ta 2.57492 5.22962 9.24619 0.509556 0.339673 1.192371 +Ta 5.22267 5.3038 5.33156 1.3354 0.250454 0.009213 +Ta 7.98999 7.90061 7.96163 -0.945486 0.84251 -0.352597 +Ta 6.68533 8.02176 5.30974 -0.632817 -0.296567 -0.005138 +Ta 9.34825 7.99677 5.29878 -1.180526 -0.264671 -0.130746 +Ta 5.33163 6.57634 7.98884 -0.009265 1.176676 -0.00019 +Ta 5.29614 9.34403 7.95803 0.264039 -1.003617 -0.12967 +Ta 8.00726 5.27369 6.70227 -0.286454 -0.101025 -2.091338 +Ta 7.97483 5.326 9.24028 -0.084847 -0.42894 1.218267 diff --git a/examples/PACKAGES/pod/Ta/XYZ/Displaced_BCC.xyz b/examples/PACKAGES/pod/Ta/XYZ/Displaced_BCC.xyz new file mode 100644 index 0000000000..f2de497d5e --- /dev/null +++ b/examples/PACKAGES/pod/Ta/XYZ/Displaced_BCC.xyz @@ -0,0 +1,504 @@ +54 +Lattice = "9.96000003815 0.0 0.0 0.0 9.96000003815 0.0 0.0 0.0 9.96000003815" Properties=species:S:1:pos:R:3:forces:R:3 energy=-631.019667 stress="48457.11 -1136.2 -2351.6499999999996 -1136.2 49582.49 -508.49999999999994 -2351.6499999999996 -508.49999999999994 49591.75" +Ta 0.03088 9.94467 0.03567 -0.612376 -0.402684 -1.345349 +Ta 1.76644 1.66184 1.44089 -1.2057 1.054325 2.428563 +Ta 3.15336 9.91786 0.09806 1.832799 -0.872674 -1.263279 +Ta 9.90797 3.4076 9.86152 0.297218 -1.020932 0.904226 +Ta 3.35029 3.41556 0.08196 -0.474781 -0.303924 -0.630438 +Ta 9.87659 0.24016 3.2897 1.017582 -2.732856 0.243285 +Ta 3.19754 9.8139 3.31195 1.086563 0.951134 0.062863 +Ta 0.08403 3.3137 3.13958 -0.885405 -1.158694 1.624432 +Ta 3.39974 3.48704 3.44694 -0.379616 -1.521174 -1.132181 +Ta 5.07318 1.57764 1.57293 -1.924629 1.561628 0.647121 +Ta 6.63264 0.09181 0.15115 -0.072574 -1.323405 -2.650495 +Ta 8.39478 1.48796 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6.4397 6.55776 9.88777 1.902994 0.646598 1.055407 +Ta 8.2046 8.46737 1.69724 -0.705785 -1.624672 0.59768 +Ta 6.47327 6.53333 3.348 1.087057 0.860747 -0.071448 +Ta 1.63781 1.56651 4.86513 0.303333 0.759117 0.988318 +Ta 9.7163 0.09312 6.79336 1.972395 -0.68173 -1.740951 +Ta 1.61582 1.57397 8.30893 0.534301 0.691166 0.33332 +Ta 3.49451 0.05066 6.70224 -2.318362 -0.853012 0.193493 +Ta 9.94977 3.38199 6.78886 -0.299979 -1.645948 -1.888923 +Ta 3.18672 3.36165 6.43952 0.586136 -0.962061 1.644513 +Ta 4.89114 1.58583 5.10545 0.895504 0.96948 -1.159718 +Ta 8.35054 1.66148 5.06446 -0.650427 1.385707 -0.230145 +Ta 4.86816 1.73116 8.31179 0.899776 0.423663 0.126451 +Ta 6.68153 9.92387 6.63426 -0.794656 0.815228 0.039522 +Ta 8.19213 1.74268 8.29407 0.709237 -0.766675 0.419655 +Ta 6.68538 3.41569 6.73237 -1.039762 -0.942693 -1.573563 +Ta 1.62301 5.03369 4.94072 -0.479437 0.708177 0.454442 +Ta 1.67811 8.17661 4.94845 -0.43286 1.033108 0.702773 +Ta 1.50449 4.90497 8.12727 2.157996 1.39217 2.121635 +Ta 9.95522 6.68722 6.7223 -1.207088 -1.014513 -2.023602 +Ta 1.45061 8.21644 8.20658 1.867458 1.404377 0.979038 +Ta 3.56471 6.75841 6.62207 -3.094311 -0.309955 1.003355 +Ta 4.86687 5.12412 5.14144 1.869234 -0.95749 -1.296573 +Ta 8.38876 4.88961 4.89775 -0.647449 1.012711 0.567511 +Ta 4.92136 8.45113 5.01625 0.770451 -1.088974 -1.090266 +Ta 8.20783 8.3489 4.81321 0.21963 0.005286 1.165586 +Ta 4.94875 4.9618 8.28572 -0.426832 0.599091 -0.345599 +Ta 8.20464 4.88251 8.34235 2.170673 2.829715 -0.757157 +Ta 5.07191 8.2117 8.40225 -1.362796 1.673933 -0.46401 +Ta 6.76974 6.82114 6.74241 -1.906068 -2.251947 -1.927455 +Ta 8.24859 8.29304 8.12672 0.501988 0.80736 3.296928 +54 +Lattice = "9.96000003815 0.0 0.0 0.0 9.96000003815 0.0 0.0 0.0 9.96000003815" Properties=species:S:1:pos:R:3:forces:R:3 energy=-631.386255 stress="48618.67 -1616.79 -530.36 -1616.79 47533.82 1218.01 -530.36 1218.01 48883.18" +Ta 9.92016 0.01438 0.03854 0.556788 -0.67783 -1.5106 +Ta 1.82311 1.70936 1.41659 -1.918774 0.138683 2.301326 +Ta 3.28553 9.91893 0.14739 0.748737 -0.469771 -1.769605 +Ta 9.87507 3.32337 9.83154 0.793708 -0.519091 0.991363 +Ta 3.3031 3.46518 0.07875 0.443248 -0.426577 -0.905273 +Ta 9.95947 0.08218 3.34696 0.739427 -0.726997 -0.766983 +Ta 3.1684 9.75979 3.2356 1.642308 1.605642 1.000091 +Ta 0.02998 3.22821 3.21978 0.370247 0.48123 0.316324 +Ta 3.32428 3.45789 3.46471 0.337827 -1.517721 -1.355537 +Ta 5.13331 1.59317 1.61007 -2.537997 2.199599 0.12697 +Ta 6.66564 0.10058 0.15795 -0.170102 -1.253786 -3.131771 +Ta 8.39979 1.53376 1.55197 -0.736293 2.568367 0.959357 +Ta 6.699 3.46643 9.78218 -1.357883 -2.290461 2.801884 +Ta 6.55739 0.19963 3.22195 1.010984 -1.898276 1.569223 +Ta 6.6614 3.19875 3.40136 0.28987 0.883996 -0.281886 +Ta 1.65474 4.95752 1.79601 -0.834231 0.053286 -1.593869 +Ta 9.95302 6.80511 0.03196 -0.079769 -1.229448 0.075092 +Ta 1.56181 8.37445 1.75774 0.103273 -1.036598 -1.620168 +Ta 3.25788 6.58258 9.89943 -0.15681 0.002856 0.109545 +Ta 9.81575 6.84635 3.22839 0.491934 -1.902197 0.607502 +Ta 3.26659 6.5421 3.20775 1.051845 1.685557 0.716388 +Ta 4.961 4.94444 1.67842 0.154733 0.132572 -0.385023 +Ta 8.39914 5.00135 1.64081 -0.85754 -0.046821 0.044073 +Ta 4.981 8.40495 1.52317 -0.154277 -1.618489 1.137429 +Ta 6.59095 6.57229 9.81082 0.516853 -0.031072 2.168022 +Ta 8.23079 8.50453 1.71947 -0.19104 -1.640479 -0.218034 +Ta 6.5189 6.4527 3.26946 1.051143 1.341567 0.195318 +Ta 1.69996 1.52396 4.92178 -0.286649 1.057284 0.327442 +Ta 9.71449 0.20654 6.76983 2.454386 -2.330371 -0.861132 +Ta 1.75395 1.54634 8.40434 -0.369274 0.99695 -0.846145 +Ta 3.36184 9.91466 6.55661 -0.545145 -0.225476 0.969587 +Ta 0.07017 3.38145 6.72746 -0.97093 -1.700112 -1.838196 +Ta 3.188 3.32611 6.41893 0.788188 -0.658484 1.70621 +Ta 4.88158 1.53321 4.98105 0.344727 0.704928 0.157548 +Ta 8.47411 1.59131 4.94665 -1.939704 1.794052 0.479038 +Ta 4.88901 1.78086 8.34967 0.243383 -0.808705 -0.52527 +Ta 6.73425 9.77434 6.70175 -1.485362 1.795728 -1.262133 +Ta 8.06248 1.71241 8.15301 1.263397 0.222212 1.789119 +Ta 6.58956 3.39493 6.70849 -0.327807 -0.793748 -1.979357 +Ta 1.72658 5.14855 4.93998 -1.319359 -0.168591 0.474034 +Ta 1.56142 8.14402 4.97342 0.414502 1.370212 0.309023 +Ta 1.49024 4.85879 8.1549 2.112914 2.183214 1.555991 +Ta 9.89805 6.74264 6.68864 -0.638427 -1.761151 -1.247128 +Ta 1.51881 8.19293 8.20586 1.126883 1.771936 0.731665 +Ta 3.53422 6.78757 6.63995 -2.202411 -1.241629 0.531987 +Ta 4.91797 5.05055 5.07395 0.97697 -0.452695 -0.680973 +Ta 8.37523 4.90856 4.86905 -0.569914 0.544987 0.445982 +Ta 4.96025 8.30839 4.98936 0.640131 -0.024991 -0.918091 +Ta 8.25393 8.41481 4.85824 -0.321351 -0.771339 0.862505 +Ta 4.98338 4.92238 8.25755 -1.037048 0.701643 -0.025492 +Ta 8.20041 4.82836 8.34047 1.93369 2.92161 -1.499861 +Ta 5.14911 8.22565 8.35035 -2.453675 1.564843 0.655552 +Ta 6.67583 6.74955 6.82036 -0.298729 -2.031929 -2.821342 +Ta 8.24568 8.22146 8.24391 1.158405 1.531882 1.928281 +54 +Lattice = "9.96000003815 0.0 0.0 0.0 9.96000003815 0.0 0.0 0.0 9.96000003815" Properties=species:S:1:pos:R:3:forces:R:3 energy=-632.575826 stress="37007.6 -3335.61 -654.2900000000001 -3335.61 41350.14000000001 729.9499999999999 -654.2900000000001 729.9499999999999 42032.22" +Ta 9.89658 0.05915 0.05605 1.036339 -0.553602 -1.509413 +Ta 1.84029 1.75247 1.5692 -1.142381 -0.38124 0.773395 +Ta 3.2103 9.87745 0.03021 0.881726 0.55755 -0.326543 +Ta 0.02515 3.41269 9.87251 -0.122739 -0.795043 1.221499 +Ta 3.43008 3.44154 0.03351 -1.7763 -1.011632 -0.445853 +Ta 9.87697 0.19214 3.32206 1.584106 -2.293162 0.196284 +Ta 3.22174 9.87812 3.28991 0.769286 0.831055 0.301207 +Ta 0.1052 3.26647 3.18262 -0.190214 0.336725 0.865636 +Ta 3.41777 3.41426 3.37277 -0.455402 -0.720753 -0.151548 +Ta 5.17196 1.58588 1.62527 -2.939961 2.107641 0.562846 +Ta 6.60208 0.22971 0.08742 0.803627 -2.595707 -2.375381 +Ta 8.43127 1.4925 1.61697 -1.259463 3.750632 -0.106891 +Ta 6.76348 3.3785 9.80186 -2.03401 -1.195377 2.585494 +Ta 6.65909 0.1949 3.2601 -0.56741 -1.409525 1.503945 +Ta 6.6316 3.23626 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3.25793 6.54382 0.621854 0.133901 0.243236 +Ta 4.92957 1.63938 4.99734 0.279261 -0.276038 0.237899 +Ta 8.42481 1.65711 4.95454 -1.326796 1.057458 1.098206 +Ta 4.84069 1.75925 8.38234 0.745716 -0.829046 -0.859739 +Ta 6.64597 9.80629 6.69075 -0.741154 2.128175 -0.430751 +Ta 8.19543 1.78177 8.30388 1.200953 -1.19775 -0.25616 +Ta 6.57343 3.34206 6.80779 0.135786 -0.186078 -2.215599 +Ta 1.6324 5.02772 5.04564 -0.039204 0.36717 -0.650982 +Ta 1.56954 8.11698 4.93801 0.230278 1.550094 0.24251 +Ta 1.44091 4.90529 8.17235 2.716493 1.617542 1.20799 +Ta 9.93346 6.67194 6.71914 -1.022256 -0.17536 -0.867865 +Ta 1.47975 8.31024 8.36713 1.004335 0.238704 -0.734919 +Ta 3.48998 6.76276 6.56515 -1.924801 -0.712464 1.159232 +Ta 4.9581 5.06922 5.0693 0.337345 -0.924942 -0.538749 +Ta 8.40596 4.88849 4.85949 -0.874232 0.467588 0.615094 +Ta 4.91272 8.41158 4.96637 0.732014 -1.112804 -0.699182 +Ta 8.15337 8.43609 4.86865 0.839591 -1.003948 0.68469 +Ta 4.9461 4.9089 8.30806 -0.155864 1.182133 -0.492917 +Ta 8.17416 4.94211 8.40779 2.376142 1.640431 -1.638172 +Ta 5.14706 8.15632 8.46125 -2.44524 1.8416 -0.879395 +Ta 6.73636 6.72505 6.79496 -1.106421 -1.283292 -2.272742 +Ta 8.21344 8.32047 8.22695 1.044823 0.536684 2.006502 +54 +Lattice = "9.96000003815 0.0 0.0 0.0 9.96000003815 0.0 0.0 0.0 9.96000003815" Properties=species:S:1:pos:R:3:forces:R:3 energy=-630.450212 stress="54872.520000000004 561.84 254.42 561.84 57576.3 3236.46 254.42 3236.46 52454.13" +Ta 9.94993 0.02472 0.14274 0.055475 -0.868863 -2.639446 +Ta 1.73941 1.62931 1.49216 0.133385 0.958345 1.334282 +Ta 3.27456 9.84431 0.06714 0.152037 0.685105 -1.338688 +Ta 9.89722 3.30899 9.8442 0.882932 -0.580173 1.896163 +Ta 3.39949 3.43937 0.07444 -1.252525 -0.603574 -1.126923 +Ta 9.95738 0.18394 3.26338 0.661235 -1.926241 0.911392 +Ta 3.30019 9.78645 3.22208 0.028724 1.660063 1.023838 +Ta 0.13719 3.26818 3.17619 -0.70546 0.166489 0.836621 +Ta 3.35898 3.53996 3.45643 -0.084938 -1.979508 -0.962122 +Ta 5.04991 1.63426 1.4814 -1.341163 1.468593 1.819665 +Ta 6.63167 0.11405 0.21537 -0.12109 -1.761401 -4.075404 +Ta 8.31494 1.42157 1.60574 0.368731 4.528905 0.569883 +Ta 6.74419 3.49221 9.84811 -2.007412 -2.167313 2.65689 +Ta 6.63412 0.20045 3.26587 -0.684628 -1.087473 1.050812 +Ta 6.74149 3.29744 3.34049 -0.536207 0.257368 0.20051 +Ta 1.65629 4.91473 1.70491 -0.099545 0.910351 -0.802777 +Ta 9.8848 6.82698 0.05792 0.376337 -1.495085 -0.415922 +Ta 1.52902 8.3382 1.76782 0.639344 -0.53398 -1.01794 +Ta 3.2842 6.59888 0.05835 -0.561013 0.262988 -0.786249 +Ta 9.8388 6.70884 3.26058 0.554427 -0.634265 0.300656 +Ta 3.29697 6.67135 3.2332 0.752046 -0.215397 0.311965 +Ta 4.97002 4.96577 1.62011 0.05044 0.104913 0.434502 +Ta 8.33172 4.99905 1.67588 -0.034233 0.026594 -0.111203 +Ta 4.97516 8.44565 1.55002 -0.020779 -1.935482 0.889879 +Ta 6.57558 6.51621 9.81153 1.066759 1.429994 2.384917 +Ta 8.25006 8.48199 1.74936 -0.452919 -1.834688 -0.031687 +Ta 6.44899 6.4711 3.23262 1.703195 1.475113 0.740876 +Ta 1.66863 1.57808 4.93069 0.431628 0.338513 0.161788 +Ta 9.72144 0.20932 6.75785 1.958848 -2.154971 -0.993231 +Ta 1.63635 1.60616 8.35046 0.463086 0.37157 -0.091186 +Ta 3.48302 0.00215 6.71334 -1.509435 -0.172883 0.010894 +Ta 9.93596 3.25148 6.70143 0.237451 -0.065117 -1.344746 +Ta 3.08129 3.29628 6.51691 2.160928 -0.13483 0.507974 +Ta 4.96743 1.5573 5.07437 0.055528 1.049799 -0.152912 +Ta 8.45292 1.6707 5.00536 -1.761269 1.037855 -0.291955 +Ta 4.94629 1.85995 8.30452 -0.162188 -1.40003 0.218906 +Ta 6.73739 9.79788 6.73002 -1.360293 2.553733 -1.038778 +Ta 8.13299 1.84164 8.23538 1.255041 -2.346864 1.564886 +Ta 6.66656 3.37782 6.84701 -0.835313 0.379035 -3.422381 +Ta 1.68024 5.12154 4.98734 -0.660796 0.080462 0.142574 +Ta 1.60982 8.10644 4.87313 0.325313 1.774663 1.223699 +Ta 1.43945 4.82885 8.10227 2.085236 1.993105 1.922899 +Ta 9.9461 6.81388 6.73985 -0.837177 -1.923205 -1.883599 +Ta 1.46223 8.29911 8.22847 1.981531 0.926889 0.882329 +Ta 3.56097 6.69411 6.63008 -2.368401 -0.099926 0.349055 +Ta 4.97662 5.05599 5.0457 0.641095 -0.663324 -0.062532 +Ta 8.47313 4.93262 4.89931 -1.205654 0.412649 0.354766 +Ta 4.99461 8.38381 5.00182 0.283353 -0.567275 -0.555014 +Ta 8.15164 8.40758 4.84002 1.070067 -0.7384 0.47295 +Ta 5.02489 5.02411 8.3462 -1.295414 -0.424201 -1.125591 +Ta 8.29233 4.81641 8.42543 1.342299 3.650693 -2.347555 +Ta 5.13768 8.20531 8.35183 -1.942023 1.3521 0.356008 +Ta 6.7424 6.82181 6.74362 -1.121731 -2.790179 -1.913012 +Ta 8.24574 8.2733 8.18525 1.245134 1.248761 2.999274 +54 +Lattice = "9.96000003815 0.0 0.0 0.0 9.96000003815 0.0 0.0 0.0 9.96000003815" Properties=species:S:1:pos:R:3:forces:R:3 energy=-631.669379 stress="43133.57 -1318.24 471.24 -1318.24 48697.43 3329.94 471.24 3329.94 47363.12" +Ta 9.94799 9.88693 0.10122 -0.263284 1.216688 -1.883794 +Ta 1.86889 1.76555 1.56581 -1.932894 -0.197466 0.799563 +Ta 3.18914 9.88171 0.13041 0.610905 0.517831 -1.648338 +Ta 9.92665 3.38968 9.84955 0.317542 -1.257416 1.688263 +Ta 3.43358 3.54499 0.1688 -1.726787 -2.050304 -2.386849 +Ta 9.82474 0.16394 3.32778 2.216383 -1.538245 -0.264099 +Ta 3.17727 9.89254 3.26737 1.70172 0.460024 0.157384 +Ta 0.07445 3.24025 3.20793 -0.069552 0.434181 0.546568 +Ta 3.36565 3.516 3.35675 0.112956 -1.917705 -0.223914 +Ta 5.16123 1.6239 1.55508 -3.303498 2.564182 1.651578 +Ta 6.55575 0.21191 0.17217 1.231731 -2.686607 -3.911866 +Ta 8.29508 1.55441 1.6632 0.089146 2.52746 -0.701653 +Ta 6.73309 3.48714 9.89848 -2.274779 -2.67868 1.66594 +Ta 6.59035 0.09173 3.21496 -0.0633 -0.576713 2.012973 +Ta 6.64791 3.2176 3.34745 0.160139 1.027979 0.160616 +Ta 1.65171 4.94471 1.7425 -0.713082 0.706387 -1.212205 +Ta 9.93323 6.79042 0.0161 -0.225077 -1.132914 -0.016869 +Ta 1.4431 8.3808 1.76113 1.378961 -0.749711 -0.52572 +Ta 3.21108 6.66508 0.00376 -0.00978 -0.476703 -0.29896 +Ta 9.81714 6.70548 3.17335 0.208961 -0.701521 1.301811 +Ta 3.21572 6.591 3.22023 1.033304 1.008256 0.532303 +Ta 4.91106 4.93792 1.58572 1.678571 2.009249 1.603115 +Ta 8.26464 4.94698 1.60854 0.497683 0.531052 0.869356 +Ta 4.90809 8.44903 1.49243 0.088267 -1.613979 1.633781 +Ta 6.59154 6.59584 9.95944 0.505361 0.227865 0.830287 +Ta 8.21527 8.54264 1.72812 -0.429569 -2.313543 -0.559364 +Ta 6.55385 6.57757 3.26324 0.271827 0.622681 0.181604 +Ta 1.75661 1.52675 4.84155 -0.633945 1.321519 1.006441 +Ta 9.87636 0.21376 6.70268 0.45418 -1.893615 -0.40218 +Ta 1.6521 1.61415 8.35169 0.600238 0.373907 0.119151 +Ta 3.44156 0.04311 6.6096 -1.495661 -0.599002 0.704379 +Ta 0.09339 3.37032 6.65029 -1.099312 -1.412438 -0.819685 +Ta 3.18042 3.28906 6.45515 0.992949 0.211285 1.220556 +Ta 5.00918 1.65807 5.12559 0.127178 -0.0364 -1.088507 +Ta 8.38565 1.61267 4.93819 -1.405672 1.604515 0.911956 +Ta 4.81649 1.82535 8.27026 1.005288 -0.428096 0.38029 +Ta 6.74177 9.88632 6.6854 -1.192978 0.733832 -0.379597 +Ta 8.06265 1.81199 8.23079 2.096046 -1.128412 0.494263 +Ta 6.62079 3.42161 6.7044 -0.241025 -0.422289 -1.432335 +Ta 1.71584 5.10974 5.01063 -0.952074 0.094302 -0.330628 +Ta 1.6423 8.21258 4.88283 -0.325763 0.887706 0.945961 +Ta 1.49636 4.82702 8.22043 2.120092 2.257811 0.840294 +Ta 9.95578 6.72188 6.72066 -0.190571 -0.973108 -1.045394 +Ta 1.57396 8.29892 8.32339 0.49698 0.587894 -0.638339 +Ta 3.53534 6.71052 6.61516 -2.080422 -0.439087 0.577691 +Ta 4.91158 5.00762 4.99897 1.141976 -0.039622 -0.08708 +Ta 8.42976 4.87775 4.88036 -0.952974 0.858021 0.171909 +Ta 4.90384 8.41136 4.98652 0.894637 -0.884584 -0.741048 +Ta 8.2864 8.42598 4.87128 -0.087899 -0.922239 0.910409 +Ta 5.03024 4.97737 8.34689 -1.018587 0.572925 -0.691072 +Ta 8.23151 4.84154 8.4374 1.578619 3.115272 -2.575512 +Ta 5.1302 8.08126 8.35768 -1.750753 2.547363 0.298061 +Ta 6.65325 6.73813 6.7005 0.162071 -1.670992 -1.976694 +Ta 8.2436 8.19187 8.19738 0.665528 1.721207 1.625195 +54 +Lattice = "9.96000003815 0.0 0.0 0.0 9.96000003815 0.0 0.0 0.0 9.96000003815" Properties=species:S:1:pos:R:3:forces:R:3 energy=-632.431277 stress="39332.07 -484.03000000000003 -591.5 -484.03000000000003 42463.85 -935.67 -591.5 -935.67 44557.78" +Ta 0.01093 0.07201 0.09451 -0.133033 -0.624676 -1.390718 +Ta 1.86279 1.76064 1.51659 -1.592195 -0.069139 1.205785 +Ta 3.2078 9.79995 0.13153 0.540433 1.454104 -1.58264 +Ta 9.85766 3.40762 9.89988 1.024661 -1.342485 0.791698 +Ta 3.38902 3.43935 0.04627 -0.448466 -0.286011 -0.80136 +Ta 9.90188 0.13348 3.29636 1.537302 -1.039386 0.836358 +Ta 3.22408 9.86832 3.24936 1.3552 0.851114 0.539138 +Ta 0.12559 3.29783 3.20677 -1.020326 -0.682337 1.223972 +Ta 3.36531 3.39767 3.43601 0.009962 -0.529326 -1.103499 +Ta 5.15746 1.68746 1.60975 -2.532105 1.453447 0.682011 +Ta 6.67484 0.22558 0.19511 -0.045042 -2.082264 -2.946332 +Ta 8.39432 1.57083 1.68829 -0.326523 2.974804 -0.552053 +Ta 6.7901 3.4905 9.84778 -2.280421 -1.914956 1.902637 +Ta 6.66098 0.16369 3.1821 -0.458515 -1.404543 2.285847 +Ta 6.68975 3.33374 3.35351 -0.189956 -0.055081 0.175264 +Ta 1.51952 4.8757 1.72333 1.250032 1.568243 -1.070974 +Ta 9.93504 6.80931 0.00911 -0.545334 -1.102829 0.05256 +Ta 1.53614 8.31731 1.75831 0.412055 0.075595 -1.050824 +Ta 3.19933 6.67436 9.9199 -0.185239 -1.027413 0.207555 +Ta 9.87719 6.84896 3.30936 0.023055 -2.415004 0.073182 +Ta 3.27549 6.6063 3.18917 0.469425 0.419811 0.76263 +Ta 5.00755 4.96297 1.63652 -0.168999 0.238458 0.154223 +Ta 8.27314 4.95228 1.66284 0.330644 1.338439 0.511823 +Ta 4.91774 8.42919 1.48115 0.474143 -1.326573 1.888404 +Ta 6.55832 6.62377 9.94221 1.26809 -0.236095 1.051695 +Ta 8.27021 8.49129 1.78853 -0.55743 -1.432265 -0.989698 +Ta 6.39844 6.56795 3.35477 1.561076 0.83826 -0.364502 +Ta 1.77582 1.5455 4.9351 -1.060253 0.494227 0.023332 +Ta 9.87126 0.15154 6.74741 0.212135 -1.347122 -0.696834 +Ta 1.74456 1.52234 8.31732 0.085858 1.095537 0.038296 +Ta 3.45815 9.88882 6.55866 -1.684608 0.594275 1.383549 +Ta 0.03304 3.29479 6.73355 -0.261879 -0.877624 -1.394156 +Ta 3.18079 3.30298 6.42253 1.207944 0.171277 1.336295 +Ta 4.9603 1.57723 4.99617 0.634253 0.567922 -0.173103 +Ta 8.3559 1.62409 5.03154 -0.530634 1.162549 -0.066204 +Ta 4.7903 1.73365 8.2792 1.03526 -0.144088 0.183756 +Ta 6.74404 9.77079 6.64995 -1.450453 2.324287 -0.166798 +Ta 8.09234 1.79785 8.24264 1.673615 -1.361805 0.313033 +Ta 6.57421 3.42967 6.77064 0.019605 -0.880931 -1.798564 +Ta 1.57913 5.11576 4.95243 0.306594 -0.25138 -0.080154 +Ta 1.69273 8.20716 4.92075 -0.341052 1.046973 0.557303 +Ta 1.43354 4.91751 8.16401 2.287861 1.338427 1.255018 +Ta 0.01425 6.67723 6.65523 -1.147897 -0.077148 -0.417608 +Ta 1.58291 8.27957 8.26309 0.342823 0.685693 0.016051 +Ta 3.42748 6.83665 6.641 -1.510001 -2.239526 0.838695 +Ta 4.97343 5.04097 5.00585 -0.037888 -0.412025 0.456637 +Ta 8.4039 4.8646 4.9179 -0.583261 0.965744 0.28682 +Ta 4.91928 8.3318 5.11892 1.250045 -0.399127 -2.452135 +Ta 8.20159 8.28199 4.88507 0.813012 0.601139 0.388164 +Ta 5.04212 4.99253 8.32778 -1.424968 0.603147 -0.546645 +Ta 8.29629 4.88656 8.35075 0.628928 2.792969 -1.330955 +Ta 5.08862 8.21773 8.50315 -0.984696 1.400694 -1.476016 +Ta 6.79769 6.74824 6.68609 -1.854116 -2.150746 -0.908504 +Ta 8.1091 8.29833 8.26479 2.601277 0.654768 1.938542 +54 +Lattice = "9.96000003815 0.0 0.0 0.0 9.96000003815 0.0 0.0 0.0 9.96000003815" Properties=species:S:1:pos:R:3:forces:R:3 energy=-630.960068 stress="47457.030000000006 -1005.83 -232.22 -1005.83 51553.91 452.42 -232.22 452.42 48272.9" +Ta 0.05485 9.94068 0.04882 -0.759723 0.349463 -1.073784 +Ta 1.85805 1.77201 1.5217 -1.724392 -0.312777 1.581767 +Ta 3.16512 9.83319 0.13832 1.061743 0.568667 -1.386846 +Ta 9.93006 3.33808 9.91253 -0.064995 -0.093866 0.630283 +Ta 3.35014 3.4521 0.05567 -0.390836 -0.380588 -0.755337 +Ta 9.83256 0.11516 3.3997 1.419777 -1.102908 -0.922237 +Ta 3.23053 9.80404 3.17024 0.958769 1.69459 1.532703 +Ta 0.01161 3.22748 3.27368 0.022937 0.373478 0.292145 +Ta 3.35601 3.5215 3.45824 0.330549 -1.676711 -0.671565 +Ta 5.17312 1.6729 1.58962 -2.671903 1.121811 0.197691 +Ta 6.67768 0.12311 0.12029 -0.440876 -1.26923 -2.349462 +Ta 8.34051 1.56504 1.62363 0.168904 1.957241 -0.015229 +Ta 6.78008 3.36169 9.8788 -1.638783 -0.833959 1.395422 +Ta 6.60936 0.19924 3.21319 -0.445878 -1.774358 1.382608 +Ta 6.66488 3.23598 3.33678 -0.05205 1.041637 0.440105 +Ta 1.55882 4.89699 1.83484 0.420221 0.664634 -1.787995 +Ta 9.92966 6.74077 0.07931 -0.240379 -0.888703 -0.594008 +Ta 1.46294 8.36123 1.80347 1.383538 -0.598636 -1.619561 +Ta 3.27604 6.65474 9.90339 -0.790555 -1.047873 0.411754 +Ta 9.88531 6.85002 3.21939 -0.582286 -2.052939 1.256318 +Ta 3.29061 6.52643 3.19139 0.073936 1.783087 1.280681 +Ta 4.89996 4.99982 1.70189 1.223371 -0.15804 -0.71227 +Ta 8.31065 5.01116 1.69232 -0.087953 0.030026 -0.109796 +Ta 4.88784 8.33857 1.51732 0.850961 -0.596673 1.090247 +Ta 6.50104 6.53275 9.80774 2.177734 -0.433205 2.899269 +Ta 8.2643 8.49938 1.67302 -0.503687 -1.58688 0.09942 +Ta 6.55463 6.57827 3.32912 0.424308 0.463881 -0.236654 +Ta 1.62393 1.56011 4.84451 0.739422 0.750623 1.039514 +Ta 9.83601 0.23425 6.80872 1.000448 -2.657832 -1.896794 +Ta 1.61133 1.59769 8.41214 1.032998 0.937424 -0.476098 +Ta 3.35598 0.02593 6.56637 -1.123068 -0.410917 1.065083 +Ta 0.09395 3.33379 6.73292 -1.590772 -1.594874 -2.032464 +Ta 3.10315 3.36912 6.45924 1.749889 -0.890546 1.008948 +Ta 4.94948 1.60844 5.13297 0.326327 0.438573 -0.854681 +Ta 8.3112 1.6084 4.98866 -0.787743 1.376575 0.740112 +Ta 4.84637 1.81183 8.24772 0.358933 -1.184604 0.522666 +Ta 6.65846 9.76479 6.73502 -0.922055 2.08298 -0.978385 +Ta 8.20906 1.73062 8.14887 0.457034 -0.533352 2.19381 +Ta 6.58641 3.34768 6.84906 -0.07115 -0.232275 -3.047979 +Ta 1.68643 5.13518 4.9899 -0.983213 0.345899 0.008163 +Ta 1.66974 8.17852 4.94291 -0.25579 1.350395 0.365493 +Ta 1.47384 4.8564 8.10261 2.294153 2.563508 2.527259 +Ta 9.88912 6.80164 6.77309 -0.120678 -1.620395 -1.826051 +Ta 1.55837 8.19547 8.30267 0.878074 1.467856 0.015021 +Ta 3.56356 6.83284 6.56625 -2.486358 -1.682642 1.765681 +Ta 4.99706 5.12232 5.11423 0.43805 -1.159229 -0.988294 +Ta 8.4671 4.91132 4.92219 -1.21811 0.738609 0.182139 +Ta 4.87329 8.34516 4.9908 1.555301 0.282701 -1.632594 +Ta 8.1534 8.37445 4.79401 0.515688 -0.19719 1.530097 +Ta 5.00952 4.94855 8.26218 -1.33193 0.185129 -0.033086 +Ta 8.21481 4.8505 8.29903 1.753267 2.042376 0.013681 +Ta 5.14988 8.12501 8.49478 -2.325196 2.631836 -1.723209 +Ta 6.79841 6.70737 6.74515 -1.373171 -1.292054 -2.073736 +Ta 8.2086 8.27306 8.2346 1.367197 1.020256 2.330032 +54 +Lattice = "9.96000003815 0.0 0.0 0.0 9.96000003815 0.0 0.0 0.0 9.96000003815" Properties=species:S:1:pos:R:3:forces:R:3 energy=-623.378198 stress="80008.25 -785.4100000000001 1601.25 -785.4100000000001 86520.39 4960.87 1601.25 4960.87 85233.93000000001" +Ta 9.95615 9.94979 0.16514 -0.137356 -0.028883 -3.40463 +Ta 1.87163 1.71307 1.41378 -1.76357 0.590114 2.267852 +Ta 3.17989 9.83685 0.10642 1.277421 0.225697 -1.841016 +Ta 9.90024 3.33884 9.82529 0.735381 -0.941566 1.77777 +Ta 3.4188 3.54303 0.14009 -1.606974 -1.518343 -1.948061 +Ta 9.8553 0.24533 3.33787 2.112303 -3.154318 -0.288821 +Ta 3.17514 9.74142 3.2 1.589191 1.94113 1.194543 +Ta 0.11128 3.26365 3.15053 -0.364264 -0.441607 0.999143 +Ta 3.37385 3.56077 3.43718 -0.10161 -1.946969 -0.790652 +Ta 5.20458 1.63365 1.50672 -4.374578 3.807338 1.826632 +Ta 6.57608 0.24353 0.2053 1.355941 -3.643228 -5.429459 +Ta 8.39734 1.42414 1.60164 -0.6903 5.287807 -0.169411 +Ta 6.79744 3.4915 9.76717 -3.482997 -2.71942 3.817554 +Ta 6.57033 0.23978 3.13517 0.116586 -1.988113 3.629484 +Ta 6.72113 3.22949 3.3633 -0.338679 0.658098 0.181119 +Ta 1.57149 4.94775 1.80091 0.075728 0.493399 -1.98724 +Ta 9.92064 6.87072 0.13795 -0.725063 -1.775537 -0.966934 +Ta 1.41785 8.41983 1.76001 1.411759 -1.132459 -0.69594 +Ta 3.14851 6.64163 0.03349 0.008652 -0.525052 -0.43074 +Ta 9.7788 6.83849 3.18243 0.240296 -2.124804 1.273631 +Ta 3.16533 6.57739 3.14068 1.48579 1.371308 1.35272 +Ta 4.90709 4.92946 1.61468 1.153866 1.203555 0.949633 +Ta 8.33316 4.92031 1.59073 -0.391861 0.974553 0.849438 +Ta 4.9596 8.47655 1.51542 -0.546245 -2.139501 1.15131 +Ta 6.44823 6.51342 9.85247 2.586298 -0.265344 3.052647 +Ta 8.17315 8.54045 1.75264 -0.705353 -2.252394 -0.493293 +Ta 6.39303 6.44322 3.27828 1.523627 1.285888 -0.061445 +Ta 1.70938 1.43709 4.84222 0.306581 1.628448 1.044131 +Ta 9.71238 0.24769 6.81385 1.995125 -2.589965 -0.973181 +Ta 1.68921 1.55889 8.35846 0.351955 0.61258 -0.208928 +Ta 3.47749 9.92814 6.63177 -2.081328 0.048903 1.244886 +Ta 0.07656 3.32278 6.77536 -1.946033 -1.979053 -2.885009 +Ta 3.07793 3.27871 6.40803 1.81774 -0.328617 1.303887 +Ta 4.90115 1.58004 5.10411 0.818241 0.705137 -0.829745 +Ta 8.43888 1.56841 5.00344 -2.225694 2.689319 0.426868 +Ta 4.81957 1.88977 8.30861 0.398342 -1.185455 -0.079158 +Ta 6.73863 9.78981 6.71678 -2.05864 2.854477 -1.371358 +Ta 8.05528 1.82891 8.19103 1.951662 -1.704639 1.321716 +Ta 6.59394 3.44619 6.83462 -0.445378 -0.730496 -3.696673 +Ta 1.65312 5.15331 5.0431 -0.703206 0.151193 -0.646398 +Ta 1.60774 8.12544 4.90328 -0.101304 1.629949 1.006095 +Ta 1.42058 4.79056 8.10344 3.354131 3.342928 2.609888 +Ta 9.92554 6.78882 6.73898 -1.110388 -1.85868 -1.874234 +Ta 1.4639 8.19238 8.28284 1.738894 1.866439 0.339074 +Ta 3.56301 6.81221 6.61544 -3.063945 -1.111905 1.132298 +Ta 4.934 5.10947 5.11506 0.832308 -0.890416 -0.494106 +Ta 8.45728 4.85519 4.78408 -1.053171 0.965832 0.968872 +Ta 4.91173 8.4049 5.06479 1.33012 -0.900003 -2.085329 +Ta 8.16172 8.38305 4.77586 0.217903 -0.195045 1.235079 +Ta 4.96219 4.997 8.25034 -1.340837 0.253721 -0.064669 +Ta 8.22081 4.83811 8.40873 2.589217 4.367823 -2.571794 +Ta 5.19313 8.07977 8.4862 -3.823089 3.630743 -0.94626 +Ta 6.77011 6.85567 6.82197 -2.081899 -4.511915 -4.402203 +Ta 8.12043 8.25909 8.1457 3.888707 1.997353 4.680418 diff --git a/examples/PACKAGES/pod/Ta/XYZ/Displaced_FCC.xyz b/examples/PACKAGES/pod/Ta/XYZ/Displaced_FCC.xyz new file mode 100644 index 0000000000..e1fbb58bbc --- /dev/null +++ b/examples/PACKAGES/pod/Ta/XYZ/Displaced_FCC.xyz @@ -0,0 +1,450 @@ +48 +Lattice = "8.39999961853 0.0 0.0 0.0 8.39999961853 0.0 0.0 0.0 12.6000003815" Properties=species:S:1:pos:R:3:forces:R:3 energy=-555.899463 stress="44324.590000000004 -88.44 -112.43 -88.44 44600.920000000006 281.49 -112.43 281.49 42648.37" +Ta 8.39872 8.3966 0.05505 0.06463 0.245549 -0.122629 +Ta 2.17054 2.11769 12.51793 -1.187171 -0.130259 0.732895 +Ta 2.0533 8.35895 2.13547 0.233297 0.276883 -0.580405 +Ta 8.38008 2.10628 2.0551 0.08252 -0.095821 -0.260646 +Ta 4.23293 0.07434 0.0467 -0.277801 -0.575764 -0.709591 +Ta 6.2651 2.18178 0.00596 0.79823 -0.246753 -0.159608 +Ta 6.25171 8.32714 2.06 0.878956 0.397963 0.635148 +Ta 4.23709 2.08122 2.04351 -0.562206 0.342387 0.661272 +Ta 0.01795 4.28026 0.03906 0.03593 -0.753743 -0.492226 +Ta 2.17486 6.29122 12.54891 -0.292549 0.564337 0.480079 +Ta 2.07869 4.28118 2.16843 0.802077 -0.587367 -0.741571 +Ta 0.03245 6.22138 2.08055 -0.303096 1.061223 0.205298 +Ta 0.05248 0.05717 4.13572 -0.808599 -0.191264 0.378476 +Ta 2.07678 2.17993 4.13839 0.013435 -0.436677 0.322097 +Ta 2.12704 8.36983 6.31443 -0.47643 0.64169 -0.334506 +Ta 8.3705 2.08925 6.34697 0.005647 -0.087278 -0.862051 +Ta 8.38688 0.07691 8.44598 -0.055963 -0.649155 -0.697661 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0.165676 +Ta 8.34652 6.37659 6.30287 0.054827 -0.339782 -0.192988 +Ta 0.03288 4.14327 8.42559 -0.136471 1.054922 -0.681011 +Ta 2.01843 6.3563 8.36368 0.358704 -0.63918 0.366829 +Ta 2.08465 4.24206 10.56487 -0.018445 0.035124 -1.175245 +Ta 8.39771 6.35777 10.52103 -0.075528 -0.463245 -0.015453 +Ta 4.18258 4.14181 4.17443 0.116808 0.364647 -0.254759 +Ta 6.22019 6.23685 4.13448 0.381966 0.454078 0.397164 +Ta 6.28851 4.24961 6.33299 0.186246 0.002802 0.096346 +Ta 4.13463 6.26413 6.29428 0.495766 0.350443 0.359588 +Ta 4.281 4.2574 8.39181 -0.903776 -0.621644 0.379359 +Ta 6.28467 6.34316 8.44502 0.157149 0.143513 -0.095499 +Ta 6.35243 4.1584 10.43469 -0.364583 0.937808 0.436386 +Ta 4.17724 6.33497 10.52826 0.308567 0.162755 -0.541855 +48 +Lattice = "8.39999961853 0.0 0.0 0.0 8.39999961853 0.0 0.0 0.0 12.6000003815" Properties=species:S:1:pos:R:3:forces:R:3 energy=-555.922478 stress="44249.71 -651.04 -186.65 -651.04 44112.909999999996 -1023.35 -186.65 -1023.35 43244.3" +Ta 0.06343 8.3606 12.52321 -0.696701 0.940785 0.465297 +Ta 2.13463 2.12169 0.0276 -1.12333 0.576705 -0.026641 +Ta 2.07364 8.36228 2.04043 -0.26239 0.268211 0.488051 +Ta 8.37571 2.16668 2.14254 0.418469 -0.605551 -0.528424 +Ta 4.12651 0.04419 0.00196 0.983012 -0.612252 -0.323205 +Ta 6.25688 2.11357 0.01148 0.864439 -0.555613 0.554016 +Ta 6.35803 0.02339 2.17882 0.004319 -0.071235 -0.60434 +Ta 4.12492 2.02962 2.07119 0.768236 0.704677 0.998809 +Ta 8.32267 4.2038 0.03156 0.384971 -0.156549 -0.15821 +Ta 2.13999 6.25061 0.01163 0.206046 -0.408259 -0.573426 +Ta 2.16033 4.27176 2.10974 -0.144662 -0.316522 0.257436 +Ta 0.07325 6.34677 2.09878 -0.79538 -0.463238 0.011227 +Ta 0.03163 8.35134 4.23884 0.243806 0.858804 0.059427 +Ta 2.09614 2.16903 4.20803 0.184215 -0.612876 -0.414497 +Ta 2.15726 8.37369 6.37727 -0.165489 0.100422 -0.659123 +Ta 0.02483 2.126 6.26528 -0.175983 -0.609909 0.638816 +Ta 8.38466 8.32281 8.34428 0.169266 -0.211404 0.509213 +Ta 2.03906 2.07515 8.33331 0.465788 0.459079 0.436569 +Ta 2.10907 0.07467 10.53386 0.194596 0.006574 -0.731867 +Ta 8.33297 2.17086 10.43991 0.550055 -0.386364 0.529968 +Ta 4.27897 4.1393 0.00645 0.009889 0.528282 0.483017 +Ta 6.32729 6.28968 12.57566 -0.264177 0.642002 0.143135 +Ta 6.36828 4.23582 2.14993 -0.643207 -0.021355 0.110192 +Ta 4.26013 6.31388 2.06529 0.111216 0.212384 0.388281 +Ta 4.14382 0.05221 4.19611 0.133795 -0.272342 0.110067 +Ta 6.35676 2.13277 4.27931 -0.64253 -0.80079 -0.286094 +Ta 6.34512 8.331 6.35294 -0.428755 0.834939 -0.239901 +Ta 4.2156 2.15214 6.2277 0.270035 -0.158319 0.779826 +Ta 4.21566 0.03803 8.38231 0.083944 0.274668 0.537654 +Ta 6.36545 2.10057 8.38811 -0.533646 0.09587 -0.966206 +Ta 6.3135 0.07881 10.48441 -0.274002 -0.668893 0.02457 +Ta 4.26171 2.16526 10.52074 -0.418059 -0.459074 -0.898808 +Ta 8.3812 4.12205 4.26058 0.319127 1.186909 -0.691015 +Ta 2.03751 6.37506 4.22969 0.912322 -0.679112 -0.028629 +Ta 2.10316 4.17066 6.25287 0.262251 0.67613 0.437224 +Ta 0.01168 6.26992 6.26445 0.470148 -0.110432 0.580066 +Ta 0.00065 4.25404 8.40936 0.720462 0.320078 -0.095225 +Ta 2.15141 6.3154 8.39974 -0.210605 -0.239741 0.525179 +Ta 2.10941 4.11716 10.53789 -0.294631 0.328036 -0.2806 +Ta 0.02774 6.34503 10.55194 0.052179 -0.561462 -0.610592 +Ta 4.27746 4.26322 4.25824 -0.303269 -0.080042 -0.881987 +Ta 6.32942 6.36807 4.26719 -0.071872 -0.096612 -0.894702 +Ta 6.34514 4.25616 6.31634 -0.236463 -0.645396 0.127271 +Ta 4.26742 6.30384 6.28532 -1.015367 0.203758 -0.319441 +Ta 4.19566 4.27408 8.40465 -0.669454 -1.290586 -0.449496 +Ta 6.21853 6.2172 8.36939 0.704437 1.092583 0.697829 +Ta 6.30129 4.2155 10.41714 0.33095 0.1172 0.467289 +Ta 4.23757 6.23742 10.53163 -0.447998 0.665832 0.302002 +48 +Lattice = "8.39999961853 0.0 0.0 0.0 8.39999961853 0.0 0.0 0.0 12.6000003815" Properties=species:S:1:pos:R:3:forces:R:3 energy=-555.800269 stress="44944.52 20.43 -53.49 20.43 46278.61 29.84 -53.49 29.84 42171.32" +Ta 8.39366 0.03327 12.53757 0.281471 -0.21858 0.714835 +Ta 2.13799 2.17663 0.08107 -0.242623 -0.691544 -0.821606 +Ta 2.1586 0.00804 2.08871 -0.840779 0.227491 0.043738 +Ta 0.07616 2.11667 2.10673 -0.564953 -0.14659 -0.53106 +Ta 4.15103 0.01208 0.04902 0.594481 0.453625 -0.068399 +Ta 6.25134 2.11148 12.51753 0.377615 -0.192108 1.200692 +Ta 6.34616 0.06815 2.1539 0.172975 -0.678259 -0.601449 +Ta 4.25478 2.13099 2.16677 0.103092 -0.008648 -0.297252 +Ta 8.32309 4.25914 0.06259 0.571757 -0.370889 -0.326093 +Ta 2.18289 6.3341 0.04696 -0.829016 -0.174777 -0.58409 +Ta 2.17634 4.18641 2.09151 -0.422429 0.255137 0.485834 +Ta 0.06508 6.22975 2.07834 -0.463567 0.907706 -0.064984 +Ta 0.03316 8.35006 4.12414 -0.730534 -0.238153 0.413363 +Ta 2.082 2.07294 4.20331 0.425673 -0.20545 -0.321985 +Ta 2.12216 0.0105 6.23718 0.020646 -0.010904 0.435072 +Ta 0.03286 2.07054 6.23343 -0.520711 -0.034403 0.247056 +Ta 8.36331 0.02515 8.43591 0.078206 -0.188894 -0.203212 +Ta 2.01725 2.02047 8.37346 0.945609 0.479423 0.375213 +Ta 2.13829 8.32424 10.45876 -0.581344 1.386424 0.908562 +Ta 8.35549 2.12524 10.51529 0.852839 -0.295749 0.265562 +Ta 4.16491 4.22554 0.0009 0.715672 -0.095676 -0.213922 +Ta 6.22371 6.32022 12.53036 0.187246 0.040385 0.908943 +Ta 6.36757 4.22353 2.09189 -0.874971 0.203062 0.00729 +Ta 4.13315 6.3638 2.09505 0.977658 -0.635482 0.37092 +Ta 4.23722 8.33801 4.14924 0.176574 0.229478 0.507526 +Ta 6.35365 2.15131 4.17453 0.12327 -0.302231 0.057467 +Ta 6.24548 0.08185 6.31737 0.13665 -0.415086 -0.30141 +Ta 4.2241 2.07465 6.23581 0.013977 0.192163 0.497879 +Ta 4.19905 8.3678 8.46852 0.198161 0.792819 -0.702669 +Ta 6.2848 2.06186 8.4824 -0.027942 0.482082 -0.848532 +Ta 6.29377 8.32663 10.54116 0.105969 0.400999 0.031916 +Ta 4.27399 2.1012 10.56089 -1.346927 0.176649 -0.650846 +Ta 0.04908 4.20115 4.17826 0.10887 0.65821 0.312297 +Ta 2.06654 6.36455 4.27901 0.165742 -0.555047 -0.271572 +Ta 2.17095 4.16446 6.22477 -0.421266 -0.000369 0.715516 +Ta 8.32881 6.3256 6.36766 0.454331 0.163972 -0.301611 +Ta 0.05742 4.18749 8.33872 0.082852 0.081218 0.003436 +Ta 2.15697 6.37663 8.42585 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0.01156 2.06262 -0.575545 -0.144242 0.553705 +Ta 8.36759 2.03815 2.01865 0.158421 0.357495 0.477149 +Ta 4.25295 8.39299 0.01959 -0.129413 -0.3983 -0.769823 +Ta 6.3041 2.15126 12.55831 -0.100908 -0.537014 0.579287 +Ta 6.31819 8.348 2.11631 -0.47465 0.826061 -0.151195 +Ta 4.12134 2.08818 2.01802 1.198272 0.44388 0.857287 +Ta 0.08271 4.2036 12.59844 -0.118028 0.163914 0.431759 +Ta 2.01753 6.35781 0.0714 0.494708 -0.055352 -1.028673 +Ta 2.08391 4.19281 2.14837 -0.158375 0.168457 0.181091 +Ta 8.38687 6.38119 2.07973 0.392875 -0.502905 0.230173 +Ta 1e-05 8.39354 4.1693 0.107276 0.205353 0.093359 +Ta 2.08062 2.07046 4.21883 0.026291 0.31706 0.006631 +Ta 2.05743 8.3971 6.26987 -0.209663 0.356146 0.194858 +Ta 8.34982 2.15852 6.27812 0.272828 -0.518433 0.131469 +Ta 0.043 0.03735 8.38109 -0.323399 0.174941 0.265006 +Ta 2.1683 2.12031 8.32959 -0.372149 0.123767 0.247418 +Ta 2.03915 0.06596 10.44595 0.608304 -0.370142 0.153462 +Ta 0.0392 2.15708 10.57335 -0.077003 -0.470665 -0.584646 +Ta 4.18371 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0.15204 -0.517119 +Ta 6.2787 2.16315 4.12282 -0.232405 -0.499866 0.253482 +Ta 6.34721 8.31974 6.30085 -0.979334 0.910385 0.303536 +Ta 4.28154 2.17035 6.32716 -0.15794 -0.615192 -0.1244 +Ta 4.18199 8.39045 8.46612 0.325504 0.011668 -0.623247 +Ta 6.26218 2.04661 8.48258 0.1676 0.725305 -0.25923 +Ta 6.23956 8.33727 10.47655 0.418626 0.454527 0.207051 +Ta 4.15476 2.10491 10.56002 -0.313925 0.116788 -0.527027 +Ta 0.01924 4.13985 4.22933 -0.14445 0.528571 -0.009114 +Ta 2.08713 6.26332 4.12939 -0.556542 0.338386 0.377019 +Ta 2.15091 4.23252 6.31161 -0.453388 -0.485864 -0.240866 +Ta 0.01574 6.34253 6.34105 0.560159 -0.626169 -0.553544 +Ta 0.06165 4.27339 8.34091 -0.693509 -0.695001 0.015426 +Ta 2.17693 6.29896 8.40088 -0.096806 0.060357 0.058203 +Ta 2.04233 4.27207 10.49743 -0.170105 0.047304 0.328134 +Ta 8.326 6.32148 10.47975 0.051179 -0.370901 0.321938 +Ta 4.17478 4.27838 4.20752 -0.040763 -0.935827 -0.576582 +Ta 6.33594 6.28787 4.27554 0.307038 0.027247 -1.208419 +Ta 6.22034 4.2468 6.22637 0.65603 -0.422269 1.121308 +Ta 4.16145 6.31917 6.2391 0.094184 0.321459 0.407157 +Ta 4.14417 4.25682 8.46183 0.755121 -0.328996 0.17207 +Ta 6.30692 6.29958 8.38648 -0.576112 -0.600141 0.013593 +Ta 6.30183 4.19292 10.57602 0.207371 0.051704 -0.883456 +Ta 4.25713 6.3237 10.54986 -0.254962 -0.198902 0.083246 +48 +Lattice = "8.39999961853 0.0 0.0 0.0 8.39999961853 0.0 0.0 0.0 12.6000003815" Properties=species:S:1:pos:R:3:forces:R:3 energy=-555.747848 stress="44613.38 397.28000000000003 -242.23 397.28000000000003 46401.21 -102.86 -242.23 -102.86 43613.280000000006" +Ta 0.02479 8.34418 0.01275 -0.16642 0.336623 -0.17578 +Ta 2.12361 2.14989 0.01237 -0.405458 -0.253401 -0.541818 +Ta 2.15668 0.05545 2.03048 -1.000877 -0.537193 0.264476 +Ta 8.38488 2.15096 2.04122 -0.226412 -0.742284 -0.216619 +Ta 4.26822 0.07709 0.05369 -1.051454 -0.974093 -0.658846 +Ta 6.22169 2.03316 12.57305 1.255557 0.920651 0.507841 +Ta 6.25622 8.38573 2.18037 0.795872 0.410847 -0.509558 +Ta 4.16678 2.07023 2.1321 0.423587 0.619136 0.258117 +Ta 0.05908 4.28115 12.57632 -0.514548 -0.229495 0.223581 +Ta 2.15681 6.25911 12.52611 -0.187265 0.793507 0.590029 +Ta 2.10607 4.20234 2.1649 -0.204517 0.52787 -0.182255 +Ta 8.33964 6.36799 2.06365 0.524674 -0.464522 0.434211 +Ta 8.32432 8.32625 4.27611 0.592658 0.021054 -0.297495 +Ta 2.02168 2.04529 4.16312 0.026264 -0.221166 0.743869 +Ta 2.16588 0.04144 6.35945 -0.460731 -0.235445 -0.58949 +Ta 0.01204 2.05369 6.35048 0.259091 0.326814 -0.495643 +Ta 0.01039 0.00368 8.3336 -0.673018 -0.236784 0.607724 +Ta 2.0362 2.11502 8.41459 0.695682 0.392328 0.347056 +Ta 2.06078 8.33946 10.46227 0.422497 0.624614 0.395156 +Ta 8.39011 2.13863 10.50323 0.037882 -0.407402 0.601189 +Ta 4.20505 4.24743 0.06234 -0.328867 -0.887587 -0.011584 +Ta 6.2258 6.25659 0.00484 0.425855 0.635452 0.199651 +Ta 6.25834 4.14378 2.03463 0.154989 0.155997 0.516394 +Ta 4.15865 6.35101 2.06568 0.13635 -0.562846 0.542472 +Ta 4.24566 0.03553 4.16912 -0.27687 0.238692 0.561637 +Ta 6.36116 2.13477 4.23864 -0.0672 0.263837 -0.212871 +Ta 6.28832 0.03663 6.33587 -0.054626 -0.825117 0.073016 +Ta 4.26921 2.03519 6.33887 -0.525339 0.940356 -0.102505 +Ta 4.20405 0.04164 8.423 0.312009 0.161766 0.440029 +Ta 6.3561 2.16604 8.38015 -0.556637 -0.443675 0.656518 +Ta 6.22231 0.06354 10.57462 0.749122 -0.629719 -0.896467 +Ta 4.23446 2.05368 10.5626 -0.759888 0.841158 -0.975855 +Ta 0.00046 4.14735 4.18932 0.123745 1.012572 -0.167229 +Ta 2.18129 6.36027 4.19805 -0.666359 0.064525 -0.022031 +Ta 2.07916 4.25676 6.35081 0.158957 -0.818787 -0.400517 +Ta 8.3474 6.21802 6.35914 0.325132 0.928801 -0.633002 +Ta 8.32754 4.20214 8.39946 0.837886 0.30854 0.750161 +Ta 2.08917 6.30707 8.37548 -0.142599 -0.403183 0.505543 +Ta 2.09792 4.22452 10.55581 0.108204 -0.342607 -0.998745 +Ta 8.34488 6.35512 10.47699 0.002323 -0.149774 0.008416 +Ta 4.12138 4.12799 4.23746 0.523048 0.17672 0.272443 +Ta 6.23634 6.28138 4.16996 -0.092966 -0.776434 0.306905 +Ta 6.36952 4.2719 6.36773 -1.008562 -0.323291 -1.151597 +Ta 4.13873 6.36014 6.35862 0.771311 -0.156347 -0.591177 +Ta 4.2281 4.26918 8.35417 -0.447945 -1.108738 0.194339 +Ta 6.2637 6.27914 8.44271 -0.036946 0.834555 0.001538 +Ta 6.25795 4.26254 10.56883 0.196157 -0.749479 0.01619 +Ta 4.19511 6.21799 10.50605 -0.003346 0.942955 -0.187417 diff --git a/examples/PACKAGES/pod/Ta/XYZ/Elastic_BCC.xyz b/examples/PACKAGES/pod/Ta/XYZ/Elastic_BCC.xyz new file mode 100644 index 0000000000..ba2d560f43 --- /dev/null +++ b/examples/PACKAGES/pod/Ta/XYZ/Elastic_BCC.xyz @@ -0,0 +1,400 @@ +2 +Lattice = "3.31180000305 0.0 0.0 0.0131999999285 3.32649993896 0.0 -0.00789999961853 -0.00710000004619 3.30480003357" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.689367 stress="4063.55 -2978.6600000000003 1761.76 -2978.6600000000003 -667.64 1596.31 1761.76 1596.31 6346.89" +Ta 0.0 0.0 0.0 -0.00044 3e-06 -2e-06 +Ta 1.6585 1.6597 1.6524 0.00044 -3e-06 2e-06 +2 +Lattice = "3.31170010567 0.0 0.0 -0.00419999985024 3.30890011787 0.0 -0.00920000020415 -0.0154999997467 3.328799963" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.689888 stress="1032.59 906.63 2045.1999999999998 906.63 1918.6499999999999 3453.7599999999998 2045.1999999999998 3453.7599999999998 -4437.12" +Ta 0.0 0.0 0.0 -0.000436 -1e-06 -2e-06 +Ta 1.6491 1.6467 1.6644 0.000436 1e-06 2e-06 +2 +Lattice = "3.3111000061 0.0 0.0 0.00810000021011 3.3273999691 0.0 -0.00889999978244 0.00870000012219 3.31040000916" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.689996 stress="1447.25 -1793.1 1960.95 -1793.1 -3771.35 -1928.0900000000001 1960.95 -1928.0900000000001 1685.23" +Ta 0.0 0.0 0.0 0.000438 -0.000443 5e-06 +Ta 1.6552 1.668 1.6552 -0.000438 0.000443 -5e-06 +2 +Lattice = "3.32399988174 0.0 0.0 -0.00179999996908 3.32139992714 0.0 -0.00359999993816 -0.00600000005215 3.31699991226" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.690957 stress="-9165.53 392.27 787.5 392.27 -8350.429999999998 1310.7 787.5 1310.7 -6953.2" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 1.6593 1.6577 1.6585 0.0 0.0 0.0 +2 +Lattice = "3.31089997292 0.0 0.0 0.0124000003561 3.32559990883 0.0 -0.001200000057 -0.0124000003561 3.3341999054" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.690521 stress="-8949.18 -2681.52 276.69 -2681.52 -13545.81 2724.27 276.69 2724.27 -16201.730000000001" +Ta 0.0 0.0 0.0 -0.000423 3e-06 0.0 +Ta 1.661 1.6566 1.6671 0.000423 -3e-06 0.0 +2 +Lattice = "3.30999994278 0.0 0.0 0.0110999997705 3.33330011368 0.0 0.00200000009499 -0.00749999983236 3.33319997787" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.69038 stress="-11410.16 -2387.02 -421.38 -2387.02 -18621.670000000002 1636.99 -421.38 1636.99 -18577.07" +Ta 0.0 0.0 0.0 0.000419 -3e-06 -1e-06 +Ta 1.6616 1.6629 1.6666 -0.000419 3e-06 1e-06 +2 +Lattice = "3.31480002403 0.0 0.0 -0.00130000000354 3.30679988861 0.0 0.0152000002563 -0.00179999996908 3.31760001183" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.689202 stress="4967.67 296.10999999999996 -3428.94 296.10999999999996 7593.91 406.16 -3428.94 406.16 4075.8900000000003" +Ta 0.0 0.0 0.0 0.000444 0.0 -4e-06 +Ta 1.6644 1.6525 1.6588 -0.000444 0.0 4e-06 +2 +Lattice = "3.30529999733 0.0 0.0 -0.00170000002254 3.32520008087 0.0 0.00170000002254 -0.00829999987036 3.32640004158" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.690482 stress="-550.9 376.95 -376.77 376.95 -6880.99 1848.91 -376.77 1848.91 -7253.42" +Ta 0.0 0.0 0.0 0.00043 -0.000434 -2e-06 +Ta 1.6527 1.6584 1.6632 -0.00043 0.000434 2e-06 +2 +Lattice = "3.32270002365 0.0 0.0 -0.00240000011399 3.32060003281 0.0 -0.0148999998346 0.00600000005215 3.30489993095" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.689902 stress="-1938.73 553.61 3301.04 553.61 -1240.33 -1332.82 3301.04 -1332.82 3793.0" +Ta 0.0 0.0 0.0 -4e-06 2e-06 -0.000435 +Ta 1.6527 1.6633 1.6524 4e-06 -2e-06 0.000435 +2 +Lattice = "3.3232998848 0.0 0.0 0.00380000006407 3.30970001221 0.0 -0.0163000002503 -0.00340000004508 3.33060002327" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.690563 stress="-9502.029999999999 -833.58 3604.52 -833.58 -5183.259999999999 750.48 3604.52 750.48 -11765.68" +Ta 0.0 0.0 0.0 -1e-06 0.000427 1e-06 +Ta 1.6554 1.6532 1.6653 1e-06 -0.000427 -1e-06 +2 +Lattice = "3.31620001793 0.0 0.0 0.00319999991916 3.31369996071 0.0 -0.00190000003204 0.00400000018999 3.31730008125" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.690207 stress="617.27 -708.54 421.95 -708.54 1415.16 -887.75 421.95 -887.75 266.22" +Ta 0.0 0.0 0.0 -0.000437 -0.000438 0.00044 +Ta 1.6587 1.6588 1.6587 0.000437 0.000438 -0.00044 +2 +Lattice = "3.32719993591 0.0 0.0 0.00240000011399 3.30349993706 0.0 0.00430000014603 -0.0038999998942 3.31030011177" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.689285 stress="138.79 -534.2 -967.78 -534.2 7805.76 865.88 -967.78 865.88 5611.4" +Ta 0.0 0.0 0.0 0.000447 -2e-06 -0.000443 +Ta 1.667 1.6498 1.6551 -0.000447 2e-06 0.000443 +2 +Lattice = "3.3218998909 0.0 0.0 0.00930000003427 3.30679988861 0.0 0.0109000001103 0.00510000018403 3.31669998169" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.689768 stress="-340.25 -2080.88 -2448.95 -2080.88 4545.72 -1144.55 -2448.95 -1144.55 1351.01" +Ta 0.0 0.0 0.0 -0.000442 -0.000437 0.000444 +Ta 1.671 1.6559 1.6584 0.000442 0.000437 -0.000444 +2 +Lattice = "3.31170010567 0.0 0.0 0.0164999999106 3.3343000412 0.0 -9.99999974738e-05 0.0138999996707 3.30570006371" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.68968 stress="-50.55 -3689.6800000000003 -1.47 -3689.6800000000003 -7274.5199999999995 -3083.4 -1.47 -3083.4 1889.91" +Ta 0.0 0.0 0.0 -0.000435 1e-06 0.000433 +Ta 1.664 1.6741 1.6529 0.000435 -1e-06 -0.000433 +2 +Lattice = "3.32259988785 0.0 0.0 0.0109999999404 3.30929994583 0.0 -0.0142000000924 -0.0140000004321 3.32019996643" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.690074 stress="-3803.7000000000003 -2463.9700000000003 3178.14 -2463.9700000000003 463.82 3109.52 3178.14 3109.52 -3014.8100000000004" +Ta 0.0 0.0 0.0 0.000872 0.000428 1.1e-05 +Ta 1.6598 1.6477 1.6601 -0.000872 -0.000428 -1.1e-05 +2 +Lattice = "3.31579995155 0.0 0.0 0.0163000002503 3.31240010262 0.0 0.00620000017807 -0.00879999995232 3.30360007286" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.688108 stress="8273.59 -3695.21 -1386.53 -3695.21 9410.130000000001 1972.81 -1386.53 1972.81 12301.0" +Ta 0.0 0.0 0.0 0.000448 -5e-06 -2e-06 +Ta 1.6692 1.6518 1.6518 -0.000448 5e-06 2e-06 +2 +Lattice = "3.31279993057 0.0 0.0 0.000699999975041 3.3220000267 0.0 -0.00209999992512 0.00410000002012 3.30430006981" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.689241 stress="5705.93 -155.59 468.56 -155.59 2710.42 -920.27 468.56 -920.27 8460.77" +Ta 0.0 0.0 0.0 -1e-06 0.000446 -0.000442 +Ta 1.6557 1.6631 1.6521 1e-06 -0.000446 0.000442 +2 +Lattice = "3.31509995461 0.0 0.0 -0.0077999997884 3.31060004234 0.0 0.0136000001803 -0.0110999997705 3.31699991226" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.68952 stress="3143.69 1764.0800000000002 -3057.7000000000003 1764.0800000000002 4618.12 2493.02 -3057.7000000000003 2493.02 2546.3" +Ta 0.0 0.0 0.0 0.000443 0.000443 -1e-06 +Ta 1.6605 1.6498 1.6585 -0.000443 -0.000443 1e-06 +2 +Lattice = "3.30970001221 0.0 0.0 -0.0141000002623 3.30669999123 0.0 -0.00380000006407 -0.0109999999404 3.30399990082" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.686278 stress="15948.689999999999 3229.23 856.13 3229.23 16943.010000000002 2508.75 856.13 2508.75 17860.57" +Ta 0.0 0.0 0.0 -4e-06 -0.000453 -3e-06 +Ta 1.6459 1.6478 1.652 4e-06 0.000453 3e-06 +2 +Lattice = "3.31279993057 0.0 0.0 0.00680000009015 3.33550000191 0.0 -0.00949999969453 -0.00449999980628 3.33489990234" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.690097 stress="-15440.51 -1462.0800000000002 2035.5400000000002 -1462.0800000000002 -22399.3 982.8 2035.5400000000002 982.8 -22219.22" +Ta 0.0 0.0 0.0 0.000418 -1e-06 0.000423 +Ta 1.6551 1.6655 1.6675 -0.000418 1e-06 -0.000423 +2 +Lattice = "3.33060002327 0.0 0.0 -0.00740000000224 3.32299995422 0.0 0.00570000009611 0.00219999998808 3.32229995728" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.690811 stress="-17578.07 1606.3700000000001 -1235.27 1606.3700000000001 -15218.79 -469.97 -1235.27 -469.97 -14998.810000000001" +Ta 0.0 0.0 0.0 0.000426 2e-06 -0.000424 +Ta 1.6645 1.6626 1.6611 -0.000426 -2e-06 0.000424 +2 +Lattice = "3.30460000038 0.0 0.0 0.00960000045598 3.32699990273 0.0 -0.0129000004381 0.00889999978244 3.33470010757" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.690266 stress="-4850.61 -2063.29 2800.95 -2063.29 -11849.39 -1958.39 2800.95 -1958.39 -14262.01" +Ta 0.0 0.0 0.0 0.000423 -0.00043 -0.000426 +Ta 1.6507 1.6679 1.6673 -0.000423 0.00043 0.000426 +2 +Lattice = "3.3166000843 0.0 0.0 0.00989999994636 3.32179999352 0.0 0.00899999961257 0.00829999987036 3.3178999424" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.690597 stress="-3926.0299999999997 -2198.55 -1990.1100000000001 -2198.55 -5568.17 -1841.1599999999999 -1990.1100000000001 -1841.1599999999999 -4321.4800000000005" +Ta 0.0 0.0 0.0 0.000428 0.00043 0.000429 +Ta 1.6678 1.6651 1.659 -0.000428 -0.00043 -0.000429 +2 +Lattice = "3.32559990883 0.0 0.0 0.0149999996647 3.32439994812 0.0 -0.0102000003681 -0.00879999995232 3.31529998779" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.690673 stress="-11060.560000000001 -3311.08 2234.96 -3311.08 -10663.09 1930.59 2234.96 1930.59 -7793.1" +Ta 0.0 0.0 0.0 3e-06 2e-06 0.000427 +Ta 1.6652 1.6578 1.6577 -3e-06 -2e-06 -0.000427 +2 +Lattice = "3.32710003853 0.0 0.0 0.0142999999225 3.31200003624 0.0 0.00529999984428 -0.00150000001304 3.3180000782" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.690551 stress="-7626.490000000001 -3148.54 -1170.5 -3148.54 -2813.94 319.88 -1170.5 319.88 -4708.87" +Ta 0.0 0.0 0.0 -0.000431 -0.000428 1e-06 +Ta 1.6733 1.6552 1.659 0.000431 0.000428 -1e-06 +2 +Lattice = "3.3218998909 0.0 0.0 0.00829999987036 3.31850004196 0.0 0.0119000002742 0.00230000005104 3.31710004807" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.690693 stress="-6193.7300000000005 -1837.26 -2623.8700000000003 -1837.26 -5083.38 -517.81 -2623.8700000000003 -517.81 -4646.26" +Ta 0.0 0.0 0.0 -0.00043 3e-06 -0.000429 +Ta 1.671 1.6604 1.6585 0.00043 -3e-06 0.000429 +2 +Lattice = "3.32940006256 0.0 0.0 -0.00769999995828 3.30390000343 0.0 -0.0120000001043 0.0147000001743 3.32710003853" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.69021 stress="-9842.3 1710.3600000000001 2678.2400000000002 1710.3600000000001 -1794.44 -3224.8100000000004 2678.2400000000002 -3224.8100000000004 -9105.6" +Ta 0.0 0.0 0.0 -0.000437 2e-06 -0.000436 +Ta 1.6548 1.6593 1.6635 0.000437 -2e-06 0.000436 +2 +Lattice = "3.30669999123 0.0 0.0 -0.0122999995947 3.31839990616 0.0 0.00789999961853 -0.0104999998584 3.31259989738" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.688943 stress="8333.89 2780.83 -1785.3000000000002 2780.83 4535.25 2375.9700000000003 -1785.3000000000002 2375.9700000000003 6440.179999999999" +Ta 0.0 0.0 0.0 0.000439 -0.000441 -5e-06 +Ta 1.6512 1.6539 1.6563 -0.000439 0.000441 5e-06 +2 +Lattice = "3.33619999886 0.0 0.0 0.00150000001304 3.30669999123 0.0 0.0163000002503 0.0137999998406 3.33039999008" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.690136 stress="-18003.329999999998 -360.51 -3576.72 -360.51 -8835.43 -2976.33 -3576.72 -2976.33 -16192.060000000001" +Ta 0.0 0.0 0.0 0.0 0.00042 -4e-06 +Ta 1.677 1.6603 1.6652 0.0 -0.00042 4e-06 +2 +Lattice = "3.30349993706 0.0 0.0 0.0162000004202 3.30900001526 0.0 -0.00700000021607 0.00680000009015 3.31489992142" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.687444 stress="14486.06 -3661.95 1582.35 -3661.95 12701.029999999999 -1541.32 1582.35 -1541.32 10767.84" +Ta 0.0 0.0 0.0 -0.00045 7e-06 -0.000453 +Ta 1.6563 1.6579 1.6574 0.00045 -7e-06 0.000453 +2 +Lattice = "3.31089997292 0.0 0.0 -0.00889999978244 3.31270003319 0.0 0.00829999987036 0.00520000001416 3.32080006599" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.689801 stress="3684.26 1974.24 -1852.3799999999999 1974.24 3114.35 -1156.8400000000001 -1852.3799999999999 -1156.8400000000001 502.12999999999994" +Ta 0.0 0.0 0.0 0.000437 -0.000437 -1e-06 +Ta 1.6552 1.6589 1.6604 -0.000437 0.000437 1e-06 +2 +Lattice = "3.31879997253 0.0 0.0 -0.0110999997705 3.31049990654 0.0 -0.0164999999106 -0.00410000002012 3.32960009575" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.690408 stress="-5855.900000000001 2413.85 3653.84 2413.85 -3177.2999999999997 882.09 3653.84 882.09 -9230.779999999999" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 1.6456 1.6532 1.6648 0.0 0.0 0.0 +2 +Lattice = "3.33170008659 0.0 0.0 0.00689999992028 3.3178999424 0.0 -0.0148000000045 0.0147000001743 3.31089997292" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.690362 stress="-10662.19 -1488.5900000000001 3240.34 -1488.5900000000001 -6300.3099999999995 -3192.45 3240.34 -3192.45 -4075.9999999999995" +Ta 0.0 0.0 0.0 4e-06 -4e-06 0.000429 +Ta 1.6619 1.6663 1.6555 -4e-06 4e-06 -0.000429 +2 +Lattice = "3.3343000412 0.0 0.0 0.00540000014007 3.32949995995 0.0 -0.0140000004321 -0.00460000010207 3.33520007133" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.688881 stress="-29339.85 -1153.21 2967.17 -1153.21 -27876.05 983.26 2967.17 983.26 -29592.94" +Ta 0.0 0.0 0.0 -0.000413 0.000412 -2e-06 +Ta 1.6628 1.6625 1.6676 0.000413 -0.000412 2e-06 +2 +Lattice = "3.31089997292 0.0 0.0 0.0131999999285 3.32349991798 0.0 -0.00669999979436 -0.00520000001416 3.33629989624" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.690515 stress="-8945.37 -2854.2900000000004 1466.4299999999998 -2854.2900000000004 -12870.23 1153.96 1466.4299999999998 1153.96 -16851.88" +Ta 0.0 0.0 0.0 0.000847 -0.000435 -0.000427 +Ta 1.6588 1.6591 1.6681 -0.000847 0.000435 0.000427 +2 +Lattice = "3.33450007439 0.0 0.0 0.0136000001803 3.32259988785 0.0 0.00700000021607 0.00400000018999 3.32060003281" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.690551 stress="-19623.16 -2954.7799999999997 -1523.28 -2954.7799999999997 -15920.310000000001 -868.95 -1523.28 -868.95 -15295.98" +Ta 0.0 0.0 0.0 -0.000424 4e-06 2e-06 +Ta 1.6775 1.6633 1.6603 0.000424 -4e-06 -2e-06 +2 +Lattice = "3.30719995499 0.0 0.0 0.00600000005215 3.30640006065 0.0 -0.00870000012219 -0.00480000022799 3.33119988441" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.689487 stress="4760.94 -1330.3100000000002 1958.3200000000002 -1330.3100000000002 5030.59 1081.68 1958.3200000000002 1081.68 -2959.67" +Ta 0.0 0.0 0.0 0.000438 -2e-06 2e-06 +Ta 1.6523 1.6508 1.6656 -0.000438 2e-06 -2e-06 +2 +Lattice = "3.32150006294 0.0 0.0 -0.000699999975041 3.30979990959 0.0 0.0129000004381 -0.0104000000283 3.31489992142" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.68986 stress="-609.8 175.89 -2883.99 175.89 3169.7000000000003 2312.35 -2883.99 2312.35 1528.81" +Ta 0.0 0.0 0.0 0.000444 -3e-06 -0.000442 +Ta 1.6669 1.6497 1.6574 -0.000444 3e-06 0.000442 +2 +Lattice = "3.30480003357 0.0 0.0 -0.00669999979436 3.31340003014 0.0 -0.00689999992028 0.0142999999225 3.3234000206" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.689288 stress="7065.76 1506.72 1557.04 1506.72 4265.53 -3227.4500000000003 1557.04 -3227.4500000000003 1046.89" +Ta 0.0 0.0 0.0 -0.000881 -0.000446 0.0 +Ta 1.6455 1.6638 1.6617 0.000881 0.000446 0.0 +2 +Lattice = "3.32389998436 0.0 0.0 -0.00850000046194 3.32249999046 0.0 -0.00889999978244 -0.00329999998212 3.33500003815" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.690457 stress="-18069.48 1814.44 1923.43 1814.44 -17623.8 707.29 1923.43 707.29 -21466.73" +Ta 0.0 0.0 0.0 -0.00042 -2e-06 -2e-06 +Ta 1.6532 1.6596 1.6675 0.00042 2e-06 2e-06 +2 +Lattice = "3.33189988136 0.0 0.0 0.0142999999225 3.31990003586 0.0 -0.00710000004619 -0.0148999998346 3.33529996872" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.689792 stress="-23150.59 -3063.23 1550.5800000000002 -3063.23 -19490.46 3197.18 1550.5800000000002 3197.18 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stress="-2208.17 3473.14 -1080.09 3473.14 -2950.43 -3225.5600000000004 -1080.09 -3225.5600000000004 -1446.74" +Ta 0.0 0.0 0.0 -0.000442 -0.000445 0.000441 +Ta 1.6533 1.6671 1.6576 0.000442 0.000445 -0.000441 +2 +Lattice = "3.31410002708 0.0 0.0 0.0126000000164 3.32780003548 0.0 0.00749999983236 -0.00620000017807 3.33170008659" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.690617 stress="-11356.33 -2713.87 -1615.29 -2713.87 -15605.029999999999 1345.96 -1615.29 1345.96 -16800.52" +Ta 0.0 0.0 0.0 -2e-06 2e-06 0.000426 +Ta 1.6671 1.6608 1.6659 2e-06 -2e-06 -0.000426 +2 +Lattice = "3.33410000801 0.0 0.0 -0.00949999969453 3.30469989777 0.0 -0.0119000002742 -0.00879999995232 3.31220006943" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.689761 stress="-6865.599999999999 2087.9500000000003 2646.9 2087.9500000000003 2545.62 1920.39 2646.9 1920.39 148.10000000000002" +Ta 0.0 0.0 0.0 0.000443 0.000436 6e-06 +Ta 1.6564 1.648 1.6561 -0.000443 -0.000436 -6e-06 +2 +Lattice = "3.32760000229 0.0 0.0 -0.00190000003204 3.31820011139 0.0 0.000500000023749 -0.0155999995768 3.33640003204" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.69027 stress="-19541.46 406.28 -110.74000000000001 406.28 -16673.960000000003 3361.5 -110.74000000000001 3361.5 -22262.14" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 1.6631 1.6513 1.6682 0.0 0.0 0.0 +2 +Lattice = "3.30819988251 0.0 0.0 0.00719999987632 3.32559990883 0.0 0.00159999995958 0.00719999987632 3.32410001755" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.690599 stress="-1982.3500000000001 -1585.1200000000001 -358.04999999999995 -1585.1200000000001 -7502.34 -1599.04 -358.04999999999995 -1599.04 -7019.8099999999995" +Ta 0.0 0.0 0.0 0.0 -2e-06 0.000434 +Ta 1.6585 1.6664 1.6621 0.0 2e-06 -0.000434 +2 +Lattice = "3.31769990921 0.0 0.0 -0.00579999992624 3.31699991226 0.0 0.00889999978244 0.0162000004202 3.3327999115" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.69061 stress="-9577.12 1230.78 -1945.3100000000002 1230.78 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Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.690688 stress="-8159.87 -1578.8500000000001 -569.48 -1578.8500000000001 -11732.89 -685.38 -569.48 -685.38 -15843.04" +Ta 0.0 0.0 0.0 -0.000422 -0.000425 1e-06 +Ta 1.6604 1.6627 1.6678 0.000422 0.000425 -1e-06 +2 +Lattice = "3.32010006905 0.0 0.0 0.0153999999166 3.31189990044 0.0 0.00710000004619 -0.0116999996826 3.3164999485" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.689988 stress="-1287.79 -3409.17 -1564.98 -3409.17 1359.31 2585.44 -1564.98 2585.44 -98.57000000000001" +Ta 0.0 0.0 0.0 -2e-06 3e-06 0.000438 +Ta 1.6713 1.6501 1.6583 2e-06 -3e-06 -0.000438 +2 +Lattice = "3.31150007248 0.0 0.0 -0.0038999998942 3.30809998512 0.0 0.0154999997467 -0.0133999995887 3.32680010796" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.689613 stress="2542.36 898.2 -3478.91 898.2 3649.25 3002.21 -3478.91 3002.21 -2359.93" +Ta 0.0 0.0 0.0 0.000437 -0.000437 -8e-06 +Ta 1.6616 1.6473 1.6634 -0.000437 0.000437 8e-06 +2 +Lattice = 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stress="-16030.460000000001 -2615.3 -1399.57 -2615.3 -9011.369999999999 1069.71 -1399.57 1069.71 -10383.800000000001" +Ta 0.0 0.0 0.0 -0.000861 6e-06 3e-06 +Ta 1.6773 1.6545 1.6592 0.000861 -6e-06 -3e-06 +2 +Lattice = "3.31769990921 0.0 0.0 -0.00949999969453 3.32529997826 0.0 0.0105999996886 0.00949999969453 3.33109998703" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.690656 stress="-12733.07 2033.6599999999999 -2291.25 2033.6599999999999 -15085.44 -2061.68 -2291.25 -2061.68 -16870.989999999998" +Ta 0.0 0.0 0.0 -3e-06 -2e-06 0.000426 +Ta 1.6594 1.6674 1.6656 3e-06 2e-06 -0.000426 +2 +Lattice = "3.32620000839 0.0 0.0 0.00270000007004 3.30970001221 0.0 0.01600000076 0.0155999995768 3.33610010147" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.690254 stress="-14323.800000000001 -620.5899999999999 -3515.58 -620.5899999999999 -9188.58 -3392.86 -3515.58 -3392.86 -17392.0" +Ta 0.0 0.0 0.0 -0.000423 0.000427 -0.000428 +Ta 1.6724 1.6627 1.668 0.000423 -0.000427 0.000428 +2 +Lattice = "3.31920003891 0.0 0.0 -0.00730000017211 3.32259988785 0.0 -0.0133999995887 -0.0131999999285 3.32820010185" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.690694 stress="-11276.81 1552.73 2911.96 1552.73 -12332.94 2876.65 2911.96 2876.65 -14073.7" +Ta 0.0 0.0 0.0 0.000425 2e-06 4e-06 +Ta 1.6493 1.6547 1.6641 -0.000425 -2e-06 -4e-06 +2 +Lattice = "3.33060002327 0.0 0.0 0.00170000002254 3.30550003052 0.0 -0.0154999997467 -0.0108000002801 3.31830000877" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.690097 stress="-7398.2 -404.2 3456.2400000000002 -404.2 607.84 2374.71 3456.2400000000002 2374.71 -3477.02" +Ta 0.0 0.0 0.0 4e-06 0.000435 0.000438 +Ta 1.6584 1.6474 1.6592 -4e-06 -0.000435 -0.000438 +2 +Lattice = "3.30870008469 0.0 0.0 0.00079999997979 3.3125 0.0 0.0129000004381 -0.0046999999322 3.3111000061" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.688402 stress="10344.23 -170.68 -2918.0299999999997 -170.68 9114.35 1063.15 -2918.0299999999997 1063.15 9572.1" +Ta 0.0 0.0 0.0 4e-06 -1e-06 -0.000447 +Ta 1.6612 1.6539 1.6555 -4e-06 1e-06 0.000447 +2 +Lattice = "3.32299995422 0.0 0.0 -0.00439999997616 3.3085000515 0.0 0.00289999996312 0.0137999998406 3.304500103" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.688669 stress="3910.4 988.25 -648.7 988.25 8614.3 -3085.0 -648.7 -3085.0 9933.490000000002" +Ta 0.0 0.0 0.0 0.000445 -0.000447 0.000446 +Ta 1.6608 1.6611 1.6523 -0.000445 0.000447 -0.000446 +2 +Lattice = "3.31419992447 0.0 0.0 -0.0108000002801 3.31520009041 0.0 0.0114000001922 -0.00249999994412 3.33610010147" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.690538 stress="-7515.75 2343.1000000000004 -2512.81 2343.1000000000004 -7800.79 565.26 -2512.81 565.26 -14362.84" +Ta 0.0 0.0 0.0 0.0 0.000428 0.000433 +Ta 1.6574 1.6564 1.6681 0.0 -0.000428 -0.000433 +2 +Lattice = "3.30870008469 0.0 0.0 -0.0105999996886 3.31060004234 0.0 0.00710000004619 -0.0164000000805 3.32909989357" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.689722 stress="2494.02 2358.67 -1602.8700000000001 2358.67 1865.98 3675.35 -1602.8700000000001 3675.35 -4043.8799999999997" +Ta 0.0 0.0 0.0 -2e-06 5e-06 0.000442 +Ta 1.6526 1.6471 1.6646 2e-06 -5e-06 -0.000442 +2 +Lattice = "3.33130002022 0.0 0.0 0.0153999999166 3.3259999752 0.0 0.00669999979436 0.00999999977648 3.31539988518" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.690581 stress="-16296.82 -3376.3999999999996 -1468.21 -3376.3999999999996 -14640.43 -2166.98 -1468.21 -2166.98 -11322.16" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 1.6767 1.668 1.6577 0.0 0.0 0.0 +2 +Lattice = "3.30430006981 0.0 0.0 0.0136000001803 3.32470011711 0.0 0.00740000000224 0.00650000013411 3.3083999157" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.688755 stress="9299.8 -3078.46 -1660.51 -3078.46 2679.5 -1477.71 -1660.51 -1477.71 7991.16" +Ta 0.0 0.0 0.0 0.000442 -4e-06 -2e-06 +Ta 1.6627 1.6656 1.6542 -0.000442 4e-06 2e-06 +2 +Lattice = "3.3273999691 0.0 0.0 0.0126999998465 3.33459997177 0.0 -0.00460000010207 0.0146000003442 3.33229994774" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.689312 stress="-25105.09 -2688.4 959.13 -2688.4 -27291.81 -3105.23 959.13 -3105.23 -26574.49" +Ta 0.0 0.0 0.0 0.000414 -7e-06 0.000415 +Ta 1.6678 1.6746 1.6662 -0.000414 7e-06 -0.000415 +2 +Lattice = "3.30520009995 0.0 0.0 -0.0137000000104 3.31570005417 0.0 -0.0162000004202 -0.0124000003561 3.30730009079" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.687388 stress="13516.93 3087.18 3651.46 3087.18 10100.35 2802.34 3651.46 2802.34 12865.9" +Ta 0.0 0.0 0.0 -0.000456 -0.000459 -0.000457 +Ta 1.6376 1.6516 1.6536 0.000456 0.000459 0.000457 +2 +Lattice = "3.31599998474 0.0 0.0 0.000699999975041 3.31730008125 0.0 0.000600000028498 -0.0154999997467 3.32500004768" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.690664 stress="-4661.23 -151.07000000000002 -130.38 -151.07000000000002 -5113.86 3419.6 -130.38 3419.6 -7531.63" +Ta 0.0 0.0 0.0 -0.000432 0.0 0.0 +Ta 1.6586 1.6509 1.6625 0.000432 0.0 0.0 +2 +Lattice = "3.3273999691 0.0 0.0 -0.0148999998346 3.32949995995 0.0 0.0137000000104 0.0154999997467 3.33450007439" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.68941 stress="-23795.190000000002 3133.63 -2900.7000000000003 3133.63 -24418.25 -3288.91 -2900.7000000000003 -3288.91 -25917.71" +Ta 0.0 0.0 0.0 3e-06 4e-06 -0.000416 +Ta 1.6631 1.6725 1.6672 -3e-06 -4e-06 0.000416 +2 +Lattice = "3.32439994812 0.0 0.0 0.00760000012815 3.31010007858 0.0 0.00590000022203 0.0038999998942 3.31290006638" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.690035 stress="-2106.9399999999996 -1695.3400000000001 -1317.1299999999999 -1695.3400000000001 2496.5299999999997 -868.58 -1317.1299999999999 -868.58 1598.99" +Ta 0.0 0.0 0.0 -0.000442 1e-06 0.000439 +Ta 1.6689 1.657 1.6565 0.000442 -1e-06 -0.000439 +2 +Lattice = "3.32430005074 0.0 0.0 0.00910000037402 3.3289000988 0.0 -0.00740000000224 0.01600000076 3.33310008049" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.690015 stress="-20472.059999999998 -1926.96 1574.3700000000001 -1926.96 -21891.98 -3433.3999999999996 1574.3700000000001 -3433.3999999999996 -23153.19" +Ta 0.0 0.0 0.0 4e-06 -0.000422 0.000423 +Ta 1.663 1.6724 1.6666 -4e-06 0.000422 -0.000423 +2 +Lattice = "3.32279992104 0.0 0.0 0.0130000002682 3.32789993286 0.0 -0.00899999961257 -0.001200000057 3.32439994812" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.690752 stress="-14810.21 -2823.7999999999997 1946.96 -2823.7999999999997 -16361.699999999999 271.0 1946.96 271.0 -15278.02" +Ta 0.0 0.0 0.0 -3e-06 0.000424 0.0 +Ta 1.6634 1.6634 1.6622 3e-06 -0.000424 0.0 +2 +Lattice = "3.30900001526 0.0 0.0 -0.0046999999322 3.33019995689 0.0 -0.00850000046194 0.00170000002254 3.30809998512" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.689825 stress="2936.71 1055.66 1878.49 1055.66 -3856.89 -383.2 1878.49 -383.2 3236.96" +Ta 0.0 0.0 0.0 -1e-06 0.000443 -0.000437 +Ta 1.6479 1.666 1.654 1e-06 -0.000443 0.000437 +2 +Lattice = "3.32730007172 0.0 0.0 -0.0148000000045 3.31719994545 0.0 0.00960000045598 -0.0111999996006 3.32929992676" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.690562 stress="-15582.82 3214.2400000000002 -2112.58 3214.2400000000002 -12428.97 2441.49 -2112.58 2441.49 -16168.56" +Ta 0.0 0.0 0.0 -0.000428 -1e-06 0.000428 +Ta 1.661 1.653 1.6647 0.000428 1e-06 -0.000428 +2 +Lattice = "3.31780004501 0.0 0.0 -0.0141000002623 3.31990003586 0.0 -0.000199999994948 -0.00460000010207 3.33559989929" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.690622 stress="-12368.81 3035.58 36.589999999999996 3035.58 -13009.29 1003.22 36.589999999999996 1003.22 -17869.59" +Ta 0.0 0.0 0.0 0.000419 -0.00042 -1e-06 +Ta 1.6518 1.6576 1.6678 -0.000419 0.00042 1e-06 +2 +Lattice = "3.31019997597 0.0 0.0 0.0127999996766 3.32069993019 0.0 0.0063000000082 -0.00170000002254 3.30509996414" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.688764 stress="8054.89 -2896.21 -1408.45 -2896.21 4644.51 375.59999999999997 -1408.45 375.59999999999997 9733.77" +Ta 0.0 0.0 0.0 -0.000446 4e-06 0.000445 +Ta 1.6646 1.6595 1.6526 0.000446 -4e-06 -0.000445 +2 +Lattice = "3.31080007553 0.0 0.0 -0.00319999991916 3.31229996681 0.0 -0.00240000011399 0.00359999993816 3.32299995422" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.690011 stress="2899.77 713.48 536.4100000000001 713.48 2419.23 -804.18 536.4100000000001 -804.18 -1023.68" +Ta 0.0 0.0 0.0 1e-06 0.000438 -1e-06 +Ta 1.6526 1.658 1.6615 -1e-06 -0.000438 1e-06 +2 +Lattice = "3.30539989471 0.0 0.0 0.00359999993816 3.31970000267 0.0 -0.0097000002861 -0.0120000001043 3.30390000343" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.687696 stress="13108.67 -840.56 2187.26 -840.56 8404.43 2733.05 2187.26 2733.05 13609.949999999999" +Ta 0.0 0.0 0.0 0.000444 0.000447 -0.000441 +Ta 1.6497 1.6539 1.6519 -0.000444 -0.000447 0.000441 +2 +Lattice = "3.31929993629 0.0 0.0 0.00240000011399 3.32459998131 0.0 0.00540000014007 0.00109999999404 3.32540011406" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.691019 stress="-10964.99 -525.81 -1177.09 -525.81 -12623.84 -241.71 -1177.09 -241.71 -12870.95" +Ta 0.0 0.0 0.0 0.000426 -0.000428 -1e-06 +Ta 1.6636 1.6628 1.6627 -0.000426 0.000428 1e-06 +2 +Lattice = "3.31080007553 0.0 0.0 0.00350000010803 3.31130003929 0.0 -0.0135000003502 0.00310000008903 3.31500005722" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.689025 stress="7287.55 -782.66 3041.1000000000004 -782.66 7135.919999999999 -692.63 3041.1000000000004 -692.63 5936.740000000001" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 1.6504 1.6572 1.6575 0.0 0.0 0.0 +2 +Lattice = "3.30800008774 0.0 0.0 -0.00200000009499 3.33439993858 0.0 0.0111999996006 0.0130000002682 3.31060004234" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.689952 stress="508.71 421.52 -2451.6800000000003 421.52 -7909.360000000001 -2885.62 -2451.6800000000003 -2885.62 -315.85999999999996" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 1.6586 1.6737 1.6553 0.0 0.0 0.0 +2 +Lattice = "3.3289000988 0.0 0.0 0.00820000004023 3.32640004158 0.0 -0.0105999996886 -0.0156999994069 3.31559991837" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.69061 stress="-14693.78 -1821.97 2311.93 -1821.97 -13931.74 3407.2 2311.93 3407.2 -10544.75" +Ta 0.0 0.0 0.0 0.000429 -0.000429 -1e-06 +Ta 1.6633 1.6553 1.6578 -0.000429 0.000429 1e-06 +2 +Lattice = "3.32290005684 0.0 0.0 0.0154999997467 3.31669998169 0.0 0.00870000012219 0.0142000000924 3.32319998741" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.690595 stress="-9023.58 -3411.2599999999998 -1934.4099999999999 -3411.2599999999998 -7071.44 -3121.81 -1934.4099999999999 -3121.81 -9087.630000000001" +Ta 0.0 0.0 0.0 0.000435 -0.000433 2e-06 +Ta 1.6736 1.6654 1.6616 -0.000435 0.000433 -2e-06 +2 +Lattice = "3.3303000927 0.0 0.0 0.0146000003442 3.31329989433 0.0 0.0110999997705 0.00760000012815 3.33520007133" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.690231 stress="-18800.98 -3140.71 -2429.11 -3140.71 -13532.06 -1652.97 -2429.11 -1652.97 -20281.1" +Ta 0.0 0.0 0.0 4e-06 -0.000419 2e-06 +Ta 1.678 1.6604 1.6676 -4e-06 0.000419 -2e-06 +2 +Lattice = "3.33489990234 0.0 0.0 0.0162000004202 3.32060003281 0.0 -0.00230000005104 0.01070000045 3.32109999657" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.690469 stress="-19225.86 -3508.14 482.12 -3508.14 -14795.67 -2294.36 482.12 -2294.36 -14933.130000000001" +Ta 0.0 0.0 0.0 -5e-06 0.000425 -0.000425 +Ta 1.6744 1.6657 1.6605 5e-06 -0.000425 0.000425 +2 +Lattice = "3.31529998779 0.0 0.0 -0.00449999980628 3.31590008736 0.0 -0.00150000001304 -0.0077999997884 3.32039999962" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.690482 stress="-1223.53 989.7099999999999 330.42 989.7099999999999 -1425.84 1726.31 330.42 1726.31 -2854.88" +Ta 0.0 0.0 0.0 0.000437 0.000437 3e-06 +Ta 1.6547 1.6541 1.6602 -0.000437 -0.000437 -3e-06 +2 +Lattice = "3.33599996567 0.0 0.0 0.0127999996766 3.31879997253 0.0 0.0046999999322 0.00219999998808 3.33610010147" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.689613 stress="-26129.239999999998 -2719.4500000000003 -1009.22 -2719.4500000000003 -20885.58 -474.41 -1009.22 -474.41 -26139.41" +Ta 0.0 0.0 0.0 0.000416 -4e-06 0.000416 +Ta 1.6768 1.6605 1.6681 -0.000416 4e-06 -0.000416 +2 +Lattice = "3.30529999733 0.0 0.0 -0.0137000000104 3.31130003929 0.0 -0.0113000003621 -0.00879999995232 3.31049990654" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.687426 stress="14036.429999999998 3100.8300000000004 2557.21 3100.8300000000004 12085.73 1993.28 2557.21 1993.28 12358.140000000001" +Ta 0.0 0.0 0.0 0.000442 -0.00045 -0.00045 +Ta 1.6402 1.6512 1.6552 -0.000442 0.00045 0.00045 +2 +Lattice = "3.30550003052 0.0 0.0 -0.00620000017807 3.30990004539 0.0 0.0144999995828 -0.00209999992512 3.33089995384" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.689562 stress="4550.63 1373.71 -3248.75 1373.71 3169.0 478.2 -3248.75 478.2 -3584.6" +Ta 0.0 0.0 0.0 4e-06 -1e-06 -0.000443 +Ta 1.6569 1.6539 1.6654 -4e-06 1e-06 0.000443 +2 +Lattice = "3.31920003891 0.0 0.0 0.0109999999404 3.31369996071 0.0 0.0155999995768 0.0151000004262 3.3273999691" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.6904 stress="-6656.91 -2444.4 -3459.77 -2444.4 -4902.92 -3339.7000000000003 -3459.77 -3339.7000000000003 -9220.65" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 1.6729 1.6644 1.6637 0.0 0.0 0.0 +2 +Lattice = "3.32829999924 0.0 0.0 0.00159999995958 3.32319998741 0.0 0.0164999999106 -0.0138999996707 3.32419991493" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.690561 stress="-16787.82 -307.25 -3575.27 -307.25 -15202.7 3000.58 -3575.27 3000.58 -15509.24" +Ta 0.0 0.0 0.0 0.0 0.000423 3e-06 +Ta 1.6732 1.6547 1.6621 0.0 -0.000423 -3e-06 +2 +Lattice = "3.33509993553 0.0 0.0 0.0 3.32529997826 0.0 0.00889999978244 0.0130000002682 3.33629989624" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.689107 stress="-28509.83 -17.12 -1893.91 -17.12 -25562.52 -2751.32 -1893.91 -2751.32 -28867.920000000002" +Ta 0.0 0.0 0.0 -2e-06 0.000408 0.00041 +Ta 1.672 1.6692 1.6682 2e-06 -0.000408 -0.00041 +2 +Lattice = "3.33400011063 0.0 0.0 -0.0162000004202 3.30960011482 0.0 -0.0131000000983 -0.0115000000224 3.31579995155" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.690145 stress="-10872.289999999999 3539.75 2881.95 3539.75 -3120.2999999999997 2484.82 2881.95 2484.82 -5070.15" +Ta 0.0 0.0 0.0 -0.00044 -0.000434 -7e-06 +Ta 1.6523 1.649 1.6579 0.00044 0.000434 7e-06 +2 +Lattice = "3.32870006561 0.0 0.0 0.00930000003427 3.33170008659 0.0 -0.00400000018999 -0.0147000001743 3.31769990921" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.690482 stress="-17992.4 -2032.8300000000002 873.85 -2032.8300000000002 -18940.809999999998 3171.19 873.85 3171.19 -14593.14" +Ta 0.0 0.0 0.0 1e-06 4e-06 0.00042 +Ta 1.667 1.6585 1.6589 -1e-06 -4e-06 -0.00042 +2 +Lattice = "3.32459998131 0.0 0.0 -0.00170000002254 3.30690002441 0.0 0.0126000000164 0.00930000003427 3.31570005417" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.689864 stress="-2068.5699999999997 357.16999999999996 -2815.44 357.16999999999996 3633.85 -2059.7599999999998 -2815.44 -2059.7599999999998 802.9" +Ta 0.0 0.0 0.0 0.000444 3e-06 -0.000442 +Ta 1.6678 1.6581 1.6578 -0.000444 -3e-06 0.000442 diff --git a/examples/PACKAGES/pod/Ta/XYZ/Elastic_FCC.xyz b/examples/PACKAGES/pod/Ta/XYZ/Elastic_FCC.xyz new file mode 100644 index 0000000000..b0f70e3e0c --- /dev/null +++ b/examples/PACKAGES/pod/Ta/XYZ/Elastic_FCC.xyz @@ -0,0 +1,600 @@ +4 +Lattice = "4.20979976654 0.0 0.0 0.00079999997979 4.19229984283 0.0 0.00139999995008 -0.00289999996312 4.20120000839" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.437936 stress="32125.329999999998 -282.22 -267.48 -282.22 28704.550000000003 301.20000000000005 -267.48 301.20000000000005 19406.25" +Ta 2.1056 -0.0014 2.1006 -0.00024 -0.000831 -4.2e-05 +Ta 2.1053 2.0961 0.0 0.00024 0.000831 4.2e-05 +Ta 0.0011 2.0947 2.1006 0.000211 -2.8e-05 -7.8e-05 +Ta 0.0 0.0 0.0 -0.000211 2.8e-05 7.8e-05 +4 +Lattice = "4.21169996262 0.0 0.0 -0.0197000000626 4.18310022354 0.0 0.0122999995947 -0.0172000005841 4.21549987793" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.438504 stress="28580.99 4661.44 -2537.73 4661.44 21736.13 3777.39 -2537.73 3777.39 15422.61" +Ta 2.112 -0.0086 2.1078 -8.5e-05 0.000609 -0.000432 +Ta 2.096 2.0916 0.0 8.5e-05 -0.000609 0.000432 +Ta -0.0037 2.083 2.1078 -7.9e-05 -0.000591 -0.00044 +Ta 0.0 0.0 0.0 7.9e-05 0.000591 0.00044 +4 +Lattice = "4.20760011673 0.0 0.0 0.00839999970049 4.19579982758 0.0 -0.0108000002801 0.00989999994636 4.19500017166" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.436378 stress="32906.770000000004 -1998.4299999999998 2448.51 -1998.4299999999998 31390.95 -2209.73 2448.51 -2209.73 20534.55" +Ta 2.1068 4.2007 2.0975 4.9e-05 0.00037 -0.000158 +Ta 2.108 2.0979 0.0 -4.9e-05 -0.00037 0.000158 +Ta -0.0012 2.1028 2.0975 4.9e-05 0.00037 -0.000158 +Ta 0.0 0.0 0.0 -4.9e-05 -0.00037 0.000158 +4 +Lattice = "4.21610021591 0.0 0.0 -0.0186000000685 4.20079994202 0.0 -0.0110999997705 -0.0149999996647 4.195499897" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.441551 stress="27882.2 4157.13 2708.72 4157.13 24066.9 3156.97 2708.72 3156.97 13737.52" +Ta 2.0839 4.1933 2.0977 6.8e-05 -4.7e-05 0.000367 +Ta 2.0987 2.1004 0.0 0.000703 0.000158 -0.000404 +Ta -0.0148 2.0929 2.0977 -0.000703 -0.000158 0.000404 +Ta 0.0 0.0 0.0 -6.8e-05 4.7e-05 -0.000367 +4 +Lattice = "4.18009996414 0.0 0.0 -0.00079999997979 4.19099998474 0.0 -0.00109999999404 -0.0186000000685 4.19029998779" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.416957 stress="47483.73 251.66 89.96 251.66 51115.740000000005 3817.67 89.96 3817.67 39271.009999999995" +Ta 2.0895 -0.0093 2.0952 -0.000287 7.5e-05 -0.000462 +Ta 2.0896 2.0955 0.0 0.000287 -7.5e-05 0.000462 +Ta 4.1791 2.0862 2.0952 0.00038 6.8e-05 -0.000503 +Ta 0.0 0.0 0.0 -0.00038 -6.8e-05 0.000503 +4 +Lattice = "4.21759986877 0.0 0.0 0.00989999994636 4.20160007477 0.0 -0.0164999999106 0.000600000028498 4.1861000061" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.440495 stress="30412.84 -2230.41 3936.28 -2230.41 27956.19 -314.22 3936.28 -314.22 16511.39" +Ta 2.1006 0.0003 2.093 -0.000512 -1.6e-05 0.000315 +Ta 2.1138 2.1008 0.0 -0.000516 -1.4e-05 -0.000327 +Ta 4.2143 2.1011 2.093 0.000516 1.4e-05 0.000327 +Ta 0.0 0.0 0.0 0.000512 1.6e-05 -0.000315 +4 +Lattice = "4.20800018311 0.0 0.0 -0.00609999988228 4.19269990921 0.0 0.0185000002384 0.00510000018403 4.20429992676" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.437972 stress="30692.39 1017.5300000000001 -3953.9 1017.5300000000001 27371.22 -937.5 -3953.9 -937.5 18526.5" +Ta 2.1071 4.1952 2.1022 0.000867 0.001178 -0.000599 +Ta 2.101 2.0964 0.0 -0.000867 -0.001178 0.000599 +Ta 4.2142 2.0989 2.1022 -3.6e-05 -0.000335 -0.000411 +Ta 0.0 0.0 0.0 3.6e-05 0.000335 0.000411 +4 +Lattice = "4.20389986038 0.0 0.0 0.0109999999404 4.21560001373 0.0 -0.0149999996647 -0.0195000004023 4.21710014343" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.44586 stress="13322.5 -1851.3999999999999 2698.2400000000002 -1851.3999999999999 15084.53 4168.71 2698.2400000000002 4168.71 3183.15" +Ta 2.0944 -0.0097 2.1085 0.000605 -0.001004 0.000354 +Ta 2.1075 2.1078 0.0 -0.000787 0.00036 -0.000493 +Ta 4.2019 2.098 2.1085 0.000145 0.000977 0.000593 +Ta 0.0 0.0 0.0 3.7e-05 -0.000333 -0.000454 +4 +Lattice = "4.20989990234 0.0 0.0 0.0194000005722 4.18979978561 0.0 0.0187999997288 -0.00710000004619 4.1998000145" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.435744 stress="32866.979999999996 -4705.08 -4510.19 -4705.08 27538.81 1684.04 -4510.19 1684.04 19619.25" +Ta 2.1338 4.1862 2.0999 -0.000654 0.000551 -0.000151 +Ta 2.1146 2.0949 0.0 0.000654 -0.000551 0.000151 +Ta 0.0191 2.0913 2.0999 0.000168 0.00073 -0.000338 +Ta 0.0 0.0 0.0 -0.000168 -0.00073 0.000338 +4 +Lattice = "4.20370006561 0.0 0.0 -0.00999999977648 4.18909978867 0.0 0.0038999998942 0.0115999998525 4.21619987488" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.438209 stress="27954.8 2323.13 -793.2399999999999 2323.13 23969.38 -2424.6400000000003 -793.2399999999999 -2424.6400000000003 15680.8" +Ta 2.1038 0.0058 2.1081 0.000328 -0.000478 -1.9e-05 +Ta 2.0969 2.0945 0.0 -0.000328 0.000478 1.9e-05 +Ta -0.003 2.1003 2.1081 -0.000328 0.000478 1.9e-05 +Ta 0.0 0.0 0.0 0.000328 -0.000478 -1.9e-05 +4 +Lattice = "4.19409990311 0.0 0.0 -0.00949999969453 4.18279981613 0.0 -0.00359999993816 0.0146000003442 4.20279979706" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.42629 stress="40994.259999999995 1984.0500000000002 678.41 1984.0500000000002 38515.95 -2950.21 678.41 -2950.21 30369.28" +Ta 2.0953 0.0073 2.1014 -0.000264 2.1e-05 -3e-06 +Ta 2.0923 2.0914 0.0 0.000264 -2.1e-05 3e-06 +Ta -0.0065 2.0987 2.1014 -0.000264 2.1e-05 -3e-06 +Ta 0.0 0.0 0.0 0.000264 -2.1e-05 3e-06 +4 +Lattice = "4.21500015259 0.0 0.0 0.00240000011399 4.2077999115 0.0 0.00559999980032 -0.00430000014603 4.19150018692" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.443301 stress="25318.89 -582.25 -1370.1399999999999 -582.25 24260.940000000002 1009.18 -1370.1399999999999 1009.18 11853.45" +Ta 2.1103 -0.0021 2.0957 2.5e-05 -0.00092 0.000616 +Ta 2.1087 2.1039 0.0 -3.1e-05 0.000243 -0.000622 +Ta 0.004 2.1017 2.0957 4e-05 0.000897 0.000626 +Ta 0.0 0.0 0.0 -3.4e-05 -0.00022 -0.000621 +4 +Lattice = "4.21619987488 0.0 0.0 -0.0207000002265 4.1875 0.0 -0.00230000005104 0.00730000017211 4.20310020447" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.439002 stress="30242.61 4765.59 418.83 4765.59 23708.24 -1576.43 418.83 -1576.43 16414.149999999998" +Ta 2.0863 4.1911 2.1015 -0.00067 0.000288 0.000472 +Ta 2.0977 2.0937 0.0 0.000637 0.000248 -0.000453 +Ta 4.2047 2.0974 2.1015 6.7e-05 -0.00028 0.000455 +Ta 0.0 0.0 0.0 -3.3e-05 -0.000255 -0.000474 +4 +Lattice = "4.21169996262 0.0 0.0 -0.0137999998406 4.18540000916 0.0 0.00350000010803 0.016799999401 4.19210004807" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.432438 stress="38865.54 2976.27 -1187.3700000000001 2976.27 32433.36 -3670.5899999999997 -1187.3700000000001 -3670.5899999999997 24012.71" +Ta 2.0938 4.1938 2.0961 0.000109 1.5e-05 -0.000266 +Ta 2.0989 2.0927 0.0 0.000626 -5.5e-05 0.000181 +Ta -0.0051 2.1011 2.0961 -0.000626 5.5e-05 -0.000181 +Ta 0.0 0.0 0.0 -0.000109 -1.5e-05 0.000266 +4 +Lattice = "4.18310022354 0.0 0.0 -0.00300000002608 4.18790006638 0.0 0.0161000005901 -0.0153999999166 4.18289995193" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.412654 stress="53423.5 705.21 -3760.97 705.21 56329.25 3452.61 -3760.97 3452.61 44823.36" +Ta 2.0996 -0.0077 2.0915 0.000209 0.000715 -0.000359 +Ta 2.09 2.094 0.0 0.000554 -0.000722 0.000333 +Ta 0.0066 2.0863 2.0915 -0.000628 -0.000725 -0.000262 +Ta 0.0 0.0 0.0 -0.000135 0.000731 0.000288 +4 +Lattice = "4.19859981537 0.0 0.0 -0.00520000001416 4.21680021286 0.0 -0.000199999994948 0.00190000003204 4.20230007172" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.443231 stress="21408.78 997.66 2.63 997.66 23951.809999999998 -420.08 2.63 -420.08 10910.34" +Ta 2.094 4.2177 2.1012 -4.8e-05 0.000221 -0.000815 +Ta 2.0967 2.1084 0.0 4.8e-05 -0.000221 0.000815 +Ta 4.1959 2.1093 2.1012 -4.8e-05 0.000221 -0.000815 +Ta 0.0 0.0 0.0 4.8e-05 -0.000221 0.000815 +4 +Lattice = "4.21309995651 0.0 0.0 0.00989999994636 4.17939996719 0.0 -0.0111999996006 -0.0109000001103 4.19469976425" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.431513 stress="38571.840000000004 -2057.94 2001.0400000000002 -2057.94 31128.620000000003 2212.8199999999997 2001.0400000000002 2212.8199999999997 25395.620000000003" +Ta 2.101 -0.0054 2.0973 -0.000812 -0.000699 0.000382 +Ta 2.1115 2.0897 0.0 -5.2e-05 0.000172 -0.000317 +Ta 4.2124 2.0842 2.0973 0.000823 0.000706 0.000273 +Ta 0.0 0.0 0.0 4.1e-05 -0.000179 -0.000337 +4 +Lattice = "4.21220016479 0.0 0.0 0.00730000017211 4.19630002975 0.0 0.00209999992512 -0.0115000000224 4.18480014801" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.435608 stress="35907.1 -1805.28 -643.2900000000001 -1805.28 32898.1 2687.74 -643.2900000000001 2687.74 21620.26" +Ta 2.1144 4.1905 2.0924 0.000371 0.000304 -3e-06 +Ta 2.1097 2.0981 0.0 0.000371 0.000304 -3e-06 +Ta 0.0047 2.0924 2.0924 -0.000371 -0.000304 3e-06 +Ta 0.0 0.0 0.0 -0.000371 -0.000304 3e-06 +4 +Lattice = "4.18069982529 0.0 0.0 -0.0109000001103 4.21169996262 0.0 -0.00529999984428 0.00520000001416 4.21330022812" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.437689 stress="23769.33 2509.14 1235.52 2509.14 31281.32 -1087.23 1235.52 -1087.23 17393.4" +Ta 2.0768 4.2143 2.1067 -0.000106 -0.000368 -0.000493 +Ta 2.0849 2.1058 0.0 0.000106 0.000368 0.000493 +Ta 4.1726 2.1084 2.1067 0.000104 0.000319 -0.000489 +Ta 0.0 0.0 0.0 -0.000104 -0.000319 0.000489 +4 +Lattice = "4.18959999084 0.0 0.0 0.0164999999106 4.20200014114 0.0 0.00899999961257 -0.0188999995589 4.19029998779" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.428447 stress="39131.659999999996 -3973.89 -2296.86 -3973.89 42258.21 4597.84 -2296.86 4597.84 29361.260000000002" +Ta 2.0993 -0.0094 2.0951 0.000613 -0.000529 0.000975 +Ta 2.1031 2.101 0.0 -0.000613 0.000529 -0.000975 +Ta 0.0128 2.0916 2.0951 -0.000208 -0.000185 0.000662 +Ta 0.0 0.0 0.0 0.000208 0.000185 -0.000662 +4 +Lattice = "4.18120002747 0.0 0.0 -0.000399999989895 4.21000003815 0.0 0.00460000010207 0.0187999997288 4.19910001755" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.432255 stress="29757.62 -182.62 -536.07 -182.62 36285.020000000004 -3344.74 -536.07 -3344.74 22592.0" +Ta 2.0929 0.0094 2.0995 -0.00013 1.7e-05 0.000285 +Ta 2.0904 2.105 0.0 0.00013 -1.7e-05 -0.000285 +Ta 0.0021 2.1144 2.0995 -0.00013 1.7e-05 0.000285 +Ta 0.0 0.0 0.0 0.00013 -1.7e-05 -0.000285 +4 +Lattice = "4.21250009537 0.0 0.0 -0.0190999992192 4.2062997818 0.0 0.0172000005841 0.0121999997646 4.1968998909" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.442315 stress="24536.86 4406.19 -4080.28 4406.19 23952.329999999998 -2854.26 -4080.28 -2854.26 11636.13" +Ta 2.1149 0.0061 2.0984 -0.00079 -0.000901 0.000821 +Ta 2.0967 2.1031 0.0 0.00079 0.000901 -0.000821 +Ta -0.0009 2.1092 2.0984 -0.00026 0.000434 0.000757 +Ta 0.0 0.0 0.0 0.00026 -0.000434 -0.000757 +4 +Lattice = "4.18179988861 0.0 0.0 0.0136000001803 4.21280002594 0.0 0.00310000008903 -0.0118000004441 4.20720005035" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.436613 stress="25874.06 -3205.31 -821.0 -3205.31 32985.54 2726.66 -821.0 2726.66 19695.18" +Ta 2.0925 -0.0059 2.1036 -0.000254 -3.3e-05 -7.2e-05 +Ta 2.0977 2.1064 0.0 0.000254 3.3e-05 7.2e-05 +Ta 0.0084 2.1005 2.1036 -0.000254 -3.3e-05 -7.2e-05 +Ta 0.0 0.0 0.0 0.000254 3.3e-05 7.2e-05 +4 +Lattice = "4.20440006256 0.0 0.0 -0.00430000014603 4.18720006943 0.0 0.0116999996826 0.0206000003964 4.19589996338" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.430825 stress="38754.51 1016.0100000000001 -2801.6 1016.0100000000001 34556.35 -4530.67 -2801.6 -4530.67 26227.129999999997" +Ta 2.108 0.0103 2.0979 0.000384 -3.4e-05 0.000554 +Ta 2.1 2.0936 0.0 0.000373 -0.000115 -0.00061 +Ta 0.0037 2.1039 2.0979 -0.000373 0.000115 0.00061 +Ta 0.0 0.0 0.0 -0.000384 3.4e-05 -0.000554 +4 +Lattice = "4.1888999939 0.0 0.0 0.0038999998942 4.20720005035 0.0 -0.0144999995828 0.0156999994069 4.19560003281" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.43312 stress="29781.53 -523.96 3434.8399999999997 -523.96 33821.21 -3382.98 3434.8399999999997 -3382.98 20448.34" +Ta 2.0911 4.215 2.0978 2.8e-05 0.00036 4.3e-05 +Ta 2.0964 2.1036 0.0 -2.8e-05 -0.00036 -4.3e-05 +Ta -0.0053 2.1114 2.0978 2.8e-05 0.00036 4.3e-05 +Ta 0.0 0.0 0.0 -2.8e-05 -0.00036 -4.3e-05 +4 +Lattice = "4.21330022812 0.0 0.0 0.000699999975041 4.1810002327 0.0 0.0054999999702 -0.00949999969453 4.19969987869" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.434347 stress="37957.909999999996 -320.79 -1076.83 -320.79 30562.539999999997 2073.23 -1076.83 2073.23 23518.02" +Ta 2.1094 -0.0047 2.0998 -8.7e-05 -0.000391 0.000502 +Ta 2.107 2.0905 0.0 8.7e-05 0.000391 -0.000502 +Ta 0.0031 2.0858 2.0998 -8.7e-05 -0.000391 0.000502 +Ta 0.0 0.0 0.0 8.7e-05 0.000391 -0.000502 +4 +Lattice = "4.20370006561 0.0 0.0 0.00340000004508 4.18830013275 0.0 -0.00089999998454 0.00980000011623 4.19320011139" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.430573 stress="38159.329999999994 -261.17 350.0 -261.17 35372.36 -2364.75 350.0 -2364.75 25174.510000000002" +Ta 2.1014 0.0049 2.0966 0.000389 -0.00053 2.4e-05 +Ta 2.1036 2.0941 0.0 -0.000389 0.00053 -2.4e-05 +Ta 0.0013 2.099 2.0966 -0.000389 0.00053 -2.4e-05 +Ta 0.0 0.0 0.0 0.000389 -0.00053 2.4e-05 +4 +Lattice = "4.20860004425 0.0 0.0 -0.00989999994636 4.20669984818 0.0 -0.0154999997467 0.00520000001416 4.21969985962" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.445665 stress="14174.23 2425.32 3028.21 2425.32 15030.34 -809.6999999999999 3028.21 -809.6999999999999 2911.0299999999997" +Ta 2.0966 0.0026 2.1098 -0.000412 -0.000614 0.000581 +Ta 2.0994 2.1033 0.0 -0.00059 0.000627 -0.000659 +Ta 4.1959 2.1059 2.1098 0.000541 0.000424 0.000445 +Ta 0.0 0.0 0.0 0.000461 -0.000437 -0.000367 +4 +Lattice = "4.19920015335 0.0 0.0 0.0185000002384 4.19920015335 0.0 -0.0126000000164 0.00540000014007 4.20139980316" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.435898 stress="32203.23 -4272.68 2945.41 -4272.68 31706.99 -1474.9 2945.41 -1474.9 21250.72" +Ta 2.0933 0.0027 2.1007 0.00043 -1.3e-05 0.000192 +Ta 2.1088 2.0996 0.0 0.00122 -8.7e-05 -0.000171 +Ta 0.003 2.1023 2.1007 -0.00122 8.7e-05 0.000171 +Ta 0.0 0.0 0.0 -0.00043 1.3e-05 -0.000192 +4 +Lattice = "4.2108001709 0.0 0.0 0.0163000002503 4.21479988098 0.0 0.01070000045 0.00499999988824 4.18380022049" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.442107 stress="28916.579999999998 -3579.5699999999997 -2277.82 -3579.5699999999997 29458.98 -1392.66 -2277.82 -1392.66 14592.84" +Ta 2.1108 0.0025 2.0919 -0.000298 4e-05 1.5e-05 +Ta 2.1136 2.1074 0.0 -0.000298 4e-05 1.5e-05 +Ta 0.0135 2.1099 2.0919 0.000298 -4e-05 -1.5e-05 +Ta 0.0 0.0 0.0 0.000298 -4e-05 -1.5e-05 +4 +Lattice = "4.19960021973 0.0 0.0 0.00079999997979 4.18790006638 0.0 -0.0054999999702 0.00499999988824 4.21040010452" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.434432 stress="33222.78 -147.47 1254.14 -147.47 29633.84 -1145.8 1254.14 -1145.8 20687.69" +Ta 2.097 0.0025 2.1052 0.00033 -1.2e-05 0.000134 +Ta 2.1002 2.094 0.0 -0.000357 -0.00057 -0.000134 +Ta 4.1972 2.0964 2.1052 0.000357 0.00057 0.000134 +Ta 0.0 0.0 0.0 -0.00033 1.2e-05 -0.000134 +4 +Lattice = "4.18860006332 0.0 0.0 0.00829999987036 4.19880008698 0.0 0.00680000009015 -0.0104999998584 4.21710014343" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.436308 stress="26865.34 -1570.0700000000002 -1633.81 -1570.0700000000002 30088.280000000002 2199.78 -1633.81 2199.78 18762.14" +Ta 2.0977 -0.0052 2.1086 0.000219 -0.000492 -0.000515 +Ta 2.0984 2.0994 0.0 0.000816 0.000404 0.000554 +Ta 0.0076 2.0942 2.1086 -0.000816 -0.000404 -0.000554 +Ta 0.0 0.0 0.0 -0.000219 0.000492 0.000515 +4 +Lattice = "4.1999001503 0.0 0.0 0.01600000076 4.18179988861 0.0 0.0184000004083 0.00219999998808 4.19189977646" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.423938 stress="45156.3 -3736.32 -4044.29 -3736.32 42163.939999999995 -272.71000000000004 -4044.29 -272.71000000000004 33401.829999999994" +Ta 2.1091 0.0011 2.0959 0.00063 0.000124 0.000424 +Ta 2.1079 2.0909 0.0 0.000645 0.000127 -0.000216 +Ta 0.0172 2.092 2.0959 -0.000645 -0.000127 0.000216 +Ta 0.0 0.0 0.0 -0.00063 -0.000124 -0.000424 +4 +Lattice = "4.18540000916 0.0 0.0 0.00910000037402 4.20340013504 0.0 -0.00449999980628 0.0206000003964 4.19199991226" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.428115 stress="33159.950000000004 -2037.96 1037.3300000000002 -2037.96 36902.979999999996 -4264.8 1037.3300000000002 -4264.8 24342.199999999997" +Ta 2.0905 0.0103 2.096 -0.000408 0.000133 9e-06 +Ta 2.0973 2.1017 0.0 -0.000408 0.000133 9e-06 +Ta 0.0023 2.112 2.096 0.000408 -0.000133 -9e-06 +Ta 0.0 0.0 0.0 0.000408 -0.000133 -9e-06 +4 +Lattice = "4.20219993591 0.0 0.0 -0.0137000000104 4.18510007858 0.0 0.0170000009239 0.000399999989895 4.19110012054" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.4269 stress="42344.0 2996.3700000000003 -4106.58 2996.3700000000003 39499.920000000006 161.89000000000001 -4106.58 161.89000000000001 29485.66" +Ta 2.1096 0.0002 2.0955 3.6e-05 -2.9e-05 0.000575 +Ta 2.0943 2.0925 0.0 -0.000498 0.000956 -0.000492 +Ta 0.0017 2.0928 2.0955 5e-06 -0.000949 0.000486 +Ta 0.0 0.0 0.0 0.000457 2.2e-05 -0.000569 +4 +Lattice = "4.18289995193 0.0 0.0 0.00159999995958 4.179500103 0.0 -0.00310000008903 0.0133999995887 4.209400177" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.421142 stress="44099.57 -461.53 789.15 -461.53 41820.810000000005 -2469.31 789.15 -2469.31 34193.81" +Ta 2.0899 0.0067 2.1047 0.000191 0.000394 1e-06 +Ta 2.0922 2.0898 0.0 0.000613 -0.00044 1.7e-05 +Ta -0.0007 2.0965 2.1047 -0.000794 -0.000378 -7e-06 +Ta 0.0 0.0 0.0 -1e-05 0.000423 -1e-05 +4 +Lattice = "4.21260023117 0.0 0.0 0.0207000002265 4.19000005722 0.0 0.00159999995958 -0.00769999995828 4.18440008163" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.432233 stress="39750.03 -4610.75 -478.2 -4610.75 34854.11 1877.37 -478.2 1877.37 25710.550000000003" +Ta 2.1071 -0.0038 2.0922 0.000289 -0.000207 -3e-06 +Ta 2.1167 2.095 0.0 -0.000289 0.000207 3e-06 +Ta 0.0112 2.0912 2.0922 -0.000287 -0.000233 1e-06 +Ta 0.0 0.0 0.0 0.000287 0.000233 -1e-06 +4 +Lattice = "4.19710016251 0.0 0.0 0.017899999395 4.18270015717 0.0 -0.00960000045598 -0.01600000076 4.20739984512" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.429408 stress="37387.92 -3190.48 1878.9499999999998 -3190.48 32357.480000000003 3103.4700000000003 1878.9499999999998 3103.4700000000003 25220.76" +Ta 2.0938 -0.008 2.1037 -0.000335 0.000327 5.2e-05 +Ta 2.1075 2.0914 0.0 0.000335 -0.000327 -5.2e-05 +Ta 0.0042 2.0834 2.1037 -0.000324 -0.000492 4.2e-05 +Ta 0.0 0.0 0.0 0.000324 0.000492 -4.2e-05 +4 +Lattice = "4.21169996262 0.0 0.0 -0.00689999992028 4.20370006561 0.0 0.00150000001304 -0.00920000020415 4.21269989014" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.445145 stress="18335.4 1673.0 -228.65 1673.0 16239.820000000002 2082.03 -228.65 2082.03 6136.77" +Ta 2.0997 4.1991 2.1063 6.7e-05 -0.000114 0.000643 +Ta 2.1024 2.1018 0.0 -9e-05 0.000831 -0.000669 +Ta -0.0027 2.0973 2.1063 9e-05 -0.000831 0.000669 +Ta 0.0 0.0 0.0 -6.7e-05 0.000114 -0.000643 +4 +Lattice = "4.19729995728 0.0 0.0 0.00370000000112 4.20749998093 0.0 0.0143999997526 -0.00310000008903 4.19150018692" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.435868 stress="32126.109999999997 -1008.08 -3338.91 -1008.08 34042.35 685.31 -3338.91 685.31 21906.06" +Ta 2.1095 4.2059 2.0958 0.000735 0.000174 -0.00065 +Ta 2.1005 2.1037 0.0 0.000783 0.000746 0.000651 +Ta 0.0091 2.1022 2.0958 -0.00125 -0.00074 -0.00065 +Ta 0.0 0.0 0.0 -0.000268 -0.00018 0.00065 +4 +Lattice = "4.18669986725 0.0 0.0 0.018200000748 4.22060012817 0.0 0.00449999980628 -0.00139999995008 4.19939994812" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.439663 stress="24909.960000000003 -4206.58 -1004.1899999999999 -4206.58 31036.64 543.86 -1004.1899999999999 543.86 16832.42" +Ta 2.0956 -0.0007 2.0997 0.000559 -2.8e-05 1e-06 +Ta 2.1025 2.1103 0.0 -0.000559 2.8e-05 -1e-06 +Ta 0.0114 2.1096 2.0997 -0.000559 2.8e-05 -1e-06 +Ta 0.0 0.0 0.0 0.000559 -2.8e-05 1e-06 +4 +Lattice = "4.1998000145 0.0 0.0 -0.0163000002503 4.19570016861 0.0 0.01070000045 -0.0124000003561 4.18389987946" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.428287 stress="41731.25 3757.21 -2445.36 3757.21 41051.920000000006 2856.2799999999997 -2445.36 2856.2799999999997 30297.370000000003" +Ta 2.1053 -0.0062 2.092 -0.00054 -0.000412 -0.000306 +Ta 2.0917 2.0978 0.0 0.00054 0.000412 0.000306 +Ta 4.197 2.0916 2.092 2.3e-05 0.0004 -0.000316 +Ta 0.0 0.0 0.0 -2.3e-05 -0.0004 0.000316 +4 +Lattice = "4.1970000267 0.0 0.0 0.0194000005722 4.1888999939 0.0 -0.00179999996908 -0.0136000001803 4.18779993057" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.424584 stress="44875.270000000004 -4458.47 289.83 -4458.47 43234.76 3197.07 289.83 3197.07 33469.479999999996" +Ta 2.0976 -0.0068 2.0939 5.4e-05 -0.000398 -1e-06 +Ta 2.1082 2.0944 0.0 -5.4e-05 0.000398 1e-06 +Ta 0.0088 2.0876 2.0939 -5.4e-05 0.000398 1e-06 +Ta 0.0 0.0 0.0 5.4e-05 -0.000398 -1e-06 +4 +Lattice = "4.18450021744 0.0 0.0 0.0130000002682 4.18849992752 0.0 -0.0195000004023 -0.00370000000112 4.18139982224" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.413045 stress="50367.32 -3261.88 3822.1099999999997 -3261.88 50402.17 705.52 3822.1099999999997 705.52 39882.66" +Ta 2.0825 -0.0018 2.0907 -5.1e-05 -0.000344 -1e-06 +Ta 2.0988 2.0943 0.0 -0.000738 -0.000336 2.6e-05 +Ta 4.1812 2.0924 2.0907 0.000738 0.000336 -2.6e-05 +Ta 0.0 0.0 0.0 5.1e-05 0.000344 1e-06 +4 +Lattice = "4.20609998703 0.0 0.0 0.0121999997646 4.20860004425 0.0 0.0104000000283 0.00490000005811 4.1810002327" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.436994 stress="32291.899999999998 -2490.73 -2201.86 -2490.73 33006.25 -463.13 -2201.86 -463.13 19860.08" +Ta 2.1204 4.211 2.0905 0.000646 0.000444 0.000147 +Ta 2.1092 2.1043 0.0 -0.000646 -0.000444 -0.000147 +Ta 0.0113 2.1067 2.0905 0.000171 0.000448 0.000145 +Ta 0.0 0.0 0.0 -0.000171 -0.000448 -0.000145 +4 +Lattice = "4.1939997673 0.0 0.0 -0.0175999999046 4.21909999847 0.0 -0.00359999993816 0.00300000002608 4.2079000473" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.443604 stress="18084.66 3671.56 781.26 3671.56 24730.91 -432.39 781.26 -432.39 9828.4" +Ta 2.0776 4.2206 2.104 0.000117 0.000438 -0.0005 +Ta 2.0882 2.1096 0.0 -0.000117 -0.000438 0.0005 +Ta -0.0106 2.1111 2.104 -1.1e-05 -0.000248 -0.000419 +Ta 0.0 0.0 0.0 1.1e-05 0.000248 0.000419 +4 +Lattice = "4.19670009613 0.0 0.0 0.0144999995828 4.20499992371 0.0 -0.0154999997467 -0.00319999991916 4.21000003815" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.439718 stress="23536.32 -3142.14 3304.68 -3142.14 26048.2 678.5 3304.68 678.5 13870.050000000001" +Ta 2.0906 -0.0016 2.105 0.0 0.0 0.0 +Ta 2.1056 2.1025 0.0 0.0 0.0 0.0 +Ta -0.0005 2.1009 2.105 0.0 0.0 0.0 +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +4 +Lattice = "4.18400001526 0.0 0.0 -0.00139999995008 4.20389986038 0.0 -0.0186000000685 -0.0144999995828 4.21430015564" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.435527 stress="26601.199999999997 224.89999999999998 3984.39 224.89999999999998 32506.140000000003 3199.5499999999997 3984.39 3199.5499999999997 20323.48" +Ta 2.0813 4.1966 2.1072 -5.7e-05 0.000574 -0.000235 +Ta 2.0913 2.102 0.0 5.7e-05 -0.000574 0.000235 +Ta -0.01 2.0947 2.1072 7.8e-05 -6.3e-05 -0.000195 +Ta 0.0 0.0 0.0 -7.8e-05 6.3e-05 0.000195 +4 +Lattice = "4.1810002327 0.0 0.0 0.00600000005215 4.22009992599 0.0 -0.00669999979436 -0.0204000007361 4.19239997864" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.434787 stress="30521.97 -1467.91 1403.6 -1467.91 38595.36 4398.91 1403.6 4398.91 23894.760000000002" +Ta 2.0872 -0.0102 2.0962 -0.000704 0.000292 6e-05 +Ta 2.0935 2.1101 0.0 -0.000115 -0.000301 -1e-06 +Ta 4.1806 2.0999 2.0962 0.000704 -0.000292 -6e-05 +Ta 0.0 0.0 0.0 0.000115 0.000301 1e-06 +4 +Lattice = "4.2076997757 0.0 0.0 -0.00329999998212 4.18240022659 0.0 0.0197999998927 -0.0142999999225 4.20949983597" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.434929 stress="33106.05 400.43 -4376.98 400.43 26345.52 2747.71 -4376.98 2747.71 20304.05" +Ta 2.1104 4.1752 2.1048 0.000619 0.000224 -0.00034 +Ta 2.1022 2.0912 0.0 0.000185 -0.00027 0.000324 +Ta 0.0083 2.084 2.1048 -0.000828 0.000293 -0.000329 +Ta 0.0 0.0 0.0 2.4e-05 -0.000248 0.000344 +4 +Lattice = "4.18709993362 0.0 0.0 -0.0137000000104 4.19210004807 0.0 -0.0206000003964 -0.00300000002608 4.2013001442" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.426499 stress="39883.59 3131.64 4730.58 3131.64 40703.380000000005 736.94 4730.58 736.94 30183.84" +Ta 2.0695 4.1906 2.1006 0.000281 -0.00046 0.000374 +Ta 2.0867 2.096 0.0 -0.000281 0.00046 -0.000374 +Ta 4.1699 2.0945 2.1006 0.000239 0.000426 0.000333 +Ta 0.0 0.0 0.0 -0.000239 -0.000426 -0.000333 +4 +Lattice = "4.19180011749 0.0 0.0 0.00350000010803 4.20699977875 0.0 0.0201999992132 -0.0141000002623 4.20459985733" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.437025 stress="28895.21 -1353.89 -4533.7300000000005 -1353.89 33286.0 2779.0699999999997 -4533.7300000000005 2779.0699999999997 20380.649999999998" +Ta 2.1095 4.1999 2.1023 0.000444 0.000256 2.5e-05 +Ta 2.0977 2.1035 0.0 -0.000444 -0.000256 -2.5e-05 +Ta 0.0119 2.0964 2.1023 -0.000371 0.000196 3.1e-05 +Ta 0.0 0.0 0.0 0.000371 -0.000196 -3.1e-05 +4 +Lattice = "4.19680023193 0.0 0.0 -0.019999999553 4.19010019302 0.0 0.0148000000045 0.00449999980628 4.19729995728" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.428937 stress="38946.02 4281.84 -3402.34 4281.84 36868.95 -1152.93 -3402.34 -1152.93 27927.85" +Ta 2.0858 4.1923 2.0986 -3.4e-05 0.000667 0.000439 +Ta 2.0884 2.0951 0.0 3.4e-05 -0.000667 -0.000439 +Ta -0.0026 2.0973 2.0986 -7.3e-05 -0.000101 0.000416 +Ta 0.0 0.0 0.0 7.3e-05 0.000101 -0.000416 +4 +Lattice = "4.21390008926 0.0 0.0 -0.0159000009298 4.2077999115 0.0 -0.0115000000224 0.00680000009015 4.19169998169" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.442516 stress="26548.37 3415.7000000000003 2464.46 3415.7000000000003 25895.34 -1426.55 2464.46 -1426.55 12731.93" +Ta 2.1012 0.0034 2.0958 -0.000117 -0.000115 0.000445 +Ta 2.099 2.1039 0.0 0.000117 0.000115 -0.000445 +Ta 4.2002 2.1073 2.0958 -0.000117 -0.000115 0.000445 +Ta 0.0 0.0 0.0 0.000117 0.000115 -0.000445 +4 +Lattice = "4.18620014191 0.0 0.0 0.00319999991916 4.18989992142 0.0 0.00359999993816 0.0201999992132 4.21029996872" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.428736 stress="36533.26 -472.27000000000004 -599.63 -472.27000000000004 38503.49 -4878.59 -599.63 -4878.59 28242.54" +Ta 2.0949 0.0101 2.1051 7.8e-05 0.000472 0.000488 +Ta 2.0947 2.095 0.0 -7.8e-05 -0.000472 -0.000488 +Ta 0.0034 2.1051 2.1051 3e-06 -0.000581 0.000458 +Ta 0.0 0.0 0.0 -3e-06 0.000581 -0.000458 +4 +Lattice = "4.18650007248 0.0 0.0 -0.020300000906 4.20889997482 0.0 0.0177999995649 -0.0108000002801 4.19799995422" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.433359 stress="31456.3 4402.04 -3820.04 4402.04 36583.71000000001 2243.03 -3820.04 2243.03 23228.44" +Ta 2.1021 -0.0054 2.099 0.000683 0.000409 2.2e-05 +Ta 2.0831 2.1045 0.0 0.000136 -0.000401 -3.2e-05 +Ta -0.0012 2.0991 2.099 -0.000683 -0.000409 -2.2e-05 +Ta 0.0 0.0 0.0 -0.000136 0.000401 3.2e-05 +4 +Lattice = "4.18569993973 0.0 0.0 -0.0201999992132 4.21250009537 0.0 0.0132999997586 -0.0038999998942 4.21120023727" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.438799 stress="22841.29 4506.599999999999 -2944.67 4506.599999999999 28994.420000000002 787.89 -2944.67 787.89 15742.92" +Ta 2.0793 4.2105 2.1056 0.00025 0.000338 -9e-06 +Ta 2.0828 2.1062 0.0 -0.000222 0.00033 -1.1e-05 +Ta -0.0034 2.1043 2.1056 -0.00025 -0.000338 9e-06 +Ta 0.0 0.0 0.0 0.000222 -0.00033 1.1e-05 +4 +Lattice = "4.20319986343 0.0 0.0 0.0133999995887 4.21220016479 0.0 0.0153000000864 0.016799999401 4.20030021667" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.441993 stress="22767.3 -2987.04 -3341.07 -2987.04 24394.9 -3697.02 -3341.07 -3697.02 11782.27" +Ta 2.1226 4.2206 2.1002 0.000406 4.3e-05 -0.000851 +Ta 2.1083 2.1061 0.0 -0.000406 -4.3e-05 0.000851 +Ta 4.2175 2.1145 2.1002 0.000406 4.3e-05 -0.000851 +Ta 0.0 0.0 0.0 -0.000406 -4.3e-05 0.000851 +4 +Lattice = "4.20020008087 0.0 0.0 0.0159000009298 4.21250009537 0.0 0.00839999970049 0.00270000007004 4.19059991837" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.439033 stress="31311.34 -2962.04 -2118.77 -2962.04 33332.84 -497.0 -2118.77 -497.0 19397.95" +Ta 2.1043 0.0014 2.0953 -0.000169 -0.000336 2e-06 +Ta 2.108 2.1063 0.0 0.000307 -0.000319 4e-06 +Ta 4.2123 2.1076 2.0953 0.000169 0.000336 -2e-06 +Ta 0.0 0.0 0.0 -0.000307 0.000319 -4e-06 +4 +Lattice = "4.19460010529 0.0 0.0 -0.00380000006407 4.20300006866 0.0 0.00710000004619 0.00289999996312 4.20419979095" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.436967 stress="28199.07 1077.27 -1364.09 1077.27 30335.760000000002 -742.39 -1364.09 -742.39 18938.510000000002" +Ta 2.1009 0.0015 2.1021 -0.000397 -0.000899 -0.000183 +Ta 2.0954 2.1015 0.0 0.000341 0.000174 0.00019 +Ta 0.0017 2.1029 2.1021 -0.000267 0.000862 -0.0002 +Ta 0.0 0.0 0.0 0.000324 -0.000137 0.000193 +4 +Lattice = "4.19649982452 0.0 0.0 0.0170000009239 4.18389987946 0.0 0.000500000023749 0.0197000000626 4.20139980316" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.427245 stress="39200.850000000006 -3187.19 -498.29 -3187.19 36589.530000000006 -4530.76 -498.29 -4530.76 27001.34" +Ta 2.0985 0.0099 2.1007 1e-05 -0.00045 2.8e-05 +Ta 2.1067 2.092 0.0 0.000706 -0.000365 -4.5e-05 +Ta 0.0088 2.1018 2.1007 -0.000706 0.000365 4.5e-05 +Ta 0.0 0.0 0.0 -1e-05 0.00045 -2.8e-05 +4 +Lattice = "4.19409990311 0.0 0.0 -0.0157999992371 4.20200014114 0.0 -0.00249999994412 -0.00449999980628 4.21129989624" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.438046 stress="26136.06 3578.57 621.48 3578.57 27841.36 1030.6 621.48 1030.6 16177.720000000001" +Ta 2.08 4.1997 2.1057 0.000264 0.000278 -0.000459 +Ta 2.0891 2.101 0.0 0.000831 -0.000264 0.000454 +Ta -0.0091 2.0987 2.1057 -0.000831 0.000264 -0.000454 +Ta 0.0 0.0 0.0 -0.000264 -0.000278 0.000459 +4 +Lattice = "4.18219995499 0.0 0.0 -0.0186999998987 4.19169998169 0.0 0.00850000046194 -0.00270000007004 4.19329977036" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.420083 stress="45896.659999999996 4350.44 -1715.56 4350.44 48179.94 571.0699999999999 -1715.56 571.0699999999999 36393.41" +Ta 2.0766 4.1903 2.0967 0.00046 0.001197 -0.000615 +Ta 2.0818 2.0959 0.0 -0.00046 -0.001197 0.000615 +Ta 4.1771 2.0945 2.0967 -0.000243 -0.00048 -0.000746 +Ta 0.0 0.0 0.0 0.000243 0.00048 0.000746 +4 +Lattice = "4.21379995346 0.0 0.0 -0.00889999978244 4.20090007782 0.0 0.00829999987036 -0.0121999997646 4.2157998085" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.445247 stress="17199.95 2060.92 -1868.0 2060.92 14754.65 2656.7 -1868.0 2656.7 4564.79" +Ta 2.111 -0.0061 2.1079 0.000429 -0.000346 -2e-05 +Ta 2.1024 2.1004 0.0 0.000445 0.000491 -1.1e-05 +Ta 4.2135 2.0943 2.1079 -0.000429 0.000346 2e-05 +Ta 0.0 0.0 0.0 -0.000445 -0.000491 1.1e-05 +4 +Lattice = "4.2171998024 0.0 0.0 -0.00249999994412 4.21280002594 0.0 0.0010000000475 -0.0208000000566 4.19570016861" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.446044 stress="19496.41 709.2 -122.84 709.2 18308.6 4583.75 -122.84 4583.75 6100.4" +Ta 2.1091 -0.0104 2.0979 0.000565 1.3e-05 -0.000312 +Ta 2.1074 2.1064 0.0 -0.000565 -1.3e-05 0.000312 +Ta -0.0007 2.096 2.0979 -0.000564 -1.2e-05 -0.000342 +Ta 0.0 0.0 0.0 0.000564 1.2e-05 0.000342 +4 +Lattice = "4.20889997482 0.0 0.0 0.0163000002503 4.17980003357 0.0 -0.00310000008903 -0.017899999395 4.2093000412" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.434472 stress="34887.090000000004 -3559.16 445.12 -3559.16 27517.510000000002 4000.3399999999997 445.12 4000.3399999999997 21214.9" +Ta 2.1029 -0.0089 2.1046 -4.5e-05 -0.000191 0.000367 +Ta 2.1126 2.0899 0.0 4.5e-05 0.000191 -0.000367 +Ta 4.2155 2.081 2.1046 -4.5e-05 -0.000191 0.000367 +Ta 0.0 0.0 0.0 4.5e-05 0.000191 -0.000367 +4 +Lattice = "4.21549987793 0.0 0.0 -0.0132999997586 4.21330022812 0.0 -0.0054999999702 0.0157999992371 4.18979978561" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.44458 stress="23231.31 2911.85 1091.22 2911.85 22696.98 -3466.5499999999997 1091.22 -3466.5499999999997 9663.7" +Ta 2.105 0.0079 2.0949 1.3e-05 0.000487 6e-06 +Ta 2.1011 2.1067 0.0 -1.3e-05 -0.000487 -6e-06 +Ta -0.0094 2.1146 2.0949 -1.3e-05 -0.000487 -6e-06 +Ta 0.0 0.0 0.0 1.3e-05 0.000487 6e-06 +4 +Lattice = "4.20329999924 0.0 0.0 0.0104000000283 4.2093000412 0.0 0.00359999993816 -0.00270000007004 4.20109987259" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.441776 stress="25420.61 -1768.14 -1189.8899999999999 -1768.14 27462.18 568.28 -1189.8899999999999 568.28 14665.82" +Ta 2.1139 4.2079 2.1005 -0.00054 0.0004 0.000307 +Ta 2.1069 2.1046 0.0 -0.000437 0.000188 -0.000353 +Ta 0.007 2.1033 2.1005 0.000437 -0.000188 0.000353 +Ta 0.0 0.0 0.0 0.00054 -0.0004 -0.000307 +4 +Lattice = "4.19390010834 0.0 0.0 -0.0154999997467 4.20030021667 0.0 0.0118000004441 -0.017100000754 4.2093000412" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.436389 stress="28175.18 3461.97 -2554.14 3461.97 29398.74 3490.6600000000003 -2554.14 3490.6600000000003 18104.420000000002" +Ta 2.1028 -0.0085 2.1047 0.000405 -0.000951 -0.000355 +Ta 2.0892 2.1001 0.0 -0.000405 0.000951 0.000355 +Ta 4.192 2.0916 2.1047 0.000387 0.000179 -0.000469 +Ta 0.0 0.0 0.0 -0.000387 -0.000179 0.000469 +4 +Lattice = "4.2079000473 0.0 0.0 -0.0097000002861 4.21920013428 0.0 -0.00490000005811 -0.00999999977648 4.20109987259" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.446416 stress="19209.399999999998 2025.1299999999999 1589.1299999999999 2025.1299999999999 20626.989999999998 2446.81 1589.1299999999999 2446.81 6438.570000000001" +Ta 2.1015 -0.005 2.1006 -2.8e-05 -0.000105 -0.000311 +Ta 2.0991 2.1096 0.0 2.8e-05 0.000105 0.000311 +Ta -0.0073 2.1046 2.1006 -2.8e-05 -0.000105 -0.000311 +Ta 0.0 0.0 0.0 2.8e-05 0.000105 0.000311 +4 +Lattice = "4.21920013428 0.0 0.0 0.00370000000112 4.21530008316 0.0 -0.001200000057 -9.99999974738e-05 4.21350002289" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.449806 stress="9066.92 -618.3199999999999 80.69 -618.3199999999999 8795.18 242.32000000000002 80.69 242.32000000000002 -3831.06" +Ta 2.109 0.0 2.1067 -0.000377 -0.000342 0.00055 +Ta 2.1115 2.1077 0.0 -0.001167 -0.000182 -0.000568 +Ta 4.2204 2.1076 2.1067 0.001167 0.000182 0.000568 +Ta 0.0 0.0 0.0 0.000377 0.000342 -0.00055 +4 +Lattice = "4.20060014725 0.0 0.0 0.00680000009015 4.19710016251 0.0 -0.0146000003442 0.0186000000685 4.17910003662" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.427189 stress="44173.07 -1484.73 3360.38 -1484.73 43201.93 -4284.93 3360.38 -4284.93 31256.18" +Ta 2.0998 4.2064 2.0896 -2.2e-05 -0.000426 -0.000366 +Ta 2.1037 2.0985 0.0 2.2e-05 0.000426 0.000366 +Ta -0.0039 2.1078 2.0896 -2.5e-05 0.000364 -0.000321 +Ta 0.0 0.0 0.0 2.5e-05 -0.000364 0.000321 +4 +Lattice = "4.18919992447 0.0 0.0 0.0135000003502 4.20279979706 0.0 -0.0119000002742 0.00999999977648 4.1875" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.427857 stress="39322.19 -2611.56 2676.7 -2611.56 42055.02 -2182.03 2676.7 -2182.03 28576.71" +Ta 2.1022 4.2078 2.0938 -0.000527 -0.000167 -0.000317 +Ta 2.1014 2.1014 0.0 -0.000703 1.2e-05 0.000454 +Ta 0.0008 2.1064 2.0938 0.000703 -1.2e-05 -0.000454 +Ta 0.0 0.0 0.0 0.000527 0.000167 0.000317 +4 +Lattice = "4.2079000473 0.0 0.0 -0.00980000011623 4.18940019608 0.0 0.0206000003964 0.0189999993891 4.21960020065" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.44004 stress="24518.6 2270.46 -4602.22 2270.46 19823.78 -4164.55 -4602.22 -4164.55 12729.210000000001" +Ta 2.1142 0.0095 2.1098 0.000377 -3.3e-05 1.1e-05 +Ta 2.099 2.0947 0.0 0.000377 -3.3e-05 1.1e-05 +Ta 0.0054 2.1042 2.1098 -0.000377 3.3e-05 -1.1e-05 +Ta 0.0 0.0 0.0 -0.000377 3.3e-05 -1.1e-05 +4 +Lattice = "4.18559980392 0.0 0.0 -0.0141000002623 4.21939992905 0.0 0.00270000007004 -0.0183000005782 4.19519996643" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.437214 stress="27548.75 3217.5699999999997 -517.42 3217.5699999999997 33898.46 4094.8900000000003 -517.42 4094.8900000000003 19872.68" +Ta 2.0941 -0.0091 2.0976 0.00078 -0.000197 -3.2e-05 +Ta 2.0857 2.1097 0.0 0.000496 0.000489 5e-06 +Ta -0.0057 2.1006 2.0976 -0.000496 -0.000489 -5e-06 +Ta 0.0 0.0 0.0 -0.00078 0.000197 3.2e-05 +4 +Lattice = "4.18179988861 0.0 0.0 -0.00949999969453 4.19159984589 0.0 0.0148000000045 0.00139999995008 4.19890022278" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.422628 stress="43385.56 2136.82 -3260.5400000000004 2136.82 46015.15 -518.6500000000001 -3260.5400000000004 -518.6500000000001 33939.47" +Ta 2.0888 4.1923 2.0995 -0.000281 -0.00027 -0.000582 +Ta 2.0861 2.0958 0.0 0.000281 0.00027 0.000582 +Ta 4.1844 2.0965 2.0995 0.000629 0.000286 -0.000561 +Ta 0.0 0.0 0.0 -0.000629 -0.000286 0.000561 +4 +Lattice = "4.20370006561 0.0 0.0 -0.0200999993831 4.21630001068 0.0 -0.0164000000805 -0.0195000004023 4.20209980011" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.443535 stress="20218.039999999997 4818.6900000000005 3580.07 4818.6900000000005 21841.62 4429.02 3580.07 4429.02 8549.369999999999" +Ta 2.0736 4.2065 2.1011 -0.000398 0.000783 -0.000458 +Ta 2.0918 2.1082 0.0 0.000398 -0.000783 0.000458 +Ta -0.0182 2.0984 2.1011 -0.000248 -0.000173 -0.000438 +Ta 0.0 0.0 0.0 0.000248 0.000173 0.000438 +4 +Lattice = "4.20109987259 0.0 0.0 0.00289999996312 4.2077999115 0.0 0.00179999996908 0.00260000000708 4.19890022278" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.439922 stress="27455.690000000002 -990.9599999999999 -176.72 -990.9599999999999 29472.14 -256.46000000000004 -176.72 -256.46000000000004 15890.19" +Ta 2.1015 0.0013 2.0994 -0.000776 -9.4e-05 0.000494 +Ta 2.102 2.1039 0.0 -0.00018 1.1e-05 -0.000461 +Ta 4.2034 2.1052 2.0994 0.000991 9.2e-05 0.000337 +Ta 0.0 0.0 0.0 -3.5e-05 -9e-06 -0.00037 +4 +Lattice = "4.20909976959 0.0 0.0 0.00279999990016 4.19089984894 0.0 0.0129000004381 0.0113000003621 4.20370006561" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.437675 stress="30559.32 -328.34999999999997 -2999.48 -328.34999999999997 26504.989999999998 -2563.55 -2999.48 -2563.55 18218.93" +Ta 2.1138 4.1965 2.1019 0.000516 0.001068 -0.000754 +Ta 2.1059 2.0955 0.0 0.000599 -0.000983 0.000746 +Ta 0.0079 2.1011 2.1019 -0.000833 -0.000415 -0.000718 +Ta 0.0 0.0 0.0 -0.000282 0.000331 0.000726 +4 +Lattice = "4.21960020065 0.0 0.0 -0.0164999999106 4.20809984207 0.0 0.00209999992512 -0.0104999998584 4.19619989395" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.445558 stress="21138.43 3552.79 -295.98 3552.79 19496.949999999997 2230.2599999999998 -295.98 2230.2599999999998 7402.18" +Ta 2.0944 4.2028 2.0981 -0.000489 0.000278 7.1e-05 +Ta 2.1016 2.104 0.0 -0.000489 0.000278 7.1e-05 +Ta -0.0072 2.0988 2.0981 0.000489 -0.000278 -7.1e-05 +Ta 0.0 0.0 0.0 0.000489 -0.000278 -7.1e-05 +4 +Lattice = "4.18620014191 0.0 0.0 0.0142000000924 4.21759986877 0.0 0.00529999984428 0.000699999975041 4.20249986649" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.439106 stress="24311.969999999998 -3207.16 -1065.08 -3207.16 30723.109999999997 -53.699999999999996 -1065.08 -53.699999999999996 16577.88" +Ta 2.11 4.2179 2.1012 -0.000734 0.000343 0.000586 +Ta 2.1002 2.1088 0.0 -0.000395 -0.000327 -0.000614 +Ta 4.1959 2.1091 2.1012 0.000856 0.000318 0.000602 +Ta 0.0 0.0 0.0 0.000273 -0.000334 -0.000574 +4 +Lattice = "4.19910001755 0.0 0.0 -0.0100999996066 4.21040010452 0.0 0.0163000002503 0.0195000004023 4.21479988098" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.443073 stress="21214.73 1620.02 -3139.49 1620.02 23804.07 -3361.12 -3139.49 -3361.12 11182.08" +Ta 2.0976 4.2201 2.1074 1.7e-05 0.000287 -2.2e-05 +Ta 2.0945 2.1052 0.0 -1.7e-05 -0.000287 2.2e-05 +Ta 4.2022 2.1149 2.1074 1.7e-05 0.000287 -2.2e-05 +Ta 0.0 0.0 0.0 -1.7e-05 -0.000287 2.2e-05 +4 +Lattice = "4.20900011063 0.0 0.0 -0.0132999997586 4.19000005722 0.0 -0.00510000018403 0.0116999996826 4.21299982071" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.4397 stress="27256.09 2922.24 1093.0500000000002 2922.24 22439.64 -2593.18 1093.0500000000002 -2593.18 14372.06" +Ta 2.102 0.0059 2.1065 -0.000435 -0.000338 0.0 +Ta 2.0979 2.095 0.0 -0.000572 0.000306 2.7e-05 +Ta -0.0092 2.1009 2.1065 0.000572 -0.000306 -2.7e-05 +Ta 0.0 0.0 0.0 0.000435 0.000338 0.0 +4 +Lattice = "4.18540000916 0.0 0.0 0.00499999988824 4.21269989014 0.0 -0.0170000009239 -0.0157999992371 4.20230007172" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.436374 stress="29413.82 -848.39 3021.03 -848.39 35818.05 3586.5499999999997 3021.03 3586.5499999999997 22359.57" +Ta 2.0892 4.2048 2.1011 0.000247 -0.000509 0.000473 +Ta 2.0952 2.1063 0.0 -0.000247 0.000509 -0.000473 +Ta 4.1794 2.0984 2.1011 0.000198 0.000499 0.000486 +Ta 0.0 0.0 0.0 -0.000198 -0.000499 -0.000486 +4 +Lattice = "4.19089984894 0.0 0.0 0.00889999978244 4.18580007553 0.0 -0.00769999995828 -0.00370000000112 4.20340013504" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.426557 stress="41786.9 -1592.19 1901.3 -1592.19 40672.780000000006 565.31 1901.3 565.31 31476.21" +Ta 2.0916 -0.0018 2.1017 9.5e-05 -0.000938 -7.3e-05 +Ta 2.0999 2.0929 0.0 -9e-06 0.000173 9e-06 +Ta 0.0006 2.091 2.1017 -9.5e-05 0.000938 7.3e-05 +Ta 0.0 0.0 0.0 9e-06 -0.000173 -9e-06 +4 +Lattice = "4.1985001564 0.0 0.0 -0.0179999992251 4.19869995117 0.0 -0.00079999997979 0.0184000004083 4.19780015945" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.434009 stress="33693.26 4132.23 124.97999999999999 4132.23 32953.46 -4050.66 124.97999999999999 -4050.66 22096.65" +Ta 2.0988 0.0092 2.0989 0.000663 0.000517 0.000224 +Ta 2.0903 2.0994 0.0 -0.000663 -0.000517 -0.000224 +Ta -0.0094 2.1086 2.0989 1.4e-05 -0.000453 7.2e-05 +Ta 0.0 0.0 0.0 -1.4e-05 0.000453 -7.2e-05 +4 +Lattice = "4.20100021362 0.0 0.0 -0.00910000037402 4.19759988785 0.0 -0.00689999992028 0.00609999988228 4.20090007782" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.436262 stress="32759.129999999997 2409.49 1583.58 2409.49 32101.69 -912.27 1583.58 -912.27 21073.66" +Ta 2.088 4.2006 2.1005 -0.001062 0.001392 -0.000497 +Ta 2.0959 2.0988 0.0 0.000982 -0.000276 0.000312 +Ta -0.008 2.1019 2.1005 -4.7e-05 -0.001302 -6.7e-05 +Ta 0.0 0.0 0.0 0.000128 0.000186 0.000252 +4 +Lattice = "4.21759986877 0.0 0.0 0.0156999994069 4.18800020218 0.0 0.00659999996424 0.0181000009179 4.18650007248" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.434505 stress="37654.36 -3876.7999999999997 -1440.8799999999999 -3876.7999999999997 32519.67 -4103.17 -1440.8799999999999 -4103.17 23829.38" +Ta 2.1278 4.197 2.0932 -0.000269 0.000298 0.000324 +Ta 2.1166 2.094 0.0 0.000269 -0.000298 -0.000324 +Ta 4.2287 2.103 2.0932 0.000297 0.000285 0.000327 +Ta 0.0 0.0 0.0 -0.000297 -0.000285 -0.000327 +4 +Lattice = "4.19199991226 0.0 0.0 0.01070000045 4.21519994736 0.0 -0.0195000004023 0.0172000005841 4.19929981232" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.438768 stress="27465.83 -1845.49 4487.129999999999 -1845.49 32725.54 -3897.0099999999998 4487.129999999999 -3897.0099999999998 17774.13" +Ta 2.0863 0.0086 2.0996 -0.000554 6.9e-05 0.000378 +Ta 2.1013 2.1076 0.0 0.000554 -6.9e-05 -0.000378 +Ta 4.1876 2.1162 2.0996 -9.3e-05 3.9e-05 0.000372 +Ta 0.0 0.0 0.0 9.3e-05 -3.9e-05 -0.000372 +4 +Lattice = "4.20120000839 0.0 0.0 -0.00980000011623 4.21460008621 0.0 0.0137000000104 -0.0104000000283 4.19080018997" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.440254 stress="26850.75 1979.56 -3070.84 1979.56 30335.71 2128.91 -3070.84 2128.91 16599.23" +Ta 2.1074 -0.0052 2.0954 0.000286 -4.3e-05 -9.2e-05 +Ta 2.0957 2.1073 0.0 -0.000286 4.3e-05 9.2e-05 +Ta 4.2031 2.1021 2.0954 0.000286 -4.3e-05 -9.2e-05 +Ta 0.0 0.0 0.0 -0.000286 4.3e-05 9.2e-05 +4 +Lattice = "4.18440008163 0.0 0.0 -0.0175000000745 4.18079996109 0.0 -0.0194000005722 0.0108000002801 4.21099996567" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.42286 stress="40368.11 3432.0 3719.6699999999996 3432.0 39974.420000000006 -1873.58 3719.6699999999996 -1873.58 31423.030000000002" +Ta 2.0825 0.0054 2.1055 -0.000359 6e-05 5.6e-05 +Ta 2.0834 2.0904 0.0 0.000359 -6e-05 -5.6e-05 +Ta 4.1659 2.0958 2.1055 0.000359 -6e-05 -5.6e-05 +Ta 0.0 0.0 0.0 -0.000359 6e-05 5.6e-05 +4 +Lattice = "4.18879985809 0.0 0.0 -0.0208000000566 4.18480014801 0.0 -0.00730000017211 -0.0186999998987 4.19089984894" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.418078 stress="45790.12 4993.91 1730.1100000000001 4993.91 45930.82 3649.4300000000003 1730.1100000000001 3649.4300000000003 35583.67" +Ta 2.0907 -0.0093 2.0955 0.000623 -0.000961 -0.000332 +Ta 2.084 2.0924 0.0 -0.000626 -0.000189 0.000487 +Ta 4.1747 2.083 2.0955 0.000372 0.001139 -0.000549 +Ta 0.0 0.0 0.0 -0.000369 1e-05 0.000393 +4 +Lattice = "4.19479990005 0.0 0.0 -0.00620000017807 4.21269989014 0.0 -0.01600000076 -0.0153000000864 4.20469999313" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.440513 stress="22841.39 1639.92 3610.02 1639.92 27085.86 3356.16 3610.02 3356.16 13927.91" +Ta 2.0894 -0.0076 2.1024 -0.000112 -0.000351 -0.000518 +Ta 2.0943 2.1064 0.0 0.00016 -0.000267 0.000412 +Ta -0.0111 2.0987 2.1024 -0.00016 0.000267 -0.000412 +Ta 0.0 0.0 0.0 0.000112 0.000351 0.000518 +4 +Lattice = "4.18660020828 0.0 0.0 -0.0172000005841 4.17999982834 0.0 -0.0137000000104 0.0121999997646 4.18389987946" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.409824 stress="54573.9 3803.25 2849.0 3803.25 53362.96 -2844.54 2849.0 -2844.54 43325.58" +Ta 2.0692 4.1861 2.092 0.000705 -1.8e-05 -0.000526 +Ta 2.0847 2.09 0.0 -0.000705 1.8e-05 0.000526 +Ta 4.1711 2.0961 2.092 0.000705 -1.8e-05 -0.000526 +Ta 0.0 0.0 0.0 -0.000705 1.8e-05 0.000526 +4 +Lattice = "4.20060014725 0.0 0.0 0.00219999998808 4.19719982147 0.0 -0.0162000004202 -0.00079999997979 4.21750020981" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.440329 stress="24420.449999999997 -556.41 3615.46 -556.41 22664.89 379.38 3615.46 379.38 13111.85" +Ta 2.0922 -0.0004 2.1088 1.1e-05 9e-05 -0.000468 +Ta 2.1014 2.0986 0.0 -1.1e-05 -9e-05 0.000468 +Ta -0.007 2.0982 2.1088 1.1e-05 9e-05 -0.000468 +Ta 0.0 0.0 0.0 -1.1e-05 -9e-05 0.000468 +4 +Lattice = "4.19640016556 0.0 0.0 0.00889999978244 4.20380020142 0.0 -0.0110999997705 0.0162000004202 4.20480012894" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.43773 stress="26565.65 -1735.6799999999998 2480.6400000000003 -1735.6799999999998 28315.010000000002 -3741.6200000000003 2480.6400000000003 -3741.6200000000003 17263.329999999998" +Ta 2.0927 0.0081 2.1024 -0.00063 -0.000147 2e-05 +Ta 2.1026 2.1019 0.0 0.00063 0.000147 -2e-05 +Ta -0.0011 2.11 2.1024 9.4e-05 3.4e-05 -2e-06 +Ta 0.0 0.0 0.0 -9.4e-05 -3.4e-05 2e-06 +4 +Lattice = "4.18130016327 0.0 0.0 0.0177999995649 4.18319988251 0.0 -0.00340000004508 -0.0187999997288 4.19859981537" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.416525 stress="45103.520000000004 -3012.21 864.34 -3012.21 46101.13 4242.0 864.34 4242.0 36460.39" +Ta 2.089 -0.0094 2.0993 -0.000372 -6.9e-05 -1.6e-05 +Ta 2.0996 2.0916 0.0 -0.000372 -6.9e-05 -1.6e-05 +Ta 0.0072 2.0822 2.0993 0.000372 6.9e-05 1.6e-05 +Ta 0.0 0.0 0.0 0.000372 6.9e-05 1.6e-05 +4 +Lattice = "4.19229984283 0.0 0.0 0.001200000057 4.20900011063 0.0 -0.0151000004262 -0.00659999996424 4.21150016785" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.440293 stress="27393.899999999998 -151.45 2769.0 -151.45 30944.28 1878.31 2769.0 1878.31 18332.49" +Ta 2.0886 -0.0033 2.1058 -0.00024 0.0 -0.000304 +Ta 2.0967 2.1045 0.0 0.00024 0.0 0.000304 +Ta 4.1853 2.1012 2.1058 0.000234 0.0 -0.000306 +Ta 0.0 0.0 0.0 -0.000234 0.0 0.000306 +4 +Lattice = "4.18419981003 0.0 0.0 0.0206000003964 4.209400177 0.0 -0.0109999999404 -0.00480000022799 4.21589994431" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.43839 stress="21338.170000000002 -4162.9 2184.87 -4162.9 28153.19 1038.1 2184.87 1038.1 15498.07" +Ta 2.1072 4.207 2.1079 -1.6e-05 9e-06 0.00028 +Ta 2.1024 2.1047 0.0 1.6e-05 -9e-06 -0.00028 +Ta 4.189 2.1023 2.1079 -1.6e-05 9e-06 0.00028 +Ta 0.0 0.0 0.0 1.6e-05 -9e-06 -0.00028 +4 +Lattice = "4.17980003357 0.0 0.0 0.00789999961853 4.21220016479 0.0 0.0197000000626 -0.00270000007004 4.2185997963" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.438916 stress="20722.52 -1865.4599999999998 -4386.49 -1865.4599999999998 29240.06 779.2900000000001 -4386.49 779.2900000000001 15461.880000000001" +Ta 2.0998 -0.0013 2.1093 -0.00064 -0.000286 9e-05 +Ta 2.0939 2.1061 0.0 -0.000872 0.000312 -7.4e-05 +Ta 4.1936 2.1048 2.1093 0.000872 -0.000312 7.4e-05 +Ta 0.0 0.0 0.0 0.00064 0.000286 -9e-05 diff --git a/examples/PACKAGES/pod/Ta/XYZ/GSF_110.xyz b/examples/PACKAGES/pod/Ta/XYZ/GSF_110.xyz new file mode 100644 index 0000000000..378878ef80 --- /dev/null +++ b/examples/PACKAGES/pod/Ta/XYZ/GSF_110.xyz @@ -0,0 +1,572 @@ +24 +Lattice = "4.69519042969 0.0 0.0 0.0 3.31999993324 0.0 0.0 0.0 53.1199989319" Properties=species:S:1:pos:R:3:forces:R:3 energy=-279.068761 stress="-2699.74 -3225.67 0.0 -3225.67 -11966.73 0.0 0.0 0.0 8811.74" +Ta 2.34759 1.66 0.09121 0.0 0.0 0.002389 +Ta 0.0 0.0 0.09121 0.0 0.0 0.002389 +Ta 0.0 1.66 2.3361 0.0 0.0 -0.010927 +Ta 2.34759 0.0 2.3361 0.0 0.0 -0.010927 +Ta 2.34759 1.66 4.68536 0.0 0.0 -0.004142 +Ta 0.0 0.0 4.68536 0.0 0.0 -0.004142 +Ta 0.0 1.66 7.03392 0.0 0.0 0.078092 +Ta 2.34759 0.0 7.03392 0.0 0.0 0.078092 +Ta 2.34759 1.66 9.38594 0.0 0.0 -0.152903 +Ta 0.0 0.0 9.38594 0.0 0.0 -0.152903 +Ta 0.0 1.66 11.73648 0.0 0.0 -0.861147 +Ta 2.34759 0.0 11.73648 0.0 0.0 -0.861147 +Ta 3.52139 2.49 14.08712 0.0 0.0 0.861147 +Ta 1.1738 0.83 14.08712 0.0 0.0 0.861147 +Ta 1.1738 2.49 16.43764 0.0 0.0 0.152903 +Ta 3.52139 0.83 16.43764 0.0 0.0 0.152903 +Ta 3.52139 2.49 18.78966 0.0 0.0 -0.078092 +Ta 1.1738 0.83 18.78966 0.0 0.0 -0.078092 +Ta 1.1738 2.49 21.13823 0.0 0.0 0.004142 +Ta 3.52139 0.83 21.13823 0.0 0.0 0.004142 +Ta 3.52139 2.49 23.48739 0.0 0.0 0.010927 +Ta 1.1738 0.83 23.48739 0.0 0.0 0.010927 +Ta 1.1738 2.49 25.73229 0.0 0.0 -0.002389 +Ta 3.52139 0.83 25.73229 0.0 0.0 -0.002389 +24 +Lattice = "4.69519042969 0.0 0.0 0.0 3.31999993324 0.0 0.0 0.0 53.1199989319" Properties=species:S:1:pos:R:3:forces:R:3 energy=-279.784296 stress="-9310.84 -724.11 -1802.3100000000002 -724.11 -7581.28 -1731.35 -1802.3100000000002 -1731.35 -145.04" +Ta 2.34759 1.66 0.09121 -0.000195 -0.00161 0.000812 +Ta 0.0 0.0 0.09121 -0.000195 -0.00161 0.000812 +Ta 0.0 1.66 2.3361 -0.000284 0.000353 -0.002185 +Ta 2.34759 0.0 2.3361 -0.000284 0.000353 -0.002185 +Ta 2.34759 1.66 4.68536 0.008799 -0.00141 -0.002306 +Ta 0.0 0.0 4.68536 0.008799 -0.00141 -0.002306 +Ta 0.0 1.66 7.03392 -0.006695 0.021282 0.017658 +Ta 2.34759 0.0 7.03392 -0.006695 0.021282 0.017658 +Ta 2.34759 1.66 9.38594 -0.014885 -0.089566 0.000145 +Ta 0.0 0.0 9.38594 -0.014885 -0.089566 0.000145 +Ta 0.0 1.66 11.73648 0.220002 0.367425 -0.11205 +Ta 2.34759 0.0 11.73648 0.220002 0.367425 -0.11205 +Ta 2.58235 1.826 14.08712 -0.220002 -0.367425 0.11205 +Ta 0.23476 0.166 14.08712 -0.220002 -0.367425 0.11205 +Ta 0.23476 1.826 16.43764 0.014885 0.089566 -0.000145 +Ta 2.58235 0.166 16.43764 0.014885 0.089566 -0.000145 +Ta 2.58235 1.826 18.78966 0.006695 -0.021282 -0.017658 +Ta 0.23476 0.166 18.78966 0.006695 -0.021282 -0.017658 +Ta 0.23476 1.826 21.13823 -0.008799 0.00141 0.002306 +Ta 2.58235 0.166 21.13823 -0.008799 0.00141 0.002306 +Ta 2.58235 1.826 23.48739 0.000284 -0.000353 0.002185 +Ta 0.23476 0.166 23.48739 0.000284 -0.000353 0.002185 +Ta 0.23476 1.826 25.73229 0.000195 0.00161 -0.000812 +Ta 2.58235 0.166 25.73229 0.000195 0.00161 -0.000812 +24 +Lattice = "4.69519042969 0.0 0.0 0.0 3.31999993324 0.0 0.0 0.0 53.1199989319" Properties=species:S:1:pos:R:3:forces:R:3 energy=-279.901657 stress="-9711.95 0.0 0.0 0.0 -7971.759999999999 0.0 0.0 0.0 -387.39" +Ta 2.34759 1.66 0.09122 0.0 0.0 -2.1e-05 +Ta 0.0 0.0 0.09122 0.0 0.0 -2.1e-05 +Ta 0.0 1.66 2.33609 0.0 0.0 0.000332 +Ta 2.34759 0.0 2.33609 0.0 0.0 0.000332 +Ta 2.34759 1.66 4.68537 0.0 0.0 0.000393 +Ta 0.0 0.0 4.68537 0.0 0.0 0.000393 +Ta 0.0 1.66 7.03419 0.0 0.0 8.4e-05 +Ta 2.34759 0.0 7.03419 0.0 0.0 8.4e-05 +Ta 2.34759 1.66 9.38555 0.0 0.0 -0.000286 +Ta 0.0 0.0 9.38555 0.0 0.0 -0.000286 +Ta 0.0 1.66 11.73665 0.0 0.0 -0.000509 +Ta 2.34759 0.0 11.73665 0.0 0.0 -0.000509 +Ta 4.69519 0.0 14.08695 0.0 0.0 0.000509 +Ta 2.3476 1.66 14.08695 0.0 0.0 0.000509 +Ta 2.3476 0.0 16.43803 0.0 0.0 0.000286 +Ta 4.69519 1.66 16.43803 0.0 0.0 0.000286 +Ta 4.69519 0.0 18.78939 0.0 0.0 -8.4e-05 +Ta 2.3476 1.66 18.78939 0.0 0.0 -8.4e-05 +Ta 2.3476 0.0 21.13822 0.0 0.0 -0.000393 +Ta 4.69519 1.66 21.13822 0.0 0.0 -0.000393 +Ta 4.69519 0.0 23.4874 0.0 0.0 -0.000332 +Ta 2.3476 1.66 23.4874 0.0 0.0 -0.000332 +Ta 2.3476 0.0 25.73228 0.0 0.0 2.1e-05 +Ta 4.69519 1.66 25.73228 0.0 0.0 2.1e-05 +24 +Lattice = "4.69519042969 0.0 0.0 0.0 3.31999993324 0.0 0.0 0.0 53.1199989319" Properties=species:S:1:pos:R:3:forces:R:3 energy=-279.584238 stress="-8455.84 -1472.71 2162.92 -1472.71 -8121.589999999999 1800.64 2162.92 1800.64 -338.96" +Ta 2.34759 1.66 0.07452 -0.000101 0.002118 -0.001067 +Ta 0.0 0.0 0.07452 -0.000101 0.002118 -0.001067 +Ta 0.0 1.66 2.31914 0.000559 -0.002302 0.001125 +Ta 2.34759 0.0 2.31914 0.000559 -0.002302 0.001125 +Ta 2.34759 1.66 4.6683 -0.011564 0.001165 -0.001122 +Ta 0.0 0.0 4.6683 -0.011564 0.001165 -0.001122 +Ta 0.0 1.66 7.0214 0.010839 -0.033575 -0.000333 +Ta 2.34759 0.0 7.0214 0.010839 -0.033575 -0.000333 +Ta 2.34759 1.66 9.36328 0.008027 0.132954 0.000561 +Ta 0.0 0.0 9.36328 0.008027 0.132954 0.000561 +Ta 0.0 1.66 11.70268 -0.232266 -0.441609 -0.001106 +Ta 2.34759 0.0 11.70268 -0.232266 -0.441609 -0.001106 +Ta 4.22567 2.988 14.12092 0.232266 0.441609 0.001106 +Ta 1.87808 1.328 14.12092 0.232266 0.441609 0.001106 +Ta 1.87808 2.988 16.4603 -0.008027 -0.132954 -0.000561 +Ta 4.22567 1.328 16.4603 -0.008027 -0.132954 -0.000561 +Ta 4.22567 2.988 18.80218 -0.010839 0.033575 0.000333 +Ta 1.87808 1.328 18.80218 -0.010839 0.033575 0.000333 +Ta 1.87808 2.988 21.15529 0.011564 -0.001165 0.001122 +Ta 4.22567 1.328 21.15529 0.011564 -0.001165 0.001122 +Ta 4.22567 2.988 23.50435 -0.000559 0.002302 -0.001125 +Ta 1.87808 1.328 23.50435 -0.000559 0.002302 -0.001125 +Ta 1.87808 2.988 25.74898 0.000101 -0.002118 0.001067 +Ta 4.22567 1.328 25.74898 0.000101 -0.002118 0.001067 +24 +Lattice = "4.69519042969 0.0 0.0 0.0 3.31999993324 0.0 0.0 0.0 53.1199989319" Properties=species:S:1:pos:R:3:forces:R:3 energy=-279.784283 stress="-9315.08 -723.62 1802.65 -723.62 -7584.349999999999 1731.7800000000002 1802.65 1731.7800000000002 -137.97" +Ta 2.34759 1.66 0.09121 0.000196 0.00161 0.000943 +Ta 0.0 0.0 0.09121 0.000196 0.00161 0.000943 +Ta 0.0 1.66 2.3361 0.000284 -0.000353 -0.002245 +Ta 2.34759 0.0 2.3361 0.000284 -0.000353 -0.002245 +Ta 2.34759 1.66 4.68536 -0.008799 0.00141 -0.002392 +Ta 0.0 0.0 4.68536 -0.008799 0.00141 -0.002392 +Ta 0.0 1.66 7.03392 0.006694 -0.021282 0.017465 +Ta 2.34759 0.0 7.03392 0.006694 -0.021282 0.017465 +Ta 2.34759 1.66 9.38594 0.014872 0.089556 -4.7e-05 +Ta 0.0 0.0 9.38594 0.014872 0.089556 -4.7e-05 +Ta 0.0 1.66 11.73648 -0.219937 -0.367391 -0.112068 +Ta 2.34759 0.0 11.73648 -0.219937 -0.367391 -0.112068 +Ta 4.46043 3.154 14.08712 0.219937 0.367391 0.112068 +Ta 2.11284 1.494 14.08712 0.219937 0.367391 0.112068 +Ta 2.11284 3.154 16.43764 -0.014872 -0.089556 4.7e-05 +Ta 4.46043 1.494 16.43764 -0.014872 -0.089556 4.7e-05 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0.0 4.68536 0.007402 -0.005681 -0.01113 +Ta 0.0 1.66 7.03392 -0.010084 0.035505 0.068653 +Ta 2.34759 0.0 7.03392 -0.010084 0.035505 0.068653 +Ta 2.34759 1.66 9.38594 0.009421 -0.162853 -0.055133 +Ta 0.0 0.0 9.38594 0.009421 -0.162853 -0.055133 +Ta 0.0 1.66 11.73648 0.194592 0.543144 -0.645035 +Ta 2.34759 0.0 11.73648 0.194592 0.543144 -0.645035 +Ta 3.05187 2.158 14.08712 -0.194592 -0.543144 0.645035 +Ta 0.70428 0.498 14.08712 -0.194592 -0.543144 0.645035 +Ta 0.70428 2.158 16.43764 -0.009421 0.162853 0.055133 +Ta 3.05187 0.498 16.43764 -0.009421 0.162853 0.055133 +Ta 3.05187 2.158 18.78966 0.010084 -0.035505 -0.068653 +Ta 0.70428 0.498 18.78966 0.010084 -0.035505 -0.068653 +Ta 0.70428 2.158 21.13823 -0.007402 0.005681 0.01113 +Ta 3.05187 0.498 21.13823 -0.007402 0.005681 0.01113 +Ta 3.05187 2.158 23.48739 0.000192 -0.002217 0.008533 +Ta 0.70428 0.498 23.48739 0.000192 -0.002217 0.008533 +Ta 0.70428 2.158 25.73229 -0.000338 0.000764 -0.003013 +Ta 3.05187 0.498 25.73229 -0.000338 0.000764 -0.003013 +24 +Lattice = "4.69519042969 0.0 0.0 0.0 3.31999993324 0.0 0.0 0.0 53.1199989319" Properties=species:S:1:pos:R:3:forces:R:3 energy=-279.55564 stress="-7951.990000000001 -1470.47 -2323.28 -1470.47 -7087.54 -2242.19 -2323.28 -2242.19 1393.38" +Ta 2.34759 1.66 0.09121 6.8e-05 -0.00218 0.002247 +Ta 0.0 0.0 0.09121 6.8e-05 -0.00218 0.002247 +Ta 0.0 1.66 2.3361 -0.000373 0.001531 -0.005318 +Ta 2.34759 0.0 2.3361 -0.000373 0.001531 -0.005318 +Ta 2.34759 1.66 4.68536 0.011743 -0.002192 -0.00859 +Ta 0.0 0.0 4.68536 0.011743 -0.002192 -0.00859 +Ta 0.0 1.66 7.03392 -0.010535 0.038081 0.052269 +Ta 2.34759 0.0 7.03392 -0.010535 0.038081 0.052269 +Ta 2.34759 1.66 9.38594 -0.00905 -0.147322 -0.015198 +Ta 0.0 0.0 9.38594 -0.00905 -0.147322 -0.015198 +Ta 0.0 1.66 11.73648 0.255618 0.52958 -0.348689 +Ta 2.34759 0.0 11.73648 0.255618 0.52958 -0.348689 +Ta 2.81711 1.992 14.08712 -0.255618 -0.52958 0.348689 +Ta 0.46952 0.332 14.08712 -0.255618 -0.52958 0.348689 +Ta 0.46952 1.992 16.43764 0.00905 0.147322 0.015198 +Ta 2.81711 0.332 16.43764 0.00905 0.147322 0.015198 +Ta 2.81711 1.992 18.78966 0.010535 -0.038081 -0.052269 +Ta 0.46952 0.332 18.78966 0.010535 -0.038081 -0.052269 +Ta 0.46952 1.992 21.13823 -0.011743 0.002192 0.00859 +Ta 2.81711 0.332 21.13823 -0.011743 0.002192 0.00859 +Ta 2.81711 1.992 23.48739 0.000373 -0.001531 0.005318 +Ta 0.46952 0.332 23.48739 0.000373 -0.001531 0.005318 +Ta 0.46952 1.992 25.73229 -6.8e-05 0.00218 -0.002247 +Ta 2.81711 0.332 25.73229 -6.8e-05 0.00218 -0.002247 +24 +Lattice = "4.69519042969 0.0 0.0 0.0 3.31999993324 0.0 0.0 0.0 53.1199989319" Properties=species:S:1:pos:R:3:forces:R:3 energy=-279.246939 stress="-7247.110000000001 -2088.01 900.26 -2088.01 -12867.95 522.24 900.26 522.24 -343.87" +Ta 2.34759 1.66 0.0313 -0.000299 2.9e-05 0.000555 +Ta 0.0 0.0 0.0313 -0.000299 2.9e-05 0.000555 +Ta 0.0 1.66 2.27588 0.000225 -0.001627 0.00115 +Ta 2.34759 0.0 2.27588 0.000225 -0.001627 0.00115 +Ta 2.34759 1.66 4.62506 -0.002747 0.002713 0.000254 +Ta 0.0 0.0 4.62506 -0.002747 0.002713 0.000254 +Ta 0.0 1.66 6.98061 0.004373 -0.018318 9.6e-05 +Ta 2.34759 0.0 6.98061 0.004373 -0.018318 9.6e-05 +Ta 2.34759 1.66 9.31312 -0.010337 0.080996 -2e-06 +Ta 0.0 0.0 9.31312 -0.010337 0.080996 -2e-06 +Ta 0.0 1.66 11.6666 -0.064509 -0.216178 0.000109 +Ta 2.34759 0.0 11.6666 -0.064509 -0.216178 0.000109 +Ta 3.75615 2.656 14.157 0.064509 0.216178 -0.000109 +Ta 1.40856 0.996 14.157 0.064509 0.216178 -0.000109 +Ta 1.40856 2.656 16.51046 0.010337 -0.080996 2e-06 +Ta 3.75615 0.996 16.51046 0.010337 -0.080996 2e-06 +Ta 3.75615 2.656 18.84297 -0.004373 0.018318 -9.6e-05 +Ta 1.40856 0.996 18.84297 -0.004373 0.018318 -9.6e-05 +Ta 1.40856 2.656 21.19853 0.002747 -0.002713 -0.000254 +Ta 3.75615 0.996 21.19853 0.002747 -0.002713 -0.000254 +Ta 3.75615 2.656 23.54761 -0.000225 0.001627 -0.00115 +Ta 1.40856 0.996 23.54761 -0.000225 0.001627 -0.00115 +Ta 1.40856 2.656 25.7922 0.000299 -2.9e-05 -0.000555 +Ta 3.75615 0.996 25.7922 0.000299 -2.9e-05 -0.000555 +24 +Lattice = "4.69519042969 0.0 0.0 0.0 3.31999993324 0.0 0.0 0.0 53.1199989319" Properties=species:S:1:pos:R:3:forces:R:3 energy=-279.302157 stress="-5999.4800000000005 -2091.2000000000003 2059.81 -2091.2000000000003 -8317.08 1933.52 2059.81 1933.52 4766.58" +Ta 2.34759 1.66 0.09121 -0.000338 0.000764 0.003027 +Ta 0.0 0.0 0.09121 -0.000338 0.000764 0.003027 +Ta 0.0 1.66 2.3361 0.000192 -0.002217 -0.008526 +Ta 2.34759 0.0 2.3361 0.000192 -0.002217 -0.008526 +Ta 2.34759 1.66 4.68536 -0.007402 0.005681 -0.011124 +Ta 0.0 0.0 4.68536 -0.007402 0.005681 -0.011124 +Ta 0.0 1.66 7.03392 0.010084 -0.035505 0.068661 +Ta 2.34759 0.0 7.03392 0.010084 -0.035505 0.068661 +Ta 2.34759 1.66 9.38594 -0.009421 0.162854 -0.055124 +Ta 0.0 0.0 9.38594 -0.009421 0.162854 -0.055124 +Ta 0.0 1.66 11.73648 -0.194591 -0.543144 -0.645027 +Ta 2.34759 0.0 11.73648 -0.194591 -0.543144 -0.645027 +Ta 3.99091 2.822 14.08712 0.194591 0.543144 0.645027 +Ta 1.64332 1.162 14.08712 0.194591 0.543144 0.645027 +Ta 1.64332 2.822 16.43764 0.009421 -0.162854 0.055124 +Ta 3.99091 1.162 16.43764 0.009421 -0.162854 0.055124 +Ta 3.99091 2.822 18.78966 -0.010084 0.035505 -0.068661 +Ta 1.64332 1.162 18.78966 -0.010084 0.035505 -0.068661 +Ta 1.64332 2.822 21.13823 0.007402 -0.005681 0.011124 +Ta 3.99091 1.162 21.13823 0.007402 -0.005681 0.011124 +Ta 3.99091 2.822 23.48739 -0.000192 0.002217 0.008526 +Ta 1.64332 1.162 23.48739 -0.000192 0.002217 0.008526 +Ta 1.64332 2.822 25.73229 0.000338 -0.000764 -0.003027 +Ta 3.99091 1.162 25.73229 0.000338 -0.000764 -0.003027 +24 +Lattice = "4.69519042969 0.0 0.0 0.0 3.31999993324 0.0 0.0 0.0 53.1199989319" Properties=species:S:1:pos:R:3:forces:R:3 energy=-279.246935 stress="-7243.7300000000005 -2085.2 -898.75 -2085.2 -12860.99 -521.24 -898.75 -521.24 -339.14" +Ta 2.34759 1.66 0.03138 0.000299 -3.1e-05 0.000674 +Ta 0.0 0.0 0.03138 0.000299 -3.1e-05 0.000674 +Ta 0.0 1.66 2.276 -0.000225 0.001628 -0.00088 +Ta 2.34759 0.0 2.276 -0.000225 0.001628 -0.00088 +Ta 2.34759 1.66 4.62485 0.002741 -0.002715 0.000469 +Ta 0.0 0.0 4.62485 0.002741 -0.002715 0.000469 +Ta 0.0 1.66 6.98003 -0.004361 0.018297 0.002362 +Ta 2.34759 0.0 6.98003 -0.004361 0.018297 0.002362 +Ta 2.34759 1.66 9.31271 0.010328 -0.080927 0.000615 +Ta 0.0 0.0 9.31271 0.010328 -0.080927 0.000615 +Ta 0.0 1.66 11.66645 0.064416 0.215971 0.000489 +Ta 2.34759 0.0 11.66645 0.064416 0.215971 0.000489 +Ta 3.28663 2.324 14.15715 -0.064416 -0.215971 -0.000489 +Ta 0.93904 0.664 14.15715 -0.064416 -0.215971 -0.000489 +Ta 0.93904 2.324 16.51087 -0.010328 0.080927 -0.000615 +Ta 3.28663 0.664 16.51087 -0.010328 0.080927 -0.000615 +Ta 3.28663 2.324 18.84355 0.004361 -0.018297 -0.002362 +Ta 0.93904 0.664 18.84355 0.004361 -0.018297 -0.002362 +Ta 0.93904 2.324 21.19874 -0.002741 0.002715 -0.000469 +Ta 3.28663 0.664 21.19874 -0.002741 0.002715 -0.000469 +Ta 3.28663 2.324 23.54749 0.000225 -0.001628 0.00088 +Ta 0.93904 0.664 23.54749 0.000225 -0.001628 0.00088 +Ta 0.93904 2.324 25.79212 -0.000299 3.1e-05 -0.000674 +Ta 3.28663 0.664 25.79212 -0.000299 3.1e-05 -0.000674 +24 +Lattice = "4.69519042969 0.0 0.0 0.0 3.31999993324 0.0 0.0 0.0 53.1199989319" Properties=species:S:1:pos:R:3:forces:R:3 energy=-279.896025 stress="-9869.42 0.0 0.0 0.0 -8124.2 0.0 0.0 0.0 -554.5600000000001" +Ta 2.34759 1.66 0.09121 0.0 0.0 0.000102 +Ta 0.0 0.0 0.09121 0.0 0.0 0.000102 +Ta 0.0 1.66 2.3361 0.0 0.0 -0.000104 +Ta 2.34759 0.0 2.3361 0.0 0.0 -0.000104 +Ta 2.34759 1.66 4.68536 0.0 0.0 0.000115 +Ta 0.0 0.0 4.68536 0.0 0.0 0.000115 +Ta 0.0 1.66 7.03392 0.0 0.0 0.002828 +Ta 2.34759 0.0 7.03392 0.0 0.0 0.002828 +Ta 2.34759 1.66 9.38594 0.0 0.0 -0.004132 +Ta 0.0 0.0 9.38594 0.0 0.0 -0.004132 +Ta 0.0 1.66 11.73648 0.0 0.0 0.001736 +Ta 2.34759 0.0 11.73648 0.0 0.0 0.001736 +Ta 2.34759 1.66 14.08712 0.0 0.0 -0.001736 +Ta 0.0 0.0 14.08712 0.0 0.0 -0.001736 +Ta 0.0 1.66 16.43764 0.0 0.0 0.004132 +Ta 2.34759 0.0 16.43764 0.0 0.0 0.004132 +Ta 2.34759 1.66 18.78966 0.0 0.0 -0.002828 +Ta 0.0 0.0 18.78966 0.0 0.0 -0.002828 +Ta 0.0 1.66 21.13823 0.0 0.0 -0.000115 +Ta 2.34759 0.0 21.13823 0.0 0.0 -0.000115 +Ta 2.34759 1.66 23.48739 0.0 0.0 0.000104 +Ta 0.0 0.0 23.48739 0.0 0.0 0.000104 +Ta 0.0 1.66 25.73229 0.0 0.0 -0.000102 +Ta 2.34759 0.0 25.73229 0.0 0.0 -0.000102 +24 +Lattice = "4.69519042969 0.0 0.0 0.0 3.31999993324 0.0 0.0 0.0 53.1199989319" Properties=species:S:1:pos:R:3:forces:R:3 energy=-279.584237 stress="-8428.63 -1472.9 -2164.32 -1472.9 -8091.21 -1800.0100000000002 -2164.32 -1800.0100000000002 -288.22999999999996" +Ta 2.34759 1.66 0.07506 0.000102 -0.002133 -0.000914 +Ta 0.0 0.0 0.07506 0.000102 -0.002133 -0.000914 +Ta 0.0 1.66 2.31974 -0.000559 0.002291 0.000397 +Ta 2.34759 0.0 2.31974 -0.000559 0.002291 0.000397 +Ta 2.34759 1.66 4.6688 0.011573 -0.001165 -0.000831 +Ta 0.0 0.0 4.6688 0.011573 -0.001165 -0.000831 +Ta 0.0 1.66 7.02184 -0.010852 0.033591 -0.000593 +Ta 2.34759 0.0 7.02184 -0.010852 0.033591 -0.000593 +Ta 2.34759 1.66 9.36366 -0.008031 -0.133014 -0.000394 +Ta 0.0 0.0 9.36366 -0.008031 -0.133014 -0.000394 +Ta 0.0 1.66 11.70273 0.232392 0.441681 -0.000156 +Ta 2.34759 0.0 11.70273 0.232392 0.441681 -0.000156 +Ta 2.81711 1.992 14.12087 -0.232392 -0.441681 0.000156 +Ta 0.46952 0.332 14.12087 -0.232392 -0.441681 0.000156 +Ta 0.46952 1.992 16.45992 0.008031 0.133014 0.000394 +Ta 2.81711 0.332 16.45992 0.008031 0.133014 0.000394 +Ta 2.81711 1.992 18.80174 0.010852 -0.033591 0.000593 +Ta 0.46952 0.332 18.80174 0.010852 -0.033591 0.000593 +Ta 0.46952 1.992 21.15479 -0.011573 0.001165 0.000831 +Ta 2.81711 0.332 21.15479 -0.011573 0.001165 0.000831 +Ta 2.81711 1.992 23.50375 0.000559 -0.002291 -0.000397 +Ta 0.46952 0.332 23.50375 0.000559 -0.002291 -0.000397 +Ta 0.46952 1.992 25.74844 -0.000102 0.002133 0.000914 +Ta 2.81711 0.332 25.74844 -0.000102 0.002133 0.000914 +24 +Lattice = "4.69519042969 0.0 0.0 0.0 3.31999993324 0.0 0.0 0.0 53.1199989319" Properties=species:S:1:pos:R:3:forces:R:3 energy=-279.124427 stress="-3757.0899999999997 -2887.24 902.0 -2887.24 -10640.1 866.64 902.0 866.64 7774.740000000001" +Ta 2.34759 1.66 0.09121 -0.000483 -0.000237 0.002307 +Ta 0.0 0.0 0.09121 -0.000483 -0.000237 0.002307 +Ta 0.0 1.66 2.3361 8.9e-05 -0.001539 -0.010324 +Ta 2.34759 0.0 2.3361 8.9e-05 -0.001539 -0.010324 +Ta 2.34759 1.66 4.68536 -0.003111 0.003535 -0.007613 +Ta 0.0 0.0 4.68536 -0.003111 0.003535 -0.007613 +Ta 0.0 1.66 7.03392 0.007146 -0.021127 0.073738 +Ta 2.34759 0.0 7.03392 0.007146 -0.021127 0.073738 +Ta 2.34759 1.66 9.38594 -0.013663 0.107342 -0.116996 +Ta 0.0 0.0 9.38594 -0.013663 0.107342 -0.116996 +Ta 0.0 1.66 11.73648 -0.067743 -0.32857 -0.821304 +Ta 2.34759 0.0 11.73648 -0.067743 -0.32857 -0.821304 +Ta 3.75615 2.656 14.08712 0.067743 0.32857 0.821304 +Ta 1.40856 0.996 14.08712 0.067743 0.32857 0.821304 +Ta 1.40856 2.656 16.43764 0.013663 -0.107342 0.116996 +Ta 3.75615 0.996 16.43764 0.013663 -0.107342 0.116996 +Ta 3.75615 2.656 18.78966 -0.007146 0.021127 -0.073738 +Ta 1.40856 0.996 18.78966 -0.007146 0.021127 -0.073738 +Ta 1.40856 2.656 21.13823 0.003111 -0.003535 0.007613 +Ta 3.75615 0.996 21.13823 0.003111 -0.003535 0.007613 +Ta 3.75615 2.656 23.48739 -8.9e-05 0.001539 0.010324 +Ta 1.40856 0.996 23.48739 -8.9e-05 0.001539 0.010324 +Ta 1.40856 2.656 25.73229 0.000483 0.000237 -0.002307 +Ta 3.75615 0.996 25.73229 0.000483 0.000237 -0.002307 +24 +Lattice = "4.69519042969 0.0 0.0 0.0 3.31999993324 0.0 0.0 0.0 53.1199989319" Properties=species:S:1:pos:R:3:forces:R:3 energy=-279.379366 stress="-7763.09 -1797.51 1889.74 -1797.51 -10164.59 1320.57 1889.74 1320.57 34.12" +Ta 2.34759 1.66 0.05376 -0.000259 0.002166 -0.001263 +Ta 0.0 0.0 0.05376 -0.000259 0.002166 -0.001263 +Ta 0.0 1.66 2.29821 0.000506 -0.00178 0.000245 +Ta 2.34759 0.0 2.29821 0.000506 -0.00178 0.000245 +Ta 2.34759 1.66 4.64698 -0.007327 0.004782 -0.001824 +Ta 0.0 0.0 4.64698 -0.007327 0.004782 -0.001824 +Ta 0.0 1.66 7.00162 0.008163 -0.030937 -0.001313 +Ta 2.34759 0.0 7.00162 0.008163 -0.030937 -0.001313 +Ta 2.34759 1.66 9.33764 -0.007098 0.132381 -0.001661 +Ta 0.0 0.0 9.33764 -0.007098 0.132381 -0.001661 +Ta 0.0 1.66 11.67998 -0.168672 -0.393164 0.000838 +Ta 2.34759 0.0 11.67998 -0.168672 -0.393164 0.000838 +Ta 3.99091 2.822 14.14362 0.168672 0.393164 -0.000838 +Ta 1.64332 1.162 14.14362 0.168672 0.393164 -0.000838 +Ta 1.64332 2.822 16.48594 0.007098 -0.132381 0.001661 +Ta 3.99091 1.162 16.48594 0.007098 -0.132381 0.001661 +Ta 3.99091 2.822 18.82196 -0.008163 0.030937 0.001313 +Ta 1.64332 1.162 18.82196 -0.008163 0.030937 0.001313 +Ta 1.64332 2.822 21.17661 0.007327 -0.004782 0.001824 +Ta 3.99091 1.162 21.17661 0.007327 -0.004782 0.001824 +Ta 3.99091 2.822 23.52528 -0.000506 0.00178 -0.000245 +Ta 1.64332 1.162 23.52528 -0.000506 0.00178 -0.000245 +Ta 1.64332 2.822 25.76974 0.000259 -0.002166 0.001263 +Ta 3.99091 1.162 25.76974 0.000259 -0.002166 0.001263 +24 +Lattice = "4.69519042969 0.0 0.0 0.0 3.31999993324 0.0 0.0 0.0 53.1199989319" Properties=species:S:1:pos:R:3:forces:R:3 energy=-279.37937 stress="-7778.34 -1797.1200000000001 -1889.07 -1797.1200000000001 -10180.85 -1319.78 -1889.07 -1319.78 5.64" +Ta 2.34759 1.66 0.0535 0.000258 -0.00217 -0.000937 +Ta 0.0 0.0 0.0535 0.000258 -0.00217 -0.000937 +Ta 0.0 1.66 2.29801 -0.000506 0.00178 -2.1e-05 +Ta 2.34759 0.0 2.29801 -0.000506 0.00178 -2.1e-05 +Ta 2.34759 1.66 4.64678 0.007324 -0.004781 -0.001649 +Ta 0.0 0.0 4.64678 0.007324 -0.004781 -0.001649 +Ta 0.0 1.66 7.00147 -0.00816 0.030933 -0.001233 +Ta 2.34759 0.0 7.00147 -0.00816 0.030933 -0.001233 +Ta 2.34759 1.66 9.33754 0.0071 -0.132353 -0.001629 +Ta 0.0 0.0 9.33754 0.0071 -0.132353 -0.001629 +Ta 0.0 1.66 11.67995 0.168627 0.393088 0.00081 +Ta 2.34759 0.0 11.67995 0.168627 0.393088 0.00081 +Ta 3.05187 2.158 14.14365 -0.168627 -0.393088 -0.00081 +Ta 0.70428 0.498 14.14365 -0.168627 -0.393088 -0.00081 +Ta 0.70428 2.158 16.48604 -0.0071 0.132353 0.001629 +Ta 3.05187 0.498 16.48604 -0.0071 0.132353 0.001629 +Ta 3.05187 2.158 18.82211 0.00816 -0.030933 0.001233 +Ta 0.70428 0.498 18.82211 0.00816 -0.030933 0.001233 +Ta 0.70428 2.158 21.17681 -0.007324 0.004781 0.001649 +Ta 3.05187 0.498 21.17681 -0.007324 0.004781 0.001649 +Ta 3.05187 2.158 23.52548 0.000506 -0.00178 2.1e-05 +Ta 0.70428 0.498 23.52548 0.000506 -0.00178 2.1e-05 +Ta 0.70428 2.158 25.77 -0.000258 0.00217 0.000937 +Ta 3.05187 0.498 25.77 -0.000258 0.00217 0.000937 +24 +Lattice = "4.69519042969 0.0 0.0 0.0 3.31999993324 0.0 0.0 0.0 53.1199989319" Properties=species:S:1:pos:R:3:forces:R:3 energy=-279.124427 stress="-3756.4 -2886.7400000000002 -901.71 -2886.7400000000002 -10639.47 -867.12 -901.71 -867.12 7774.14" +Ta 2.34759 1.66 0.09121 0.000483 0.000237 0.002314 +Ta 0.0 0.0 0.09121 0.000483 0.000237 0.002314 +Ta 0.0 1.66 2.3361 -8.8e-05 0.001538 -0.010267 +Ta 2.34759 0.0 2.3361 -8.8e-05 0.001538 -0.010267 +Ta 2.34759 1.66 4.68536 0.003111 -0.003535 -0.007607 +Ta 0.0 0.0 4.68536 0.003111 -0.003535 -0.007607 +Ta 0.0 1.66 7.03392 -0.007146 0.021127 0.073723 +Ta 2.34759 0.0 7.03392 -0.007146 0.021127 0.073723 +Ta 2.34759 1.66 9.38594 0.013663 -0.10734 -0.116992 +Ta 0.0 0.0 9.38594 0.013663 -0.10734 -0.116992 +Ta 0.0 1.66 11.73648 0.067747 0.328568 -0.821295 +Ta 2.34759 0.0 11.73648 0.067747 0.328568 -0.821295 +Ta 3.28663 2.324 14.08712 -0.067747 -0.328568 0.821295 +Ta 0.93904 0.664 14.08712 -0.067747 -0.328568 0.821295 +Ta 0.93904 2.324 16.43764 -0.013663 0.10734 0.116992 +Ta 3.28663 0.664 16.43764 -0.013663 0.10734 0.116992 +Ta 3.28663 2.324 18.78966 0.007146 -0.021127 -0.073723 +Ta 0.93904 0.664 18.78966 0.007146 -0.021127 -0.073723 +Ta 0.93904 2.324 21.13823 -0.003111 0.003535 0.007607 +Ta 3.28663 0.664 21.13823 -0.003111 0.003535 0.007607 +Ta 3.28663 2.324 23.48739 8.8e-05 -0.001538 0.010267 +Ta 0.93904 0.664 23.48739 8.8e-05 -0.001538 0.010267 +Ta 0.93904 2.324 25.73229 -0.000483 -0.000237 -0.002314 +Ta 3.28663 0.664 25.73229 -0.000483 -0.000237 -0.002314 +24 +Lattice = "4.69519042969 0.0 0.0 0.0 3.31999993324 0.0 0.0 0.0 53.1199989319" Properties=species:S:1:pos:R:3:forces:R:3 energy=-279.901657 stress="-9712.87 0.0 0.0 0.0 -7972.25 0.0 0.0 0.0 -388.31" +Ta 2.34759 1.66 0.09122 0.0 0.0 -1.6e-05 +Ta 0.0 0.0 0.09122 0.0 0.0 -1.6e-05 +Ta 0.0 1.66 2.33609 0.0 0.0 0.000319 +Ta 2.34759 0.0 2.33609 0.0 0.0 0.000319 +Ta 2.34759 1.66 4.68537 0.0 0.0 0.0004 +Ta 0.0 0.0 4.68537 0.0 0.0 0.0004 +Ta 0.0 1.66 7.03419 0.0 0.0 9.3e-05 +Ta 2.34759 0.0 7.03419 0.0 0.0 9.3e-05 +Ta 2.34759 1.66 9.38555 0.0 0.0 -0.000298 +Ta 0.0 0.0 9.38555 0.0 0.0 -0.000298 +Ta 0.0 1.66 11.73665 0.0 0.0 -0.000507 +Ta 2.34759 0.0 11.73665 0.0 0.0 -0.000507 +Ta 2.34759 1.66 14.08695 0.0 0.0 0.000507 +Ta 0.0 0.0 14.08695 0.0 0.0 0.000507 +Ta 0.0 1.66 16.43803 0.0 0.0 0.000298 +Ta 2.34759 0.0 16.43803 0.0 0.0 0.000298 +Ta 2.34759 1.66 18.78939 0.0 0.0 -9.3e-05 +Ta 0.0 0.0 18.78939 0.0 0.0 -9.3e-05 +Ta 0.0 1.66 21.13822 0.0 0.0 -0.0004 +Ta 2.34759 0.0 21.13822 0.0 0.0 -0.0004 +Ta 2.34759 1.66 23.4874 0.0 0.0 -0.000319 +Ta 0.0 0.0 23.4874 0.0 0.0 -0.000319 +Ta 0.0 1.66 25.73228 0.0 0.0 1.6e-05 +Ta 2.34759 0.0 25.73228 0.0 0.0 1.6e-05 +24 +Lattice = "4.69519042969 0.0 0.0 0.0 3.31999993324 0.0 0.0 0.0 53.1199989319" Properties=species:S:1:pos:R:3:forces:R:3 energy=-279.79264 stress="-9277.630000000001 -706.52 -1762.12 -706.52 -7720.29 -1609.51 -1762.12 -1609.51 -420.21999999999997" +Ta 2.34759 1.66 0.0871 -0.000184 -0.001656 0.000674 +Ta 0.0 0.0 0.0871 -0.000184 -0.001656 0.000674 +Ta 0.0 1.66 2.332 -0.000294 0.000423 0.000306 +Ta 2.34759 0.0 2.332 -0.000294 0.000423 0.000306 +Ta 2.34759 1.66 4.68156 0.008643 -0.001357 -0.001853 +Ta 0.0 0.0 4.68156 0.008643 -0.001357 -0.001853 +Ta 0.0 1.66 7.03137 -0.006924 0.020397 -0.000275 +Ta 2.34759 0.0 7.03137 -0.006924 0.020397 -0.000275 +Ta 2.34759 1.66 9.38022 -0.01463 -0.087628 0.000622 +Ta 0.0 0.0 9.38022 -0.01463 -0.087628 0.000622 +Ta 0.0 1.66 11.72434 0.214497 0.348769 -0.000686 +Ta 2.34759 0.0 11.72434 0.214497 0.348769 -0.000686 +Ta 2.58235 1.826 14.09926 -0.214497 -0.348769 0.000686 +Ta 0.23476 0.166 14.09926 -0.214497 -0.348769 0.000686 +Ta 0.23476 1.826 16.44336 0.01463 0.087628 -0.000622 +Ta 2.58235 0.166 16.44336 0.01463 0.087628 -0.000622 +Ta 2.58235 1.826 18.79221 0.006924 -0.020397 0.000275 +Ta 0.23476 0.166 18.79221 0.006924 -0.020397 0.000275 +Ta 0.23476 1.826 21.14203 -0.008643 0.001357 0.001853 +Ta 2.58235 0.166 21.14203 -0.008643 0.001357 0.001853 +Ta 2.58235 1.826 23.49149 0.000294 -0.000423 -0.000306 +Ta 0.23476 0.166 23.49149 0.000294 -0.000423 -0.000306 +Ta 0.23476 1.826 25.7364 0.000184 0.001656 -0.000674 +Ta 2.58235 0.166 25.7364 0.000184 0.001656 -0.000674 +24 +Lattice = "4.69519042969 0.0 0.0 0.0 3.31999993324 0.0 0.0 0.0 53.1199989319" Properties=species:S:1:pos:R:3:forces:R:3 energy=-279.896025 stress="-9868.86 0.0 0.0 0.0 -8124.259999999999 0.0 0.0 0.0 -554.9" +Ta 2.34759 1.66 0.09121 0.0 0.0 0.000107 +Ta 0.0 0.0 0.09121 0.0 0.0 0.000107 +Ta 0.0 1.66 2.3361 0.0 0.0 -9.8e-05 +Ta 2.34759 0.0 2.3361 0.0 0.0 -9.8e-05 +Ta 2.34759 1.66 4.68536 0.0 0.0 0.000111 +Ta 0.0 0.0 4.68536 0.0 0.0 0.000111 +Ta 0.0 1.66 7.03392 0.0 0.0 0.002832 +Ta 2.34759 0.0 7.03392 0.0 0.0 0.002832 +Ta 2.34759 1.66 9.38594 0.0 0.0 -0.004127 +Ta 0.0 0.0 9.38594 0.0 0.0 -0.004127 +Ta 0.0 1.66 11.73648 0.0 0.0 0.001737 +Ta 2.34759 0.0 11.73648 0.0 0.0 0.001737 +Ta 4.69519 0.0 14.08712 0.0 0.0 -0.001737 +Ta 2.3476 1.66 14.08712 0.0 0.0 -0.001737 +Ta 2.3476 0.0 16.43764 0.0 0.0 0.004127 +Ta 4.69519 1.66 16.43764 0.0 0.0 0.004127 +Ta 4.69519 0.0 18.78966 0.0 0.0 -0.002832 +Ta 2.3476 1.66 18.78966 0.0 0.0 -0.002832 +Ta 2.3476 0.0 21.13823 0.0 0.0 -0.000111 +Ta 4.69519 1.66 21.13823 0.0 0.0 -0.000111 +Ta 4.69519 0.0 23.48739 0.0 0.0 9.8e-05 +Ta 2.3476 1.66 23.48739 0.0 0.0 9.8e-05 +Ta 2.3476 0.0 25.73229 0.0 0.0 -0.000107 +Ta 4.69519 1.66 25.73229 0.0 0.0 -0.000107 +24 +Lattice = "4.69519042969 0.0 0.0 0.0 3.31999993324 0.0 0.0 0.0 53.1199989319" Properties=species:S:1:pos:R:3:forces:R:3 energy=-279.206496 stress="-6761.16 -2211.9399999999996 0.0 -2211.9399999999996 -14026.06 0.0 0.0 0.0 -201.45" +Ta 2.34759 1.66 0.026 0.0 0.0 -0.000166 +Ta 0.0 0.0 0.026 0.0 0.0 -0.000166 +Ta 0.0 1.66 2.2705 0.0 0.0 -0.000442 +Ta 2.34759 0.0 2.2705 0.0 0.0 -0.000442 +Ta 2.34759 1.66 4.61955 0.0 0.0 -0.001018 +Ta 0.0 0.0 4.61955 0.0 0.0 -0.001018 +Ta 0.0 1.66 6.97451 0.0 0.0 0.001141 +Ta 2.34759 0.0 6.97451 0.0 0.0 0.001141 +Ta 2.34759 1.66 9.30496 0.0 0.0 0.000143 +Ta 0.0 0.0 9.30496 0.0 0.0 0.000143 +Ta 0.0 1.66 11.66343 0.0 0.0 0.002124 +Ta 2.34759 0.0 11.66343 0.0 0.0 0.002124 +Ta 3.52139 2.49 14.16017 0.0 0.0 -0.002124 +Ta 1.1738 0.83 14.16017 0.0 0.0 -0.002124 +Ta 1.1738 2.49 16.51862 0.0 0.0 -0.000143 +Ta 3.52139 0.83 16.51862 0.0 0.0 -0.000143 +Ta 3.52139 2.49 18.84907 0.0 0.0 -0.001141 +Ta 1.1738 0.83 18.84907 0.0 0.0 -0.001141 +Ta 1.1738 2.49 21.20404 0.0 0.0 0.001018 +Ta 3.52139 0.83 21.20404 0.0 0.0 0.001018 +Ta 3.52139 2.49 23.55299 0.0 0.0 0.000442 +Ta 1.1738 0.83 23.55299 0.0 0.0 0.000442 +Ta 1.1738 2.49 25.7975 0.0 0.0 0.000166 +Ta 3.52139 0.83 25.7975 0.0 0.0 0.000166 +24 +Lattice = "4.69519042969 0.0 0.0 0.0 3.31999993324 0.0 0.0 0.0 53.1199989319" Properties=species:S:1:pos:R:3:forces:R:3 energy=-279.55564 stress="-7951.26 -1470.33 2322.88 -1470.33 -7086.45 2241.6200000000003 2322.88 2241.6200000000003 1394.24" +Ta 2.34759 1.66 0.09121 -6.8e-05 0.00218 0.002238 +Ta 0.0 0.0 0.09121 -6.8e-05 0.00218 0.002238 +Ta 0.0 1.66 2.3361 0.000372 -0.001531 -0.005316 +Ta 2.34759 0.0 2.3361 0.000372 -0.001531 -0.005316 +Ta 2.34759 1.66 4.68536 -0.011743 0.002192 -0.008604 +Ta 0.0 0.0 4.68536 -0.011743 0.002192 -0.008604 +Ta 0.0 1.66 7.03392 0.010535 -0.038081 0.05226 +Ta 2.34759 0.0 7.03392 0.010535 -0.038081 0.05226 +Ta 2.34759 1.66 9.38594 0.00905 0.147322 -0.015204 +Ta 0.0 0.0 9.38594 0.00905 0.147322 -0.015204 +Ta 0.0 1.66 11.73648 -0.255617 -0.52958 -0.348696 +Ta 2.34759 0.0 11.73648 -0.255617 -0.52958 -0.348696 +Ta 4.22567 2.988 14.08712 0.255617 0.52958 0.348696 +Ta 1.87808 1.328 14.08712 0.255617 0.52958 0.348696 +Ta 1.87808 2.988 16.43764 -0.00905 -0.147322 0.015204 +Ta 4.22567 1.328 16.43764 -0.00905 -0.147322 0.015204 +Ta 4.22567 2.988 18.78966 -0.010535 0.038081 -0.05226 +Ta 1.87808 1.328 18.78966 -0.010535 0.038081 -0.05226 +Ta 1.87808 2.988 21.13823 0.011743 -0.002192 0.008604 +Ta 4.22567 1.328 21.13823 0.011743 -0.002192 0.008604 +Ta 4.22567 2.988 23.48739 -0.000372 0.001531 0.005316 +Ta 1.87808 1.328 23.48739 -0.000372 0.001531 0.005316 +Ta 1.87808 2.988 25.73229 6.8e-05 -0.00218 -0.002238 +Ta 4.22567 1.328 25.73229 6.8e-05 -0.00218 -0.002238 +24 +Lattice = "4.69519042969 0.0 0.0 0.0 3.31999993324 0.0 0.0 0.0 53.1199989319" Properties=species:S:1:pos:R:3:forces:R:3 energy=-279.79264 stress="-9276.56 -705.96 1761.7 -705.96 -7718.9800000000005 1609.3500000000001 1761.7 1609.3500000000001 -417.65000000000003" +Ta 2.34759 1.66 0.08713 0.000184 0.001656 0.000681 +Ta 0.0 0.0 0.08713 0.000184 0.001656 0.000681 +Ta 0.0 1.66 2.33202 0.000294 -0.000424 0.000309 +Ta 2.34759 0.0 2.33202 0.000294 -0.000424 0.000309 +Ta 2.34759 1.66 4.68158 -0.008643 0.001357 -0.001844 +Ta 0.0 0.0 4.68158 -0.008643 0.001357 -0.001844 +Ta 0.0 1.66 7.03138 0.006924 -0.020398 -0.000267 +Ta 2.34759 0.0 7.03138 0.006924 -0.020398 -0.000267 +Ta 2.34759 1.66 9.38023 0.01463 0.087629 0.00063 +Ta 0.0 0.0 9.38023 0.01463 0.087629 0.00063 +Ta 0.0 1.66 11.72434 -0.214496 -0.34877 -0.000676 +Ta 2.34759 0.0 11.72434 -0.214496 -0.34877 -0.000676 +Ta 4.46043 3.154 14.09926 0.214496 0.34877 0.000676 +Ta 2.11284 1.494 14.09926 0.214496 0.34877 0.000676 +Ta 2.11284 3.154 16.44335 -0.01463 -0.087629 -0.00063 +Ta 4.46043 1.494 16.44335 -0.01463 -0.087629 -0.00063 +Ta 4.46043 3.154 18.7922 -0.006924 0.020398 0.000267 +Ta 2.11284 1.494 18.7922 -0.006924 0.020398 0.000267 +Ta 2.11284 3.154 21.14201 0.008643 -0.001357 0.001844 +Ta 4.46043 1.494 21.14201 0.008643 -0.001357 0.001844 +Ta 4.46043 3.154 23.49147 -0.000294 0.000424 -0.000309 +Ta 2.11284 1.494 23.49147 -0.000294 0.000424 -0.000309 +Ta 2.11284 3.154 25.73637 -0.000184 -0.001656 -0.000681 +Ta 4.46043 1.494 25.73637 -0.000184 -0.001656 -0.000681 diff --git a/examples/PACKAGES/pod/Ta/XYZ/GSF_112.xyz b/examples/PACKAGES/pod/Ta/XYZ/GSF_112.xyz new file mode 100644 index 0000000000..71e317e259 --- /dev/null +++ b/examples/PACKAGES/pod/Ta/XYZ/GSF_112.xyz @@ -0,0 +1,704 @@ +30 +Lattice = "5.75041007996 0.0 0.0 0.0 4.69518995285 0.0 0.0 0.0 39.8400001526" Properties=species:S:1:pos:R:3:forces:R:3 energy=-345.175835 stress="-13147.16 0.0 -3780.86 0.0 -8634.359999999999 0.0 -3780.86 0.0 -262.94" +Ta 0.9892 0.0 2.67612 0.024552 0.0 -0.00195 +Ta 0.00727 2.34759 4.02628 0.020645 0.0 9.3e-05 +Ta 2.88247 2.34759 4.02628 0.020645 0.0 9.3e-05 +Ta 0.17997 0.0 0.13381 0.04617 0.0 -0.000386 +Ta 3.05517 0.0 0.13381 0.04617 0.0 -0.000386 +Ta 1.87083 2.34759 1.2728 -0.032821 0.0 -0.001196 +Ta 4.74604 2.34759 1.2728 -0.032821 0.0 -0.001196 +Ta 3.86441 0.0 2.67612 0.024552 0.0 -0.00195 +Ta 0.94648 2.34759 6.72012 0.031811 0.0 0.000572 +Ta 0.00117 0.0 8.09323 0.426675 0.0 0.000202 +Ta 2.87637 0.0 8.09323 0.426675 0.0 0.000202 +Ta 1.91123 0.0 5.35809 -0.1254 0.0 0.000587 +Ta 4.78644 0.0 5.35809 -0.1254 0.0 0.000587 +Ta 3.82169 2.34759 6.72012 0.031811 0.0 0.000572 +Ta 1.9168 2.34759 9.40413 -0.175762 0.0 0.000278 +Ta 4.79201 2.34759 9.40413 -0.175762 0.0 0.000278 +Ta 2.10731 0.0 10.91795 0.187758 0.0 0.000468 +Ta 1.162 2.34759 12.2439 -0.520663 0.0 0.000295 +Ta 4.0372 2.34759 12.2439 -0.520663 0.0 0.000295 +Ta 4.98252 0.0 10.91795 0.187758 0.0 0.000468 +Ta 2.10121 2.34759 14.96595 0.131217 0.0 0.000175 +Ta 1.11928 0.0 16.30656 -0.015432 0.0 6e-06 +Ta 3.99448 0.0 16.30656 -0.015432 0.0 6e-06 +Ta 3.11285 2.34759 17.71541 0.007977 0.0 0.000401 +Ta 0.23765 2.34759 17.71541 0.007977 0.0 0.000401 +Ta 3.07245 0.0 13.62798 0.021452 0.0 0.000107 +Ta 0.19725 0.0 13.62798 0.021452 0.0 0.000107 +Ta 4.97642 2.34759 14.96595 0.131217 0.0 0.000175 +Ta 1.92851 0.0 18.85304 -0.028176 0.0 0.00035 +Ta 4.80372 0.0 18.85304 -0.028176 0.0 0.00035 +30 +Lattice = "5.75041007996 0.0 0.0 0.0 4.69518995285 0.0 0.0 0.0 39.8400001526" Properties=species:S:1:pos:R:3:forces:R:3 energy=-346.361714 stress="-10339.27 0.0 -4235.839999999999 0.0 -10300.0 0.0 -4235.839999999999 0.0 -143.8" +Ta 0.9892 0.0 2.71788 0.039491 0.0 -0.003174 +Ta 0.00727 2.34759 4.0686 -0.006941 0.0 0.000225 +Ta 2.88247 2.34759 4.0686 -0.006941 0.0 0.000225 +Ta 0.17997 0.0 0.18084 0.006017 0.0 -0.000536 +Ta 3.05517 0.0 0.18084 0.006017 0.0 -0.000536 +Ta 1.87083 2.34759 1.32379 -0.009843 0.0 -0.001904 +Ta 4.74604 2.34759 1.32379 -0.009843 0.0 -0.001904 +Ta 3.86441 0.0 2.71788 0.039491 0.0 -0.003174 +Ta 0.94648 2.34759 6.76401 0.031952 0.0 0.001417 +Ta 0.00117 0.0 8.13836 0.170121 0.0 0.00142 +Ta 2.87637 0.0 8.13836 0.170121 0.0 0.00142 +Ta 1.91123 0.0 5.41435 -0.068665 0.0 0.001093 +Ta 4.78644 0.0 5.41435 -0.068665 0.0 0.001093 +Ta 3.82169 2.34759 6.76401 0.031952 0.0 0.001417 +Ta 1.9168 2.34759 9.47269 0.56983 0.0 0.001115 +Ta 4.79201 2.34759 9.47269 0.56983 0.0 0.001115 +Ta 1.24475 0.0 10.85237 -0.591123 0.0 0.000193 +Ta 0.29944 2.34759 12.20261 -0.170693 0.0 -0.00076 +Ta 3.17464 2.34759 12.20261 -0.170693 0.0 -0.00076 +Ta 4.11996 0.0 10.85237 -0.591123 0.0 0.000193 +Ta 1.23865 2.34759 14.90362 0.062003 0.0 -0.000147 +Ta 0.25672 0.0 16.25811 0.014238 0.0 6.7e-05 +Ta 3.13192 0.0 16.25811 0.014238 0.0 6.7e-05 +Ta 2.25029 2.34759 17.65366 -0.022348 0.0 0.000828 +Ta 5.1255 2.34759 17.65366 -0.022348 0.0 0.000828 +Ta 2.20989 0.0 13.56973 -0.01066 0.0 -0.000183 +Ta 5.0851 0.0 13.56973 -0.01066 0.0 -0.000183 +Ta 4.11386 2.34759 14.90362 0.062003 0.0 -0.000147 +Ta 1.06595 0.0 18.79472 -0.01338 0.0 0.000344 +Ta 3.94116 0.0 18.79472 -0.01338 0.0 0.000344 +30 +Lattice = "5.75041007996 0.0 0.0 0.0 4.69518995285 0.0 0.0 0.0 39.8400001526" Properties=species:S:1:pos:R:3:forces:R:3 energy=-345.795524 stress="-11480.130000000001 0.0 -5932.89 0.0 -5542.72 0.0 -5932.89 0.0 3462.38" +Ta 0.9892 0.0 2.7203 0.054393 0.0 0.051613 +Ta 0.00727 2.34759 4.07239 0.011422 0.0 0.01044 +Ta 2.88247 2.34759 4.07239 0.011422 0.0 0.01044 +Ta 0.17997 0.0 0.18449 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16.2663 -0.029184 0.0 8.5e-05 +Ta 4.55046 2.34759 17.66134 0.026269 0.0 -0.000704 +Ta 1.67526 2.34759 17.66134 0.026269 0.0 -0.000704 +Ta 4.51005 0.0 13.57023 0.044788 0.0 0.000159 +Ta 1.63485 0.0 13.57023 0.044788 0.0 0.000159 +Ta 0.66361 2.34759 14.91622 -0.038582 0.0 0.000491 +Ta 3.36612 0.0 18.80388 0.004104 0.0 0.000717 +Ta 0.49092 0.0 18.80388 0.004104 0.0 0.000717 +30 +Lattice = "5.75041007996 0.0 0.0 0.0 4.69518995285 0.0 0.0 0.0 39.8400001526" Properties=species:S:1:pos:R:3:forces:R:3 energy=-345.319406 stress="-11416.52 0.0 -757.17 0.0 -9138.949999999999 0.0 -757.17 0.0 -340.37" +Ta 0.9892 0.0 2.6792 -0.016362 0.0 0.000549 +Ta 0.00727 2.34759 4.0346 0.061621 0.0 0.000282 +Ta 2.88247 2.34759 4.0346 0.061621 0.0 0.000282 +Ta 0.17997 0.0 0.13955 0.017834 0.0 -0.000235 +Ta 3.05517 0.0 0.13955 0.017834 0.0 -0.000235 +Ta 1.87083 2.34759 1.28166 -0.013104 0.0 -5.3e-05 +Ta 4.74604 2.34759 1.28166 -0.013104 0.0 -5.3e-05 +Ta 3.86441 0.0 2.6792 -0.016362 0.0 0.000549 +Ta 0.94648 2.34759 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0.000446 +Ta 4.79201 2.34759 9.43202 -0.708973 0.0 0.000446 +Ta 2.96987 0.0 10.89606 0.708813 0.0 0.000528 +Ta 2.02457 2.34759 12.26428 -0.203649 0.0 0.002064 +Ta 4.89977 2.34759 12.26428 -0.203649 0.0 0.002064 +Ta 0.09467 0.0 10.89606 0.708813 0.0 0.000528 +Ta 2.96377 2.34759 14.9433 0.014742 0.0 -0.000587 +Ta 1.98184 0.0 16.28932 -0.077212 0.0 0.001835 +Ta 4.85704 0.0 16.28932 -0.077212 0.0 0.001835 +Ta 3.97542 2.34759 17.69607 0.052551 0.0 -9.3e-05 +Ta 1.10022 2.34759 17.69607 0.052551 0.0 -9.3e-05 +Ta 3.93501 0.0 13.59778 0.097817 0.0 0.000127 +Ta 1.05981 0.0 13.59778 0.097817 0.0 0.000127 +Ta 0.08857 2.34759 14.9433 0.014742 0.0 -0.000587 +Ta 2.79108 0.0 18.83554 -0.009805 0.0 -0.001124 +Ta 5.66629 0.0 18.83554 -0.009805 0.0 -0.001124 +30 +Lattice = "5.75041007996 0.0 0.0 0.0 4.69518995285 0.0 0.0 0.0 39.8400001526" Properties=species:S:1:pos:R:3:forces:R:3 energy=-345.98566 stress="-11481.859999999999 0.0 3919.02 0.0 -10708.259999999998 0.0 3919.02 0.0 -234.91" +Ta 0.9892 0.0 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2195.0699999999997 0.0 -6268.24 0.0 2195.0699999999997 0.0 6817.8099999999995" +Ta 0.9892 0.0 2.7203 -0.023223 0.0 0.001016 +Ta 0.00727 2.34759 4.07239 0.069003 0.0 0.068642 +Ta 2.88247 2.34759 4.07239 0.069003 0.0 0.068642 +Ta 0.17997 0.0 0.18449 0.005805 0.0 -0.024588 +Ta 3.05517 0.0 0.18449 0.005805 0.0 -0.024588 +Ta 1.87083 2.34759 1.32776 -0.003386 0.0 0.004796 +Ta 4.74604 2.34759 1.32776 -0.003386 0.0 0.004796 +Ta 3.86441 0.0 2.7203 -0.023223 0.0 0.001016 +Ta 0.94648 2.34759 6.77133 -0.15941 0.0 0.086585 +Ta 0.00117 0.0 8.1367 0.254346 0.0 -0.687398 +Ta 2.87637 0.0 8.1367 0.254346 0.0 -0.687398 +Ta 1.91123 0.0 5.41489 -0.007273 0.0 0.083064 +Ta 4.78644 0.0 5.41489 -0.007273 0.0 0.083064 +Ta 3.82169 2.34759 6.77133 -0.15941 0.0 0.086585 +Ta 1.9168 2.34759 9.48769 -0.854831 0.0 -0.81341 +Ta 4.79201 2.34759 9.48769 -0.854831 0.0 -0.81341 +Ta 2.96987 0.0 10.83871 0.856404 0.0 0.869919 +Ta 2.02457 2.34759 12.20409 -0.204616 0.0 0.570902 +Ta 4.89977 2.34759 12.20409 -0.204616 0.0 0.570902 +Ta 0.09467 0.0 10.83871 0.856404 0.0 0.869919 +Ta 2.96377 2.34759 14.90296 -0.014831 0.0 -0.080565 +Ta 1.98184 0.0 16.25507 -0.069492 0.0 -0.116436 +Ta 4.85704 0.0 16.25507 -0.069492 0.0 -0.116436 +Ta 3.97542 2.34759 17.64762 0.035331 0.0 0.046498 +Ta 1.10022 2.34759 17.64762 0.035331 0.0 0.046498 +Ta 3.93501 0.0 13.56045 0.105163 0.0 -0.067164 +Ta 1.05981 0.0 13.56045 0.105163 0.0 -0.067164 +Ta 0.08857 2.34759 14.90296 -0.014831 0.0 -0.080565 +Ta 2.79108 0.0 18.79091 0.011012 0.0 0.058138 +Ta 5.66629 0.0 18.79091 0.011012 0.0 0.058138 +30 +Lattice = "5.75041007996 0.0 0.0 0.0 4.69518995285 0.0 0.0 0.0 39.8400001526" Properties=species:S:1:pos:R:3:forces:R:3 energy=-346.593523 stress="-9415.82 0.0 -282.14 0.0 -11858.18 0.0 -282.14 0.0 174.85" +Ta 0.9892 0.0 2.7203 0.00126 0.0 -0.000951 +Ta 0.00727 2.34759 4.07239 0.002425 0.0 -0.000721 +Ta 2.88247 2.34759 4.07239 0.002425 0.0 -0.000721 +Ta 0.17997 0.0 0.18449 0.003483 0.0 -0.001569 +Ta 3.05517 0.0 0.18449 0.003483 0.0 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-0.00171 0.0 0.000333 +Ta 1.92238 0.0 13.56045 -0.00171 0.0 0.000333 +Ta 0.95113 2.34759 14.90296 -0.002425 0.0 0.000721 +Ta 3.65364 0.0 18.79091 -0.003483 0.0 0.001569 +Ta 0.77844 0.0 18.79091 -0.003483 0.0 0.001569 +30 +Lattice = "5.75041007996 0.0 0.0 0.0 4.69518995285 0.0 0.0 0.0 39.8400001526" Properties=species:S:1:pos:R:3:forces:R:3 energy=-345.281949 stress="-11560.39 0.0 -4653.08 0.0 -2434.16 0.0 -4653.08 0.0 6566.94" +Ta 0.9892 0.0 2.7203 0.050194 0.0 0.096189 +Ta 0.00727 2.34759 4.07239 0.024666 0.0 0.022454 +Ta 2.88247 2.34759 4.07239 0.024666 0.0 0.022454 +Ta 0.17997 0.0 0.18449 0.022221 0.0 -0.035876 +Ta 3.05517 0.0 0.18449 0.022221 0.0 -0.035876 +Ta 1.87083 2.34759 1.32776 -0.018007 0.0 -0.028654 +Ta 4.74604 2.34759 1.32776 -0.018007 0.0 -0.028654 +Ta 3.86441 0.0 2.7203 0.050194 0.0 0.096189 +Ta 0.94648 2.34759 6.77133 0.035097 0.0 -0.05687 +Ta 0.00117 0.0 8.1367 0.39639 0.0 -0.242712 +Ta 2.87637 0.0 8.1367 0.39639 0.0 -0.242712 +Ta 1.91123 0.0 5.41489 -0.174932 0.0 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Properties=species:S:1:pos:R:3:forces:R:3 energy=-345.928661 stress="-9145.630000000001 0.0 4495.89 0.0 -8704.09 0.0 4495.89 0.0 4121.84" +Ta 0.9892 0.0 2.7203 -0.037192 0.0 -0.008535 +Ta 0.00727 2.34759 4.07239 0.046799 0.0 0.059571 +Ta 2.88247 2.34759 4.07239 0.046799 0.0 0.059571 +Ta 0.17997 0.0 0.18449 0.009422 0.0 -0.012097 +Ta 3.05517 0.0 0.18449 0.009422 0.0 -0.012097 +Ta 1.87083 2.34759 1.32776 -0.005981 0.0 0.006654 +Ta 4.74604 2.34759 1.32776 -0.005981 0.0 0.006654 +Ta 3.86441 0.0 2.7203 -0.037192 0.0 -0.008535 +Ta 0.94648 2.34759 6.77133 -0.141158 0.0 0.065062 +Ta 0.00117 0.0 8.1367 -0.005041 0.0 -0.535781 +Ta 2.87637 0.0 8.1367 -0.005041 0.0 -0.535781 +Ta 1.91123 0.0 5.41489 0.047966 0.0 0.052967 +Ta 4.78644 0.0 5.41489 0.047966 0.0 0.052967 +Ta 3.82169 2.34759 6.77133 -0.141158 0.0 0.065062 +Ta 1.9168 2.34759 9.48769 -0.807767 0.0 -0.37656 +Ta 4.79201 2.34759 9.48769 -0.807767 0.0 -0.37656 +Ta 3.25739 0.0 10.83871 0.80662 0.0 0.413175 +Ta 2.31209 2.34759 12.20409 0.049763 0.0 0.478936 +Ta 5.18729 2.34759 12.20409 0.049763 0.0 0.478936 +Ta 0.38219 0.0 10.83871 0.80662 0.0 0.413175 +Ta 3.25129 2.34759 14.90296 -0.059966 0.0 -0.070617 +Ta 2.26936 0.0 16.25507 -0.058332 0.0 -0.070148 +Ta 5.14456 0.0 16.25507 -0.058332 0.0 -0.070148 +Ta 4.26294 2.34759 17.64762 0.034688 0.0 0.021628 +Ta 1.38774 2.34759 17.64762 0.034688 0.0 0.021628 +Ta 4.22253 0.0 13.56045 0.107399 0.0 -0.061704 +Ta 1.34733 0.0 13.56045 0.107399 0.0 -0.061704 +Ta 0.37609 2.34759 14.90296 -0.059966 0.0 -0.070617 +Ta 3.0786 0.0 18.79091 0.01278 0.0 0.037448 +Ta 0.2034 0.0 18.79091 0.01278 0.0 0.037448 +30 +Lattice = "5.75041007996 0.0 0.0 0.0 4.69518995285 0.0 0.0 0.0 39.8400001526" Properties=species:S:1:pos:R:3:forces:R:3 energy=-345.111657 stress="-8100.32 0.0 -1129.41 0.0 -4564.69 0.0 -1129.41 0.0 8777.64" +Ta 0.9892 0.0 2.7203 -0.002999 0.0 0.02667 +Ta 0.00727 2.34759 4.07239 0.054882 0.0 0.061699 +Ta 2.88247 2.34759 4.07239 0.054882 0.0 0.061699 +Ta 0.17997 0.0 0.18449 -0.00101 0.0 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0.8127 2.34759 17.64762 0.020235 0.0 0.058633 +Ta 3.64749 0.0 13.56045 0.091771 0.0 -0.007909 +Ta 0.77229 0.0 13.56045 0.091771 0.0 -0.007909 +Ta 5.55146 2.34759 14.90296 0.046884 0.0 -0.018316 +Ta 2.50356 0.0 18.79091 -0.009823 0.0 0.055977 +Ta 5.37876 0.0 18.79091 -0.009823 0.0 0.055977 +30 +Lattice = "5.75041007996 0.0 0.0 0.0 4.69518995285 0.0 0.0 0.0 39.8400001526" Properties=species:S:1:pos:R:3:forces:R:3 energy=-346.367123 stress="-9925.11 0.0 -4252.58 0.0 -9690.35 0.0 -4252.58 0.0 528.8000000000001" +Ta 0.9892 0.0 2.7203 0.036893 0.0 0.011121 +Ta 0.00727 2.34759 4.07239 0.003739 0.0 -0.008403 +Ta 2.88247 2.34759 4.07239 0.003739 0.0 -0.008403 +Ta 0.17997 0.0 0.18449 0.001677 0.0 -0.008529 +Ta 3.05517 0.0 0.18449 0.001677 0.0 -0.008529 +Ta 1.87083 2.34759 1.32776 -0.006125 0.0 -0.007305 +Ta 4.74604 2.34759 1.32776 -0.006125 0.0 -0.007305 +Ta 3.86441 0.0 2.7203 0.036893 0.0 0.011121 +Ta 0.94648 2.34759 6.77133 0.047105 0.0 -0.045187 +Ta 0.00117 0.0 8.1367 0.149771 0.0 0.043481 +Ta 2.87637 0.0 8.1367 0.149771 0.0 0.043481 +Ta 1.91123 0.0 5.41489 -0.082659 0.0 0.037224 +Ta 4.78644 0.0 5.41489 -0.082659 0.0 0.037224 +Ta 3.82169 2.34759 6.77133 0.047105 0.0 -0.045187 +Ta 1.9168 2.34759 9.48769 0.609504 0.0 -0.160261 +Ta 4.79201 2.34759 9.48769 0.609504 0.0 -0.160261 +Ta 1.24475 0.0 10.83871 -0.628777 0.0 0.151816 +Ta 0.29944 2.34759 12.20409 -0.151337 0.0 -0.040462 +Ta 3.17464 2.34759 12.20409 -0.151337 0.0 -0.040462 +Ta 4.11996 0.0 10.83871 -0.628777 0.0 0.151816 +Ta 1.23865 2.34759 14.90296 0.077509 0.0 -0.040594 +Ta 0.25672 0.0 16.25507 0.005483 0.0 -0.00975 +Ta 3.13192 0.0 16.25507 0.005483 0.0 -0.00975 +Ta 2.25029 2.34759 17.64762 -0.026269 0.0 0.012323 +Ta 5.1255 2.34759 17.64762 -0.026269 0.0 0.012323 +Ta 2.20989 0.0 13.56045 -0.027306 0.0 0.063713 +Ta 5.0851 0.0 13.56045 -0.027306 0.0 0.063713 +Ta 4.11386 2.34759 14.90296 0.077509 0.0 -0.040594 +Ta 1.06595 0.0 18.79091 -0.009208 0.0 0.000812 +Ta 3.94116 0.0 18.79091 -0.009208 0.0 0.000812 +30 +Lattice = "5.75041007996 0.0 0.0 0.0 4.69518995285 0.0 0.0 0.0 39.8400001526" Properties=species:S:1:pos:R:3:forces:R:3 energy=-346.582565 stress="-9596.72 0.0 -296.27 0.0 -12032.57 0.0 -296.27 0.0 -26.450000000000003" +Ta 0.9892 0.0 2.71997 0.001254 0.0 -0.000998 +Ta 0.00727 2.34759 4.07216 0.002375 0.0 -0.000846 +Ta 2.88247 2.34759 4.07216 0.002375 0.0 -0.000846 +Ta 0.17997 0.0 0.18409 0.004062 0.0 -0.001188 +Ta 3.05517 0.0 0.18409 0.004062 0.0 -0.001188 +Ta 1.87083 2.34759 1.32736 -0.001515 0.0 -0.001063 +Ta 4.74604 2.34759 1.32736 -0.001515 0.0 -0.001063 +Ta 3.86441 0.0 2.71997 0.001254 0.0 -0.000998 +Ta 0.94648 2.34759 6.77121 -0.000474 0.0 -0.000276 +Ta 0.00117 0.0 8.13671 0.001992 0.0 -0.000431 +Ta 2.87637 0.0 8.13671 0.001992 0.0 -0.000431 +Ta 1.91123 0.0 5.41479 0.001951 0.0 -0.000915 +Ta 4.78644 0.0 5.41479 0.001951 0.0 -0.000915 +Ta 3.82169 2.34759 6.77121 -0.000474 0.0 -0.000276 +Ta 1.9168 2.34759 9.48769 0.0 0.0 0.0 +Ta 4.79201 2.34759 9.48769 0.0 0.0 0.0 +Ta 0.95723 0.0 10.8387 -0.001992 0.0 0.000431 +Ta 0.01192 2.34759 12.20421 0.000474 0.0 0.000276 +Ta 2.88712 2.34759 12.20421 0.000474 0.0 0.000276 +Ta 3.83244 0.0 10.8387 -0.001992 0.0 0.000431 +Ta 0.95113 2.34759 14.90319 -0.002375 0.0 0.000846 +Ta 5.71961 0.0 16.2554 -0.001254 0.0 0.000998 +Ta 2.8444 0.0 16.2554 -0.001254 0.0 0.000998 +Ta 1.96277 2.34759 17.64802 0.001515 0.0 0.001063 +Ta 4.83798 2.34759 17.64802 0.001515 0.0 0.001063 +Ta 1.92237 0.0 13.56055 -0.001951 0.0 0.000915 +Ta 4.79758 0.0 13.56055 -0.001951 0.0 0.000915 +Ta 3.82634 2.34759 14.90319 -0.002375 0.0 0.000846 +Ta 0.77843 0.0 18.79131 -0.004062 0.0 0.001188 +Ta 3.65364 0.0 18.79131 -0.004062 0.0 0.001188 +30 +Lattice = "5.75041007996 0.0 0.0 0.0 4.69518995285 0.0 0.0 0.0 39.8400001526" Properties=species:S:1:pos:R:3:forces:R:3 energy=-344.91356 stress="-9331.87 0.0 -3483.6 0.0 -3070.65 0.0 -3483.6 0.0 10023.91" +Ta 0.9892 0.0 2.7203 0.020761 0.0 0.069829 +Ta 0.00727 2.34759 4.07239 0.031416 0.0 0.042888 +Ta 2.88247 2.34759 4.07239 0.031416 0.0 0.042888 +Ta 0.17997 0.0 0.18449 0.008231 0.0 -0.040672 +Ta 3.05517 0.0 0.18449 0.008231 0.0 -0.040672 +Ta 1.87083 2.34759 1.32776 -0.006968 0.0 -0.013357 +Ta 4.74604 2.34759 1.32776 -0.006968 0.0 -0.013357 +Ta 3.86441 0.0 2.7203 0.020761 0.0 0.069829 +Ta 0.94648 2.34759 6.77133 -0.012614 0.0 0.0322 +Ta 0.00117 0.0 8.1367 0.6286 0.0 -0.362527 +Ta 2.87637 0.0 8.1367 0.6286 0.0 -0.362527 +Ta 1.91123 0.0 5.41489 -0.117602 0.0 -0.047411 +Ta 4.78644 0.0 5.41489 -0.117602 0.0 -0.047411 +Ta 3.82169 2.34759 6.77133 -0.012614 0.0 0.0322 +Ta 1.9168 2.34759 9.48769 -0.731669 0.0 -1.341165 +Ta 4.79201 2.34759 9.48769 -0.731669 0.0 -1.341165 +Ta 2.39483 0.0 10.83871 0.796655 0.0 1.335154 +Ta 1.44952 2.34759 12.20409 -0.719661 0.0 0.218469 +Ta 4.32472 2.34759 12.20409 -0.719661 0.0 0.218469 +Ta 5.27004 0.0 10.83871 0.796655 0.0 1.335154 +Ta 2.38873 2.34759 14.90296 0.115505 0.0 0.057838 +Ta 1.4068 0.0 16.25507 -0.048364 0.0 -0.136512 +Ta 4.282 0.0 16.25507 -0.048364 0.0 -0.136512 +Ta 3.40038 2.34759 17.64762 0.008342 0.0 0.049918 +Ta 0.52518 2.34759 17.64762 0.008342 0.0 0.049918 +Ta 3.35997 0.0 13.56045 0.043395 0.0 0.085984 +Ta 0.48477 0.0 13.56045 0.043395 0.0 0.085984 +Ta 5.26394 2.34759 14.90296 0.115505 0.0 0.057838 +Ta 2.21604 0.0 18.79091 -0.016029 0.0 0.049364 +Ta 5.09124 0.0 18.79091 -0.016029 0.0 0.049364 +30 +Lattice = "5.75041007996 0.0 0.0 0.0 4.69518995285 0.0 0.0 0.0 39.8400001526" Properties=species:S:1:pos:R:3:forces:R:3 energy=-345.836703 stress="-13121.27 0.0 -5634.91 0.0 -8850.33 0.0 -5634.91 0.0 -251.82" +Ta 0.9892 0.0 2.69946 0.050014 0.0 0.000282 +Ta 0.00727 2.34759 4.05025 0.000899 0.0 -0.000628 +Ta 2.88247 2.34759 4.05025 0.000899 0.0 -0.000628 +Ta 0.17997 0.0 0.16024 0.025286 0.0 -0.000329 +Ta 3.05517 0.0 0.16024 0.025286 0.0 -0.000329 +Ta 1.87083 2.34759 1.30033 -0.022784 0.0 0.0001 +Ta 4.74604 2.34759 1.30033 -0.022784 0.0 0.0001 +Ta 3.86441 0.0 2.69946 0.050014 0.0 0.000282 +Ta 0.94648 2.34759 6.74132 0.018982 0.0 0.000803 +Ta 0.00117 0.0 8.1136 0.294678 0.0 -7e-05 +Ta 2.87637 0.0 8.1136 0.294678 0.0 -7e-05 +Ta 1.91123 0.0 5.39201 -0.117735 0.0 -0.000184 +Ta 4.78644 0.0 5.39201 -0.117735 0.0 -0.000184 +Ta 3.82169 2.34759 6.74132 0.018982 0.0 0.000803 +Ta 1.9168 2.34759 9.44202 0.717113 0.0 3.7e-05 +Ta 4.79201 2.34759 9.44202 0.717113 0.0 3.7e-05 +Ta 1.53227 0.0 10.88381 -0.754498 0.0 3.7e-05 +Ta 0.58696 2.34759 12.229 -0.304417 0.0 -0.000673 +Ta 3.46216 2.34759 12.229 -0.304417 0.0 -0.000673 +Ta 4.40748 0.0 10.88381 -0.754498 0.0 3.7e-05 +Ta 1.52617 2.34759 14.92821 0.111991 0.0 0.000677 +Ta 0.54424 0.0 16.27854 0.000794 0.0 -0.00097 +Ta 3.41944 0.0 16.27854 0.000794 0.0 -0.00097 +Ta 2.53781 2.34759 17.67931 -0.020042 0.0 -0.001378 +Ta 5.41302 2.34759 17.67931 -0.020042 0.0 -0.001378 +Ta 2.49741 0.0 13.59913 0.010142 0.0 0.001166 +Ta 5.37262 0.0 13.59913 0.010142 0.0 0.001166 +Ta 4.40138 2.34759 14.92821 0.111991 0.0 0.000677 +Ta 1.35347 0.0 18.81813 -0.010421 0.0 0.001129 +Ta 4.22868 0.0 18.81813 -0.010421 0.0 0.001129 +30 +Lattice = "5.75041007996 0.0 0.0 0.0 4.69518995285 0.0 0.0 0.0 39.8400001526" Properties=species:S:1:pos:R:3:forces:R:3 energy=-344.984307 stress="-10564.03 0.0 -4829.4 0.0 -2612.55 0.0 -4829.4 0.0 9464.02" +Ta 0.9892 0.0 2.7203 0.037412 0.0 0.099042 +Ta 0.00727 2.34759 4.07239 0.028536 0.0 0.023468 +Ta 2.88247 2.34759 4.07239 0.028536 0.0 0.023468 +Ta 0.17997 0.0 0.18449 0.023555 0.0 -0.042618 +Ta 3.05517 0.0 0.18449 0.023555 0.0 -0.042618 +Ta 1.87083 2.34759 1.32776 -0.016108 0.0 -0.021017 +Ta 4.74604 2.34759 1.32776 -0.016108 0.0 -0.021017 +Ta 3.86441 0.0 2.7203 0.037412 0.0 0.099042 +Ta 0.94648 2.34759 6.77133 0.046477 0.0 0.002765 +Ta 0.00117 0.0 8.1367 0.514609 0.0 -0.283847 +Ta 2.87637 0.0 8.1367 0.514609 0.0 -0.283847 +Ta 1.91123 0.0 5.41489 -0.163272 0.0 -0.078622 +Ta 4.78644 0.0 5.41489 -0.163272 0.0 -0.078622 +Ta 3.82169 2.34759 6.77133 0.046477 0.0 0.002765 +Ta 1.9168 2.34759 9.48769 -0.094634 0.0 -1.114901 +Ta 4.79201 2.34759 9.48769 -0.094634 0.0 -1.114901 +Ta 2.10731 0.0 10.83871 0.096153 0.0 1.054366 +Ta 1.162 2.34759 12.20409 -0.593943 0.0 0.202897 +Ta 4.0372 2.34759 12.20409 -0.593943 0.0 0.202897 +Ta 4.98252 0.0 10.83871 0.096153 0.0 1.054366 +Ta 2.10121 2.34759 14.90296 0.169155 0.0 0.056551 +Ta 1.11928 0.0 16.25507 -0.031734 0.0 -0.113985 +Ta 3.99448 0.0 16.25507 -0.031734 0.0 -0.113985 +Ta 3.11285 2.34759 17.64762 -0.01565 0.0 0.02811 +Ta 0.23765 2.34759 17.64762 -0.01565 0.0 0.02811 +Ta 3.07245 0.0 13.56045 0.006275 0.0 0.144107 +Ta 0.19725 0.0 13.56045 0.006275 0.0 0.144107 +Ta 4.97642 2.34759 14.90296 0.169155 0.0 0.056551 +Ta 1.92851 0.0 18.79091 -0.00683 0.0 0.043685 +Ta 4.80372 0.0 18.79091 -0.00683 0.0 0.043685 +30 +Lattice = "5.75041007996 0.0 0.0 0.0 4.69518995285 0.0 0.0 0.0 39.8400001526" Properties=species:S:1:pos:R:3:forces:R:3 energy=-346.393931 stress="-9438.37 0.0 3529.1 0.0 -11318.58 0.0 3529.1 0.0 1838.01" +Ta 0.9892 0.0 2.7203 -0.028288 0.0 -0.004272 +Ta 0.00727 2.34759 4.07239 0.01665 0.0 0.029245 +Ta 2.88247 2.34759 4.07239 0.01665 0.0 0.029245 +Ta 0.17997 0.0 0.18449 0.006746 0.0 -0.001633 +Ta 3.05517 0.0 0.18449 0.006746 0.0 -0.001633 +Ta 1.87083 2.34759 1.32776 -0.000473 0.0 -3e-05 +Ta 4.74604 2.34759 1.32776 -0.000473 0.0 -3e-05 +Ta 3.86441 0.0 2.7203 -0.028288 0.0 -0.004272 +Ta 0.94648 2.34759 6.77133 -0.081349 0.0 0.034571 +Ta 0.00117 0.0 8.1367 -0.101274 0.0 -0.252924 +Ta 2.87637 0.0 8.1367 -0.101274 0.0 -0.252924 +Ta 1.91123 0.0 5.41489 0.063888 0.0 0.002877 +Ta 4.78644 0.0 5.41489 0.063888 0.0 0.002877 +Ta 3.82169 2.34759 6.77133 -0.081349 0.0 0.034571 +Ta 1.9168 2.34759 9.48769 -0.523826 0.0 -0.065241 +Ta 4.79201 2.34759 9.48769 -0.523826 0.0 -0.065241 +Ta 3.54491 0.0 10.83871 0.531471 0.0 0.075625 +Ta 2.59961 2.34759 12.20409 0.108678 0.0 0.237898 +Ta 5.47481 2.34759 12.20409 0.108678 0.0 0.237898 +Ta 0.66971 0.0 10.83871 0.531471 0.0 0.075625 +Ta 3.53881 2.34759 14.90296 -0.061771 0.0 -0.016484 +Ta 2.55688 0.0 16.25507 -0.022115 0.0 -0.025346 +Ta 5.43208 0.0 16.25507 -0.022115 0.0 -0.025346 +Ta 4.55046 2.34759 17.64762 0.021554 0.0 0.004745 +Ta 1.67526 2.34759 17.64762 0.021554 0.0 0.004745 +Ta 4.51005 0.0 13.56045 0.060372 0.0 -0.032886 +Ta 1.63485 0.0 13.56045 0.060372 0.0 -0.032886 +Ta 0.66361 2.34759 14.90296 -0.061771 0.0 -0.016484 +Ta 3.36612 0.0 18.79091 0.009737 0.0 0.013855 +Ta 0.49092 0.0 18.79091 0.009737 0.0 0.013855 diff --git a/examples/PACKAGES/pod/Ta/XYZ/Liquid.xyz b/examples/PACKAGES/pod/Ta/XYZ/Liquid.xyz new file mode 100644 index 0000000000..1bf7814567 --- /dev/null +++ b/examples/PACKAGES/pod/Ta/XYZ/Liquid.xyz @@ -0,0 +1,306 @@ +100 +Lattice = "12.6055002213 0.0 0.0 0.0 12.6055002213 0.0 0.0 0.0 12.6055002213" Properties=species:S:1:pos:R:3:forces:R:3 energy=-1105.601723 stress="41522.36 -10028.6 5843.19 -10028.6 44080.57 10402.62 5843.19 10402.62 34745.600000000006" +Ta 0.43107 3.74888 0.07776 -0.335192 0.399751 2.053897 +Ta 1.60366 2.09108 2.35693 -3.868362 -1.228623 -1.515572 +Ta 4.15329 1.55338 2.45739 1.505017 -0.176525 -0.218711 +Ta 2.64801 1.89114 12.39607 0.25781 1.51672 2.137521 +Ta 7.24215 1.70209 1.79979 -0.11292 -2.198189 -0.337499 +Ta 10.95446 2.67458 1.59213 -0.965217 -1.195646 -0.253554 +Ta 9.27673 0.87789 3.43116 1.643765 0.347467 -1.593945 +Ta 2.03607 6.61594 1.61137 2.535752 0.592029 1.82052 +Ta 5.49317 3.20146 0.58262 -0.862046 0.984883 -1.598913 +Ta 3.04231 4.31908 2.00353 0.620511 -1.092947 -1.508929 +Ta 4.95339 6.14708 0.65118 -1.365205 -2.865106 2.363303 +Ta 7.52643 4.18623 2.31722 0.746021 1.167867 -1.110257 +Ta 12.27295 5.1198 2.52809 0.765074 0.812857 1.098129 +Ta 9.25719 7.32072 1.58199 0.215508 0.987987 1.690552 +Ta 10.53635 5.29937 0.6285 -0.28915 -1.601915 -1.639854 +Ta 1.90384 9.1638 3.00286 0.22302 2.303078 2.48401 +Ta 3.80372 8.76382 0.84403 -1.139535 0.518969 0.980714 +Ta 6.20544 8.3316 1.50988 2.193636 0.909931 -1.013726 +Ta 8.06784 5.83681 12.25104 -1.350407 0.626007 -0.379155 +Ta 0.31897 6.90336 0.10643 -5.3666 -0.250563 -1.141097 +Ta 11.55436 9.51362 3.34931 0.547949 -2.202531 -1.917224 +Ta 10.78092 9.16961 0.43619 2.93789 -2.957858 -2.910142 +Ta 1.24862 9.5832 0.57435 -1.713064 -0.323209 -1.423673 +Ta 5.81406 11.77176 1.54406 1.638754 0.219842 1.61986 +Ta 10.13103 11.22875 1.38321 -1.800705 4.539384 2.649159 +Ta 0.34899 0.35649 6.1042 -1.407332 -2.793672 0.622672 +Ta 2.3232 1.67801 4.77877 -0.05644 2.09227 -0.734316 +Ta 7.49734 2.52339 4.64715 -2.007496 -0.115682 0.14042 +Ta 9.77964 2.17772 5.83529 3.713057 -1.608783 0.411426 +Ta 12.08877 2.91076 4.07847 -1.520526 -1.704707 -0.587973 +Ta 1.76078 4.6877 4.47668 1.413545 -7.499735 -1.858957 +Ta 4.98999 4.11433 3.79876 0.289553 -1.316969 -0.292034 +Ta 6.76353 5.11499 5.45587 -3.138755 0.635253 -4.508867 +Ta 8.18843 6.66761 6.69958 1.823722 2.515733 1.945463 +Ta 9.26522 5.32398 3.90117 2.522311 -2.914637 0.434012 +Ta 11.70087 5.41848 5.49634 -0.91363 0.599933 0.511554 +Ta 1.65165 6.89091 4.56552 -4.64308 7.078545 2.907672 +Ta 3.88906 7.3482 3.69272 4.376913 -1.607122 -3.387251 +Ta 3.78056 9.22669 5.62637 -1.173755 -0.484115 1.473183 +Ta 7.2778 6.86119 3.31305 -1.712746 -0.762926 0.612453 +Ta 8.43315 9.5977 2.96474 -0.068906 0.588767 0.305611 +Ta 8.32391 9.49805 7.04669 1.283119 0.857479 -0.056213 +Ta 9.74646 7.68415 4.88166 1.553537 2.838279 -1.262714 +Ta 0.20242 11.9595 3.59124 0.480807 0.704331 -0.139582 +Ta 0.92234 9.81536 5.6286 -0.676685 -0.718246 -1.353345 +Ta 2.97319 11.83837 4.92159 0.124172 -2.5278 -0.825427 +Ta 4.81042 10.11638 3.25804 -0.00158 0.832634 1.353808 +Ta 5.10938 0.86525 4.93901 1.123663 0.063599 1.236154 +Ta 7.61412 11.73973 4.74754 -0.814736 -0.047356 -0.545511 +Ta 10.33697 11.30643 4.67815 -0.528432 -0.050872 2.228917 +Ta 0.27884 2.84477 6.49144 0.360201 1.903395 2.778998 +Ta 2.01197 0.93667 8.3625 1.378708 0.191326 -1.606266 +Ta 5.95649 1.56866 7.7316 -3.530422 2.114153 0.082888 +Ta 7.99571 0.37668 7.3238 3.086708 -0.94535 -1.566298 +Ta 9.75758 2.05273 9.00324 -1.78926 -0.869367 -0.765594 +Ta 7.0553 1.30554 10.35383 -0.468981 0.451781 -0.424135 +Ta 3.31072 3.02847 6.68212 2.374838 -0.044278 1.652536 +Ta 1.94786 5.25704 7.02637 -4.869392 -0.604143 3.206895 +Ta 5.58301 4.41656 7.69055 -0.012085 -1.275371 2.405145 +Ta 8.49696 4.09995 6.94038 1.731209 -2.887879 -0.17644 +Ta 11.05285 4.3866 7.9546 0.367601 1.162168 1.374681 +Ta 0.98645 7.70557 8.0109 1.110298 0.078167 -0.561606 +Ta 4.08075 5.84992 6.03442 1.908693 2.469334 -1.250813 +Ta 6.48069 8.76967 5.22823 0.114255 -0.523517 -0.733113 +Ta 3.57803 8.81681 8.5928 -0.66732 -1.171187 1.154754 +Ta 7.84056 7.36674 9.41266 2.673183 -2.160921 0.812097 +Ta 5.68236 7.53635 7.81446 0.283447 -0.99061 -1.738751 +Ta 10.93798 7.78281 7.44991 -0.183664 0.008309 0.251959 +Ta 9.9392 9.29803 9.66467 -1.179107 -2.844565 -1.936143 +Ta 3.27502 11.20914 7.71694 -1.605014 0.866048 -1.920371 +Ta 5.80571 11.2039 6.87956 0.570374 -0.917997 -1.21799 +Ta 6.62643 9.54017 9.251 -2.194588 1.730297 1.398058 +Ta 8.37506 11.43578 9.44763 -1.003205 1.254061 1.409533 +Ta 10.64763 11.60302 8.34425 0.22912 1.878017 -4.253745 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-0.58882 -1.012186 0.957519 +Ta 10.50201 6.92143 10.75604 -0.179214 -0.360035 0.514513 +Ta 0.20749 8.75375 10.46189 -1.586508 0.42554 -0.709369 +Ta 2.55072 10.18804 10.88287 1.336488 2.096133 -1.047152 +Ta 4.96405 12.00073 9.46535 1.226786 1.399389 2.14847 +Ta 2.9582 11.89523 1.24555 -0.497007 -1.084677 0.372878 +Ta 5.43899 10.20671 12.04447 0.457816 0.156284 -2.53866 +Ta 7.88861 11.67933 12.19294 -0.209863 1.614617 -0.260277 +Ta 11.22489 11.04751 10.7648 2.246152 1.517056 4.384995 +100 +Lattice = "12.6055002213 0.0 0.0 0.0 12.6055002213 0.0 0.0 0.0 12.6055002213" Properties=species:S:1:pos:R:3:forces:R:3 energy=-1099.673012 stress="64329.38 4705.339999999999 16428.34 4705.339999999999 41963.4 -4448.86 16428.34 -4448.86 54142.01" +Ta 0.38188 4.35838 0.74564 -0.727255 -2.684915 -1.502186 +Ta 1.34891 1.23814 1.97516 -0.901556 -0.105425 1.00657 +Ta 3.91629 1.3428 2.33074 3.786054 2.848263 -0.971111 +Ta 2.50882 2.14034 12.20579 -0.262289 0.109978 0.538412 +Ta 8.20217 1.50457 1.09255 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8.73043 9.80728 2.84372 -0.269419 -1.581451 0.380496 +Ta 8.3667 9.63065 6.92756 1.753511 2.485611 1.143484 +Ta 11.10448 8.19971 4.67383 -2.984282 1.041303 -1.700702 +Ta 12.33138 11.59365 3.22318 2.360024 -1.006585 -0.789645 +Ta 12.53349 9.89403 5.63928 3.735451 -1.567194 1.41596 +Ta 3.05157 11.96433 3.46769 -2.586656 -4.605553 1.003837 +Ta 5.53812 9.74587 3.73544 -0.624627 0.711032 0.321477 +Ta 5.17764 0.08755 4.56072 0.792806 1.090161 2.480897 +Ta 7.64882 11.92872 4.33422 1.371203 -2.646937 -1.592811 +Ta 10.26273 11.13472 4.99862 -1.516508 -2.562682 1.139746 +Ta 0.63147 2.19678 6.67724 -1.933442 4.953146 -0.194708 +Ta 2.39775 1.15536 7.89766 1.566886 -5.944045 0.931194 +Ta 5.33276 1.28983 7.19797 -1.126761 0.854886 -2.020746 +Ta 7.89352 0.43228 6.56287 1.13823 0.267818 2.364431 +Ta 8.88305 1.54913 9.09168 1.934009 3.681926 -0.69568 +Ta 6.00124 2.16677 9.5598 8.252345 -1.117748 2.215338 +Ta 2.66739 3.83317 7.06559 2.190193 -4.842621 2.418064 +Ta 0.44413 5.53507 7.53921 0.172202 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0.06721 10.62363 1.061812 0.946373 0.815892 +Ta 3.83384 2.56871 9.64718 -1.450486 1.088741 1.78581 +Ta 4.91898 0.74942 12.23402 2.069575 0.652415 -1.682263 +Ta 10.35682 1.29618 11.60881 -1.007516 -0.380767 -0.681798 +Ta 12.25089 0.25724 0.5674 -1.167993 -0.553636 -1.082113 +Ta 12.05792 1.27062 8.79257 -1.958821 -0.199606 3.512891 +Ta 0.94154 6.36726 9.79464 -0.470327 -1.562595 2.388469 +Ta 1.55131 2.94376 9.49017 -5.482202 3.713318 2.157258 +Ta 2.83736 5.28335 12.23429 0.21999 -0.856343 -0.328898 +Ta 3.28912 5.72925 9.20121 2.590913 0.102617 0.278337 +Ta 5.23966 4.63128 11.01018 -0.510883 -1.107745 -0.843113 +Ta 8.09196 3.41706 12.13822 -0.502547 -2.144772 0.04882 +Ta 8.1563 4.57839 10.05093 0.383882 0.414866 -3.808578 +Ta 10.79442 4.02679 10.93553 1.752466 -1.881501 1.268269 +Ta 2.71931 8.02403 11.22143 2.049893 -0.963189 1.387113 +Ta 5.73731 7.44013 11.32002 -4.676222 3.883048 -2.762461 +Ta 8.16217 8.96831 11.31638 0.374044 -1.476354 1.757164 +Ta 10.92094 6.50569 10.08481 -2.942535 0.663572 0.583517 +Ta 0.13295 8.72748 10.50938 -1.244418 2.69593 0.1167 +Ta 2.76073 10.72733 11.03757 0.159817 -0.598944 -1.675276 +Ta 4.565 12.20225 9.16074 -0.475524 -0.325595 2.074182 +Ta 3.333 11.65103 0.9196 -2.017399 0.539865 -1.533111 +Ta 5.52052 10.58245 11.86999 -0.929433 -0.112136 -1.59182 +Ta 7.97547 11.45742 0.05805 -0.0746 0.038856 -1.899211 +Ta 11.12836 11.17255 11.09073 -0.284488 0.783851 1.570373 +100 +Lattice = "12.6055002213 0.0 0.0 0.0 12.6055002213 0.0 0.0 0.0 12.6055002213" Properties=species:S:1:pos:R:3:forces:R:3 energy=-1121.31506 stress="6315.33 3551.01 1290.84 3551.01 7373.36 -1793.4699999999998 1290.84 -1793.4699999999998 -4190.5599999999995" +Ta 0.64937 3.12625 0.43144 -0.384771 0.95129 0.165479 +Ta 1.36715 0.72175 2.1191 -0.396084 1.361974 -0.172418 +Ta 4.5846 1.15642 2.6142 -0.373595 0.78336 -1.848167 +Ta 3.4656 2.34361 0.38597 -2.224767 -1.381119 -1.370954 +Ta 7.88853 1.1719 1.55114 -0.598212 -0.078923 1.145428 +Ta 10.07282 2.82479 1.63047 1.639511 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1.279331 1.42035 2.206812 +Ta 10.71239 11.30092 1.18755 -0.759539 -2.842687 -0.44627 +Ta 0.12647 0.57355 5.6744 1.485357 -0.339908 0.72473 +Ta 2.40387 1.53268 4.75274 0.971096 -0.38073 0.869134 +Ta 6.4354 2.09058 4.44464 1.8115 0.323829 -0.954613 +Ta 10.29448 1.87908 6.14933 -0.973544 0.673823 0.524211 +Ta 12.13409 2.64826 3.96133 1.041975 -0.146906 -0.101053 +Ta 1.89139 4.2711 5.14514 -1.126257 1.765095 -1.172303 +Ta 4.29285 3.26764 5.49838 1.359585 0.954058 -0.894642 +Ta 6.22054 4.99782 4.76901 -0.57103 0.193676 0.659475 +Ta 8.73015 5.75307 5.41647 0.977001 1.137808 0.707847 +Ta 9.46292 3.6411 4.00924 0.208171 -0.619736 1.487252 +Ta 11.80799 5.28602 5.31887 -1.14111 -1.708079 1.708749 +Ta 1.42351 7.04153 5.51044 0.442962 1.999421 -1.932131 +Ta 3.99608 6.77694 4.00068 0.020115 -0.082585 -0.562723 +Ta 3.50684 9.23442 5.21977 0.277684 0.652346 0.809939 +Ta 6.82787 7.1376 3.15953 0.461297 -1.023286 -0.200358 +Ta 9.15017 9.16521 3.22539 0.975528 -0.406877 -2.361923 +Ta 9.03229 9.22399 5.76536 -0.96211 0.660671 1.97306 +Ta 11.42908 7.93297 4.71336 -1.075725 2.179405 -1.299081 +Ta 0.05087 11.06881 3.63544 0.18806 -0.894103 -2.497085 +Ta 0.61823 10.14934 5.99785 0.964288 -1.323025 0.615744 +Ta 2.87244 11.55729 3.56061 -0.950735 -1.383789 -0.752604 +Ta 6.21349 9.52465 3.78915 -1.000365 1.509307 0.554842 +Ta 5.15602 12.31549 4.62675 0.565237 -0.704465 1.119632 +Ta 8.08827 11.62648 3.35101 -0.339071 0.461047 0.284645 +Ta 10.68985 11.76775 5.34052 -2.452377 -2.887406 0.054989 +Ta 0.14268 2.96019 7.28952 -1.17741 0.302926 -1.013001 +Ta 1.79625 1.2317 8.73242 1.145361 -3.820996 -0.45811 +Ta 5.07039 1.39926 7.46358 -0.781338 0.724617 -1.541559 +Ta 7.57216 0.49788 6.56353 0.962384 0.05587 -0.04513 +Ta 9.27827 2.61852 8.92732 0.176007 -0.879678 -0.926458 +Ta 6.54771 2.47044 9.38651 2.190569 0.166399 1.077573 +Ta 2.76284 3.40149 7.77645 3.137421 -0.183358 -0.704336 +Ta 1.46964 5.59388 7.81661 -3.887251 -0.228325 -0.342894 +Ta 5.28247 4.64737 8.03918 0.338155 -1.923057 0.116762 +Ta 7.44449 3.18893 6.73322 1.141594 1.207491 -0.292546 +Ta 11.12935 5.21434 8.64857 -1.612825 -2.999306 -1.714386 +Ta 1.54461 8.15093 8.61321 0.347763 2.086893 -0.257285 +Ta 3.74639 6.51293 6.87702 0.959722 -0.501443 -1.452222 +Ta 6.16432 8.04946 6.35417 0.023322 -2.311879 -2.364886 +Ta 4.17774 8.81779 8.33178 -1.45671 1.390508 1.192928 +Ta 8.79674 7.34098 7.76356 0.744674 0.017978 0.615727 +Ta 6.3995 6.81915 8.95492 -2.56268 0.245528 -0.18037 +Ta 11.65865 7.47829 7.15549 -0.141642 0.63044 2.199066 +Ta 10.36878 9.3845 9.0403 -0.66872 0.230975 -0.20666 +Ta 3.44367 12.01539 7.00233 -1.966426 -2.282219 -0.555493 +Ta 6.18022 10.72879 6.38769 -0.159595 0.636574 0.422497 +Ta 6.60979 9.53788 8.62428 1.893523 1.309962 1.811685 +Ta 7.82809 11.91798 9.44419 -1.75495 0.501787 1.526707 +Ta 9.83162 12.15132 7.88212 0.675577 0.0338 -0.256919 +Ta 12.33473 11.37557 8.23941 1.476837 0.086277 1.652827 +Ta 1.26867 0.5664 11.43089 0.552369 0.109749 -1.014297 +Ta 4.11323 2.51574 10.31659 -0.216484 0.602173 -0.337403 +Ta 6.1981 1.3171 12.07577 -0.840924 -1.268238 -1.122831 +Ta 8.93316 0.96241 11.49866 0.200771 0.591493 -0.447815 +Ta 11.51202 0.95161 12.55636 0.023759 0.436473 0.983974 +Ta 11.74771 1.34839 9.48403 -0.672837 0.114932 -0.4313 +Ta 0.37088 6.14613 10.23785 1.469982 0.175809 2.274858 +Ta 1.53343 3.45239 10.16056 -2.401632 0.95373 1.427778 +Ta 2.97984 4.88656 12.27482 -1.163376 -0.933805 -0.832442 +Ta 3.23113 5.88226 9.89191 1.644345 0.515055 -2.001086 +Ta 5.83202 4.76093 11.09154 -1.265112 -0.209543 -0.313576 +Ta 8.18149 3.7694 12.32031 -0.908072 -2.871898 -1.645014 +Ta 8.28389 5.18304 9.86813 1.06209 -0.729605 -0.590042 +Ta 10.60165 3.38032 11.14631 2.294652 0.864636 -1.210164 +Ta 2.16602 8.04842 12.06324 1.617599 0.103075 -0.814791 +Ta 5.19763 7.5131 11.34985 -0.346409 1.752742 -0.487937 +Ta 7.92875 8.24785 10.61624 0.728867 1.077493 1.692555 +Ta 10.42049 6.95313 10.57826 -0.286476 0.160363 0.370268 +Ta 12.38682 9.14199 11.43376 -0.594871 0.767297 -0.960584 +Ta 2.2479 10.73902 9.80504 -0.028268 0.335889 0.421595 +Ta 4.91854 12.45236 9.55661 -0.382663 -1.868957 -0.192626 +Ta 3.60604 12.29562 12.33442 -0.6243 -0.490257 0.799831 +Ta 5.45536 10.4337 11.30531 0.355343 -0.806764 -0.469902 +Ta 8.0691 11.11452 12.46882 0.894574 0.749785 -0.70888 +Ta 10.68626 11.50854 10.77779 0.440455 -1.251201 0.450872 diff --git a/examples/PACKAGES/pod/Ta/XYZ/Surface.xyz b/examples/PACKAGES/pod/Ta/XYZ/Surface.xyz new file mode 100644 index 0000000000..d22d2ee956 --- /dev/null +++ b/examples/PACKAGES/pod/Ta/XYZ/Surface.xyz @@ -0,0 +1,250 @@ +24 +Lattice = "4.69519013405 0.0 0.0 0.0 3.32 0.0 0.0 0.0 53.12" Properties=species:S:1:pos:R:3:forces:R:3 energy=-279.911828 stress="-9651.84 0.0 0.0 0.0 -7622.87 0.0 0.0 0.0 -272.58" +Ta 2.34759 1.66 0.09121 0.0 0.0 0.001057 +Ta 0.0 0.0 0.09121 0.0 0.0 0.001057 +Ta 0.0 1.66 2.3361 0.0 0.0 0.000335 +Ta 2.34759 0.0 2.3361 0.0 0.0 0.000335 +Ta 2.34759 1.66 4.68536 0.0 0.0 0.000274 +Ta 0.0 0.0 4.68536 0.0 0.0 0.000274 +Ta 0.0 1.66 7.03392 0.0 0.0 0.000349 +Ta 2.34759 0.0 7.03392 0.0 0.0 0.000349 +Ta 2.34759 1.66 9.38594 0.0 0.0 -0.000481 +Ta 0.0 0.0 9.38594 0.0 0.0 -0.000481 +Ta 0.0 1.66 11.73648 0.0 0.0 -0.000487 +Ta 2.34759 0.0 11.73648 0.0 0.0 -0.000487 +Ta 2.34759 1.66 14.08712 0.0 0.0 0.000487 +Ta 0.0 0.0 14.08712 0.0 0.0 0.000487 +Ta 0.0 1.66 16.43764 0.0 0.0 0.000481 +Ta 2.34759 0.0 16.43764 0.0 0.0 0.000481 +Ta 2.34759 1.66 18.78966 0.0 0.0 -0.000349 +Ta 0.0 0.0 18.78966 0.0 0.0 -0.000349 +Ta 0.0 1.66 21.13823 0.0 0.0 -0.000274 +Ta 2.34759 0.0 21.13823 0.0 0.0 -0.000274 +Ta 2.34759 1.66 23.48739 0.0 0.0 -0.000335 +Ta 0.0 0.0 23.48739 0.0 0.0 -0.000335 +Ta 0.0 1.66 25.73229 0.0 0.0 -0.001057 +Ta 2.34759 0.0 25.73229 0.0 0.0 -0.001057 +48 +Lattice = "6.64001325846 0.0 0.0 0.0 6.64001325846 0.0 0.0 0.0 39.84" Properties=species:S:1:pos:R:3:forces:R:3 energy=-555.359452 stress="-6438.73 0.0 0.0 0.0 -6438.73 0.0 0.0 0.0 -286.5" +Ta 1.66001 1.66 1.62137 0.0 0.0 -3e-05 +Ta 0.0 0.0 0.17247 0.0 0.0 0.00038 +Ta 1.66001 1.66 4.98756 0.0 0.0 0.000833 +Ta 0.0 0.0 3.27999 0.0 0.0 0.000359 +Ta 1.66001 1.66 8.28844 0.0 0.0 0.00041 +Ta 0.0 0.0 6.62582 0.0 0.0 6.6e-05 +Ta 1.66001 1.66 11.63419 0.0 0.0 -6.6e-05 +Ta 0.0 0.0 9.97156 0.0 0.0 -0.00041 +Ta 1.66001 1.66 14.98001 0.0 0.0 -0.000359 +Ta 0.0 0.0 13.27244 0.0 0.0 -0.000833 +Ta 1.66001 1.66 18.08753 0.0 0.0 -0.00038 +Ta 0.0 0.0 16.63864 0.0 0.0 3e-05 +Ta 1.66001 4.98001 1.62137 0.0 0.0 -3e-05 +Ta 0.0 3.32001 0.17247 0.0 0.0 0.00038 +Ta 1.66001 4.98001 4.98756 0.0 0.0 0.000833 +Ta 0.0 3.32001 3.27999 0.0 0.0 0.000359 +Ta 1.66001 4.98001 8.28844 0.0 0.0 0.00041 +Ta 0.0 3.32001 6.62582 0.0 0.0 6.6e-05 +Ta 1.66001 4.98001 11.63419 0.0 0.0 -6.6e-05 +Ta 0.0 3.32001 9.97156 0.0 0.0 -0.00041 +Ta 1.66001 4.98001 14.98001 0.0 0.0 -0.000359 +Ta 0.0 3.32001 13.27244 0.0 0.0 -0.000833 +Ta 1.66001 4.98001 18.08753 0.0 0.0 -0.00038 +Ta 0.0 3.32001 16.63864 0.0 0.0 3e-05 +Ta 4.98002 1.66 1.62137 0.0 0.0 -3e-05 +Ta 3.32001 0.0 0.17247 0.0 0.0 0.00038 +Ta 4.98002 1.66 4.98756 0.0 0.0 0.000833 +Ta 3.32001 0.0 3.27999 0.0 0.0 0.000359 +Ta 4.98002 1.66 8.28844 0.0 0.0 0.00041 +Ta 3.32001 0.0 6.62582 0.0 0.0 6.6e-05 +Ta 4.98002 1.66 11.63419 0.0 0.0 -6.6e-05 +Ta 3.32001 0.0 9.97156 0.0 0.0 -0.00041 +Ta 4.98002 1.66 14.98001 0.0 0.0 -0.000359 +Ta 3.32001 0.0 13.27244 0.0 0.0 -0.000833 +Ta 4.98002 1.66 18.08753 0.0 0.0 -0.00038 +Ta 3.32001 0.0 16.63864 0.0 0.0 3e-05 +Ta 4.98002 4.98001 1.62137 0.0 0.0 -3e-05 +Ta 3.32001 3.32001 0.17247 0.0 0.0 0.00038 +Ta 4.98002 4.98001 4.98756 0.0 0.0 0.000833 +Ta 3.32001 3.32001 3.27999 0.0 0.0 0.000359 +Ta 4.98002 4.98001 8.28844 0.0 0.0 0.00041 +Ta 3.32001 3.32001 6.62582 0.0 0.0 6.6e-05 +Ta 4.98002 4.98001 11.63419 0.0 0.0 -6.6e-05 +Ta 3.32001 3.32001 9.97156 0.0 0.0 -0.00041 +Ta 4.98002 4.98001 14.98001 0.0 0.0 -0.000359 +Ta 3.32001 3.32001 13.27244 0.0 0.0 -0.000833 +Ta 4.98002 4.98001 18.08753 0.0 0.0 -0.00038 +Ta 3.32001 3.32001 16.63864 0.0 0.0 3e-05 +40 +Lattice = "4.69518993616 0.0 0.0 0.0 8.13231015027 0.0 0.0 0.0 36.52" Properties=species:S:1:pos:R:3:forces:R:3 energy=-459.216162 stress="-27041.87 0.0 0.0 0.0 -26744.41 19.599999999999998 0.0 19.599999999999998 -29530.539999999997" +Ta 2.34759 6.77692 0.9584 0.0 0.00104 0.266836 +Ta 0.0 2.71077 0.9584 0.0 0.00104 0.266836 +Ta 2.34759 4.06615 0.0 0.0 -0.000781 2.01398 +Ta 2.34759 4.06615 2.8752 0.0 0.002127 -0.707743 +Ta 0.0 5.42154 1.9168 0.0 -0.0035 -1.222398 +Ta 2.34759 6.77692 3.83361 0.0 0.000551 -0.353108 +Ta 0.0 0.0 0.0 0.0 -0.000781 2.01398 +Ta 0.0 0.0 2.8752 0.0 0.002127 -0.707743 +Ta 2.34759 1.35538 1.9168 0.0 -0.0035 -1.222398 +Ta 0.0 2.71077 3.83361 0.0 0.000551 -0.353108 +Ta 0.0 5.42154 4.79201 0.0 0.001693 -0.22097 +Ta 2.34759 6.77692 6.70881 0.0 0.000422 -0.070866 +Ta 2.34759 1.35538 4.79201 0.0 0.001693 -0.22097 +Ta 0.0 2.71077 6.70881 0.0 0.000422 -0.070866 +Ta 2.34759 4.06615 5.75041 0.0 -0.000841 0.251247 +Ta 2.34759 4.06615 8.62561 0.0 -0.000554 0.023395 +Ta 0.0 5.42154 7.66721 0.0 -0.000869 -0.03418 +Ta 0.0 0.0 5.75041 0.0 -0.000841 0.251247 +Ta 0.0 0.0 8.62561 0.0 -0.000554 0.023395 +Ta 2.34759 1.35538 7.66721 0.0 -0.000869 -0.03418 +Ta 0.0 5.42154 10.5424 0.0 0.000869 0.03418 +Ta 2.34759 6.77692 9.58401 0.0 0.000554 -0.023395 +Ta 2.34759 6.77692 12.4592 0.0 0.000841 -0.251247 +Ta 2.34759 1.35538 10.5424 0.0 0.000869 0.03418 +Ta 0.0 2.71077 9.58401 0.0 0.000554 -0.023395 +Ta 0.0 2.71077 12.4592 0.0 0.000841 -0.251247 +Ta 2.34759 4.06615 11.5008 0.0 -0.000422 0.070866 +Ta 0.0 5.42154 13.4176 0.0 -0.001693 0.22097 +Ta 0.0 0.0 11.5008 0.0 -0.000422 0.070866 +Ta 2.34759 1.35538 13.4176 0.0 -0.001693 0.22097 +Ta 2.34759 4.06615 14.376 0.0 -0.000551 0.353108 +Ta 0.0 5.42154 16.2928 0.0 0.0035 1.222398 +Ta 2.34759 6.77692 15.3344 0.0 -0.002127 0.707743 +Ta 2.34759 6.77692 18.2096 0.0 0.000781 -2.01398 +Ta 0.0 0.0 14.376 0.0 -0.000551 0.353108 +Ta 2.34759 1.35538 16.2928 0.0 0.0035 1.222398 +Ta 0.0 2.71077 15.3344 0.0 -0.002127 0.707743 +Ta 0.0 2.71077 18.2096 0.0 0.000781 -2.01398 +Ta 2.34759 4.06615 17.2512 0.0 -0.00104 -0.266836 +Ta 0.0 0.0 17.2512 0.0 -0.00104 -0.266836 +40 +Lattice = "4.69518993616 0.0 0.0 0.0 8.13231015027 0.0 0.0 0.0 36.52" Properties=species:S:1:pos:R:3:forces:R:3 energy=-461.144076 stress="-6214.78 0.0 0.0 0.0 -6110.78 11.43 0.0 11.43 -124.44" +Ta 2.34759 6.77677 1.02996 0.0 4.9e-05 0.000956 +Ta 0.0 2.71062 1.02996 0.0 4.9e-05 0.000956 +Ta 2.34759 4.06617 0.30181 0.0 -0.000436 0.000304 +Ta 2.34759 4.0661 2.9333 0.0 0.000405 -0.000621 +Ta 0.0 5.42161 1.81457 0.0 -0.000256 -0.000454 +Ta 2.34759 6.77673 3.82136 0.0 0.000483 0.001188 +Ta 0.0 2e-05 0.30181 0.0 -0.000436 0.000304 +Ta 0.0 8.13226 2.9333 0.0 0.000405 -0.000621 +Ta 2.34759 1.35545 1.81457 0.0 -0.000256 -0.000454 +Ta 0.0 2.71058 3.82136 0.0 0.000483 0.001188 +Ta 0.0 5.42171 4.75865 0.0 -0.000286 3.9e-05 +Ta 2.34759 6.77697 6.68474 0.0 0.000174 0.001115 +Ta 2.34759 1.35555 4.75865 0.0 -0.000286 3.9e-05 +Ta 0.0 2.71082 6.68474 0.0 0.000174 0.001115 +Ta 2.34759 4.06631 5.76725 0.0 0.000154 -0.0006 +Ta 2.34759 4.0661 8.64133 0.0 0.000311 0.000365 +Ta 0.0 5.42175 7.66351 0.0 -0.000264 -0.00059 +Ta 0.0 0.00016 5.76725 0.0 0.000154 -0.0006 +Ta 0.0 -5e-05 8.64133 0.0 0.000311 0.000365 +Ta 2.34759 1.35559 7.66351 0.0 -0.000264 -0.00059 +Ta 0.0 5.42176 10.5454 0.0 -0.000164 0.000261 +Ta 2.34759 6.77681 9.56856 0.0 0.000347 -0.001383 +Ta 2.34759 6.77657 12.44226 0.0 0.000206 0.000791 +Ta 2.34759 1.3556 10.5454 0.0 -0.000164 0.000261 +Ta 0.0 2.71066 9.56856 0.0 0.000347 -0.001383 +Ta 0.0 2.71042 12.44226 0.0 0.000206 0.000791 +Ta 2.34759 4.06598 11.52478 0.0 0.000279 -0.00135 +Ta 0.0 5.42175 13.45118 0.0 -0.000329 -0.001033 +Ta 0.0 8.13214 11.52478 0.0 0.000279 -0.00135 +Ta 2.34759 1.35559 13.45118 0.0 -0.000329 -0.001033 +Ta 2.34759 4.06624 14.38799 0.0 0.000351 -0.000576 +Ta 0.0 5.4218 16.39523 0.0 -0.000453 0.0004 +Ta 2.34759 6.77687 15.2766 0.0 0.000189 0.001532 +Ta 2.34759 6.77657 17.90814 0.0 -0.000603 -0.00011 +Ta 0.0 9e-05 14.38799 0.0 0.000351 -0.000576 +Ta 2.34759 1.35564 16.39523 0.0 -0.000453 0.0004 +Ta 0.0 2.71072 15.2766 0.0 0.000189 0.001532 +Ta 0.0 2.71042 17.90814 0.0 -0.000603 -0.00011 +Ta 2.34759 4.06617 17.17945 0.0 -0.000157 -0.000235 +Ta 0.0 2e-05 17.17945 0.0 -0.000157 -0.000235 +24 +Lattice = "4.69519013405 0.0 0.0 0.0 3.32 0.0 0.0 0.0 53.12" Properties=species:S:1:pos:R:3:forces:R:3 energy=-279.635146 stress="-21250.23 0.0 0.0 0.0 -20345.210000000003 0.0 0.0 0.0 -14676.96" +Ta 2.34759 1.66 0.0 0.0 0.0 0.48507 +Ta 0.0 0.0 0.0 0.0 0.0 0.48507 +Ta 0.0 1.66 2.34759 0.0 0.0 -0.412878 +Ta 2.34759 0.0 2.34759 0.0 0.0 -0.412878 +Ta 2.34759 1.66 4.69519 0.0 0.0 -0.096961 +Ta 0.0 0.0 4.69519 0.0 0.0 -0.096961 +Ta 0.0 1.66 7.04278 0.0 0.0 0.008179 +Ta 2.34759 0.0 7.04278 0.0 0.0 0.008179 +Ta 2.34759 1.66 9.39038 0.0 0.0 -0.003881 +Ta 0.0 0.0 9.39038 0.0 0.0 -0.003881 +Ta 0.0 1.66 11.738 0.0 0.0 0.002591 +Ta 2.34759 0.0 11.738 0.0 0.0 0.002591 +Ta 2.34759 1.66 14.0856 0.0 0.0 -0.002591 +Ta 0.0 0.0 14.0856 0.0 0.0 -0.002591 +Ta 0.0 1.66 16.4332 0.0 0.0 0.003881 +Ta 2.34759 0.0 16.4332 0.0 0.0 0.003881 +Ta 2.34759 1.66 18.7808 0.0 0.0 -0.008179 +Ta 0.0 0.0 18.7808 0.0 0.0 -0.008179 +Ta 0.0 1.66 21.1284 0.0 0.0 0.096961 +Ta 2.34759 0.0 21.1284 0.0 0.0 0.096961 +Ta 2.34759 1.66 23.4759 0.0 0.0 0.412878 +Ta 0.0 0.0 23.4759 0.0 0.0 0.412878 +Ta 0.0 1.66 25.8235 0.0 0.0 -0.48507 +Ta 2.34759 0.0 25.8235 0.0 0.0 -0.48507 +30 +Lattice = "5.75040976524 0.0 0.0 0.0 4.69518993616 0.0 0.0 0.0 39.84" Properties=species:S:1:pos:R:3:forces:R:3 energy=-346.592525 stress="-9399.49 0.0 -208.25 0.0 -11819.32 0.0 -208.25 0.0 132.24" +Ta 0.9892 0.0 2.7203 0.001551 0.0 -0.000488 +Ta 0.00727 2.34759 4.07239 0.001169 0.0 -0.000766 +Ta 2.88247 2.34759 4.07239 0.001169 0.0 -0.000766 +Ta 0.17997 0.0 0.18449 0.002466 0.0 -0.001108 +Ta 3.05517 0.0 0.18449 0.002466 0.0 -0.001108 +Ta 1.87083 2.34759 1.32776 -0.000874 0.0 -0.001517 +Ta 4.74604 2.34759 1.32776 -0.000874 0.0 -0.001517 +Ta 3.86441 0.0 2.7203 0.001551 0.0 -0.000488 +Ta 0.94648 2.34759 6.77133 0.00042 0.0 -0.000294 +Ta 0.00117 0.0 8.1367 0.000452 0.0 9.6e-05 +Ta 2.87637 0.0 8.1367 0.000452 0.0 9.6e-05 +Ta 1.91123 0.0 5.41489 0.001544 0.0 -5.7e-05 +Ta 4.78644 0.0 5.41489 0.001544 0.0 -5.7e-05 +Ta 3.82169 2.34759 6.77133 0.00042 0.0 -0.000294 +Ta 0.95723 0.0 10.83871 -0.000452 0.0 -9.6e-05 +Ta 0.01192 2.34759 12.20409 -0.00042 0.0 0.000294 +Ta 2.88712 2.34759 12.20409 -0.00042 0.0 0.000294 +Ta 1.9168 2.34759 9.48769 0.0 0.0 0.0 +Ta 4.79201 2.34759 9.48769 0.0 0.0 0.0 +Ta 3.83244 0.0 10.83871 -0.000452 0.0 -9.6e-05 +Ta 0.95113 2.34759 14.90296 -0.001169 0.0 0.000766 +Ta 5.71961 0.0 16.25507 -0.001551 0.0 0.000488 +Ta 2.8444 0.0 16.25507 -0.001551 0.0 0.000488 +Ta 1.96277 2.34759 17.64762 0.000874 0.0 0.001517 +Ta 4.83798 2.34759 17.64762 0.000874 0.0 0.001517 +Ta 1.92237 0.0 13.56045 -0.001544 0.0 5.7e-05 +Ta 4.79758 0.0 13.56045 -0.001544 0.0 5.7e-05 +Ta 3.82634 2.34759 14.90296 -0.001169 0.0 0.000766 +Ta 0.77843 0.0 18.79091 -0.002466 0.0 0.001108 +Ta 3.65364 0.0 18.79091 -0.002466 0.0 0.001108 +30 +Lattice = "5.75040976524 0.0 0.0 0.0 4.69518993616 0.0 0.0 0.0 39.84" Properties=species:S:1:pos:R:3:forces:R:3 energy=-345.744506 stress="-26530.08 0.0 -2915.02 0.0 -25603.77 0.0 -2915.02 0.0 -21262.54" +Ta 0.9584 0.0 2.71077 0.048753 0.0 -0.789488 +Ta 0.0 2.34759 4.06615 0.000543 0.0 0.103698 +Ta 2.8752 2.34759 4.06615 0.000543 0.0 0.103698 +Ta 0.0 0.0 0.0 0.302653 0.0 1.1858 +Ta 2.8752 0.0 0.0 0.302653 0.0 1.1858 +Ta 1.9168 2.34759 1.35538 -0.326078 0.0 -0.402735 +Ta 4.79201 2.34759 1.35538 -0.326078 0.0 -0.402735 +Ta 3.83361 0.0 2.71077 0.048753 0.0 -0.789488 +Ta 0.9584 2.34759 6.77692 -0.058605 0.0 -0.050501 +Ta 0.0 0.0 8.13231 0.022525 0.0 0.111412 +Ta 2.8752 0.0 8.13231 0.022525 0.0 0.111412 +Ta 1.9168 0.0 5.42154 0.017191 0.0 -0.139574 +Ta 4.79201 0.0 5.42154 0.017191 0.0 -0.139574 +Ta 3.83361 2.34759 6.77692 -0.058605 0.0 -0.050501 +Ta 0.9584 0.0 10.8431 -0.022525 0.0 -0.111412 +Ta 0.0 2.34759 12.1985 0.058605 0.0 0.050501 +Ta 2.8752 2.34759 12.1985 0.058605 0.0 0.050501 +Ta 1.9168 2.34759 9.48769 0.0 0.0 0.0 +Ta 4.79201 2.34759 9.48769 0.0 0.0 0.0 +Ta 3.83361 0.0 10.8431 -0.022525 0.0 -0.111412 +Ta 0.9584 2.34759 14.9092 -0.000543 0.0 -0.103698 +Ta 0.0 0.0 16.2646 -0.048753 0.0 0.789488 +Ta 2.8752 0.0 16.2646 -0.048753 0.0 0.789488 +Ta 1.9168 2.34759 17.62 0.326078 0.0 0.402735 +Ta 4.79201 2.34759 17.62 0.326078 0.0 0.402735 +Ta 1.9168 0.0 13.5538 -0.017191 0.0 0.139574 +Ta 4.79201 0.0 13.5538 -0.017191 0.0 0.139574 +Ta 3.83361 2.34759 14.9092 -0.000543 0.0 -0.103698 +Ta 0.9584 0.0 18.9754 -0.302653 0.0 -1.1858 +Ta 3.83361 0.0 18.9754 -0.302653 0.0 -1.1858 diff --git a/examples/PACKAGES/pod/Ta/XYZ/Volume_A15.xyz b/examples/PACKAGES/pod/Ta/XYZ/Volume_A15.xyz new file mode 100644 index 0000000000..41e9be5a6d --- /dev/null +++ b/examples/PACKAGES/pod/Ta/XYZ/Volume_A15.xyz @@ -0,0 +1,300 @@ +8 +Lattice = "6.7 0.0 0.0 0.0 6.7 0.0 0.0 0.0 6.7" Properties=species:S:1:pos:R:3:forces:R:3 energy=-66.990732 stress="-312387.88 0.0 -0.0 0.0 -312387.88 0.0 -0.0 0.0 -312387.88" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 3.35 3.35 3.35 0.0 0.0 0.0 +Ta 1.675 3.35 0.0 0.0 0.0 0.0 +Ta 5.025 3.35 0.0 0.0 0.0 0.0 +Ta 0.0 1.675 3.35 0.0 0.0 0.0 +Ta 0.0 5.025 3.35 0.0 0.0 0.0 +Ta 3.35 0.0 1.675 0.0 0.0 0.0 +Ta 3.35 0.0 5.025 0.0 0.0 0.0 +8 +Lattice = "4.6 0.0 0.0 0.0 4.6 0.0 0.0 0.0 4.6" Properties=species:S:1:pos:R:3:forces:R:3 energy=-72.957807 stress="1835613.98 0.0 -0.0 0.0 1835613.98 0.0 -0.0 0.0 1835613.98" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 2.3 2.3 2.3 0.0 0.0 0.0 +Ta 1.15 2.3 0.0 0.0 0.0 0.0 +Ta 3.45 2.3 0.0 0.0 0.0 0.0 +Ta 0.0 1.15 2.3 0.0 0.0 0.0 +Ta 0.0 3.45 2.3 0.0 0.0 0.0 +Ta 2.3 0.0 1.15 0.0 0.0 0.0 +Ta 2.3 0.0 3.45 0.0 0.0 0.0 +8 +Lattice = "5.2 0.0 0.0 0.0 5.2 0.0 0.0 0.0 5.2" Properties=species:S:1:pos:R:3:forces:R:3 energy=-94.145745 stress="145354.31 0.0 0.0 0.0 145354.31 -0.0 0.0 -0.0 145354.31" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 2.6 2.6 2.6 0.0 0.0 0.0 +Ta 1.3 2.6 0.0 0.0 0.0 0.0 +Ta 3.9 2.6 0.0 0.0 0.0 0.0 +Ta 0.0 1.3 2.6 0.0 0.0 0.0 +Ta 0.0 3.9 2.6 0.0 0.0 0.0 +Ta 2.6 0.0 1.3 0.0 0.0 0.0 +Ta 2.6 0.0 3.9 0.0 0.0 0.0 +8 +Lattice = "5.3 0.0 0.0 0.0 5.3 0.0 0.0 0.0 5.3" Properties=species:S:1:pos:R:3:forces:R:3 energy=-94.554682 stress="18038.98 0.0 -0.0 0.0 18038.98 -0.0 -0.0 -0.0 18038.98" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 2.65 2.65 2.65 0.0 0.0 0.0 +Ta 1.325 2.65 0.0 0.0 0.0 0.0 +Ta 3.975 2.65 0.0 0.0 0.0 0.0 +Ta 0.0 1.325 2.65 0.0 0.0 0.0 +Ta 0.0 3.975 2.65 0.0 0.0 0.0 +Ta 2.65 0.0 1.325 0.0 0.0 0.0 +Ta 2.65 0.0 3.975 0.0 0.0 0.0 +8 +Lattice = "4.7 0.0 0.0 0.0 4.7 0.0 0.0 0.0 4.7" Properties=species:S:1:pos:R:3:forces:R:3 energy=-79.438363 stress="1385239.49 0.0 0.0 0.0 1385239.49 0.0 0.0 0.0 1385239.49" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 2.35 2.35 2.35 0.0 0.0 0.0 +Ta 1.175 2.35 0.0 0.0 0.0 0.0 +Ta 3.525 2.35 0.0 0.0 0.0 0.0 +Ta 0.0 1.175 2.35 0.0 0.0 0.0 +Ta 0.0 3.525 2.35 0.0 0.0 0.0 +Ta 2.35 0.0 1.175 0.0 0.0 0.0 +Ta 2.35 0.0 3.525 0.0 0.0 0.0 +8 +Lattice = "6.6 0.0 0.0 0.0 6.6 0.0 0.0 0.0 6.6" Properties=species:S:1:pos:R:3:forces:R:3 energy=-69.627817 stress="-324717.99 0.0 0.0 0.0 -324717.99 0.0 0.0 0.0 -324717.99" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 3.3 3.3 3.3 0.0 0.0 0.0 +Ta 1.65 3.3 0.0 0.0 0.0 0.0 +Ta 4.95 3.3 0.0 0.0 0.0 0.0 +Ta 0.0 1.65 3.3 0.0 0.0 0.0 +Ta 0.0 4.95 3.3 0.0 0.0 0.0 +Ta 3.3 0.0 1.65 0.0 0.0 0.0 +Ta 3.3 0.0 4.95 0.0 0.0 0.0 +8 +Lattice = "6.1 0.0 0.0 0.0 6.1 0.0 0.0 0.0 6.1" Properties=species:S:1:pos:R:3:forces:R:3 energy=-82.604907 stress="-350351.07 0.0 0.0 0.0 -350351.07 0.0 0.0 0.0 -350351.07" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 3.05 3.05 3.05 0.0 0.0 0.0 +Ta 1.525 3.05 0.0 0.0 0.0 0.0 +Ta 4.575 3.05 0.0 0.0 0.0 0.0 +Ta 0.0 1.525 3.05 0.0 0.0 0.0 +Ta 0.0 4.575 3.05 0.0 0.0 0.0 +Ta 3.05 0.0 1.525 0.0 0.0 0.0 +Ta 3.05 0.0 4.575 0.0 0.0 0.0 +8 +Lattice = "4.0 0.0 0.0 0.0 4.0 0.0 0.0 0.0 4.0" Properties=species:S:1:pos:R:3:forces:R:3 energy=14.89048 stress="8403695.620000001 0.0 0.0 0.0 8403695.620000001 0.0 0.0 0.0 8403695.620000001" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 2.0 2.0 2.0 0.0 0.0 0.0 +Ta 1.0 2.0 0.0 0.0 0.0 0.0 +Ta 3.0 2.0 0.0 0.0 0.0 0.0 +Ta 0.0 1.0 2.0 0.0 0.0 0.0 +Ta 0.0 3.0 2.0 0.0 0.0 0.0 +Ta 2.0 0.0 1.0 0.0 0.0 0.0 +Ta 2.0 0.0 3.0 0.0 0.0 0.0 +8 +Lattice = "5.4 0.0 0.0 0.0 5.4 0.0 0.0 0.0 5.4" Properties=species:S:1:pos:R:3:forces:R:3 energy=-94.367599 stress="-83756.66 -0.0 0.0 -0.0 -83756.66 -0.0 0.0 -0.0 -83756.66" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 2.7 2.7 2.7 0.0 0.0 0.0 +Ta 1.35 2.7 0.0 0.0 0.0 0.0 +Ta 4.05 2.7 0.0 0.0 0.0 0.0 +Ta 0.0 1.35 2.7 0.0 0.0 0.0 +Ta 0.0 4.05 2.7 0.0 0.0 0.0 +Ta 2.7 0.0 1.35 0.0 0.0 0.0 +Ta 2.7 0.0 4.05 0.0 0.0 0.0 +8 +Lattice = "5.8 0.0 0.0 0.0 5.8 0.0 0.0 0.0 5.8" Properties=species:S:1:pos:R:3:forces:R:3 energy=-89.248227 stress="-305522.26 0.0 0.0 0.0 -305522.26 -0.0 0.0 -0.0 -305522.26" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 2.9 2.9 2.9 0.0 0.0 0.0 +Ta 1.45 2.9 0.0 0.0 0.0 0.0 +Ta 4.35 2.9 0.0 0.0 0.0 0.0 +Ta 0.0 1.45 2.9 0.0 0.0 0.0 +Ta 0.0 4.35 2.9 0.0 0.0 0.0 +Ta 2.9 0.0 1.45 0.0 0.0 0.0 +Ta 2.9 0.0 4.35 0.0 0.0 0.0 +8 +Lattice = "5.9 0.0 0.0 0.0 5.9 0.0 0.0 0.0 5.9" Properties=species:S:1:pos:R:3:forces:R:3 energy=-87.211997 stress="-328516.14999999997 -0.0 0.0 -0.0 -328516.14999999997 0.0 0.0 0.0 -328516.14999999997" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 2.95 2.95 2.95 0.0 0.0 0.0 +Ta 1.475 2.95 0.0 0.0 0.0 0.0 +Ta 4.425 2.95 0.0 0.0 0.0 0.0 +Ta 0.0 1.475 2.95 0.0 0.0 0.0 +Ta 0.0 4.425 2.95 0.0 0.0 0.0 +Ta 2.95 0.0 1.475 0.0 0.0 0.0 +Ta 2.95 0.0 4.425 0.0 0.0 0.0 +8 +Lattice = "5.5 0.0 0.0 0.0 5.5 0.0 0.0 0.0 5.5" Properties=species:S:1:pos:R:3:forces:R:3 energy=-93.66897 stress="-164011.68000000002 -0.0 0.0 -0.0 -164011.68000000002 0.0 0.0 0.0 -164011.68000000002" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 2.75 2.75 2.75 0.0 0.0 0.0 +Ta 1.375 2.75 0.0 0.0 0.0 0.0 +Ta 4.125 2.75 0.0 0.0 0.0 0.0 +Ta 0.0 1.375 2.75 0.0 0.0 0.0 +Ta 0.0 4.125 2.75 0.0 0.0 0.0 +Ta 2.75 0.0 1.375 0.0 0.0 0.0 +Ta 2.75 0.0 4.125 0.0 0.0 0.0 +8 +Lattice = "4.1 0.0 0.0 0.0 4.1 0.0 0.0 0.0 4.1" Properties=species:S:1:pos:R:3:forces:R:3 energy=-7.989166 stress="6580211.09 0.0 0.0 0.0 6580211.09 0.0 0.0 0.0 6580211.09" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 2.05 2.05 2.05 0.0 0.0 0.0 +Ta 1.025 2.05 0.0 0.0 0.0 0.0 +Ta 3.075 2.05 0.0 0.0 0.0 0.0 +Ta 0.0 1.025 2.05 0.0 0.0 0.0 +Ta 0.0 3.075 2.05 0.0 0.0 0.0 +Ta 2.05 0.0 1.025 0.0 0.0 0.0 +Ta 2.05 0.0 3.075 0.0 0.0 0.0 +8 +Lattice = "6.0 0.0 0.0 0.0 6.0 0.0 0.0 0.0 6.0" Properties=species:S:1:pos:R:3:forces:R:3 energy=-84.982834 stress="-342905.56 0.0 -0.0 0.0 -342905.56 -0.0 -0.0 -0.0 -342905.56" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 3.0 3.0 3.0 0.0 0.0 0.0 +Ta 1.5 3.0 0.0 0.0 0.0 0.0 +Ta 4.5 3.0 0.0 0.0 0.0 0.0 +Ta 0.0 1.5 3.0 0.0 0.0 0.0 +Ta 0.0 4.5 3.0 0.0 0.0 0.0 +Ta 3.0 0.0 1.5 0.0 0.0 0.0 +Ta 3.0 0.0 4.5 0.0 0.0 0.0 +8 +Lattice = "5.6 0.0 0.0 0.0 5.6 0.0 0.0 0.0 5.6" Properties=species:S:1:pos:R:3:forces:R:3 energy=-92.536373 stress="-225855.3 0.0 -0.0 0.0 -225855.3 0.0 -0.0 0.0 -225855.3" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 2.8 2.8 2.8 0.0 0.0 0.0 +Ta 1.4 2.8 0.0 0.0 0.0 0.0 +Ta 4.2 2.8 0.0 0.0 0.0 0.0 +Ta 0.0 1.4 2.8 0.0 0.0 0.0 +Ta 0.0 4.2 2.8 0.0 0.0 0.0 +Ta 2.8 0.0 1.4 0.0 0.0 0.0 +Ta 2.8 0.0 4.2 0.0 0.0 0.0 +8 +Lattice = "4.2 0.0 0.0 0.0 4.2 0.0 0.0 0.0 4.2" Properties=species:S:1:pos:R:3:forces:R:3 energy=-26.77612 stress="5138714.33 -0.0 -0.0 -0.0 5138714.33 0.0 -0.0 0.0 5138714.33" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 2.1 2.1 2.1 0.0 0.0 0.0 +Ta 1.05 2.1 0.0 0.0 0.0 0.0 +Ta 3.15 2.1 0.0 0.0 0.0 0.0 +Ta 0.0 1.05 2.1 0.0 0.0 0.0 +Ta 0.0 3.15 2.1 0.0 0.0 0.0 +Ta 2.1 0.0 1.05 0.0 0.0 0.0 +Ta 2.1 0.0 3.15 0.0 0.0 0.0 +8 +Lattice = "6.3 0.0 0.0 0.0 6.3 0.0 0.0 0.0 6.3" Properties=species:S:1:pos:R:3:forces:R:3 energy=-77.544107 stress="-349968.45 0.0 0.0 0.0 -349968.45 0.0 0.0 0.0 -349968.45" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 3.15 3.15 3.15 0.0 0.0 0.0 +Ta 1.575 3.15 0.0 0.0 0.0 0.0 +Ta 4.725 3.15 0.0 0.0 0.0 0.0 +Ta 0.0 1.575 3.15 0.0 0.0 0.0 +Ta 0.0 4.725 3.15 0.0 0.0 0.0 +Ta 3.15 0.0 1.575 0.0 0.0 0.0 +Ta 3.15 0.0 4.725 0.0 0.0 0.0 +8 +Lattice = "6.2 0.0 0.0 0.0 6.2 0.0 0.0 0.0 6.2" Properties=species:S:1:pos:R:3:forces:R:3 energy=-80.114217 stress="-352410.12 0.0 0.0 0.0 -352410.12 0.0 0.0 0.0 -352410.12" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 3.1 3.1 3.1 0.0 0.0 0.0 +Ta 1.55 3.1 0.0 0.0 0.0 0.0 +Ta 4.65 3.1 0.0 0.0 0.0 0.0 +Ta 0.0 1.55 3.1 0.0 0.0 0.0 +Ta 0.0 4.65 3.1 0.0 0.0 0.0 +Ta 3.1 0.0 1.55 0.0 0.0 0.0 +Ta 3.1 0.0 4.65 0.0 0.0 0.0 +8 +Lattice = "4.3 0.0 0.0 0.0 4.3 0.0 0.0 0.0 4.3" Properties=species:S:1:pos:R:3:forces:R:3 energy=-42.143041 stress="4001608.1 -0.0 -0.0 -0.0 4001608.1 -0.0 -0.0 -0.0 4001608.1" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 2.15 2.15 2.15 0.0 0.0 0.0 +Ta 1.075 2.15 0.0 0.0 0.0 0.0 +Ta 3.225 2.15 0.0 0.0 0.0 0.0 +Ta 0.0 1.075 2.15 0.0 0.0 0.0 +Ta 0.0 3.225 2.15 0.0 0.0 0.0 +Ta 2.15 0.0 1.075 0.0 0.0 0.0 +Ta 2.15 0.0 3.225 0.0 0.0 0.0 +8 +Lattice = "5.7 0.0 0.0 0.0 5.7 0.0 0.0 0.0 5.7" Properties=species:S:1:pos:R:3:forces:R:3 energy=-91.040671 stress="-272236.58 -0.0 0.0 -0.0 -272236.58 -0.0 0.0 -0.0 -272236.58" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 2.85 2.85 2.85 0.0 0.0 0.0 +Ta 1.425 2.85 0.0 0.0 0.0 0.0 +Ta 4.275 2.85 0.0 0.0 0.0 0.0 +Ta 0.0 1.425 2.85 0.0 0.0 0.0 +Ta 0.0 4.275 2.85 0.0 0.0 0.0 +Ta 2.85 0.0 1.425 0.0 0.0 0.0 +Ta 2.85 0.0 4.275 0.0 0.0 0.0 +8 +Lattice = "4.8 0.0 0.0 0.0 4.8 0.0 0.0 0.0 4.8" Properties=species:S:1:pos:R:3:forces:R:3 energy=-84.499231 stress="1025744.96 -0.0 -0.0 -0.0 1025744.96 -0.0 -0.0 -0.0 1025744.96" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 2.4 2.4 2.4 0.0 0.0 0.0 +Ta 1.2 2.4 0.0 0.0 0.0 0.0 +Ta 3.6 2.4 0.0 0.0 0.0 0.0 +Ta 0.0 1.2 2.4 0.0 0.0 0.0 +Ta 0.0 3.6 2.4 0.0 0.0 0.0 +Ta 2.4 0.0 1.2 0.0 0.0 0.0 +Ta 2.4 0.0 3.6 0.0 0.0 0.0 +8 +Lattice = "6.9 0.0 0.0 0.0 6.9 0.0 0.0 0.0 6.9" Properties=species:S:1:pos:R:3:forces:R:3 energy=-61.825173 stress="-284789.87 -0.0 -0.0 -0.0 -284789.87 -0.0 -0.0 -0.0 -284789.87" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 3.45 3.45 3.45 0.0 0.0 0.0 +Ta 1.725 3.45 0.0 0.0 0.0 0.0 +Ta 5.175 3.45 0.0 0.0 0.0 0.0 +Ta 0.0 1.725 3.45 0.0 0.0 0.0 +Ta 0.0 5.175 3.45 0.0 0.0 0.0 +Ta 3.45 0.0 1.725 0.0 0.0 0.0 +Ta 3.45 0.0 5.175 0.0 0.0 0.0 +8 +Lattice = "5.0 0.0 0.0 0.0 5.0 0.0 0.0 0.0 5.0" Properties=species:S:1:pos:R:3:forces:R:3 energy=-91.156873 stress="496748.23 -0.0 0.0 -0.0 496748.23 0.0 0.0 0.0 496748.23" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 2.5 2.5 2.5 0.0 0.0 0.0 +Ta 1.25 2.5 0.0 0.0 0.0 0.0 +Ta 3.75 2.5 0.0 0.0 0.0 0.0 +Ta 0.0 1.25 2.5 0.0 0.0 0.0 +Ta 0.0 3.75 2.5 0.0 0.0 0.0 +Ta 2.5 0.0 1.25 0.0 0.0 0.0 +Ta 2.5 0.0 3.75 0.0 0.0 0.0 +8 +Lattice = "4.4 0.0 0.0 0.0 4.4 0.0 0.0 0.0 4.4" Properties=species:S:1:pos:R:3:forces:R:3 energy=-54.658744 stress="3103602.33 0.0 -0.0 0.0 3103602.33 -0.0 -0.0 -0.0 3103602.33" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 2.2 2.2 2.2 0.0 0.0 0.0 +Ta 1.1 2.2 0.0 0.0 0.0 0.0 +Ta 3.3 2.2 0.0 0.0 0.0 0.0 +Ta 0.0 1.1 2.2 0.0 0.0 0.0 +Ta 0.0 3.3 2.2 0.0 0.0 0.0 +Ta 2.2 0.0 1.1 0.0 0.0 0.0 +Ta 2.2 0.0 3.3 0.0 0.0 0.0 +8 +Lattice = "6.5 0.0 0.0 0.0 6.5 0.0 0.0 0.0 6.5" Properties=species:S:1:pos:R:3:forces:R:3 energy=-72.277255 stress="-335267.83999999997 -0.0 -0.0 -0.0 -335267.83999999997 -0.0 -0.0 -0.0 -335267.83999999997" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 3.25 3.25 3.25 0.0 0.0 0.0 +Ta 1.625 3.25 0.0 0.0 0.0 0.0 +Ta 4.875 3.25 0.0 0.0 0.0 0.0 +Ta 0.0 1.625 3.25 0.0 0.0 0.0 +Ta 0.0 4.875 3.25 0.0 0.0 0.0 +Ta 3.25 0.0 1.625 0.0 0.0 0.0 +Ta 3.25 0.0 4.875 0.0 0.0 0.0 +8 +Lattice = "6.4 0.0 0.0 0.0 6.4 0.0 0.0 0.0 6.4" Properties=species:S:1:pos:R:3:forces:R:3 energy=-74.923334 stress="-344004.72000000003 -0.0 -0.0 -0.0 -344004.72000000003 -0.0 -0.0 -0.0 -344004.72000000003" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 3.2 3.2 3.2 0.0 0.0 0.0 +Ta 1.6 3.2 0.0 0.0 0.0 0.0 +Ta 4.8 3.2 0.0 0.0 0.0 0.0 +Ta 0.0 1.6 3.2 0.0 0.0 0.0 +Ta 0.0 4.8 3.2 0.0 0.0 0.0 +Ta 3.2 0.0 1.6 0.0 0.0 0.0 +Ta 3.2 0.0 4.8 0.0 0.0 0.0 +8 +Lattice = "4.5 0.0 0.0 0.0 4.5 0.0 0.0 0.0 4.5" Properties=species:S:1:pos:R:3:forces:R:3 energy=-64.798066 stress="2398125.0500000003 0.0 0.0 0.0 2398125.0500000003 0.0 0.0 0.0 2398125.0500000003" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 2.25 2.25 2.25 0.0 0.0 0.0 +Ta 1.125 2.25 0.0 0.0 0.0 0.0 +Ta 3.375 2.25 0.0 0.0 0.0 0.0 +Ta 0.0 1.125 2.25 0.0 0.0 0.0 +Ta 0.0 3.375 2.25 0.0 0.0 0.0 +Ta 2.25 0.0 1.125 0.0 0.0 0.0 +Ta 2.25 0.0 3.375 0.0 0.0 0.0 +8 +Lattice = "5.1 0.0 0.0 0.0 5.1 0.0 0.0 0.0 5.1" Properties=species:S:1:pos:R:3:forces:R:3 energy=-93.048342 stress="302698.75 0.0 -0.0 0.0 302698.75 -0.0 -0.0 -0.0 302698.75" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 2.55 2.55 2.55 0.0 0.0 0.0 +Ta 1.275 2.55 0.0 0.0 0.0 0.0 +Ta 3.825 2.55 0.0 0.0 0.0 0.0 +Ta 0.0 1.275 2.55 0.0 0.0 0.0 +Ta 0.0 3.825 2.55 0.0 0.0 0.0 +Ta 2.55 0.0 1.275 0.0 0.0 0.0 +Ta 2.55 0.0 3.825 0.0 0.0 0.0 +8 +Lattice = "6.8 0.0 0.0 0.0 6.8 0.0 0.0 0.0 6.8" Properties=species:S:1:pos:R:3:forces:R:3 energy=-64.38702 stress="-298814.67 0.0 0.0 0.0 -298814.67 0.0 0.0 0.0 -298814.67" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 3.4 3.4 3.4 0.0 0.0 0.0 +Ta 1.7 3.4 0.0 0.0 0.0 0.0 +Ta 5.1 3.4 0.0 0.0 0.0 0.0 +Ta 0.0 1.7 3.4 0.0 0.0 0.0 +Ta 0.0 5.1 3.4 0.0 0.0 0.0 +Ta 3.4 0.0 1.7 0.0 0.0 0.0 +Ta 3.4 0.0 5.1 0.0 0.0 0.0 +8 +Lattice = "4.9 0.0 0.0 0.0 4.9 0.0 0.0 0.0 4.9" Properties=species:S:1:pos:R:3:forces:R:3 energy=-88.352871 stress="734688.7400000001 0.0 0.0 0.0 734688.7400000001 -0.0 0.0 -0.0 734688.7400000001" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 2.45 2.45 2.45 0.0 0.0 0.0 +Ta 1.225 2.45 0.0 0.0 0.0 0.0 +Ta 3.675 2.45 0.0 0.0 0.0 0.0 +Ta 0.0 1.225 2.45 0.0 0.0 0.0 +Ta 0.0 3.675 2.45 0.0 0.0 0.0 +Ta 2.45 0.0 1.225 0.0 0.0 0.0 +Ta 2.45 0.0 3.675 0.0 0.0 0.0 diff --git a/examples/PACKAGES/pod/Ta/XYZ/Volume_BCC.xyz b/examples/PACKAGES/pod/Ta/XYZ/Volume_BCC.xyz new file mode 100644 index 0000000000..1a43270892 --- /dev/null +++ b/examples/PACKAGES/pod/Ta/XYZ/Volume_BCC.xyz @@ -0,0 +1,84 @@ +2 +Lattice = "4.2 0.0 0.0 0.0 4.2 0.0 0.0 0.0 4.2" Properties=species:S:1:pos:R:3:forces:R:3 energy=-16.763625 stress="-315811.75 0.0 0.0 0.0 -315811.75 0.0 0.0 0.0 -315811.75" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 2.1 2.1 2.1 0.0 0.0 0.0 +2 +Lattice = "2.4 0.0 0.0 0.0 2.4 0.0 0.0 0.0 2.4" Properties=species:S:1:pos:R:3:forces:R:3 energy=16.314145 stress="13221145.45 0.0 -0.0 0.0 13221145.45 0.0 -0.0 0.0 13221145.45" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 1.2 1.2 1.2 0.0 0.0 0.0 +2 +Lattice = "3.0 0.0 0.0 0.0 3.0 0.0 0.0 0.0 3.0" Properties=species:S:1:pos:R:3:forces:R:3 energy=-21.209071 stress="1054433.87 -0.0 0.0 -0.0 1054433.87 -0.0 0.0 -0.0 1054433.87" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 1.5 1.5 1.5 0.0 0.0 0.0 +2 +Lattice = "2.8 0.0 0.0 0.0 2.8 0.0 0.0 0.0 2.8" Properties=species:S:1:pos:R:3:forces:R:3 energy=-15.780524 stress="2609201.0100000002 0.0 -0.0 0.0 2609201.0100000002 0.0 -0.0 0.0 2609201.0100000002" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 1.4 1.4 1.4 0.0 0.0 0.0 +2 +Lattice = "2.9 0.0 0.0 0.0 2.9 0.0 0.0 0.0 2.9" Properties=species:S:1:pos:R:3:forces:R:3 energy=-19.002205 stress="1696212.8900000001 0.0 0.0 0.0 1696212.8900000001 0.0 0.0 0.0 1696212.8900000001" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 1.45 1.45 1.45 0.0 0.0 0.0 +2 +Lattice = "3.1 0.0 0.0 0.0 3.1 0.0 0.0 0.0 3.1" Properties=species:S:1:pos:R:3:forces:R:3 energy=-22.620568 stress="596204.8200000001 0.0 0.0 0.0 596204.8200000001 0.0 0.0 0.0 596204.8200000001" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 1.55 1.55 1.55 0.0 0.0 0.0 +2 +Lattice = "2.5 0.0 0.0 0.0 2.5 0.0 0.0 0.0 2.5" Properties=species:S:1:pos:R:3:forces:R:3 energy=4.096885 stress="8866538.459999999 0.0 0.0 0.0 8866538.459999999 -0.0 0.0 -0.0 8866538.459999999" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 1.25 1.25 1.25 0.0 0.0 0.0 +2 +Lattice = "2.2 0.0 0.0 0.0 2.2 0.0 0.0 0.0 2.2" Properties=species:S:1:pos:R:3:forces:R:3 energy=56.26276 stress="29925857.27 -0.0 -0.0 -0.0 29925857.27 -0.0 -0.0 -0.0 29925857.27" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 1.1 1.1 1.1 0.0 0.0 0.0 +2 +Lattice = "3.6 0.0 0.0 0.0 3.6 0.0 0.0 0.0 3.6" Properties=species:S:1:pos:R:3:forces:R:3 energy=-22.585113 stress="-294769.07 0.0 0.0 0.0 -294769.07 0.0 0.0 0.0 -294769.07" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 1.8 1.8 1.8 0.0 0.0 0.0 +2 +Lattice = "3.7 0.0 0.0 0.0 3.7 0.0 0.0 0.0 3.7" Properties=species:S:1:pos:R:3:forces:R:3 energy=-21.795501 stress="-334343.07 0.0 0.0 0.0 -334343.07 -0.0 0.0 -0.0 -334343.07" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 1.85 1.85 1.85 0.0 0.0 0.0 +2 +Lattice = "2.3 0.0 0.0 0.0 2.3 0.0 0.0 0.0 2.3" Properties=species:S:1:pos:R:3:forces:R:3 energy=33.110078 stress="19804876.43 0.0 0.0 0.0 19804876.43 -0.0 0.0 -0.0 19804876.43" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 1.15 1.15 1.15 0.0 0.0 0.0 +2 +Lattice = "3.8 0.0 0.0 0.0 3.8 0.0 0.0 0.0 3.8" Properties=species:S:1:pos:R:3:forces:R:3 energy=-20.885998 stress="-353363.87 -0.0 0.0 -0.0 -353363.87 -0.0 0.0 -0.0 -353363.87" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 1.9 1.9 1.9 0.0 0.0 0.0 +2 +Lattice = "3.4 0.0 0.0 0.0 3.4 0.0 0.0 0.0 3.4" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.601336 stress="-119086.12999999999 0.0 -0.0 0.0 -119086.12999999999 0.0 -0.0 0.0 -119086.12999999999" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 1.7 1.7 1.7 0.0 0.0 0.0 +2 +Lattice = "3.5 0.0 0.0 0.0 3.5 0.0 0.0 0.0 3.5" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.207313 stress="-226389.97 0.0 -0.0 0.0 -226389.97 0.0 -0.0 0.0 -226389.97" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 1.75 1.75 1.75 0.0 0.0 0.0 +2 +Lattice = "3.9 0.0 0.0 0.0 3.9 0.0 0.0 0.0 3.9" Properties=species:S:1:pos:R:3:forces:R:3 energy=-19.898089 stress="-356527.42 0.0 -0.0 0.0 -356527.42 0.0 -0.0 0.0 -356527.42" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 1.95 1.95 1.95 0.0 0.0 0.0 +2 +Lattice = "3.2 0.0 0.0 0.0 3.2 0.0 0.0 0.0 3.2" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.405474 stress="270245.51 -0.0 0.0 -0.0 270245.51 -0.0 0.0 -0.0 270245.51" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 1.6 1.6 1.6 0.0 0.0 0.0 +2 +Lattice = "2.6 0.0 0.0 0.0 2.6 0.0 0.0 0.0 2.6" Properties=species:S:1:pos:R:3:forces:R:3 energy=-4.781324 stress="5944705.43 -0.0 0.0 -0.0 5944705.43 -0.0 0.0 -0.0 5944705.43" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 1.3 1.3 1.3 0.0 0.0 0.0 +2 +Lattice = "4.0 0.0 0.0 0.0 4.0 0.0 0.0 0.0 4.0" Properties=species:S:1:pos:R:3:forces:R:3 energy=-18.864936 stress="-349512.61 -0.0 -0.0 -0.0 -349512.61 0.0 -0.0 0.0 -349512.61" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 2.0 2.0 2.0 0.0 0.0 0.0 +2 +Lattice = "4.1 0.0 0.0 0.0 4.1 0.0 0.0 0.0 4.1" Properties=species:S:1:pos:R:3:forces:R:3 energy=-17.813086 stress="-334971.81 0.0 0.0 0.0 -334971.81 0.0 0.0 0.0 -334971.81" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 2.05 2.05 2.05 0.0 0.0 0.0 +2 +Lattice = "2.7 0.0 0.0 0.0 2.7 0.0 0.0 0.0 2.7" Properties=species:S:1:pos:R:3:forces:R:3 energy=-11.197201 stress="3964027.36 0.0 0.0 0.0 3964027.36 0.0 0.0 0.0 3964027.36" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 1.35 1.35 1.35 0.0 0.0 0.0 +2 +Lattice = "3.3 0.0 0.0 0.0 3.3 0.0 0.0 0.0 3.3" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.696705 stress="39945.84 -0.0 -0.0 -0.0 39945.84 0.0 -0.0 0.0 39945.84" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 1.65 1.65 1.65 0.0 0.0 0.0 diff --git a/examples/PACKAGES/pod/Ta/XYZ/Volume_FCC.xyz b/examples/PACKAGES/pod/Ta/XYZ/Volume_FCC.xyz new file mode 100644 index 0000000000..48c577b507 --- /dev/null +++ b/examples/PACKAGES/pod/Ta/XYZ/Volume_FCC.xyz @@ -0,0 +1,186 @@ +4 +Lattice = "3.4 0.0 0.0 0.0 3.4 0.0 0.0 0.0 3.4" Properties=species:S:1:pos:R:3:forces:R:3 energy=-19.075994 stress="4059178.91 0.0 -0.0 0.0 4059178.91 0.0 -0.0 0.0 4059178.91" +Ta 0.0 0.0 0.0 0 0 0 +Ta 1.7 1.7 0.0 0 0 0 +Ta 1.7 0.0 1.7 0 0 0 +Ta 0.0 1.7 1.7 0 0 0 +4 +Lattice = "5.2 0.0 0.0 0.0 5.2 0.0 0.0 0.0 5.2" Properties=species:S:1:pos:R:3:forces:R:3 energy=-34.873619 stress="-326647.94999999995 0.0 0.0 0.0 -326647.94999999995 -0.0 0.0 -0.0 -326647.94999999995" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 2.6 2.6 0.0 0.0 0.0 0.0 +Ta 2.6 0.0 2.6 0.0 0.0 0.0 +Ta 0.0 2.6 2.6 0.0 0.0 0.0 +4 +Lattice = "4.6 0.0 0.0 0.0 4.6 0.0 0.0 0.0 4.6" Properties=species:S:1:pos:R:3:forces:R:3 energy=-43.950003 stress="-296256.79000000004 -0.0 -0.0 -0.0 -296256.79000000004 0.0 -0.0 0.0 -296256.79000000004" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 2.3 2.3 0.0 0.0 0.0 0.0 +Ta 2.3 0.0 2.3 0.0 0.0 0.0 +Ta 0.0 2.3 2.3 0.0 0.0 0.0 +4 +Lattice = "3.8 0.0 0.0 0.0 3.8 0.0 0.0 0.0 3.8" Properties=species:S:1:pos:R:3:forces:R:3 energy=-40.991909 stress="1079302.71 0.0 0.0 0.0 1079302.71 0.0 0.0 0.0 1079302.71" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 1.9 1.9 0.0 0.0 0.0 0.0 +Ta 1.9 0.0 1.9 0.0 0.0 0.0 +Ta 0.0 1.9 1.9 0.0 0.0 0.0 +4 +Lattice = "3.9 0.0 0.0 0.0 3.9 0.0 0.0 0.0 3.9" Properties=species:S:1:pos:R:3:forces:R:3 energy=-43.453929 stress="713769.5499999999 0.0 0.0 0.0 713769.5499999999 -0.0 0.0 -0.0 713769.5499999999" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 1.95 1.95 0.0 0.0 0.0 0.0 +Ta 1.95 0.0 1.95 0.0 0.0 0.0 +Ta 0.0 1.95 1.95 0.0 0.0 0.0 +4 +Lattice = "4.7 0.0 0.0 0.0 4.7 0.0 0.0 0.0 4.7" Properties=species:S:1:pos:R:3:forces:R:3 energy=-42.686077 stress="-325547.88 0.0 0.0 0.0 -325547.88 0.0 0.0 0.0 -325547.88" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 2.35 2.35 0.0 0.0 0.0 0.0 +Ta 2.35 0.0 2.35 0.0 0.0 0.0 +Ta 0.0 2.35 2.35 0.0 0.0 0.0 +4 +Lattice = "5.3 0.0 0.0 0.0 5.3 0.0 0.0 0.0 5.3" Properties=species:S:1:pos:R:3:forces:R:3 energy=-33.224653 stress="-312088.68 0.0 0.0 0.0 -312088.68 0.0 0.0 0.0 -312088.68" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 2.65 2.65 0.0 0.0 0.0 0.0 +Ta 2.65 0.0 2.65 0.0 0.0 0.0 +Ta 0.0 2.65 2.65 0.0 0.0 0.0 +4 +Lattice = "3.5 0.0 0.0 0.0 3.5 0.0 0.0 0.0 3.5" Properties=species:S:1:pos:R:3:forces:R:3 energy=-26.862709 stress="2990127.38 0.0 0.0 0.0 2990127.38 -0.0 0.0 -0.0 2990127.38" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 1.75 1.75 0.0 0.0 0.0 0.0 +Ta 1.75 0.0 1.75 0.0 0.0 0.0 +Ta 0.0 1.75 1.75 0.0 0.0 0.0 +4 +Lattice = "5.8 0.0 0.0 0.0 5.8 0.0 0.0 0.0 5.8" Properties=species:S:1:pos:R:3:forces:R:3 energy=-25.519883 stress="-222839.06 0.0 -0.0 0.0 -222839.06 -0.0 -0.0 -0.0 -222839.06" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 2.9 2.9 0.0 0.0 0.0 0.0 +Ta 2.9 0.0 2.9 0.0 0.0 0.0 +Ta 0.0 2.9 2.9 0.0 0.0 0.0 +4 +Lattice = "3.2 0.0 0.0 0.0 3.2 0.0 0.0 0.0 3.2" Properties=species:S:1:pos:R:3:forces:R:3 energy=3.463071 stress="7429287.470000001 0.0 -0.0 0.0 7429287.470000001 -0.0 -0.0 -0.0 7429287.470000001" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 1.6 1.6 0.0 0.0 0.0 0.0 +Ta 1.6 0.0 1.6 0.0 0.0 0.0 +Ta 0.0 1.6 1.6 0.0 0.0 0.0 +4 +Lattice = "5.4 0.0 0.0 0.0 5.4 0.0 0.0 0.0 5.4" Properties=species:S:1:pos:R:3:forces:R:3 energy=-31.59595 stress="-295489.55 0.0 0.0 0.0 -295489.55 -0.0 0.0 -0.0 -295489.55" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 2.7 2.7 0.0 0.0 0.0 0.0 +Ta 2.7 0.0 2.7 0.0 0.0 0.0 +Ta 0.0 2.7 2.7 0.0 0.0 0.0 +4 +Lattice = "4.0 0.0 0.0 0.0 4.0 0.0 0.0 0.0 4.0" Properties=species:S:1:pos:R:3:forces:R:3 energy=-45.100466 stress="426831.86 0.0 -0.0 0.0 426831.86 0.0 -0.0 0.0 426831.86" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 2.0 2.0 0.0 0.0 0.0 0.0 +Ta 2.0 0.0 2.0 0.0 0.0 0.0 +Ta 0.0 2.0 2.0 0.0 0.0 0.0 +4 +Lattice = "4.1 0.0 0.0 0.0 4.1 0.0 0.0 0.0 4.1" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.052258 stress="204707.15999999997 -0.0 0.0 -0.0 204707.15999999997 -0.0 0.0 -0.0 204707.15999999997" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 2.05 2.05 0.0 0.0 0.0 0.0 +Ta 2.05 0.0 2.05 0.0 0.0 0.0 +Ta 0.0 2.05 2.05 0.0 0.0 0.0 +4 +Lattice = "5.5 0.0 0.0 0.0 5.5 0.0 0.0 0.0 5.5" Properties=species:S:1:pos:R:3:forces:R:3 energy=-30.001189 stress="-277646.68 0.0 0.0 0.0 -277646.68 -0.0 0.0 -0.0 -277646.68" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 2.75 2.75 0.0 0.0 0.0 0.0 +Ta 2.75 0.0 2.75 0.0 0.0 0.0 +Ta 0.0 2.75 2.75 0.0 0.0 0.0 +4 +Lattice = "6.0 0.0 0.0 0.0 6.0 0.0 0.0 0.0 6.0" Properties=species:S:1:pos:R:3:forces:R:3 energy=-22.8504 stress="-187574.33000000002 -0.0 -0.0 -0.0 -187574.33000000002 0.0 -0.0 0.0 -187574.33000000002" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 3.0 3.0 0.0 0.0 0.0 0.0 +Ta 3.0 0.0 3.0 0.0 0.0 0.0 +Ta 0.0 3.0 3.0 0.0 0.0 0.0 +4 +Lattice = "3.3 0.0 0.0 0.0 3.3 0.0 0.0 0.0 3.3" Properties=species:S:1:pos:R:3:forces:R:3 energy=-9.164691 stress="5458905.82 0.0 -0.0 0.0 5458905.82 0.0 -0.0 0.0 5458905.82" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 1.65 1.65 0.0 0.0 0.0 0.0 +Ta 1.65 0.0 1.65 0.0 0.0 0.0 +Ta 0.0 1.65 1.65 0.0 0.0 0.0 +4 +Lattice = "5.9 0.0 0.0 0.0 5.9 0.0 0.0 0.0 5.9" Properties=species:S:1:pos:R:3:forces:R:3 energy=-24.150343 stress="-204945.0 0.0 -0.0 0.0 -204945.0 0.0 -0.0 0.0 -204945.0" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 2.95 2.95 0.0 0.0 0.0 0.0 +Ta 2.95 0.0 2.95 0.0 0.0 0.0 +Ta 0.0 2.95 2.95 0.0 0.0 0.0 +4 +Lattice = "4.2 0.0 0.0 0.0 4.2 0.0 0.0 0.0 4.2" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.426795 stress="36447.14 -0.0 0.0 -0.0 36447.14 -0.0 0.0 -0.0 36447.14" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 2.1 2.1 0.0 0.0 0.0 0.0 +Ta 2.1 0.0 2.1 0.0 0.0 0.0 +Ta 0.0 2.1 2.1 0.0 0.0 0.0 +4 +Lattice = "5.6 0.0 0.0 0.0 5.6 0.0 0.0 0.0 5.6" Properties=species:S:1:pos:R:3:forces:R:3 energy=-28.451145 stress="-259709.67 0.0 0.0 0.0 -259709.67 -0.0 0.0 -0.0 -259709.67" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 2.8 2.8 0.0 0.0 0.0 0.0 +Ta 2.8 0.0 2.8 0.0 0.0 0.0 +Ta 0.0 2.8 2.8 0.0 0.0 0.0 +4 +Lattice = "3.0 0.0 0.0 0.0 3.0 0.0 0.0 0.0 3.0" Properties=species:S:1:pos:R:3:forces:R:3 energy=40.341566 stress="13905054.1 0.0 0.0 0.0 13905054.1 0.0 0.0 0.0 13905054.1" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 1.5 1.5 0.0 0.0 0.0 0.0 +Ta 1.5 0.0 1.5 0.0 0.0 0.0 +Ta 0.0 1.5 1.5 0.0 0.0 0.0 +4 +Lattice = "3.1 0.0 0.0 0.0 3.1 0.0 0.0 0.0 3.1" Properties=species:S:1:pos:R:3:forces:R:3 energy=19.617912 stress="10138102.870000001 -0.0 0.0 -0.0 10138102.870000001 -0.0 0.0 -0.0 10138102.870000001" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 1.55 1.55 0.0 0.0 0.0 0.0 +Ta 1.55 0.0 1.55 0.0 0.0 0.0 +Ta 0.0 1.55 1.55 0.0 0.0 0.0 +4 +Lattice = "5.7 0.0 0.0 0.0 5.7 0.0 0.0 0.0 5.7" Properties=species:S:1:pos:R:3:forces:R:3 energy=-26.954384 stress="-241322.06 0.0 -0.0 0.0 -241322.06 0.0 -0.0 0.0 -241322.06" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 2.85 2.85 0.0 0.0 0.0 0.0 +Ta 2.85 0.0 2.85 0.0 0.0 0.0 +Ta 0.0 2.85 2.85 0.0 0.0 0.0 +4 +Lattice = "4.3 0.0 0.0 0.0 4.3 0.0 0.0 0.0 4.3" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.323696 stress="-90447.06999999999 0.0 0.0 0.0 -90447.06999999999 -0.0 0.0 -0.0 -90447.06999999999" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 2.15 2.15 0.0 0.0 0.0 0.0 +Ta 2.15 0.0 2.15 0.0 0.0 0.0 +Ta 0.0 2.15 2.15 0.0 0.0 0.0 +4 +Lattice = "4.4 0.0 0.0 0.0 4.4 0.0 0.0 0.0 4.4" Properties=species:S:1:pos:R:3:forces:R:3 energy=-45.828947 stress="-183778.61 0.0 0.0 0.0 -183778.61 0.0 0.0 0.0 -183778.61" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 2.2 2.2 0.0 0.0 0.0 0.0 +Ta 2.2 0.0 2.2 0.0 0.0 0.0 +Ta 0.0 2.2 2.2 0.0 0.0 0.0 +4 +Lattice = "5.0 0.0 0.0 0.0 5.0 0.0 0.0 0.0 5.0" Properties=species:S:1:pos:R:3:forces:R:3 energy=-38.16029 stress="-345892.4 -0.0 -0.0 -0.0 -345892.4 0.0 -0.0 0.0 -345892.4" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 2.5 2.5 0.0 0.0 0.0 0.0 +Ta 2.5 0.0 2.5 0.0 0.0 0.0 +Ta 0.0 2.5 2.5 0.0 0.0 0.0 +4 +Lattice = "3.6 0.0 0.0 0.0 3.6 0.0 0.0 0.0 3.6" Properties=species:S:1:pos:R:3:forces:R:3 energy=-32.919741 stress="2180370.41 0.0 0.0 0.0 2180370.41 -0.0 0.0 -0.0 2180370.41" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 1.8 1.8 0.0 0.0 0.0 0.0 +Ta 1.8 0.0 1.8 0.0 0.0 0.0 +Ta 0.0 1.8 1.8 0.0 0.0 0.0 +4 +Lattice = "4.8 0.0 0.0 0.0 4.8 0.0 0.0 0.0 4.8" Properties=species:S:1:pos:R:3:forces:R:3 energy=-41.272675 stress="-341505.95 0.0 0.0 0.0 -341505.95 -0.0 0.0 -0.0 -341505.95" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 2.4 2.4 0.0 0.0 0.0 0.0 +Ta 2.4 0.0 2.4 0.0 0.0 0.0 +Ta 0.0 2.4 2.4 0.0 0.0 0.0 +4 +Lattice = "4.9 0.0 0.0 0.0 4.9 0.0 0.0 0.0 4.9" Properties=species:S:1:pos:R:3:forces:R:3 energy=-39.753322 stress="-347458.42 0.0 -0.0 0.0 -347458.42 0.0 -0.0 0.0 -347458.42" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 2.45 2.45 0.0 0.0 0.0 0.0 +Ta 2.45 0.0 2.45 0.0 0.0 0.0 +Ta 0.0 2.45 2.45 0.0 0.0 0.0 +4 +Lattice = "3.7 0.0 0.0 0.0 3.7 0.0 0.0 0.0 3.7" Properties=species:S:1:pos:R:3:forces:R:3 energy=-37.547435 stress="1562535.85 0.0 0.0 0.0 1562535.85 -0.0 0.0 -0.0 1562535.85" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 1.85 1.85 0.0 0.0 0.0 0.0 +Ta 1.85 0.0 1.85 0.0 0.0 0.0 +Ta 0.0 1.85 1.85 0.0 0.0 0.0 +4 +Lattice = "5.1 0.0 0.0 0.0 5.1 0.0 0.0 0.0 5.1" Properties=species:S:1:pos:R:3:forces:R:3 energy=-36.52595 stress="-338327.71 -0.0 -0.0 -0.0 -338327.71 0.0 -0.0 0.0 -338327.71" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 2.55 2.55 0.0 0.0 0.0 0.0 +Ta 2.55 0.0 2.55 0.0 0.0 0.0 +Ta 0.0 2.55 2.55 0.0 0.0 0.0 +4 +Lattice = "4.5 0.0 0.0 0.0 4.5 0.0 0.0 0.0 4.5" Properties=species:S:1:pos:R:3:forces:R:3 energy=-45.016087 stress="-250456.02 -0.0 -0.0 -0.0 -250456.02 0.0 -0.0 0.0 -250456.02" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 2.25 2.25 0.0 0.0 0.0 0.0 +Ta 2.25 0.0 2.25 0.0 0.0 0.0 +Ta 0.0 2.25 2.25 0.0 0.0 0.0 diff --git a/examples/PACKAGES/pod/Ta/in.fitpod b/examples/PACKAGES/pod/Ta/in.fitpod new file mode 100644 index 0000000000..7b932558ea --- /dev/null +++ b/examples/PACKAGES/pod/Ta/in.fitpod @@ -0,0 +1,5 @@ +# Demonstrate fitpod for POD potential + +units metal +fitpod Ta_param.pod Ta_data.pod + diff --git a/examples/PACKAGES/pod/Ta/in.pod b/examples/PACKAGES/pod/Ta/in.pod new file mode 100644 index 0000000000..866ee40549 --- /dev/null +++ b/examples/PACKAGES/pod/Ta/in.pod @@ -0,0 +1,47 @@ +# Demonstrate POD Ta potential + +# Initialize simulation + +variable nsteps index 100 +variable nrep equal 4 +variable a equal 3.316 +units metal + +# generate the box and atom positions using a BCC lattice + +variable nx equal ${nrep} +variable ny equal ${nrep} +variable nz equal ${nrep} + +boundary p p p + +lattice bcc $a +region box block 0 ${nx} 0 ${ny} 0 ${nz} +create_box 1 box +create_atoms 1 box + +mass 1 180.88 + + +# POD potential +pair_style pod +pair_coeff * * Ta_param.pod Ta_coeff.pod Ta + +# Setup output + +thermo 10 +thermo_modify norm yes + +# Set up NVE run + +timestep 0.5e-3 +neighbor 1.0 bin +neigh_modify once no every 1 delay 0 check yes + +# Run MD + +velocity all create 300.0 4928459 loop geom +fix 1 all nve +run ${nsteps} + + diff --git a/examples/PACKAGES/pod/Ta/log.1Dec22.fitpod.g++.1 b/examples/PACKAGES/pod/Ta/log.1Dec22.fitpod.g++.1 new file mode 100644 index 0000000000..92bf7ede2d --- /dev/null +++ b/examples/PACKAGES/pod/Ta/log.1Dec22.fitpod.g++.1 @@ -0,0 +1,114 @@ +LAMMPS (3 Nov 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Demonstrate fitpod for POD potential + +units metal +fitpod Ta_param.pod Ta_data.pod +Reading potential file Ta_param.pod with DATE: 2022-11-30 +**************** Begin of POD Potentials **************** +species: Ta +periodic boundary conditions: 1 1 1 +inner cut-off radius: 1 +outer cut-off radius: 5 +bessel polynomial degree: 3 +inverse polynomial degree: 6 +one-body potential: 1 +two-body potential: 3 6 6 +three-body potential: 3 6 5 5 +four-body SNAP potential: 0 0 +quadratic POD potential: 0 +number of basis functions for one-body potential: 1 +number of basis functions for two-body potential: 6 +number of basis functions for three-body potential: 25 +number of basis functions for four-body potential: 0 +number of descriptors for one-body potential: 1 +number of descriptors for two-body potential: 6 +number of descriptors for three-body potential: 25 +number of descriptors for four-body potential: 0 +number of descriptors for quadratic POD potential: 0 +total number of descriptors for all potentials: 32 +**************** End of POD Potentials **************** + +**************** Begin of Data File **************** +file format: extxyz +file extension: xyz +path to training data set: XYZ +path to test data set: XYZ +training fraction: 1 +test fraction: 1 +randomize training data set: 1 +randomize test data set: 1 +error analysis for training data set: 1 +error analysis for test data set: 0 +energy/force calculation for training data set: 0 +energy/force calculation for test data set: 0 +fitting weight for energy: 100 +fitting weight for force: 1 +fitting weight for stress: 0 +**************** End of Data File **************** +**************** Begin of Training Data Set **************** +--------------------------------------------------------------- + data file | number of configurations | number of atoms +--------------------------------------------------------------- + Displaced_A15.xyz | 9 | 576 + Displaced_BCC.xyz | 9 | 486 + Displaced_FCC.xyz | 9 | 432 + Elastic_BCC.xyz | 100 | 200 + Elastic_FCC.xyz | 100 | 400 + GSF_110.xyz | 22 | 528 + GSF_112.xyz | 22 | 660 + Liquid.xyz | 3 | 300 + Surface.xyz | 7 | 236 + Volume_A15.xyz | 30 | 240 + Volume_BCC.xyz | 21 | 42 + Volume_FCC.xyz | 31 | 124 +--------------------------------------------------------------- +number of files: 12 +number of configurations in all files: 363 +number of atoms in all files: 4224 +minimum number of atoms: 2 +maximum number of atoms: 100 +**************** End of Training Data Set **************** +**************** Begin of Memory Allocation **************** +maximum number of atoms in periodic domain: 100 +maximum number of atoms in extended domain: 2700 +maximum number of neighbors in extended domain: 270000 +size of double memory: 223201 +size of int memory: 14709 +size of descriptor matrix: 32 x 32 +**************** End of Memory Allocation **************** +**************** Begin of Least-Squares Fitting **************** +Configuration: # 1 +Configuration: # 101 +Configuration: # 201 +Configuration: # 301 +**************** End of Least-Squares Fitting **************** +**************** Begin of Error Calculation **************** +Configuration: # 1 +Configuration: # 101 +Configuration: # 201 +Configuration: # 301 +**************** End of Error Calculation **************** +**************** Begin of Error Analysis for the Training Data Set **************** +--------------------------------------------------------------------------------------------------- + File | # configs | # atoms | MAE energy | RMSE energy | MAE force | RMSE force +--------------------------------------------------------------------------------------------------- +Displaced_A15.xyz 9 576 0.011286 0.011334 0.113353 0.141650 +Displaced_BCC.xyz 9 486 0.012178 0.014005 0.240613 0.312191 +Displaced_FCC.xyz 9 432 0.001445 0.001591 0.082688 0.103800 +Elastic_BCC.xyz 100 200 0.004452 0.004783 0.000010 0.000013 +Elastic_FCC.xyz 100 400 0.002865 0.002923 0.000146 0.000207 +GSF_110.xyz 22 528 0.005804 0.006853 0.047276 0.097819 +GSF_112.xyz 22 660 0.010588 0.011555 0.123342 0.191090 +Liquid.xyz 3 300 0.013161 0.015355 0.567536 0.757847 +Surface.xyz 7 236 0.025400 0.037555 0.096121 0.295623 +Volume_A15.xyz 30 240 0.039281 0.048678 0.000000 0.000000 +Volume_BCC.xyz 21 42 0.049766 0.067554 0.000000 0.000000 +Volume_FCC.xyz 31 124 0.030056 0.041738 0.000000 0.000000 +--------------------------------------------------------------------------------------------------- +All files 363 4224 0.012917 0.025797 0.122473 0.260052 +--------------------------------------------------------------------------------------------------- +**************** End of Error Analysis for the Training Data Set **************** + +Total wall time: 0:00:01 diff --git a/examples/PACKAGES/pod/Ta/log.1Dec22.fitpod.g++.4 b/examples/PACKAGES/pod/Ta/log.1Dec22.fitpod.g++.4 new file mode 100644 index 0000000000..698636c4ba --- /dev/null +++ b/examples/PACKAGES/pod/Ta/log.1Dec22.fitpod.g++.4 @@ -0,0 +1,114 @@ +LAMMPS (3 Nov 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Demonstrate fitpod for POD potential + +units metal +fitpod Ta_param.pod Ta_data.pod +Reading potential file Ta_param.pod with DATE: 2022-11-30 +**************** Begin of POD Potentials **************** +species: Ta +periodic boundary conditions: 1 1 1 +inner cut-off radius: 1 +outer cut-off radius: 5 +bessel polynomial degree: 3 +inverse polynomial degree: 6 +one-body potential: 1 +two-body potential: 3 6 6 +three-body potential: 3 6 5 5 +four-body SNAP potential: 0 0 +quadratic POD potential: 0 +number of basis functions for one-body potential: 1 +number of basis functions for two-body potential: 6 +number of basis functions for three-body potential: 25 +number of basis functions for four-body potential: 0 +number of descriptors for one-body potential: 1 +number of descriptors for two-body potential: 6 +number of descriptors for three-body potential: 25 +number of descriptors for four-body potential: 0 +number of descriptors for quadratic POD potential: 0 +total number of descriptors for all potentials: 32 +**************** End of POD Potentials **************** + +**************** Begin of Data File **************** +file format: extxyz +file extension: xyz +path to training data set: XYZ +path to test data set: XYZ +training fraction: 1 +test fraction: 1 +randomize training data set: 1 +randomize test data set: 1 +error analysis for training data set: 1 +error analysis for test data set: 0 +energy/force calculation for training data set: 0 +energy/force calculation for test data set: 0 +fitting weight for energy: 100 +fitting weight for force: 1 +fitting weight for stress: 0 +**************** End of Data File **************** +**************** Begin of Training Data Set **************** +--------------------------------------------------------------- + data file | number of configurations | number of atoms +--------------------------------------------------------------- + Displaced_A15.xyz | 9 | 576 + Displaced_BCC.xyz | 9 | 486 + Displaced_FCC.xyz | 9 | 432 + Elastic_BCC.xyz | 100 | 200 + Elastic_FCC.xyz | 100 | 400 + GSF_110.xyz | 22 | 528 + GSF_112.xyz | 22 | 660 + Liquid.xyz | 3 | 300 + Surface.xyz | 7 | 236 + Volume_A15.xyz | 30 | 240 + Volume_BCC.xyz | 21 | 42 + Volume_FCC.xyz | 31 | 124 +--------------------------------------------------------------- +number of files: 12 +number of configurations in all files: 363 +number of atoms in all files: 4224 +minimum number of atoms: 2 +maximum number of atoms: 100 +**************** End of Training Data Set **************** +**************** Begin of Memory Allocation **************** +maximum number of atoms in periodic domain: 100 +maximum number of atoms in extended domain: 2700 +maximum number of neighbors in extended domain: 270000 +size of double memory: 223201 +size of int memory: 14709 +size of descriptor matrix: 32 x 32 +**************** End of Memory Allocation **************** +**************** Begin of Least-Squares Fitting **************** +Configuration: # 1 +Configuration: # 101 +Configuration: # 201 +Configuration: # 301 +**************** End of Least-Squares Fitting **************** +**************** Begin of Error Calculation **************** +Configuration: # 1 +Configuration: # 101 +Configuration: # 201 +Configuration: # 301 +**************** End of Error Calculation **************** +**************** Begin of Error Analysis for the Training Data Set **************** +--------------------------------------------------------------------------------------------------- + File | # configs | # atoms | MAE energy | RMSE energy | MAE force | RMSE force +--------------------------------------------------------------------------------------------------- +Displaced_A15.xyz 9 576 0.011286 0.011334 0.113353 0.141650 +Displaced_BCC.xyz 9 486 0.012178 0.014005 0.240613 0.312191 +Displaced_FCC.xyz 9 432 0.001445 0.001591 0.082688 0.103800 +Elastic_BCC.xyz 100 200 0.004452 0.004783 0.000010 0.000013 +Elastic_FCC.xyz 100 400 0.002865 0.002923 0.000146 0.000207 +GSF_110.xyz 22 528 0.005804 0.006853 0.047276 0.097819 +GSF_112.xyz 22 660 0.010588 0.011555 0.123342 0.191090 +Liquid.xyz 3 300 0.013161 0.015355 0.567536 0.757847 +Surface.xyz 7 236 0.025400 0.037555 0.096121 0.295623 +Volume_A15.xyz 30 240 0.039281 0.048678 0.000000 0.000000 +Volume_BCC.xyz 21 42 0.049766 0.067554 0.000000 0.000000 +Volume_FCC.xyz 31 124 0.030056 0.041738 0.000000 0.000000 +--------------------------------------------------------------------------------------------------- +All files 363 4224 0.012917 0.025797 0.122473 0.260052 +--------------------------------------------------------------------------------------------------- +**************** End of Error Analysis for the Training Data Set **************** + +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/pod/Ta/log.1Dec22.pod.g++.1 b/examples/PACKAGES/pod/Ta/log.1Dec22.pod.g++.1 new file mode 100644 index 0000000000..eceb9f5dec --- /dev/null +++ b/examples/PACKAGES/pod/Ta/log.1Dec22.pod.g++.1 @@ -0,0 +1,143 @@ +LAMMPS (3 Nov 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Demonstrate POD Ta potential + +# Initialize simulation + +variable nsteps index 100 +variable nrep equal 4 +variable a equal 3.316 +units metal + +# generate the box and atom positions using a BCC lattice + +variable nx equal ${nrep} +variable nx equal 4 +variable ny equal ${nrep} +variable ny equal 4 +variable nz equal ${nrep} +variable nz equal 4 + +boundary p p p + +lattice bcc $a +lattice bcc 3.316 +Lattice spacing in x,y,z = 3.316 3.316 3.316 +region box block 0 ${nx} 0 ${ny} 0 ${nz} +region box block 0 4 0 ${ny} 0 ${nz} +region box block 0 4 0 4 0 ${nz} +region box block 0 4 0 4 0 4 +create_box 1 box +Created orthogonal box = (0 0 0) to (13.264 13.264 13.264) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 128 atoms + using lattice units in orthogonal box = (0 0 0) to (13.264 13.264 13.264) + create_atoms CPU = 0.000 seconds + +mass 1 180.88 + + +# POD potential +pair_style pod +pair_coeff * * Ta_param.pod Ta_coeff.pod Ta +Reading potential file Ta_param.pod with DATE: 2022-11-30 +**************** Begin of POD Potentials **************** +species: Ta +periodic boundary conditions: 1 1 1 +inner cut-off radius: 1 +outer cut-off radius: 5 +bessel polynomial degree: 3 +inverse polynomial degree: 6 +one-body potential: 1 +two-body potential: 3 6 6 +three-body potential: 3 6 5 5 +four-body SNAP potential: 0 0 +quadratic POD potential: 0 +number of basis functions for one-body potential: 1 +number of basis functions for two-body potential: 6 +number of basis functions for three-body potential: 25 +number of basis functions for four-body potential: 0 +number of descriptors for one-body potential: 1 +number of descriptors for two-body potential: 6 +number of descriptors for three-body potential: 25 +number of descriptors for four-body potential: 0 +number of descriptors for quadratic POD potential: 0 +total number of descriptors for all potentials: 32 +**************** End of POD Potentials **************** + + +# Setup output + +thermo 10 +thermo_modify norm yes + +# Set up NVE run + +timestep 0.5e-3 +neighbor 1.0 bin +neigh_modify once no every 1 delay 0 check yes + +# Run MD + +velocity all create 300.0 4928459 loop geom +fix 1 all nve +run ${nsteps} +run 100 +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6 + ghost atom cutoff = 6 + binsize = 3, bins = 5 5 5 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair pod, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.082 | 3.082 | 3.082 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 300 -11.841512 0 -11.803037 -15933.622 + 10 296.91721 -11.841117 0 -11.803037 -15691.904 + 20 287.83555 -11.839952 0 -11.803037 -14982.977 + 30 273.25574 -11.838082 0 -11.803037 -13853.44 + 40 253.98821 -11.835611 0 -11.803037 -12375.459 + 50 231.10664 -11.832676 0 -11.803037 -10639.774 + 60 205.8844 -11.829441 0 -11.803037 -8747.2222 + 70 179.71599 -11.826085 0 -11.803037 -6799.8371 + 80 154.02711 -11.822791 0 -11.803037 -4892.7805 + 90 130.17821 -11.819732 0 -11.803036 -3108.1226 + 100 109.36842 -11.817063 0 -11.803036 -1510.9592 +Loop time of 2.21355 on 1 procs for 100 steps with 128 atoms + +Performance: 1.952 ns/day, 12.298 hours/ns, 45.176 timesteps/s, 5.783 katom-step/s +99.9% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 2.2126 | 2.2126 | 2.2126 | 0.0 | 99.96 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.00039011 | 0.00039011 | 0.00039011 | 0.0 | 0.02 +Output | 0.00018205 | 0.00018205 | 0.00018205 | 0.0 | 0.01 +Modify | 0.00014707 | 0.00014707 | 0.00014707 | 0.0 | 0.01 +Other | | 0.0002439 | | | 0.01 + +Nlocal: 128 ave 128 max 128 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 727 ave 727 max 727 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 7424 ave 7424 max 7424 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 7424 +Ave neighs/atom = 58 +Neighbor list builds = 0 +Dangerous builds = 0 + + +Total wall time: 0:00:02 diff --git a/examples/PACKAGES/pod/Ta/log.1Dec22.pod.g++.4 b/examples/PACKAGES/pod/Ta/log.1Dec22.pod.g++.4 new file mode 100644 index 0000000000..ace3943c12 --- /dev/null +++ b/examples/PACKAGES/pod/Ta/log.1Dec22.pod.g++.4 @@ -0,0 +1,143 @@ +LAMMPS (3 Nov 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Demonstrate POD Ta potential + +# Initialize simulation + +variable nsteps index 100 +variable nrep equal 4 +variable a equal 3.316 +units metal + +# generate the box and atom positions using a BCC lattice + +variable nx equal ${nrep} +variable nx equal 4 +variable ny equal ${nrep} +variable ny equal 4 +variable nz equal ${nrep} +variable nz equal 4 + +boundary p p p + +lattice bcc $a +lattice bcc 3.316 +Lattice spacing in x,y,z = 3.316 3.316 3.316 +region box block 0 ${nx} 0 ${ny} 0 ${nz} +region box block 0 4 0 ${ny} 0 ${nz} +region box block 0 4 0 4 0 ${nz} +region box block 0 4 0 4 0 4 +create_box 1 box +Created orthogonal box = (0 0 0) to (13.264 13.264 13.264) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 128 atoms + using lattice units in orthogonal box = (0 0 0) to (13.264 13.264 13.264) + create_atoms CPU = 0.000 seconds + +mass 1 180.88 + + +# POD potential +pair_style pod +pair_coeff * * Ta_param.pod Ta_coeff.pod Ta +Reading potential file Ta_param.pod with DATE: 2022-11-30 +**************** Begin of POD Potentials **************** +species: Ta +periodic boundary conditions: 1 1 1 +inner cut-off radius: 1 +outer cut-off radius: 5 +bessel polynomial degree: 3 +inverse polynomial degree: 6 +one-body potential: 1 +two-body potential: 3 6 6 +three-body potential: 3 6 5 5 +four-body SNAP potential: 0 0 +quadratic POD potential: 0 +number of basis functions for one-body potential: 1 +number of basis functions for two-body potential: 6 +number of basis functions for three-body potential: 25 +number of basis functions for four-body potential: 0 +number of descriptors for one-body potential: 1 +number of descriptors for two-body potential: 6 +number of descriptors for three-body potential: 25 +number of descriptors for four-body potential: 0 +number of descriptors for quadratic POD potential: 0 +total number of descriptors for all potentials: 32 +**************** End of POD Potentials **************** + + +# Setup output + +thermo 10 +thermo_modify norm yes + +# Set up NVE run + +timestep 0.5e-3 +neighbor 1.0 bin +neigh_modify once no every 1 delay 0 check yes + +# Run MD + +velocity all create 300.0 4928459 loop geom +fix 1 all nve +run ${nsteps} +run 100 +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6 + ghost atom cutoff = 6 + binsize = 3, bins = 5 5 5 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair pod, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.062 | 3.062 | 3.062 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 300 -11.841512 0 -11.803037 -15933.622 + 10 296.91721 -11.841117 0 -11.803037 -15691.904 + 20 287.83555 -11.839952 0 -11.803037 -14982.977 + 30 273.25574 -11.838082 0 -11.803037 -13853.44 + 40 253.98821 -11.835611 0 -11.803037 -12375.459 + 50 231.10664 -11.832676 0 -11.803037 -10639.774 + 60 205.8844 -11.829441 0 -11.803037 -8747.2222 + 70 179.71599 -11.826085 0 -11.803037 -6799.8371 + 80 154.02711 -11.822791 0 -11.803037 -4892.7805 + 90 130.17821 -11.819732 0 -11.803036 -3108.1226 + 100 109.36842 -11.817063 0 -11.803036 -1510.9592 +Loop time of 0.638221 on 4 procs for 100 steps with 128 atoms + +Performance: 6.769 ns/day, 3.546 hours/ns, 156.686 timesteps/s, 20.056 katom-step/s +99.4% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.59009 | 0.60345 | 0.61657 | 1.3 | 94.55 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.020708 | 0.033858 | 0.047324 | 5.5 | 5.31 +Output | 0.00021209 | 0.00022669 | 0.00026379 | 0.0 | 0.04 +Modify | 0.00012321 | 0.00012709 | 0.00013646 | 0.0 | 0.02 +Other | | 0.00056 | | | 0.09 + +Nlocal: 32 ave 32 max 32 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 431 ave 431 max 431 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 1856 ave 1856 max 1856 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 7424 +Ave neighs/atom = 58 +Neighbor list builds = 0 +Dangerous builds = 0 + + +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/pod/Ta_Quadratic/Ta_coefficients.pod b/examples/PACKAGES/pod/Ta_Quadratic/Ta_coefficients.pod new file mode 100644 index 0000000000..19a1263bff --- /dev/null +++ b/examples/PACKAGES/pod/Ta_Quadratic/Ta_coefficients.pod @@ -0,0 +1,183 @@ +POD_coefficients: 182 +-4.35181 +3.57833 +-2.25499 +-4.84612 +2.06319 +-1.17070 +0.23842 +9.17159 +36.02380 +16.65293 +-141.18389 +37.17631 +0.46029 +-9.76145 +-0.03678 +15.64520 +2.29801 +0.02143 +2.69734 +-0.35337 +0.51108 +-2.36290 +0.18617 +-0.13079 +1.02665 +0.21514 +0.08076 +-0.28347 +-0.45059 +-0.24762 +-1.13671 +-0.30577 +0.60504 +-0.31285 +0.10638 +0.06958 +0.21962 +0.10426 +0.80241 +11.41434 +10.26118 +0.03871 +-18.86071 +4.47376 +-1.76865 +0.92507 +-0.42650 +-0.35847 +0.56613 +0.79353 +5.65244 +-8.75326 +6.22216 +4.34659 +10.19995 +-6.53345 +7.16628 +-2.19246 +-5.90780 +-3.52168 +7.97278 +-0.21108 +-0.01016 +-0.01023 +-0.03088 +-0.10222 +0.05366 +0.08037 +-3.17607 +3.45670 +0.79279 +2.38325 +-0.69796 +1.44779 +-0.03351 +0.05645 +-0.01901 +0.01923 +0.05401 +0.02095 +1.45657 +-1.58808 +-1.41187 +-2.18121 +3.04892 +-1.09293 +3.03780 +-1.07247 +-0.50261 +-0.81151 +0.35996 +-0.64601 +-0.04245 +-0.00112 +0.02894 +-0.04382 +-0.06556 +-0.00052 +4.67527 +-0.11816 +-1.52428 +0.17075 +0.20231 +-0.36857 +0.61745 +-0.20190 +0.00816 +-0.16194 +-0.12948 +0.02136 +-2.19267 +-0.62508 +-0.20029 +0.27620 +-0.58116 +0.21791 +-1.82301 +0.32164 +0.64550 +0.11580 +-0.02438 +0.08056 +0.19537 +-0.04119 +-0.00323 +-0.06530 +-0.02547 +0.01404 +0.22333 +0.48190 +0.10715 +0.25684 +-0.65069 +0.31428 +-0.06946 +-0.11924 +-0.05467 +-0.12105 +-0.03980 +0.00295 +-2.14415 +-0.82347 +-0.23084 +0.24926 +-0.36679 +0.16710 +1.20411 +0.47757 +0.11104 +-0.09587 +0.03722 +-0.00309 +-0.29879 +0.06463 +0.10236 +0.02276 +-0.06012 +0.02985 +12.06878 +3.39996 +-0.85590 +0.77481 +-1.13392 +0.40511 +-0.08006 +0.07161 +0.05978 +0.02407 +-0.06031 +0.02307 +-10.24102 +-2.49354 +1.14053 +-0.70454 +0.99990 +-0.33863 +2.43470 +1.16557 +0.23708 +-0.03482 +-0.05280 +0.02735 diff --git a/examples/PACKAGES/pod/Ta_Quadratic/Ta_data.pod b/examples/PACKAGES/pod/Ta_Quadratic/Ta_data.pod new file mode 100644 index 0000000000..2aed5d60dd --- /dev/null +++ b/examples/PACKAGES/pod/Ta_Quadratic/Ta_data.pod @@ -0,0 +1,20 @@ +file_format extxyz +file_extension xyz + +path_to_training_data_set "../Ta/XYZ" +path_to_test_data_set "../Ta/XYZ" + +fitting_weight_energy 100.0 +fitting_weight_force 1.0 +fitting_regularization_parameter 1e-10 + +error_analysis_for_training_data_set 1 +error_analysis_for_test_data_set 0 + +# Add the following basename to the name of output files +basename_for_output_files Ta + +# number of digits after the decimal point for pod coefficients +precision_for_pod_coefficients 5 + + diff --git a/examples/PACKAGES/pod/Ta_Quadratic/Ta_param.pod b/examples/PACKAGES/pod/Ta_Quadratic/Ta_param.pod new file mode 100644 index 0000000000..adfe772d10 --- /dev/null +++ b/examples/PACKAGES/pod/Ta_Quadratic/Ta_param.pod @@ -0,0 +1,33 @@ +# DATE: 2022-11-30 UNITS: metal CONTRIBUTOR: Ngoc Cuong Nguyen, exapde@gmail.com CITATION: https://arxiv.org/abs/2209.02362 +# chemical element symbols +species Ta + +# periodic boundary conditions +pbc 1 1 1 + +# inner cut-off radius +rin 1.0 + +# outer cut-off radius +rcut 5.0 + +# polynomial degrees for radial basis functions +bessel_polynomial_degree 3 +inverse_polynomial_degree 6 + +# one-body potential +onebody 1 + +# two-body linear POD potential +twobody_number_radial_basis_functions 6 + +# three-body linear POD potential +threebody_number_radial_basis_functions 5 +threebody_number_angular_basis_functions 5 + +# four-body linear SNAP potential +fourbody_snap_twojmax 0 + +# quadratic POD potential +quadratic_pod_potential 1 + diff --git a/examples/PACKAGES/pod/Ta_Quadratic/Ta_training_analysis.pod b/examples/PACKAGES/pod/Ta_Quadratic/Ta_training_analysis.pod new file mode 100644 index 0000000000..f7f3910f93 --- /dev/null +++ b/examples/PACKAGES/pod/Ta_Quadratic/Ta_training_analysis.pod @@ -0,0 +1,387 @@ +# Displaced_A15.xyz + config # atoms energy DFT energy energy error force DFT force force error + 1 64 -754.2481469 -754.220443 0.0004328736542 8.011514932 8.398670477 0.06376626471 + 2 64 -753.8045627 -753.865255 0.0009483170919 9.036675474 9.134430545 0.07283331622 + 3 64 -754.1013213 -754.0221 0.001237833587 8.637024563 9.017261102 0.06364803016 + 4 64 -754.2847415 -754.279613 8.013259279e-05 8.107730847 8.381725092 0.0651017527 + 5 64 -753.8382044 -753.777209 0.0009530524751 9.104259346 9.478314477 0.07200166218 + 6 64 -754.0793448 -754.048643 0.0004797149516 8.152199121 8.465317938 0.06707944664 + 7 64 -754.3310528 -754.317603 0.0002101527451 7.944092757 8.127690491 0.05987173847 + 8 64 -754.0070856 -753.969161 0.0005925723559 9.179444115 9.425464952 0.06695321977 + 9 64 -754.1450603 -754.141988 4.800421744e-05 8.574171053 8.821346913 0.06628509806 +# Displaced_BCC.xyz + config # atoms energy DFT energy energy error force DFT force force error + 10 54 -630.8081936 -631.019667 0.003916173668 15.97497492 16.625876 0.1021118884 + 11 54 -631.4580137 -631.719595 0.004844098796 15.24068909 15.58666626 0.1043856899 + 12 54 -631.1667565 -631.386255 0.004064786135 15.46091763 15.92378883 0.1062824237 + 13 54 -632.3004944 -632.575826 0.005098733889 14.42619736 14.55977162 0.09839143245 + 14 54 -630.0894752 -630.450212 0.006680311898 16.78432817 16.96340726 0.108510231 + 15 54 -631.3402507 -631.669379 0.006094968579 15.82894198 16.05757315 0.1000888506 + 16 54 -632.0447348 -632.431277 0.007158188469 14.73098392 14.69810718 0.09621570623 + 17 54 -630.7186534 -630.960068 0.004470640569 15.62236513 15.99073148 0.1063789504 + 18 54 -623.3884972 -623.378198 0.0001907256206 23.97393076 24.67640432 0.1519105242 +# Displaced_FCC.xyz + config # atoms energy DFT energy energy error force DFT force force error + 19 48 -556.0112402 -555.899463 0.002328692595 5.300795182 6.084617063 0.07215984282 + 20 48 -555.9884375 -555.922478 0.001374155755 5.509767105 6.297071211 0.08438733778 + 21 48 -555.8765557 -555.800269 0.001589305952 5.420812181 6.021098636 0.07404420713 + 22 48 -556.2511473 -556.196151 0.00114575707 4.54185517 5.127955094 0.06609457327 + 23 48 -555.6590667 -555.488929 0.003544534966 6.087062872 7.050223459 0.09107544933 + 24 48 -556.1020654 -556.027926 0.001544570012 5.048523316 5.611881174 0.06751585758 + 25 48 -556.0607473 -555.968399 0.001923922354 5.20975666 5.979217189 0.08024051191 + 26 48 -556.0598013 -556.047132 0.0002639447837 4.995519809 5.544452585 0.07745365182 + 27 48 -555.8256423 -555.747848 0.001620713741 5.762702449 6.47892568 0.08480579641 +# Elastic_BCC.xyz + config # atoms energy DFT energy energy error force DFT force force error + 28 2 -23.69025375 -23.689367 0.0004433760298 0.0006229109944 0.0006222748589 9.850145246e-07 + 29 2 -23.690768 -23.689888 0.000440000226 0.000618183093 0.0006166052222 1.005028422e-06 + 30 2 -23.69082186 -23.689996 0.0004129297806 0.0008798074771 0.0008810425642 1.74843114e-06 + 31 2 -23.69166748 -23.690957 0.0003552393384 1.000599337e-06 0 4.011213572e-07 + 32 2 -23.69137648 -23.690521 0.0004277400529 0.0005992883433 0.0005982273815 7.219128625e-07 + 33 2 -23.69120607 -23.69038 0.0004130356748 0.0005947953498 0.0005925723585 9.949545518e-07 + 34 2 -23.6900782 -23.689202 0.0004381010976 0.000626333442 0.0006279363025 1.11150918e-06 + 35 2 -23.69121642 -23.690482 0.0003672088756 0.0008635087452 0.0008640138888 1.400552377e-06 + 36 2 -23.69074792 -23.689902 0.0004229607524 0.0006176587851 0.0006152154094 9.894653378e-07 + 37 2 -23.6914111 -23.690563 0.0004240511901 0.00060523674 0.0006038725031 4.148446495e-07 + 38 2 -23.69095105 -23.690207 0.0003720260028 0.001071999141 0.00107369735 7.195432847e-07 + 39 2 -23.69007856 -23.689285 0.0003967815187 0.0008875288751 0.000890013483 1.187800698e-06 + 40 2 -23.69061639 -23.689768 0.0004241948328 0.001078744596 0.001080249045 1.098539288e-06 + 41 2 -23.69064479 -23.68968 0.0004823961198 0.0008702112502 0.0008680034562 8.482029159e-07 + 42 2 -23.6910243 -23.690074 0.0004751500988 0.00136892629 0.001373818765 2.351923075e-06 + 43 2 -23.68910107 -23.688108 0.0004965356565 0.0006334703054 0.0006336134468 5.99047899e-07 + 44 2 -23.69003986 -23.689241 0.0003994297476 0.0008886652258 0.0008880101351 1.319383612e-06 + 45 2 -23.69042994 -23.68952 0.0004549687915 0.0008868886746 0.0008860011287 4.687853177e-07 + 46 2 -23.68738487 -23.686278 0.0005534349406 0.0006426679338 0.0006406777661 9.71847259e-07 + 47 2 -23.69095089 -23.690097 0.000426944902 0.0008409063968 0.0008410160522 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0.0008843760681 0.001650878554 0.0001728225821 +# GSF_110.xyz + config # atoms energy DFT energy energy error force DFT force force error + 228 24 -278.9717069 -279.068761 0.00404392159 1.716820058 1.756353161 0.02195806777 + 229 24 -279.8354387 -279.784296 0.002130947259 0.8360146768 0.9057668891 0.02306494032 + 230 24 -279.920921 -279.901657 0.0008026665456 0.2958425102 0.001565946359 0.01411644012 + 231 24 -279.6113309 -279.584238 0.001128868858 1.136927341 1.035572248 0.02681094686 + 232 24 -279.8354404 -279.784283 0.002131557037 0.8360110766 0.9056396189 0.0230536352 + 233 24 -279.3024349 -279.302158 1.153693867e-05 1.736732164 1.771965137 0.0337612822 + 234 24 -279.5958842 -279.55564 0.001676842348 1.457718728 1.405626506 0.02601747541 + 235 24 -279.1575825 -279.246939 0.003723188855 0.7701800349 0.4813964151 0.04047321686 + 236 24 -279.3024374 -279.302157 1.168449864e-05 1.736735452 1.771953347 0.03376037562 + 237 24 -279.1575945 -279.246935 0.003722519724 0.7692674812 0.4809484798 0.04044518496 + 238 24 -279.9208868 -279.896025 0.001035908286 0.2963183655 0.01060549839 0.01410249268 + 239 24 -279.6115694 -279.584237 0.001138851225 1.137705592 1.035836121 0.02686761868 + 240 24 -279.0645289 -279.124427 0.002495753535 1.763755884 1.809545887 0.03536481445 + 241 24 -279.3562358 -279.379366 0.0009637580399 1.070359709 0.8982692706 0.03586364626 + 242 24 -279.3561336 -279.37937 0.0009681812755 1.070186817 0.898081355 0.03582333417 + 243 24 -279.0645273 -279.124427 0.002495821471 1.76375235 1.809523374 0.03536506787 + 244 24 -279.920921 -279.901657 0.0008026665457 0.2958425115 0.001570374478 0.01411414901 + 245 24 -279.835369 -279.79264 0.001780376458 0.7694167211 0.8392614852 0.02365582641 + 246 24 -279.9208868 -279.896025 0.001035908286 0.2963183642 0.01060243293 0.01410272845 + 247 24 -279.0819585 -279.206496 0.005189062307 0.5487881184 0.005326518563 0.03225762846 + 248 24 -279.5958869 -279.55564 0.001676953548 1.457718908 1.4056319 0.0260184492 + 249 24 -279.8353874 -279.79264 0.00178114169 0.7694019544 0.8392625708 0.02365755724 +# GSF_112.xyz + config # atoms energy DFT energy energy error force DFT force force error + 250 30 -345.1958147 -345.175835 0.0006659891847 1.417828523 1.057395322 0.04924265533 + 251 30 -346.4091655 -346.361714 0.00158171544 1.014644749 1.220284939 0.04659092137 + 252 30 -345.9623041 -345.795524 0.00555933642 1.67846042 2.112860875 0.06265038152 + 253 30 -345.1047773 -345.164602 0.001994155137 1.81758407 1.765832199 0.05258058282 + 254 30 -346.5687926 -346.593523 0.0008243469243 0.5266157132 0.01148867129 0.03755503081 + 255 30 -346.4165138 -346.396186 0.000677592277 1.101956155 0.9954683928 0.04399110273 + 256 30 -345.2521555 -345.319406 0.002241683384 2.024012114 1.772040852 0.05936121329 + 257 30 -345.5898529 -345.594794 0.0001647017128 2.048144748 1.516014157 0.06040124074 + 258 30 -346.0297766 -345.98566 0.001470553801 1.767327567 1.406252265 0.0524370388 + 259 30 -345.5053827 -345.383994 0.004046291647 1.336428827 0.963574308 0.05104898331 + 260 30 -346.5686343 -346.582564 0.0004643235194 0.5264211967 0.0126740587 0.03760970063 + 261 30 -345.4208874 -345.452139 0.001041721437 3.011664984 2.787719406 0.06345649604 + 262 30 -346.5687923 -346.593523 0.0008243564189 0.5266290267 0.01148834 0.03755658657 + 263 30 -345.4303119 -345.281949 0.004945431293 1.947208693 1.873142686 0.05337068276 + 264 30 -345.9593201 -345.928661 0.001021971125 2.36272379 2.100874472 0.0500210761 + 265 30 -345.0137679 -345.111657 0.003262969466 3.193781636 3.358068319 0.0653642582 + 266 30 -346.4078757 -346.367123 0.00135842305 1.085591177 1.335797131 0.04639233515 + 267 30 -346.5685865 -346.582565 0.000465950677 0.5264876602 0.01254743735 0.03760888491 + 268 30 -344.8663405 -344.91356 0.00157398253 2.930409434 3.441834403 0.06926997464 + 269 30 -345.9709087 -345.836703 0.00447352268 1.391835322 1.608769148 0.05570538969 + 270 30 -345.0229889 -344.984307 0.001289396737 2.372017585 2.542628782 0.05571754983 + 271 30 -346.4089446 -346.393931 0.0005004538568 1.297845709 1.211680725 0.04319349627 +# Liquid.xyz + config # atoms energy DFT energy energy error force DFT force force error + 272 100 -1105.559726 -1105.601723 0.0004199685213 30.70196318 31.39853886 0.2273901981 + 273 100 -1099.629534 -1099.673012 0.0004347839505 31.9864667 32.03167218 0.2226202822 + 274 100 -1121.431681 -1121.31506 0.001166208152 21.23863487 20.81076453 0.2037539182 +# Surface.xyz + config # atoms energy DFT energy energy error force DFT force force error + 275 24 -279.9208871 -279.911828 0.0003774638802 0.296319206 0.002753093533 0.01433131366 + 276 48 -554.2414777 -555.359452 0.02329113138 1.363109763 0.003020630398 0.05738251122 + 277 40 -459.5808396 -459.216162 0.009116939427 3.331498127 5.0461364 0.07877996732 + 278 40 -460.5932468 -461.144076 0.01377073069 0.885446861 0.005582740008 0.03813346389 + 279 24 -279.8214987 -279.635146 0.007764695863 0.9820115882 1.288799837 0.01857542284 + 280 30 -346.5687934 -346.592525 0.000791054458 0.5266151802 0.008446203407 0.03726635334 + 281 30 -346.0051972 -345.744506 0.008689705343 2.2667395 3.124961367 0.06591070418 +# Volume_A15.xyz + config # atoms energy DFT energy energy error force DFT force force error + 282 8 -67.00264006 -66.990732 0.001488507429 1.215939804e-14 0 2.243358855e-15 + 283 8 -72.95775649 -72.957807 6.314313802e-06 8.336427488e-14 0 1.123457519e-14 + 284 8 -94.15079086 -94.145745 0.0006307320297 1.643238761e-14 0 2.292400473e-15 + 285 8 -94.55576973 -94.554682 0.0001359665592 8.781810015e-15 0 1.347934763e-15 + 286 8 -79.41651001 -79.438363 0.002731624081 2.791146139e-14 0 4.283068402e-15 + 287 8 -69.63190551 -69.627817 0.0005110639107 2.797159709e-15 0 4.945407509e-16 + 288 8 -82.61402421 -82.604907 0.001139651578 5.50518588e-15 0 8.533393899e-16 + 289 8 14.88715331 14.89048 0.0004158363277 2.277623074e-13 0 3.606918366e-14 + 290 8 -94.356027 -94.367599 0.001446500568 1.370656518e-14 0 1.897531383e-15 + 291 8 -89.24943611 -89.248227 0.0001511386032 1.664774127e-14 0 2.375992921e-15 + 292 8 -87.22359359 -87.211997 0.001449574005 7.983033839e-15 0 1.375635716e-15 + 293 8 -93.64917628 -93.66897 0.002474215442 2.161830962e-15 0 3.67529118e-16 + 294 8 -7.974970933 -7.989166 0.001774383436 5.099416125e-13 0 6.946546112e-14 + 295 8 -84.99735699 -84.982834 0.001815374179 2.170443421e-15 0 3.781697178e-16 + 296 8 -92.51696438 -92.536373 0.002426077641 3.718860295e-14 0 5.973231169e-15 + 297 8 -26.79883513 -26.77612 0.002839390901 2.233715834e-13 0 3.517493235e-14 + 298 8 -77.53738471 -77.544107 0.0008402860664 4.491324709e-15 0 6.054184931e-16 + 299 8 -80.11476756 -80.114217 6.882047834e-05 5.913998758e-15 0 9.669637776e-16 + 300 8 -42.12903277 -42.143041 0.00175102843 2.422750345e-13 0 3.585193613e-14 + 301 8 -91.02990945 -91.040671 0.001345193709 6.975614512e-15 0 1.271552308e-15 + 302 8 -84.50933128 -84.499231 0.001262535287 7.403156156e-14 0 1.406889651e-14 + 303 8 -61.79844785 -61.825173 0.00334064406 6.607450367e-15 0 1.159662644e-15 + 304 8 -91.13057634 -91.156873 0.003287081921 4.951266629e-15 0 8.926959288e-16 + 305 8 -54.64916673 -54.658744 0.001197159343 1.762087937e-13 0 2.65881147e-14 + 306 8 -72.27319254 -72.277255 0.000507807722 1.012753197e-15 0 1.548963504e-16 + 307 8 -74.91471828 -74.923334 0.001076965039 5.031158658e-15 0 8.218252467e-16 + 308 8 -64.81833234 -64.798066 0.002533292377 2.413198886e-14 0 3.886792508e-15 + 309 8 -93.03489737 -93.048342 0.001680578381 1.933770811e-14 0 2.823007783e-15 + 310 8 -64.39098016 -64.38702 0.0004950203573 5.491439235e-15 0 7.035387897e-16 + 311 8 -88.36401111 -88.352871 0.001392513469 2.448818319e-14 0 4.111150078e-15 +# Volume_BCC.xyz + config # atoms energy DFT energy energy error force DFT force force error + 312 2 -16.76594324 -16.763625 0.001159120926 6.976263305e-16 0 2.428612866e-16 + 313 2 16.313727 16.314145 0.0002090019872 8.554299543e-13 0 3.258747439e-13 + 314 2 -21.21034404 -21.209071 0.0006365184639 6.640073969e-15 0 2.236638531e-15 + 315 2 -15.78459679 -15.780524 0.002036394156 5.203101774e-14 0 1.833927975e-14 + 316 2 -18.99841037 -19.002205 0.001897313323 1.54524867e-14 0 5.273488075e-15 + 317 2 -22.62451928 -22.620568 0.001975641435 2.616505909e-15 0 8.627358087e-16 + 318 2 4.098164524 4.096885 0.0006397621932 1.343238339e-13 0 4.308474873e-14 + 319 2 56.26275599 56.26276 2.005140033e-06 4.519068948e-12 0 1.619606237e-12 + 320 2 -22.58944013 -22.585113 0.002163564374 5.342497709e-16 0 1.665334537e-16 + 321 2 -21.79724015 -21.795501 0.0008695727187 1.356336346e-15 0 5.088522196e-16 + 322 2 33.11015633 33.110078 3.916319966e-05 9.447550921e-13 0 3.146094496e-13 + 323 2 -20.88315873 -20.885998 0.001419633105 7.79136136e-16 0 2.683038976e-16 + 324 2 -23.59568896 -23.601336 0.002823519876 1.786193989e-15 0 4.786425072e-16 + 325 2 -23.20858072 -23.207313 0.0006338593044 1.587616402e-15 0 5.168500994e-16 + 326 2 -19.89310508 -19.898089 0.002491959911 5.484204741e-15 0 2.212350673e-15 + 327 2 -23.40543383 -23.405474 2.008348612e-05 1.53358588e-15 0 5.31475905e-16 + 328 2 -4.78389031 -4.781324 0.001283154883 1.032154003e-13 0 2.824014171e-14 + 329 2 -18.86311291 -18.864936 0.0009115426575 7.879846534e-16 0 3.053113318e-16 + 330 2 -17.81642586 -17.813086 0.001669928234 3.605555037e-16 0 9.945747929e-17 + 331 2 -11.19369732 -11.197201 0.001751838472 4.930421981e-14 0 1.82568081e-14 + 332 2 -23.68308621 -23.696705 0.00680939721 1.854348399e-15 0 6.493648212e-16 +# Volume_FCC.xyz + config # atoms energy DFT energy energy error force DFT force force error + 333 4 -19.07363593 -19.075994 0.0005895165228 4.539228243e-14 0 9.571047658e-15 + 334 4 -34.87911159 -34.873619 0.001373146366 4.198460887e-16 0 9.425330886e-17 + 335 4 -43.95312211 -43.950003 0.0007797776247 2.024630393e-15 0 4.763261544e-16 + 336 4 -40.99484531 -40.991909 0.0007340787492 7.390350347e-15 0 1.496325488e-15 + 337 4 -43.44688588 -43.453929 0.001760780713 4.008514517e-15 0 1.003087756e-15 + 338 4 -42.69057262 -42.686077 0.00112390473 2.201304978e-15 0 5.507566336e-16 + 339 4 -33.2256766 -33.224653 0.0002559009775 2.053725049e-16 0 5.088522196e-17 + 340 4 -26.86518979 -26.862709 0.0006201985978 3.140235603e-14 0 7.073764388e-15 + 341 4 -25.52095379 -25.519883 0.000267698747 6.385007894e-16 0 1.350193105e-16 + 342 4 3.462101351 3.463071 0.0002424122902 9.859120235e-14 0 2.313607928e-14 + 343 4 -31.59322682 -31.59595 0.0006807955537 2.683163594e-16 0 6.85215773e-17 + 344 4 -45.10086835 -45.100466 0.0001005869681 1.851345213e-15 0 4.233676619e-16 + 345 4 -46.05341345 -46.052258 0.0002888617397 5.706396539e-16 0 1.230208065e-16 + 346 4 -29.99832747 -30.001189 0.000715381888 4.217055326e-16 0 9.772275581e-17 + 347 4 -22.85257323 -22.8504 0.0005433065144 5.289057803e-16 0 1.249000903e-16 + 348 4 -9.165925355 -9.164691 0.0003085886251 6.994099953e-14 0 1.740903428e-14 + 349 4 -24.14844551 -24.150343 0.0004743734227 3.331030455e-16 0 7.459310947e-17 + 350 4 -46.43546878 -46.426795 0.002168446119 3.110946892e-15 0 8.45388574e-16 + 351 4 -28.4512672 -28.451145 3.054899355e-05 7.027034849e-15 0 2.024133176e-15 + 352 4 40.34134283 40.341566 5.579222461e-05 4.132267104e-13 0 1.032726433e-13 + 353 4 19.61887601 19.617912 0.0002410019119 1.957059783e-13 0 4.973561211e-14 + 354 4 -26.95747285 -26.954384 0.0007722115981 4.151755412e-16 0 1.006139616e-16 + 355 4 -46.33491981 -46.323696 0.002805952031 2.472781231e-15 0 6.375108774e-16 + 356 4 -45.83316789 -45.828947 0.001055221357 1.149213664e-14 0 3.283108739e-15 + 357 4 -38.16058672 -38.16029 7.417901943e-05 5.394515869e-16 0 1.214306433e-16 + 358 4 -32.91257361 -32.919741 0.001791847013 3.667266479e-14 0 9.583190722e-15 + 359 4 -41.2675262 -41.272675 0.001287200608 1.447869656e-14 0 4.164533482e-15 + 360 4 -39.74460491 -39.753322 0.002179272067 5.980937198e-16 0 1.292283933e-16 + 361 4 -37.55548161 -37.547435 0.002011651484 1.56813803e-14 0 3.793478841e-15 + 362 4 -36.53186907 -36.52595 0.00147976637 2.125160163e-16 0 4.741577501e-17 + 363 4 -45.01550152 -45.016087 0.0001463706371 1.97327102e-15 0 4.891920202e-16 diff --git a/examples/PACKAGES/pod/Ta_Quadratic/Ta_training_errors.pod b/examples/PACKAGES/pod/Ta_Quadratic/Ta_training_errors.pod new file mode 100644 index 0000000000..78f600d5cb --- /dev/null +++ b/examples/PACKAGES/pod/Ta_Quadratic/Ta_training_errors.pod @@ -0,0 +1,20 @@ +**************** Begin of Error Analysis for the Training Data Set **************** +--------------------------------------------------------------------------------------------------- + File | # configs | # atoms | MAE energy | RMSE energy | MAE force | RMSE force +--------------------------------------------------------------------------------------------------- +Displaced_A15.xyz 9 576 0.000554 0.000680 0.066393 0.083014 +Displaced_BCC.xyz 9 486 0.004724 0.005103 0.108253 0.139461 +Displaced_FCC.xyz 9 432 0.001704 0.001900 0.077531 0.097471 +Elastic_BCC.xyz 100 200 0.000444 0.000446 0.000001 0.000002 +Elastic_FCC.xyz 100 400 0.000273 0.000327 0.000110 0.000163 +GSF_110.xyz 22 528 0.001852 0.002260 0.027302 0.044765 +GSF_112.xyz 22 660 0.001839 0.002404 0.051415 0.080350 +Liquid.xyz 3 300 0.000674 0.000758 0.217921 0.276109 +Surface.xyz 7 236 0.009115 0.011661 0.047949 0.105123 +Volume_A15.xyz 30 240 0.001407 0.001693 0.000000 0.000000 +Volume_BCC.xyz 21 42 0.001497 0.002077 0.000000 0.000000 +Volume_FCC.xyz 31 124 0.000870 0.001139 0.000000 0.000000 +--------------------------------------------------------------------------------------------------- +All files 363 4224 0.001053 0.002171 0.059051 0.106960 +--------------------------------------------------------------------------------------------------- +**************** End of Error Analysis for the Training Data Set **************** diff --git a/examples/PACKAGES/pod/Ta_Quadratic/in.fitpod b/examples/PACKAGES/pod/Ta_Quadratic/in.fitpod new file mode 100644 index 0000000000..7b932558ea --- /dev/null +++ b/examples/PACKAGES/pod/Ta_Quadratic/in.fitpod @@ -0,0 +1,5 @@ +# Demonstrate fitpod for POD potential + +units metal +fitpod Ta_param.pod Ta_data.pod + diff --git a/examples/PACKAGES/pod/Ta_Quadratic/in.pod b/examples/PACKAGES/pod/Ta_Quadratic/in.pod new file mode 100644 index 0000000000..bde2df00a1 --- /dev/null +++ b/examples/PACKAGES/pod/Ta_Quadratic/in.pod @@ -0,0 +1,47 @@ +# Demonstrate POD Ta potential + +# Initialize simulation + +variable nsteps index 100 +variable nrep equal 4 +variable a equal 3.316 +units metal + +# generate the box and atom positions using a BCC lattice + +variable nx equal ${nrep} +variable ny equal ${nrep} +variable nz equal ${nrep} + +boundary p p p + +lattice bcc $a +region box block 0 ${nx} 0 ${ny} 0 ${nz} +create_box 1 box +create_atoms 1 box + +mass 1 180.88 + + +# POD potential +pair_style pod +pair_coeff * * Ta_param.pod Ta_coefficients.pod Ta + +# Setup output + +thermo 10 +thermo_modify norm yes + +# Set up NVE run + +timestep 0.5e-3 +neighbor 1.0 bin +neigh_modify once no every 1 delay 0 check yes + +# Run MD + +velocity all create 300.0 4928459 loop geom +fix 1 all nve +run ${nsteps} + + diff --git a/examples/PACKAGES/pod/Ta_Quadratic/log.1Dec22.fitpod.g++.1 b/examples/PACKAGES/pod/Ta_Quadratic/log.1Dec22.fitpod.g++.1 new file mode 100644 index 0000000000..6e5e4cd78b --- /dev/null +++ b/examples/PACKAGES/pod/Ta_Quadratic/log.1Dec22.fitpod.g++.1 @@ -0,0 +1,114 @@ +LAMMPS (3 Nov 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Demonstrate fitpod for POD potential + +units metal +fitpod Ta_param.pod Ta_data.pod +Reading potential file Ta_param.pod with DATE: 2022-11-30 +**************** Begin of POD Potentials **************** +species: Ta +periodic boundary conditions: 1 1 1 +inner cut-off radius: 1 +outer cut-off radius: 5 +bessel polynomial degree: 3 +inverse polynomial degree: 6 +one-body potential: 1 +two-body potential: 3 6 6 +three-body potential: 3 6 5 5 +four-body SNAP potential: 0 0 +quadratic POD potential: 1 +number of basis functions for one-body potential: 1 +number of basis functions for two-body potential: 6 +number of basis functions for three-body potential: 25 +number of basis functions for four-body potential: 0 +number of descriptors for one-body potential: 1 +number of descriptors for two-body potential: 6 +number of descriptors for three-body potential: 25 +number of descriptors for four-body potential: 0 +number of descriptors for quadratic POD potential: 150 +total number of descriptors for all potentials: 182 +**************** End of POD Potentials **************** + +**************** Begin of Data File **************** +file format: extxyz +file extension: xyz +path to training data set: ../Ta/XYZ +path to test data set: ../Ta/XYZ +training fraction: 1 +test fraction: 1 +randomize training data set: 1 +randomize test data set: 1 +error analysis for training data set: 1 +error analysis for test data set: 0 +energy/force calculation for training data set: 0 +energy/force calculation for test data set: 0 +fitting weight for energy: 100 +fitting weight for force: 1 +fitting weight for stress: 0 +**************** End of Data File **************** +**************** Begin of Training Data Set **************** +--------------------------------------------------------------- + data file | number of configurations | number of atoms +--------------------------------------------------------------- + Displaced_A15.xyz | 9 | 576 + Displaced_BCC.xyz | 9 | 486 + Displaced_FCC.xyz | 9 | 432 + Elastic_BCC.xyz | 100 | 200 + Elastic_FCC.xyz | 100 | 400 + GSF_110.xyz | 22 | 528 + GSF_112.xyz | 22 | 660 + Liquid.xyz | 3 | 300 + Surface.xyz | 7 | 236 + Volume_A15.xyz | 30 | 240 + Volume_BCC.xyz | 21 | 42 + Volume_FCC.xyz | 31 | 124 +--------------------------------------------------------------- +number of files: 12 +number of configurations in all files: 363 +number of atoms in all files: 4224 +minimum number of atoms: 2 +maximum number of atoms: 100 +**************** End of Training Data Set **************** +**************** Begin of Memory Allocation **************** +maximum number of atoms in periodic domain: 100 +maximum number of atoms in extended domain: 2700 +maximum number of neighbors in extended domain: 270000 +size of double memory: 223201 +size of int memory: 14709 +size of descriptor matrix: 182 x 182 +**************** End of Memory Allocation **************** +**************** Begin of Least-Squares Fitting **************** +Configuration: # 1 +Configuration: # 101 +Configuration: # 201 +Configuration: # 301 +**************** End of Least-Squares Fitting **************** +**************** Begin of Error Calculation **************** +Configuration: # 1 +Configuration: # 101 +Configuration: # 201 +Configuration: # 301 +**************** End of Error Calculation **************** +**************** Begin of Error Analysis for the Training Data Set **************** +--------------------------------------------------------------------------------------------------- + File | # configs | # atoms | MAE energy | RMSE energy | MAE force | RMSE force +--------------------------------------------------------------------------------------------------- +Displaced_A15.xyz 9 576 0.000554 0.000680 0.066393 0.083014 +Displaced_BCC.xyz 9 486 0.004724 0.005103 0.108253 0.139461 +Displaced_FCC.xyz 9 432 0.001704 0.001900 0.077531 0.097471 +Elastic_BCC.xyz 100 200 0.000444 0.000446 0.000001 0.000002 +Elastic_FCC.xyz 100 400 0.000273 0.000327 0.000110 0.000163 +GSF_110.xyz 22 528 0.001852 0.002260 0.027302 0.044765 +GSF_112.xyz 22 660 0.001839 0.002404 0.051415 0.080350 +Liquid.xyz 3 300 0.000674 0.000758 0.217921 0.276109 +Surface.xyz 7 236 0.009115 0.011661 0.047949 0.105123 +Volume_A15.xyz 30 240 0.001407 0.001693 0.000000 0.000000 +Volume_BCC.xyz 21 42 0.001497 0.002077 0.000000 0.000000 +Volume_FCC.xyz 31 124 0.000870 0.001139 0.000000 0.000000 +--------------------------------------------------------------------------------------------------- +All files 363 4224 0.001053 0.002171 0.059051 0.106960 +--------------------------------------------------------------------------------------------------- +**************** End of Error Analysis for the Training Data Set **************** + +Total wall time: 0:00:01 diff --git a/examples/PACKAGES/pod/Ta_Quadratic/log.1Dec22.fitpod.g++.4 b/examples/PACKAGES/pod/Ta_Quadratic/log.1Dec22.fitpod.g++.4 new file mode 100644 index 0000000000..ddc559c6c0 --- /dev/null +++ b/examples/PACKAGES/pod/Ta_Quadratic/log.1Dec22.fitpod.g++.4 @@ -0,0 +1,114 @@ +LAMMPS (3 Nov 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Demonstrate fitpod for POD potential + +units metal +fitpod Ta_param.pod Ta_data.pod +Reading potential file Ta_param.pod with DATE: 2022-11-30 +**************** Begin of POD Potentials **************** +species: Ta +periodic boundary conditions: 1 1 1 +inner cut-off radius: 1 +outer cut-off radius: 5 +bessel polynomial degree: 3 +inverse polynomial degree: 6 +one-body potential: 1 +two-body potential: 3 6 6 +three-body potential: 3 6 5 5 +four-body SNAP potential: 0 0 +quadratic POD potential: 1 +number of basis functions for one-body potential: 1 +number of basis functions for two-body potential: 6 +number of basis functions for three-body potential: 25 +number of basis functions for four-body potential: 0 +number of descriptors for one-body potential: 1 +number of descriptors for two-body potential: 6 +number of descriptors for three-body potential: 25 +number of descriptors for four-body potential: 0 +number of descriptors for quadratic POD potential: 150 +total number of descriptors for all potentials: 182 +**************** End of POD Potentials **************** + +**************** Begin of Data File **************** +file format: extxyz +file extension: xyz +path to training data set: ../Ta/XYZ +path to test data set: ../Ta/XYZ +training fraction: 1 +test fraction: 1 +randomize training data set: 1 +randomize test data set: 1 +error analysis for training data set: 1 +error analysis for test data set: 0 +energy/force calculation for training data set: 0 +energy/force calculation for test data set: 0 +fitting weight for energy: 100 +fitting weight for force: 1 +fitting weight for stress: 0 +**************** End of Data File **************** +**************** Begin of Training Data Set **************** +--------------------------------------------------------------- + data file | number of configurations | number of atoms +--------------------------------------------------------------- + Displaced_A15.xyz | 9 | 576 + Displaced_BCC.xyz | 9 | 486 + Displaced_FCC.xyz | 9 | 432 + Elastic_BCC.xyz | 100 | 200 + Elastic_FCC.xyz | 100 | 400 + GSF_110.xyz | 22 | 528 + GSF_112.xyz | 22 | 660 + Liquid.xyz | 3 | 300 + Surface.xyz | 7 | 236 + Volume_A15.xyz | 30 | 240 + Volume_BCC.xyz | 21 | 42 + Volume_FCC.xyz | 31 | 124 +--------------------------------------------------------------- +number of files: 12 +number of configurations in all files: 363 +number of atoms in all files: 4224 +minimum number of atoms: 2 +maximum number of atoms: 100 +**************** End of Training Data Set **************** +**************** Begin of Memory Allocation **************** +maximum number of atoms in periodic domain: 100 +maximum number of atoms in extended domain: 2700 +maximum number of neighbors in extended domain: 270000 +size of double memory: 223201 +size of int memory: 14709 +size of descriptor matrix: 182 x 182 +**************** End of Memory Allocation **************** +**************** Begin of Least-Squares Fitting **************** +Configuration: # 1 +Configuration: # 101 +Configuration: # 201 +Configuration: # 301 +**************** End of Least-Squares Fitting **************** +**************** Begin of Error Calculation **************** +Configuration: # 1 +Configuration: # 101 +Configuration: # 201 +Configuration: # 301 +**************** End of Error Calculation **************** +**************** Begin of Error Analysis for the Training Data Set **************** +--------------------------------------------------------------------------------------------------- + File | # configs | # atoms | MAE energy | RMSE energy | MAE force | RMSE force +--------------------------------------------------------------------------------------------------- +Displaced_A15.xyz 9 576 0.000554 0.000680 0.066393 0.083014 +Displaced_BCC.xyz 9 486 0.004724 0.005103 0.108253 0.139461 +Displaced_FCC.xyz 9 432 0.001704 0.001900 0.077531 0.097471 +Elastic_BCC.xyz 100 200 0.000444 0.000446 0.000001 0.000002 +Elastic_FCC.xyz 100 400 0.000273 0.000327 0.000110 0.000163 +GSF_110.xyz 22 528 0.001852 0.002260 0.027302 0.044765 +GSF_112.xyz 22 660 0.001839 0.002404 0.051415 0.080350 +Liquid.xyz 3 300 0.000674 0.000758 0.217921 0.276109 +Surface.xyz 7 236 0.009115 0.011661 0.047949 0.105123 +Volume_A15.xyz 30 240 0.001407 0.001693 0.000000 0.000000 +Volume_BCC.xyz 21 42 0.001497 0.002077 0.000000 0.000000 +Volume_FCC.xyz 31 124 0.000870 0.001139 0.000000 0.000000 +--------------------------------------------------------------------------------------------------- +All files 363 4224 0.001053 0.002171 0.059051 0.106960 +--------------------------------------------------------------------------------------------------- +**************** End of Error Analysis for the Training Data Set **************** + +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/pod/Ta_Quadratic/log.1Dec22.pod.g++.1 b/examples/PACKAGES/pod/Ta_Quadratic/log.1Dec22.pod.g++.1 new file mode 100644 index 0000000000..1635479223 --- /dev/null +++ b/examples/PACKAGES/pod/Ta_Quadratic/log.1Dec22.pod.g++.1 @@ -0,0 +1,143 @@ +LAMMPS (3 Nov 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Demonstrate POD Ta potential + +# Initialize simulation + +variable nsteps index 100 +variable nrep equal 4 +variable a equal 3.316 +units metal + +# generate the box and atom positions using a BCC lattice + +variable nx equal ${nrep} +variable nx equal 4 +variable ny equal ${nrep} +variable ny equal 4 +variable nz equal ${nrep} +variable nz equal 4 + +boundary p p p + +lattice bcc $a +lattice bcc 3.316 +Lattice spacing in x,y,z = 3.316 3.316 3.316 +region box block 0 ${nx} 0 ${ny} 0 ${nz} +region box block 0 4 0 ${ny} 0 ${nz} +region box block 0 4 0 4 0 ${nz} +region box block 0 4 0 4 0 4 +create_box 1 box +Created orthogonal box = (0 0 0) to (13.264 13.264 13.264) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 128 atoms + using lattice units in orthogonal box = (0 0 0) to (13.264 13.264 13.264) + create_atoms CPU = 0.000 seconds + +mass 1 180.88 + + +# POD potential +pair_style pod +pair_coeff * * Ta_param.pod Ta_coefficients.pod Ta +Reading potential file Ta_param.pod with DATE: 2022-11-30 +**************** Begin of POD Potentials **************** +species: Ta +periodic boundary conditions: 1 1 1 +inner cut-off radius: 1 +outer cut-off radius: 5 +bessel polynomial degree: 3 +inverse polynomial degree: 6 +one-body potential: 1 +two-body potential: 3 6 6 +three-body potential: 3 6 5 5 +four-body SNAP potential: 0 0 +quadratic POD potential: 1 +number of basis functions for one-body potential: 1 +number of basis functions for two-body potential: 6 +number of basis functions for three-body potential: 25 +number of basis functions for four-body potential: 0 +number of descriptors for one-body potential: 1 +number of descriptors for two-body potential: 6 +number of descriptors for three-body potential: 25 +number of descriptors for four-body potential: 0 +number of descriptors for quadratic POD potential: 150 +total number of descriptors for all potentials: 182 +**************** End of POD Potentials **************** + + +# Setup output + +thermo 10 +thermo_modify norm yes + +# Set up NVE run + +timestep 0.5e-3 +neighbor 1.0 bin +neigh_modify once no every 1 delay 0 check yes + +# Run MD + +velocity all create 300.0 4928459 loop geom +fix 1 all nve +run ${nsteps} +run 100 +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6 + ghost atom cutoff = 6 + binsize = 3, bins = 5 5 5 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair pod, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.082 | 3.082 | 3.082 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 300 -11.84932 0 -11.810845 12965.331 + 10 296.47479 -11.848868 0 -11.810845 12992.863 + 20 286.0912 -11.847536 0 -11.810845 13077.505 + 30 269.42142 -11.845399 0 -11.810845 13223.909 + 40 247.39188 -11.842573 0 -11.810845 13436.937 + 50 221.23616 -11.839219 0 -11.810845 13718.879 + 60 192.42749 -11.835524 0 -11.810845 14066.912 + 70 162.5922 -11.831697 0 -11.810845 14471.57 + 80 133.40727 -11.827954 0 -11.810845 14916.653 + 90 106.48844 -11.824502 0 -11.810844 15380.602 + 100 83.277725 -11.821525 0 -11.810844 15838.941 +Loop time of 2.21094 on 1 procs for 100 steps with 128 atoms + +Performance: 1.954 ns/day, 12.283 hours/ns, 45.230 timesteps/s, 5.789 katom-step/s +99.9% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 2.21 | 2.21 | 2.21 | 0.0 | 99.96 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.00036776 | 0.00036776 | 0.00036776 | 0.0 | 0.02 +Output | 0.00019486 | 0.00019486 | 0.00019486 | 0.0 | 0.01 +Modify | 0.00016419 | 0.00016419 | 0.00016419 | 0.0 | 0.01 +Other | | 0.0002416 | | | 0.01 + +Nlocal: 128 ave 128 max 128 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 727 ave 727 max 727 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 7424 ave 7424 max 7424 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 7424 +Ave neighs/atom = 58 +Neighbor list builds = 0 +Dangerous builds = 0 + + +Total wall time: 0:00:02 diff --git a/examples/PACKAGES/pod/Ta_Quadratic/log.1Dec22.pod.g++.4 b/examples/PACKAGES/pod/Ta_Quadratic/log.1Dec22.pod.g++.4 new file mode 100644 index 0000000000..0a9472c23e --- /dev/null +++ b/examples/PACKAGES/pod/Ta_Quadratic/log.1Dec22.pod.g++.4 @@ -0,0 +1,143 @@ +LAMMPS (3 Nov 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Demonstrate POD Ta potential + +# Initialize simulation + +variable nsteps index 100 +variable nrep equal 4 +variable a equal 3.316 +units metal + +# generate the box and atom positions using a BCC lattice + +variable nx equal ${nrep} +variable nx equal 4 +variable ny equal ${nrep} +variable ny equal 4 +variable nz equal ${nrep} +variable nz equal 4 + +boundary p p p + +lattice bcc $a +lattice bcc 3.316 +Lattice spacing in x,y,z = 3.316 3.316 3.316 +region box block 0 ${nx} 0 ${ny} 0 ${nz} +region box block 0 4 0 ${ny} 0 ${nz} +region box block 0 4 0 4 0 ${nz} +region box block 0 4 0 4 0 4 +create_box 1 box +Created orthogonal box = (0 0 0) to (13.264 13.264 13.264) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 128 atoms + using lattice units in orthogonal box = (0 0 0) to (13.264 13.264 13.264) + create_atoms CPU = 0.000 seconds + +mass 1 180.88 + + +# POD potential +pair_style pod +pair_coeff * * Ta_param.pod Ta_coefficients.pod Ta +Reading potential file Ta_param.pod with DATE: 2022-11-30 +**************** Begin of POD Potentials **************** +species: Ta +periodic boundary conditions: 1 1 1 +inner cut-off radius: 1 +outer cut-off radius: 5 +bessel polynomial degree: 3 +inverse polynomial degree: 6 +one-body potential: 1 +two-body potential: 3 6 6 +three-body potential: 3 6 5 5 +four-body SNAP potential: 0 0 +quadratic POD potential: 1 +number of basis functions for one-body potential: 1 +number of basis functions for two-body potential: 6 +number of basis functions for three-body potential: 25 +number of basis functions for four-body potential: 0 +number of descriptors for one-body potential: 1 +number of descriptors for two-body potential: 6 +number of descriptors for three-body potential: 25 +number of descriptors for four-body potential: 0 +number of descriptors for quadratic POD potential: 150 +total number of descriptors for all potentials: 182 +**************** End of POD Potentials **************** + + +# Setup output + +thermo 10 +thermo_modify norm yes + +# Set up NVE run + +timestep 0.5e-3 +neighbor 1.0 bin +neigh_modify once no every 1 delay 0 check yes + +# Run MD + +velocity all create 300.0 4928459 loop geom +fix 1 all nve +run ${nsteps} +run 100 +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6 + ghost atom cutoff = 6 + binsize = 3, bins = 5 5 5 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair pod, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.062 | 3.062 | 3.062 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 300 -11.84932 0 -11.810845 12965.331 + 10 296.47479 -11.848868 0 -11.810845 12992.863 + 20 286.0912 -11.847536 0 -11.810845 13077.505 + 30 269.42142 -11.845399 0 -11.810845 13223.909 + 40 247.39188 -11.842573 0 -11.810845 13436.937 + 50 221.23616 -11.839219 0 -11.810845 13718.879 + 60 192.42749 -11.835524 0 -11.810845 14066.912 + 70 162.5922 -11.831697 0 -11.810845 14471.57 + 80 133.40727 -11.827954 0 -11.810845 14916.653 + 90 106.48844 -11.824502 0 -11.810844 15380.602 + 100 83.277725 -11.821525 0 -11.810844 15838.941 +Loop time of 0.680827 on 4 procs for 100 steps with 128 atoms + +Performance: 6.345 ns/day, 3.782 hours/ns, 146.880 timesteps/s, 18.801 katom-step/s +99.3% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.66292 | 0.66527 | 0.66845 | 0.3 | 97.72 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.011041 | 0.014313 | 0.01666 | 1.9 | 2.10 +Output | 0.00023806 | 0.00027584 | 0.00038453 | 0.0 | 0.04 +Modify | 0.00015182 | 0.00015927 | 0.00016433 | 0.0 | 0.02 +Other | | 0.0008078 | | | 0.12 + +Nlocal: 32 ave 32 max 32 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 431 ave 431 max 431 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 1856 ave 1856 max 1856 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 7424 +Ave neighs/atom = 58 +Neighbor list builds = 0 +Dangerous builds = 0 + + +Total wall time: 0:00:00 diff --git a/lib/mlpod/Install.py b/lib/mlpod/Install.py new file mode 100644 index 0000000000..0a0979c2ee --- /dev/null +++ b/lib/mlpod/Install.py @@ -0,0 +1,97 @@ +#!/usr/bin/env python + +""" +Install.py tool to do a generic build of a library +soft linked to by many of the lib/Install.py files +used to automate the steps described in the corresponding lib/README +""" + +from __future__ import print_function +import sys, os, subprocess +from argparse import ArgumentParser + +sys.path.append('..') +from install_helpers import get_cpus, fullpath + +parser = ArgumentParser(prog='Install.py', + description="LAMMPS library build wrapper script") + +HELP = """ +Syntax from src dir: make lib-libname args="-m machine -e suffix" +Syntax from lib dir: python Install.py -m machine -e suffix + +libname = name of lib dir (e.g. atc, h5md, meam, poems, etc) +specify -m and optionally -e, order does not matter + +Examples: + +make lib-poems args="-m serial" # build POEMS lib with same settings as in the serial Makefile in src +make lib-colvars args="-m mpi" # build COLVARS lib with same settings as in the mpi Makefile in src +make lib-meam args="-m ifort" # build MEAM lib with custom Makefile.ifort (using Intel Fortran) +""" + +# parse and process arguments + +parser.add_argument("-m", "--machine", + help="suffix of a /Makefile.* file used for compiling this library") +parser.add_argument("-e", "--extramake", + help="set EXTRAMAKE variable in /Makefile. to Makefile.lammps.") + +args = parser.parse_args() + +# print help message and exit, if neither build nor path options are given +if not args.machine and not args.extramake: + parser.print_help() + sys.exit(HELP) + +machine = args.machine +extraflag = args.extramake +if extraflag: + suffix = args.extramake +else: + suffix = 'empty' + +# set lib from working dir + +cwd = fullpath('.') +lib = os.path.basename(cwd) + +# create Makefile.auto as copy of Makefile.machine +# reset EXTRAMAKE if requested + +if not os.path.exists("Makefile.%s" % machine): + sys.exit("lib/%s/Makefile.%s does not exist" % (lib, machine)) + +lines = open("Makefile.%s" % machine, 'r').readlines() +fp = open("Makefile.auto", 'w') + +has_extramake = False +for line in lines: + words = line.split() + if len(words) == 3 and words[0] == "EXTRAMAKE" and words[1] == '=': + has_extramake = True + if extraflag: + line = line.replace(words[2], "Makefile.lammps.%s" % suffix) + fp.write(line) + +fp.close() + +# make the library via Makefile.auto optionally with parallel make +n_cpus = get_cpus() + +print("Building lib%s.a ..." % lib) +cmd = "make -f Makefile.auto clean; make -f Makefile.auto -j%d" % n_cpus +try: + txt = subprocess.check_output(cmd, shell=True, stderr=subprocess.STDOUT) + print(txt.decode('UTF-8')) +except subprocess.CalledProcessError as e: + print("Make failed with:\n %s" % e.output.decode('UTF-8')) + sys.exit(1) + +if os.path.exists("lib%s.a" % lib): + print("Build was successful") +else: + sys.exit("Build of lib/%s/lib%s.a was NOT successful" % (lib, lib)) + +if has_extramake and not os.path.exists("Makefile.lammps"): + print("WARNING: lib/%s/Makefile.lammps was NOT created" % lib) diff --git a/lib/mlpod/Makefile.lammps.empty b/lib/mlpod/Makefile.lammps.empty new file mode 100644 index 0000000000..bf467a20c3 --- /dev/null +++ b/lib/mlpod/Makefile.lammps.empty @@ -0,0 +1,5 @@ +# Settings that the LAMMPS build will import when this package library is used + +mlpod_SYSINC = +mlpod_SYSLIB = +mlpod_SYSPATH = diff --git a/lib/mlpod/Makefile.lammps.installed b/lib/mlpod/Makefile.lammps.installed new file mode 100644 index 0000000000..d8b0d41225 --- /dev/null +++ b/lib/mlpod/Makefile.lammps.installed @@ -0,0 +1,5 @@ +# Settings that the LAMMPS build will import when this package library is used + +mlpod_SYSINC = +mlpod_SYSLIB = -lblas -llapack +mlpod_SYSPATH = diff --git a/lib/mlpod/Makefile.lammps.linalg b/lib/mlpod/Makefile.lammps.linalg new file mode 100644 index 0000000000..cb4d78df99 --- /dev/null +++ b/lib/mlpod/Makefile.lammps.linalg @@ -0,0 +1,5 @@ +# Settings that the LAMMPS build will import when this package library is used + +mlpod_SYSINC = +mlpod_SYSLIB = -llinalg -lgfortran +mlpod_SYSPATH = -L../../lib/linalg$(LIBOBJDIR) diff --git a/lib/mlpod/Makefile.mpi b/lib/mlpod/Makefile.mpi new file mode 100644 index 0000000000..05b6ee642a --- /dev/null +++ b/lib/mlpod/Makefile.mpi @@ -0,0 +1,48 @@ +SHELL = /bin/sh + +# which file will be copied to Makefile.lammps + +EXTRAMAKE = Makefile.lammps.linalg + +# ------ DEFINITIONS ------ + +LIB = libmlpod.a +OBJ = $(SRC:.cpp=.o) + +# ------ SETTINGS ------ + +# include any MPI settings needed for the ELECTRODE library to build with +# the same MPI library that LAMMPS is built with + +CC = mpicxx +CCFLAGS = -O3 -fPIC -DMPICH_IGNORE_CXX_SEEK -DOMPI_SKIP_MPICXX=1 + +ARCHIVE = ar +ARCHFLAG = -rc +DEPFLAGS = -M +#LINK = +#LINKFLAGS = +USRLIB = +SYSLIB = + +# ------ MAKE PROCEDURE ------ + +lib: $(OBJ) + $(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ) + @cp $(EXTRAMAKE) Makefile.lammps + +# ------ COMPILE RULES ------ + +%.o:%.cpp + $(CC) $(CCFLAGS) -c $< -o $@ +%.d:%.cpp + $(CC) $(CCFLAGS) $(DEPFLAGS) $< > $@ + +# ------ DEPENDENCIES ------ + +DEPENDS = $(OBJ:.o=.d) + +# ------ CLEAN ------ + +clean: + -rm -f *.d *~ $(OBJ) $(LIB) diff --git a/lib/mlpod/Makefile.serial b/lib/mlpod/Makefile.serial new file mode 100644 index 0000000000..54e819ee38 --- /dev/null +++ b/lib/mlpod/Makefile.serial @@ -0,0 +1,48 @@ +SHELL = /bin/sh + +# which file will be copied to Makefile.lammps + +EXTRAMAKE = Makefile.lammps.linalg + +# ------ DEFINITIONS ------ + +LIB = libmlpod.a +OBJ = $(SRC:.cpp=.o) + +# ------ SETTINGS ------ + +# include any MPI settings needed for the mlpod library to build with +# the same MPI library that LAMMPS is built with + +CC = g++ +CCFLAGS = -O3 -fPIC -I../../src/STUBS + +ARCHIVE = ar +ARCHFLAG = -rc +DEPFLAGS = -M +#LINK = +#LINKFLAGS = +USRLIB = +SYSLIB = + +# ------ MAKE PROCEDURE ------ + +lib: $(OBJ) + $(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ) + @cp $(EXTRAMAKE) Makefile.lammps + +# ------ COMPILE RULES ------ + +%.o:%.cpp + $(CC) $(CCFLAGS) -c $< -o $@ +%.d:%.cpp + $(CC) $(CCFLAGS) $(DEPFLAGS) $< > $@ + +# ------ DEPENDENCIES ------ + +DEPENDS = $(OBJ:.o=.d) + +# ------ CLEAN ------ + +clean: + -rm -f *.d *~ $(OBJ) $(LIB) diff --git a/potentials/README b/potentials/README index 4df315a7f2..c234f5f48b 100644 --- a/potentials/README +++ b/potentials/README @@ -104,6 +104,7 @@ mliap MLIAP potential mliap.descriptor MLIAP potential descriptor mliap.model MLIAP potential model nb3b.harmonic nonbonded 3-body harmonic potential +pod ML potential with proper orthogonal descriptors (POD) poly polymorphic 3-body potential reax ReaxFF potential (see README.reax for more info) smtbq second moment tight binding QEq (SMTBQ) potential diff --git a/potentials/Ta_coeff.pod b/potentials/Ta_coeff.pod new file mode 100644 index 0000000000..c8943bb889 --- /dev/null +++ b/potentials/Ta_coeff.pod @@ -0,0 +1,33 @@ +POD_coefficients: 32 +-4.44242 +4.10219 +-2.36987 +-3.92184 +0.83796 +-0.79457 +0.26230 +-21.24294 +-15.38460 +-38.44056 +8.29872 +-42.54514 +2.79976 +3.76109 +5.23499 +0.04878 +2.96006 +0.09101 +-0.19257 +-0.24326 +-0.16735 +0.53738 +0.02236 +-0.00154 +0.02488 +-0.00565 +0.07672 +-0.05894 +-0.05604 +-0.12664 +0.11723 +0.00262 diff --git a/potentials/Ta_param.pod b/potentials/Ta_param.pod new file mode 100644 index 0000000000..888dcb1b34 --- /dev/null +++ b/potentials/Ta_param.pod @@ -0,0 +1,38 @@ +# DATE: 2022-11-30 UNITS: metal CONTRIBUTOR: Ngoc Cuong Nguyen, exapde@gmail.com CITATION: https://arxiv.org/abs/2209.02362 +# chemical element symbols +species Ta + +# periodic boundary conditions +pbc 1 1 1 + +# inner cut-off radius +rin 1.0 + +# outer cut-off radius +rcut 5.0 + +# polynomial degrees for radial basis functions +bessel_polynomial_degree 3 +inverse_polynomial_degree 6 + +# one-body potential +onebody 1 + +# two-body linear POD potential +twobody_number_radial_basis_functions 6 + +# three-body linear POD potential +threebody_number_radial_basis_functions 5 +threebody_number_angular_basis_functions 5 + +# four-body linear SNAP potential +fourbody_snap_twojmax 0 + +# quadratic POD potential +quadratic_pod_potential 0 + +# Add the following basename to the name of output files +basename_for_output_files Ta + +# number of digits after the decimal point +precision_for_pod_coefficients 5 diff --git a/src/.gitignore b/src/.gitignore index ba1acae20e..0fbd54afcd 100644 --- a/src/.gitignore +++ b/src/.gitignore @@ -57,6 +57,13 @@ /pair_pace.cpp /pair_pace.h +/pair_pod.cpp +/pair_pod.h +/fitpod_command.cpp +/fitpod_command.h +/mlpod.cpp +/mlpod.h + /fix_polarize*.cpp /fix_polarize*.h /*_dielectric.cpp diff --git a/src/ADIOS/Install.sh b/src/ADIOS/Install.sh index bd0acb1414..0ee2c5428e 100644 --- a/src/ADIOS/Install.sh +++ b/src/ADIOS/Install.sh @@ -69,7 +69,7 @@ adios_SYSLIB=${ADIOS2_LIB} fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*ADIOS.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*ADIOS.*$/d' ../Makefile.package.settings # multiline form needed for BSD sed on Macs sed -i -e '4 i \ include ../ADIOS/Makefile.lammps @@ -85,7 +85,7 @@ elif (test $1 = 0) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*ADIOS.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*ADIOS.*$/d' ../Makefile.package.settings fi rm -f Makefile.lammps diff --git a/src/ATC/Install.sh b/src/ATC/Install.sh index e1dacdd7d6..2194685f92 100755 --- a/src/ATC/Install.sh +++ b/src/ATC/Install.sh @@ -60,7 +60,7 @@ if (test $1 = 1) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*atc.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*atc.*$/d' ../Makefile.package.settings # multiline form needed for BSD sed on Macs sed -i -e '4 i \ include ..\/..\/lib\/atc\/Makefile.lammps @@ -74,7 +74,7 @@ elif (test $1 = 0) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*atc.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*atc.*$/d' ../Makefile.package.settings fi fi diff --git a/src/AWPMD/Install.sh b/src/AWPMD/Install.sh index 70e87c3fbc..0e2e2d3473 100755 --- a/src/AWPMD/Install.sh +++ b/src/AWPMD/Install.sh @@ -46,7 +46,7 @@ if (test $1 = 1) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*awpmd.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*awpmd.*$/d' ../Makefile.package.settings # multiline form needed for BSD sed on Macs sed -i -e '4 i \ include ..\/..\/lib\/awpmd\/Makefile.lammps @@ -60,7 +60,7 @@ elif (test $1 = 0) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*awpmd.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*awpmd.*$/d' ../Makefile.package.settings fi fi diff --git a/src/COLVARS/Install.sh b/src/COLVARS/Install.sh index d67883a416..ebabfd7a1e 100755 --- a/src/COLVARS/Install.sh +++ b/src/COLVARS/Install.sh @@ -47,7 +47,7 @@ if (test $1 = 1) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*colvars.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*colvars.*$/d' ../Makefile.package.settings # multiline form needed for BSD sed on Macs sed -i -e '4 i \ include ..\/..\/lib\/colvars\/Makefile.lammps @@ -62,7 +62,7 @@ elif (test $1 = 0) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*colvars.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*colvars.*$/d' ../Makefile.package.settings fi fi diff --git a/src/COMPRESS/Install.sh b/src/COMPRESS/Install.sh index ab9dac33dc..c0d926cba4 100755 --- a/src/COMPRESS/Install.sh +++ b/src/COMPRESS/Install.sh @@ -44,7 +44,7 @@ if (test $1 = 1) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*compress.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*compress.*$/d' ../Makefile.package.settings # multiline form needed for BSD sed on Macs sed -i -e '4 i \ include ..\/..\/lib\/compress\/Makefile.lammps @@ -58,7 +58,7 @@ elif (test $1 = 0) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*compress.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*compress.*$/d' ../Makefile.package.settings fi fi diff --git a/src/ELECTRODE/Install.sh b/src/ELECTRODE/Install.sh index 65d0b404da..561df0dce0 100755 --- a/src/ELECTRODE/Install.sh +++ b/src/ELECTRODE/Install.sh @@ -49,11 +49,11 @@ if (test $1 = 1) then sed -i -e 's|^PKG_SYSLIB =[ \t]*|&$(electrode_SYSLIB) |' ../Makefile.package fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*electrode.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*electrode.*$/d' ../Makefile.package.settings # multiline form needed for BSD sed on Macs sed -i -e '4 i \ - include ..\/..\/lib\/electrode\/Makefile.lammps - ' ../Makefile.package.settings +include ..\/..\/lib\/electrode\/Makefile.lammps +' ../Makefile.package.settings fi elif (test $1 = 0) then @@ -61,7 +61,7 @@ elif (test $1 = 0) then sed -i -e 's/[^ \t]*electrode[^ \t]* //g' ../Makefile.package fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*electrode.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*electrode.*$/d' ../Makefile.package.settings fi fi diff --git a/src/ELECTRODE/boundary_correction.cpp b/src/ELECTRODE/boundary_correction.cpp index feda3af4f9..8e622c170f 100644 --- a/src/ELECTRODE/boundary_correction.cpp +++ b/src/ELECTRODE/boundary_correction.cpp @@ -19,34 +19,18 @@ #include "atom.h" #include "comm.h" +#include "domain.h" #include "force.h" +#include "kspace.h" using namespace LAMMPS_NS; -// use EW3DC slab correction -// BoundaryCorrection::BoundaryCorrection(LAMMPS *lmp) : Pointers(lmp) {} -void BoundaryCorrection::setup(double x, double y, double z) +double BoundaryCorrection::get_volume() { - xprd_wire = x; - yprd_wire = y; - zprd_slab = z; - volume = x * y * z; - area = x * y; - qqrd2e = force->qqrd2e; - scale = 1.0; -} -void BoundaryCorrection::setup(double x, double y, double z, double g) -{ - xprd_wire = x; - yprd_wire = y; - zprd_slab = z; - volume = x * y * z; - area = x * y; - qqrd2e = force->qqrd2e; - scale = 1.0; - g_ewald = g; + return domain->xprd * force->kspace->wire_volfactor * domain->yprd * + force->kspace->wire_volfactor * domain->zprd * force->kspace->slab_volfactor; } std::vector BoundaryCorrection::gather_recvcounts(int n) diff --git a/src/ELECTRODE/boundary_correction.h b/src/ELECTRODE/boundary_correction.h index b729207b6c..3fec90f8d2 100644 --- a/src/ELECTRODE/boundary_correction.h +++ b/src/ELECTRODE/boundary_correction.h @@ -27,20 +27,10 @@ class BoundaryCorrection : protected Pointers { BoundaryCorrection(LAMMPS *); virtual void vector_corr(double *, int, int, bool){}; virtual void matrix_corr(bigint *, double **){}; - virtual void compute_corr(double, double, int, int, double &, double *){}; - void setup(double, double, double); - void setup(double, double, double, double); + virtual void compute_corr(double, int, int, double &, double *){}; protected: - double area; - double volume; - double xprd_wire; - double yprd_wire; - double zprd_slab; - double qqrd2e; - double scale; - double g_ewald; - + double get_volume(); std::vector gather_jmat(bigint *); std::vector gather_recvcounts(int); std::vector gather_displs(const std::vector &); diff --git a/src/ELECTRODE/electrode_matrix.cpp b/src/ELECTRODE/electrode_matrix.cpp index 484e524041..1362026eb3 100644 --- a/src/ELECTRODE/electrode_matrix.cpp +++ b/src/ELECTRODE/electrode_matrix.cpp @@ -82,7 +82,9 @@ void ElectrodeMatrix::compute_array(double **array, bool timer_flag) MPI_Barrier(world); if (timer_flag && (comm->me == 0)) utils::logmesg(lmp, fmt::format("KSpace time: {:.4g} s\n", MPI_Wtime() - kspace_time)); + //cout << array[0][0] << ", " << array[0][1] << endl; pair_contribution(array); + //cout << array[0][0] << ", " << array[0][1] << endl; self_contribution(array); electrode_kspace->compute_matrix_corr(&mpos[0], array); if (tfflag) tf_contribution(array); @@ -110,7 +112,7 @@ void ElectrodeMatrix::pair_contribution(double **array) int nlocal = atom->nlocal; int newton_pair = force->newton_pair; - double etaij = eta * eta / sqrt(2.0 * eta * eta); // see mw ewald theory eq. (29)-(30) + double const etaij = eta * eta / sqrt(2.0 * eta * eta); // see mw ewald theory eq. (29)-(30) // neighbor list will be ready because called from post_neighbor inum = list->inum; diff --git a/src/ELECTRODE/electrode_vector.cpp b/src/ELECTRODE/electrode_vector.cpp index 4b99973fc7..1a1b877406 100644 --- a/src/ELECTRODE/electrode_vector.cpp +++ b/src/ELECTRODE/electrode_vector.cpp @@ -25,10 +25,12 @@ #include "force.h" #include "group.h" #include "kspace.h" +#include "math_const.h" #include "neigh_list.h" #include "pair.h" using namespace LAMMPS_NS; +using namespace MathConst; ElectrodeVector::ElectrodeVector(LAMMPS *lmp, int sensor_group, int source_group, double eta, bool invert_source) : @@ -41,6 +43,7 @@ ElectrodeVector::ElectrodeVector(LAMMPS *lmp, int sensor_group, int source_group ngroup = group->count(igroup); source_grpbit = group->bitmask[source_group]; this->eta = eta; + tfflag = false; kspace_time_total = 0; pair_time_total = 0; @@ -79,6 +82,14 @@ void ElectrodeVector::setup(class Pair *fix_pair, class NeighList *fix_neighlist /* ---------------------------------------------------------------------- */ +void ElectrodeVector::setup_tf(const std::map &tf_types) +{ + tfflag = true; + this->tf_types = tf_types; +} + +/* ---------------------------------------------------------------------- */ + void ElectrodeVector::compute_vector(double *vector) { MPI_Barrier(world); @@ -86,6 +97,8 @@ void ElectrodeVector::compute_vector(double *vector) // pair double pair_start_time = MPI_Wtime(); pair_contribution(vector); + self_contribution(vector); + if (tfflag) tf_contribution(vector); MPI_Barrier(world); pair_time_total += MPI_Wtime() - pair_start_time; // kspace @@ -105,6 +118,7 @@ void ElectrodeVector::compute_vector(double *vector) void ElectrodeVector::pair_contribution(double *vector) { + double const etaij = eta * MY_ISQRT2; double **x = atom->x; double *q = atom->q; int *type = atom->type; @@ -121,6 +135,7 @@ void ElectrodeVector::pair_contribution(double *vector) int const i = ilist[ii]; bool const i_in_sensor = (mask[i] & groupbit); bool const i_in_source = !!(mask[i] & source_grpbit) != invert_source; + if (!(i_in_sensor || i_in_source)) continue; double const xtmp = x[i][0]; double const ytmp = x[i][1]; double const ztmp = x[i][2]; @@ -144,12 +159,53 @@ void ElectrodeVector::pair_contribution(double *vector) double const rinv = 1.0 / r; double aij = rinv; aij *= ElectrodeMath::safe_erfc(g_ewald * r); - aij -= ElectrodeMath::safe_erfc(eta * r) * rinv; + if (invert_source) + aij -= ElectrodeMath::safe_erfc(eta * r) * rinv; + else + aij -= ElectrodeMath::safe_erfc(etaij * r) * rinv; if (i_in_sensor) { vector[i] += aij * q[j]; - } else if (j_in_sensor) { - vector[j] += aij * q[i]; + //} else if (j_in_sensor) { } + if (j_in_sensor && (!invert_source || !i_in_sensor)) { vector[j] += aij * q[i]; } } } } + +/* ---------------------------------------------------------------------- */ + +void ElectrodeVector::self_contribution(double *vector) +{ + int const inum = list->inum; + int *mask = atom->mask; + int *ilist = list->ilist; + double *q = atom->q; + + const double selfint = 2.0 / MY_PIS * g_ewald; + const double preta = MY_SQRT2 / MY_PIS; + + for (int ii = 0; ii < inum; ii++) { + int const i = ilist[ii]; + bool const i_in_sensor = (mask[i] & groupbit); + bool const i_in_source = !!(mask[i] & source_grpbit) != invert_source; + if (i_in_sensor && i_in_source) vector[i] += (preta * eta - selfint) * q[i]; + } +} + +/* ---------------------------------------------------------------------- */ + +void ElectrodeVector::tf_contribution(double *vector) +{ + int const inum = list->inum; + int *mask = atom->mask; + int *type = atom->type; + int *ilist = list->ilist; + double *q = atom->q; + + for (int ii = 0; ii < inum; ii++) { + int const i = ilist[ii]; + bool const i_in_sensor = (mask[i] & groupbit); + bool const i_in_source = !!(mask[i] & source_grpbit) != invert_source; + if (i_in_sensor && i_in_source) vector[i] += tf_types[type[i]] * q[i]; + } +} diff --git a/src/ELECTRODE/electrode_vector.h b/src/ELECTRODE/electrode_vector.h index cd3117a31f..e7f637dd2d 100644 --- a/src/ELECTRODE/electrode_vector.h +++ b/src/ELECTRODE/electrode_vector.h @@ -19,6 +19,7 @@ #define LMP_ELECTRODE_VECTOR_H #include "pointers.h" +#include namespace LAMMPS_NS { @@ -27,6 +28,7 @@ class ElectrodeVector : protected Pointers { ElectrodeVector(class LAMMPS *, int, int, double, bool); ~ElectrodeVector() override; void setup(class Pair *, class NeighList *, bool); + void setup_tf(const std::map &); void compute_vector(double *); int igroup, source_group; @@ -36,11 +38,15 @@ class ElectrodeVector : protected Pointers { bigint ngroup; double **cutsq; double g_ewald, eta; + bool tfflag; + std::map tf_types; class Pair *pair; class NeighList *list; class ElectrodeKSpace *electrode_kspace; void pair_contribution(double *); + void self_contribution(double *); + void tf_contribution(double *); double kspace_time_total; double pair_time_total; diff --git a/src/ELECTRODE/ewald_electrode.cpp b/src/ELECTRODE/ewald_electrode.cpp index 9d9dbdcd07..a0a081deb0 100644 --- a/src/ELECTRODE/ewald_electrode.cpp +++ b/src/ELECTRODE/ewald_electrode.cpp @@ -32,6 +32,7 @@ #include #include +#include using namespace LAMMPS_NS; using namespace MathConst; @@ -40,7 +41,7 @@ using namespace MathConst; /* ---------------------------------------------------------------------- */ -EwaldElectrode::EwaldElectrode(LAMMPS *lmp) : Ewald(lmp) +EwaldElectrode::EwaldElectrode(LAMMPS *lmp) : Ewald(lmp), boundcorr(nullptr) { eikr_step = -1; } @@ -88,6 +89,7 @@ void EwaldElectrode::init() }; int periodicity_2d[] = {1, 1, 0}; int periodicity_1d[] = {0, 0, 1}; + if (boundcorr != nullptr) delete boundcorr; if (slabflag == 1) { // EW3Dc dipole correction if (!equal_periodicity(periodicity_2d)) @@ -301,7 +303,6 @@ void EwaldElectrode::setup() memory->create3d_offset(sn, -kmax, kmax, 3, nmax, "ewald/electrode:sn"); kmax_created = kmax; } - boundcorr->setup(xprd_wire, yprd_wire, zprd_slab, g_ewald); // pre-compute Ewald coefficients @@ -418,7 +419,7 @@ void EwaldElectrode::compute(int eflag, int vflag) for (int j = 0; j < 6; j++) vatom[i][j] *= q[i] * qscale; } - boundcorr->compute_corr(qsum, slab_volfactor, eflag_atom, eflag_global, energy, eatom); + boundcorr->compute_corr(qsum, eflag_atom, eflag_global, energy, eatom); } /* ---------------------------------------------------------------------- */ @@ -1007,7 +1008,8 @@ void EwaldElectrode::compute_matrix(bigint *imat, double **matrix, bool /* timer n++; } - // TODO check if ((bigint) kxmax+1)*ngroup overflows ... + if (((bigint) kxmax + 1) * ngroup > INT_MAX) + error->all(FLERR, "kmax is too large, integer overflows might occur."); memory->create(csx_all, ((bigint) kxmax + 1) * ngroup, "ewald/electrode:csx_all"); memory->create(snx_all, ((bigint) kxmax + 1) * ngroup, "ewald/electrode:snx_all"); @@ -1018,15 +1020,12 @@ void EwaldElectrode::compute_matrix(bigint *imat, double **matrix, bool /* timer memory->create(jmat, ngroup, "ewald/electrode:jmat"); - int *recvcounts, *displs; // TODO allgather requires int for displs but - // displs might overflow! + int *recvcounts, *displs; memory->create(recvcounts, nprocs, "ewald/electrode:recvcounts"); memory->create(displs, nprocs, "ewald/electrode:displs"); // gather subsets global cs and sn int n = (kxmax + 1) * ngrouplocal; - // TODO check if (kxmax+1)*ngrouplocal, etc. - // overflows int n! typically kxmax small MPI_Allgather(&n, 1, MPI_INT, recvcounts, 1, MPI_INT, world); displs[0] = 0; diff --git a/src/ELECTRODE/fix_electrode_conp.cpp b/src/ELECTRODE/fix_electrode_conp.cpp index a5069f819d..73c029a61f 100644 --- a/src/ELECTRODE/fix_electrode_conp.cpp +++ b/src/ELECTRODE/fix_electrode_conp.cpp @@ -18,6 +18,7 @@ #include "fix_electrode_conp.h" #include "atom.h" +#include "citeme.h" #include "comm.h" #include "compute.h" #include "domain.h" @@ -46,34 +47,52 @@ using namespace LAMMPS_NS; using namespace MathConst; +#define SMALL 1e-16 + extern "C" { void dgetrf_(const int *M, const int *N, double *A, const int *lda, int *ipiv, int *info); void dgetri_(const int *N, double *A, const int *lda, const int *ipiv, double *work, const int *lwork, int *info); } -enum { CONST, EQUAL }; -enum { - V, // voltage - QSB, // q_sb - MC, // macro_capacitance - ME // macro_elastance -}; +static const char cite_fix_electrode[] = + "fix electrode command:\n\n" + "@article{Ahrens2022\n" + "author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\\ss}ner, " + "Robert H.},\n" + "doi = {10.1063/5.0099239},\n" + "title = {{ELECTRODE: An electrochemistry package for LAMMPS}},\n" + "journal = {The Journal of Chemical Physics},\n" + "year = {2022}\n" + "volume = {157},\n" + "pages = {084801},\n" + "}\n"; // 0 1 2 3 4 // fix fxupdate group1 electrode/conp pot1 eta couple group2 pot2 FixElectrodeConp::FixElectrodeConp(LAMMPS *lmp, int narg, char **arg) : - Fix(lmp, narg, arg), f_inv(nullptr), f_mat(nullptr), f_vec(nullptr), array_compute(nullptr), - ele_vector(nullptr), capacitance(nullptr), pair(nullptr), mat_neighlist(nullptr), - vec_neighlist(nullptr), recvcounts(nullptr), displs(nullptr), iele_gathered(nullptr), - buf_gathered(nullptr), potential_i(nullptr), potential_iele(nullptr), charge_iele(nullptr) + Fix(lmp, narg, arg), elyt_vector(nullptr), elec_vector(nullptr), capacitance(nullptr), + elastance(nullptr), pair(nullptr), mat_neighlist(nullptr), vec_neighlist(nullptr), + recvcounts(nullptr), displs(nullptr), iele_gathered(nullptr), buf_gathered(nullptr), + potential_i(nullptr), potential_iele(nullptr) { - read_inv = read_mat = false; + if (lmp->citeme) lmp->citeme->add(cite_fix_electrode); + // fix.h output flags + scalar_flag = 1; + vector_flag = 1; + extscalar = 1; + extvector = 0; + extarray = 0; + + bool default_algo = true; + algo = Algo::MATRIX_INV; + matrix_algo = true; + cg_threshold = 0.; + write_inv = write_mat = write_vec = read_inv = read_mat = false; symm = false; ffield = false; thermo_time = 0.; - scalar_flag = 1; - vector_flag = 1; + top_group = 0; intelflag = false; tfflag = false; @@ -81,19 +100,20 @@ FixElectrodeConp::FixElectrodeConp(LAMMPS *lmp, int narg, char **arg) : update_time = 0; mult_time = 0; + n_call = n_cg_step = 0; // read fix command fixname = std::string(arg[0]); groups = std::vector(1, igroup); group_bits = std::vector(1, groupbit); group_psi_var_names = std::vector(1); - group_psi_var_styles = std::vector(1, CONST); + group_psi_var_styles = std::vector(1, VarStyle::CONST); group_psi = std::vector(1); etypes_neighlists = false; if (strstr(arg[3], "v_") == arg[3]) { std::string vname = arg[3]; group_psi_var_names[0] = vname.substr(2); - group_psi_var_styles[0] = EQUAL; + group_psi_var_styles[0] = VarStyle::EQUAL; } else group_psi[0] = utils::numeric(FLERR, arg[3], false, lmp); char *eta_str = arg[4]; @@ -110,50 +130,51 @@ FixElectrodeConp::FixElectrodeConp(LAMMPS *lmp, int narg, char **arg) : if (strstr(arg[iarg], "v_") == arg[iarg]) { std::string vname = arg[iarg]; group_psi_var_names.push_back(vname.substr(2)); - group_psi_var_styles.push_back(EQUAL); + group_psi_var_styles.push_back(VarStyle::EQUAL); group_psi.push_back(0.); } else { std::string null; group_psi_var_names.push_back(null); - group_psi_var_styles.push_back(CONST); + group_psi_var_styles.push_back(VarStyle::CONST); group_psi.push_back(utils::numeric(FLERR, arg[iarg], false, lmp)); } - } else if ((strncmp(arg[iarg], "symm", 4) == 0)) { - if (iarg + 2 > narg) error->all(FLERR, "Need yes/no command after symm keyword"); - char *symm_arg = arg[++iarg]; - if ((strcmp(symm_arg, "yes") == 0) || (strcmp(symm_arg, "on") == 0)) { - symm = true; - } else if ((strcmp(symm_arg, "no") == 0) || (strcmp(symm_arg, "off") == 0)) { - symm = false; + } else if ((strcmp(arg[iarg], "algo") == 0)) { + if (!default_algo) error->one(FLERR, fmt::format("Algorithm can be set once, only")); + default_algo = false; + if (iarg + 2 > narg) error->all(FLERR, "Need one argument after algo command"); + char *algo_arg = arg[++iarg]; + bool cg_algo = false; + if ((strcmp(algo_arg, "mat_inv") == 0)) { + algo = Algo::MATRIX_INV; + matrix_algo = true; + } else if ((strcmp(algo_arg, "mat_cg") == 0)) { + algo = Algo::MATRIX_CG; + matrix_algo = true; + cg_algo = true; + } else if ((strcmp(algo_arg, "cg") == 0)) { + algo = Algo::CG; + matrix_algo = false; + cg_algo = true; } else { - error->all(FLERR, "Invalid argument after symm keyword"); + error->all(FLERR, "Invalid argument after algo keyword"); + } + if (cg_algo) { + if (iarg + 2 > narg) error->all(FLERR, "Need one argument after algo *cg command"); + cg_threshold = utils::numeric(FLERR, arg[++iarg], false, lmp); } } else if ((strncmp(arg[iarg], "write", 5) == 0)) { if (iarg + 2 > narg) error->all(FLERR, "Need one argument after write command"); - if (comm->me == 0) { - if ((strcmp(arg[iarg], "write_inv") == 0)) { // capacitance matrix - f_inv = fopen(arg[++iarg], "w"); - if (f_inv == nullptr) - error->one(FLERR, - fmt::format("Cannot open capacitance matrix file {}: {}", arg[iarg], - utils::getsyserror())); - } else if ((strcmp(arg[iarg], "write_mat") == 0)) { // b vector - f_mat = fopen(arg[++iarg], "w"); - if (f_mat == nullptr) - error->one(FLERR, - fmt::format("Cannot open elastance matrix file {}: {}", arg[iarg], - utils::getsyserror())); - } else if ((strcmp(arg[iarg], "write_vec") == 0)) { // b vector - f_vec = fopen(arg[++iarg], "w"); - if (f_vec == nullptr) - error->one( - FLERR, - fmt::format("Cannot open vector file {}: {}", arg[iarg], utils::getsyserror())); - } else { - error->all(FLERR, "Illegal fix electrode/conp command with write"); - } + if ((strcmp(arg[iarg], "write_inv") == 0)) { // capacitance matrix + write_inv = true; + output_file_inv = arg[++iarg]; + } else if ((strcmp(arg[iarg], "write_mat") == 0)) { // elastance matrix + write_mat = true; + output_file_mat = arg[++iarg]; + } else if ((strcmp(arg[iarg], "write_vec") == 0)) { // b vector + write_vec = true; + output_file_vec = arg[++iarg]; } else { - iarg++; + error->all(FLERR, "Illegal fix electrode/conp command with write"); } } else if ((strncmp(arg[iarg], "read", 4) == 0)) { if (iarg + 2 > narg) error->all(FLERR, "Need one argument after read command"); @@ -166,12 +187,6 @@ FixElectrodeConp::FixElectrodeConp(LAMMPS *lmp, int narg, char **arg) : } else { error->all(FLERR, "Illegal fix electrode/conp command with read"); } - } else if ((strcmp(arg[iarg], "etypes") == 0)) { - if (iarg + 2 > narg) error->all(FLERR, "Need one argument after etypes command"); - int ilo, ihi; - utils::bounds(FLERR, arg[++iarg], 1, atom->ntypes, ilo, ihi, error); - for (int i = ilo; i <= ihi; ++i) etypes.push_back(i); - etypes_neighlists = true; } else if ((strcmp(arg[iarg], "temp") == 0)) { if (iarg + 4 > narg) error->all(FLERR, "Need three arguments after temp command"); if (strcmp(this->style, "electrode/thermo") != 0) @@ -179,16 +194,13 @@ FixElectrodeConp::FixElectrodeConp(LAMMPS *lmp, int narg, char **arg) : thermo_temp = force->boltz / force->qe2f * utils::numeric(FLERR, arg[++iarg], false, lmp); thermo_time = utils::numeric(FLERR, arg[++iarg], false, lmp); thermo_init = utils::inumeric(FLERR, arg[++iarg], false, lmp); + // toggle parameters + } else if ((strcmp(arg[iarg], "etypes") == 0)) { + etypes_neighlists = utils::logical(FLERR, arg[++iarg], false, lmp); + } else if ((strncmp(arg[iarg], "symm", 4) == 0)) { + symm = utils::logical(FLERR, arg[++iarg], false, lmp); } else if ((strcmp(arg[iarg], "ffield") == 0)) { - if (iarg + 2 > narg) error->all(FLERR, "Need yes/no command after ffield keyword"); - char *ffield_arg = arg[++iarg]; - if ((strcmp(ffield_arg, "yes") == 0) || (strcmp(ffield_arg, "on") == 0)) { - ffield = true; - } else if ((strcmp(ffield_arg, "no") == 0) || (strcmp(ffield_arg, "off") == 0)) { - ffield = false; - } else { - error->all(FLERR, "Invalid argument after ffield keyword"); - } + ffield = utils::logical(FLERR, arg[++iarg], false, lmp); } else { error->all(FLERR, "Illegal fix electrode/conp command"); } @@ -206,23 +218,38 @@ FixElectrodeConp::FixElectrodeConp(LAMMPS *lmp, int narg, char **arg) : igroup = group->find(union_group); if (igroup < 0) error->all(FLERR, "Failed to create union of groups"); // construct computes - ele_vector = new ElectrodeVector(lmp, igroup, igroup, eta, true); - if (!(read_inv || read_mat)) { array_compute = new ElectrodeMatrix(lmp, igroup, eta); } - - // error checks + need_array_compute = !(read_inv || read_mat) && matrix_algo; + need_elec_vector = algo == Algo::CG; + elyt_vector = new ElectrodeVector(lmp, igroup, igroup, eta, true); + if (need_elec_vector) elec_vector = new ElectrodeVector(lmp, igroup, igroup, eta, false); assert(groups.size() == group_bits.size()); assert(groups.size() == group_psi.size()); assert(groups.size() == group_psi_var_styles.size()); assert(groups.size() == group_psi_var_names.size()); - assert(igroup == ele_vector->igroup); - if (!(read_mat || read_inv)) assert(igroup == array_compute->igroup); + assert(igroup == elyt_vector->igroup); + if (need_elec_vector) assert(igroup == elec_vector->igroup); + if (algo != Algo::MATRIX_INV) { + if (read_inv || write_inv) + error->all( + FLERR, + "Selected algorithm does not use inverted matrix. Cannot read/write inverted matrix."); + } + if (!matrix_algo && (read_mat || write_mat || write_vec)) { + error->all(FLERR, + "Selected algorithm does not use matrix. Cannot read/write matrix or vector."); + } if (read_inv && read_mat) error->all(FLERR, "Cannot read matrix from two files"); - if (f_mat && read_inv) + if (write_mat && read_inv) error->all(FLERR, "Cannot write elastance matrix if reading capacitance matrix " "from file"); num_of_groups = static_cast(groups.size()); size_vector = num_of_groups; + array_flag = !!(algo == Algo::MATRIX_INV); + if (array_flag) { + size_array_rows = num_of_groups; + size_array_cols = 2 + 2 * num_of_groups; + } // check groups are consistent int *mask = atom->mask; @@ -243,15 +270,17 @@ FixElectrodeConp::FixElectrodeConp(LAMMPS *lmp, int narg, char **arg) : groupbit = group->bitmask[igroup]; ngroup = group->count(igroup); - accel_interface = new ElectrodeAccelInterface(lmp); + accel_interface = std::unique_ptr(new ElectrodeAccelInterface(lmp)); - memory->create(iele_gathered, ngroup, "FixElectrode:iele_gathered"); - memory->create(buf_gathered, ngroup, "FixElectrode:buf_gathered"); - memory->create(potential_iele, ngroup, "FixElectrode:potential_iele"); - memory->create(charge_iele, ngroup, "FixElectrode:charge_iele"); + if (matrix_algo) { + memory->create(iele_gathered, ngroup, "FixElectrode:iele_gathered"); + memory->create(buf_gathered, ngroup, "FixElectrode:buf_gathered"); + memory->create(potential_iele, ngroup, "FixElectrode:potential_iele"); + } atom->add_callback(Atom::GROW); // atomvec track local electrode atoms comm_reverse = 1; + comm_forward = 1; nlocalele = 0; @@ -260,12 +289,6 @@ FixElectrodeConp::FixElectrodeConp(LAMMPS *lmp, int narg, char **arg) : /* ---------------------------------------------------------------------- */ -// 0 1 2 3 return 4 if successful -// fix_modify fxupdate set v [group] [var] -// fix_modify fxupdate set qsb [group] [var] -// 0 1 2 3 4 return 5 if successful -// fix_modify fxupdate set mc [group1] [group2] [var] -// fix_modify fxupdate set me [group1] [group2] [var] int FixElectrodeConp::modify_param(int narg, char **arg) { if (strcmp(arg[0], "tf") == 0) { @@ -306,49 +329,6 @@ int FixElectrodeConp::modify_param(int narg, char **arg) timer_flag = utils::logical(FLERR, arg[1], false, lmp); return 2; - } else if (strcmp(arg[0], "set") == 0) { - if (strcmp(arg[1], "v") == 0 || strcmp(arg[1], "qsb") == 0) { - if (narg != 4) - error->all(FLERR, - fmt::format("Incorrect number of arguments for fix_modify set {}", arg[1])); - int outputgrp = groupnum_from_name(arg[2]); - int outputvar = input->variable->find(arg[3]); - if (outputvar < 0) - error->all(FLERR, - fmt::format("Variable {} for fix_modify electrode does not exist", arg[3])); - if (!input->variable->internalstyle(outputvar)) - error->all(FLERR, - fmt::format("Variable {} for fix_modify electrode is invalid style", arg[3])); - if (strcmp(arg[1], "v") == 0) - setvars_types.push_back(V); - else - setvars_types.push_back(QSB); - setvars_groups.push_back(outputgrp); - setvars_vars.push_back(outputvar); - return 4; - } else if (strcmp(arg[1], "mc") == 0 || strcmp(arg[1], "me") == 0) { - if (narg != 5) - error->all(FLERR, - fmt::format("Incorrect number of arguments for fix_modify set {}", arg[1])); - int outputgrpi = groupnum_from_name(arg[2]); - int outputgrpj = groupnum_from_name(arg[3]); - int outputgrpij = outputgrpi * num_of_groups + outputgrpj; - int outputvar = input->variable->find(arg[4]); - if (outputvar < 0) - error->all(FLERR, - fmt::format("Variable {} for fix_modify electrode does not exist", arg[4])); - if (!input->variable->internalstyle(outputvar)) - error->all(FLERR, - fmt::format("Variable {} for fix_modify electrode is invalid style", arg[4])); - if (strcmp(arg[1], "mc") == 0) - setvars_types.push_back(MC); - else - setvars_types.push_back(ME); - setvars_groups.push_back(outputgrpij); - setvars_vars.push_back(outputvar); - return 5; - } else - error->all(FLERR, "Invalid set option for fix_modify electrode"); } else error->all(FLERR, "Invalid argument for fix_modify electrode"); return 0; @@ -392,6 +372,12 @@ void FixElectrodeConp::init() } if (pair == nullptr) error->all(FLERR, "Fix electrode couldn't find a Coulombic pair style"); + // error if more than one fix electrode/* + int count = 0; + for (int i = 0; i < modify->nfix; i++) + if (strncmp(modify->fix[i]->style, "electrode", 9) == 0) count++; + if (count > 1) error->all(FLERR, "More than one fix electrode"); + // check for package intel accel_interface->intel_find_fix(); if (etypes_neighlists) @@ -436,7 +422,7 @@ void FixElectrodeConp::post_constructor() input->variable->set(fmt::format("{} equal f_{}[{}]", var_vtop, fixname, 1 + top_group)); input->variable->set(fmt::format("{} equal (v_{}-v_{})/lz", var_efield, var_vbot, var_vtop)); // check for other efields and warn if found - if (modify->get_fix_by_style("efield").size() > 0) + if (modify->get_fix_by_style("efield").size() > 0 && comm->me == 0) error->warning(FLERR, "Other efield fixes found -- please make sure this is intended!"); // call fix command: // fix [varstem]_efield all efield 0.0 0.0 [var_vdiff]/lz @@ -452,10 +438,6 @@ void FixElectrodeConp::setup_post_neighbor() int *mask = atom->mask; tagint *tag = atom->tag; - // setvars asserts: - assert(setvars_groups.size() == setvars_vars.size()); - assert(setvars_groups.size() == setvars_types.size()); - // if Thomas-Fermi, make sure all electrode atoms have parameters if (tfflag) { int unset_tf = 0; @@ -471,7 +453,7 @@ void FixElectrodeConp::setup_post_neighbor() // get equal-style variable ids: group_psi_var_ids = std::vector(num_of_groups, -1); for (int g = 0; g < num_of_groups; g++) { - if (group_psi_var_styles[g] == CONST) continue; + if (group_psi_var_styles[g] == VarStyle::CONST) continue; const char *var_name = group_psi_var_names[g].c_str(); int var_id = input->variable->find(var_name); if (var_id < 0) @@ -485,22 +467,11 @@ void FixElectrodeConp::setup_post_neighbor() // pair and list setups: evscale = force->qe2f / force->qqrd2e; - ele_vector->setup(pair, vec_neighlist, timer_flag); - if (!(read_mat || read_inv)) { - if (etypes_neighlists) neighbor->build_one(mat_neighlist, 0); - array_compute->setup(tag_to_iele, pair, mat_neighlist); - if (tfflag) { array_compute->setup_tf(tf_types); } + elyt_vector->setup(pair, vec_neighlist, timer_flag); + if (need_elec_vector) { + elec_vector->setup(pair, mat_neighlist, timer_flag); + if (tfflag) elec_vector->setup_tf(tf_types); } - // setup psi with target potentials - iele_to_group = std::vector(ngroup, -1); - sd_vectors = std::vector>(num_of_groups, std::vector(ngroup)); - sb_charges = std::vector(num_of_groups); - for (int i = 0; i < nlocal; i++) { - for (int g = 0; g < num_of_groups; g++) { - if (mask[i] & group_bits[g]) { iele_to_group[tag_to_iele[tag[i]]] = g; } - } - } - MPI_Allreduce(MPI_IN_PLACE, &iele_to_group.front(), ngroup, MPI_INT, MPI_MAX, world); auto const order_matrix = [](std::vector order, double **mat) { size_t n = order.size(); @@ -512,51 +483,93 @@ void FixElectrodeConp::setup_post_neighbor() return ordered_mat; }; - // capacitance matrix - memory->create(capacitance, ngroup, ngroup, "fix_electrode:capacitance"); - if (read_inv) { - read_from_file(input_file_inv, capacitance, "capacitance"); - } else { - // temporarily hold elastance in "capacitance" + if (matrix_algo) { + + sd_vectors = std::vector>(num_of_groups, std::vector(ngroup)); + sb_charges = std::vector(num_of_groups); + iele_to_group = std::vector(ngroup, -1); + for (int i = 0; i < nlocal; i++) { + for (int g = 0; g < num_of_groups; g++) { + if (mask[i] & group_bits[g]) { iele_to_group[tag_to_iele[tag[i]]] = g; } + } + } + MPI_Allreduce(MPI_IN_PLACE, &iele_to_group.front(), ngroup, MPI_INT, MPI_MAX, world); + + memory->create(elastance, ngroup, ngroup, "fix_electrode:matrix"); if (read_mat) - read_from_file(input_file_mat, capacitance, "elastance"); - else - array_compute->compute_array(capacitance, timer_flag); - if (f_mat && !(read_inv)) - write_to_file(f_mat, taglist_bygroup, order_matrix(group_idx, capacitance)); - invert(); // TODO uncommented lots of stuff here - } - if (symm) symmetrize(); + read_from_file(input_file_mat, elastance, "elastance"); + else if (!read_inv) { + if (etypes_neighlists) neighbor->build_one(mat_neighlist, 0); + auto array_compute = std::unique_ptr(new ElectrodeMatrix(lmp, igroup, eta)); + array_compute->setup(tag_to_iele, pair, mat_neighlist); + if (tfflag) { array_compute->setup_tf(tf_types); } + array_compute->compute_array(elastance, timer_flag); + } // write_mat before proceeding + if (comm->me == 0 && write_mat) { + auto f_mat = fopen(output_file_mat.c_str(), "w"); + if (f_mat == nullptr) + error->one(FLERR, + fmt::format("Cannot open elastance matrix file {}: {}", output_file_mat, + utils::getsyserror())); + write_to_file(f_mat, taglist_bygroup, order_matrix(group_idx, elastance)); + fclose(f_mat); + } + if (algo == Algo::MATRIX_INV) { + capacitance = elastance; + elastance = nullptr; + if (read_inv) + read_from_file(input_file_inv, capacitance, "capacitance"); + else + invert(); + if (symm) symmetrize(); - // build sd vectors and macro matrices - MPI_Barrier(world); - double start = MPI_Wtime(); - if (ffield) { - compute_sd_vectors_ffield(); - } else { - compute_sd_vectors(); + // build sd vectors and macro matrices + MPI_Barrier(world); + double start = MPI_Wtime(); + if (ffield) { + compute_sd_vectors_ffield(); + } else { + compute_sd_vectors(); + } + compute_macro_matrices(); + MPI_Barrier(world); + if (timer_flag && (comm->me == 0)) + utils::logmesg( + lmp, fmt::format("SD-vector and macro matrices time: {:.4g} s\n", MPI_Wtime() - start)); + } } - compute_macro_matrices(); - MPI_Barrier(world); - if (timer_flag && (comm->me == 0)) - utils::logmesg( - lmp, fmt::format("SD-vector and macro matrices time: {:.4g} s\n", MPI_Wtime() - start)); - // initial charges and b vector update_charges(); // write to files, ordered by group - memset(potential_i, 0, atom->nmax * sizeof(double)); - ele_vector->compute_vector(potential_i); - if (force->newton_pair) comm->reverse_comm(this); - buffer_and_gather(potential_i, potential_iele); - if (comm->me == 0) { - if (f_vec) { + if (write_vec) { + memset(potential_i, 0, atom->nmax * sizeof(double)); + elyt_vector->compute_vector(potential_i); + if (force->newton_pair) comm->reverse_comm(this); + buffer_and_gather(potential_i, potential_iele); + if (comm->me == 0) { + auto f_vec = fopen(output_file_vec.c_str(), "w"); + if (f_vec == nullptr) + error->one( + FLERR, + fmt::format("Cannot open vector file {}: {}", output_file_vec, utils::getsyserror())); std::vector> vec(ngroup, std::vector(1)); for (int i = 0; i < ngroup; i++) { vec[group_idx[i]][0] = potential_iele[i]; } write_to_file(f_vec, taglist_bygroup, vec); + fclose(f_vec); + } + } + + if (write_inv) { + if (comm->me == 0) { + auto f_inv = fopen(output_file_inv.c_str(), "w"); + if (f_inv == nullptr) + error->one(FLERR, + fmt::format("Cannot open capacitance matrix file {}: {}", output_file_inv, + utils::getsyserror())); + write_to_file(f_inv, taglist_bygroup, order_matrix(group_idx, capacitance)); + fclose(f_inv); } - if (f_inv) { write_to_file(f_inv, taglist_bygroup, order_matrix(group_idx, capacitance)); } } } @@ -567,13 +580,15 @@ void FixElectrodeConp::setup_pre_reverse(int eflag, int /*vflag*/) // correct forces for initial timestep gausscorr(eflag, true); self_energy(eflag); - potential_energy(eflag); + // potential_energy(eflag); // not always part of the energy, depending on ensemble, therefore + // removed } /* ---------------------------------------------------------------------- */ void FixElectrodeConp::invert() { + assert(algo == Algo::MATRIX_INV); MPI_Barrier(world); double invert_time = MPI_Wtime(); if (timer_flag && (comm->me == 0)) utils::logmesg(lmp, "CONP inverting matrix\n"); @@ -596,6 +611,11 @@ void FixElectrodeConp::invert() void FixElectrodeConp::symmetrize() { // S matrix to enforce charge neutrality constraint + if (read_inv && comm->me == 0) + error->warning(FLERR, + "Symmetrizing matrix from file. Make sure the provided matrix has not been " + "symmetrized yet."); + assert(algo == Algo::MATRIX_INV); std::vector AinvE(ngroup, 0.); double EAinvE = 0.0; for (int i = 0; i < ngroup; i++) { @@ -614,6 +634,10 @@ void FixElectrodeConp::symmetrize() void FixElectrodeConp::setup_pre_exchange() // create_taglist { + nlocalele_outdated = 1; // force regather + // + if (!matrix_algo) return; + int *mask = atom->mask; int const nlocal = atom->nlocal; int const nprocs = comm->nprocs; @@ -626,21 +650,21 @@ void FixElectrodeConp::setup_pre_exchange() // create_taglist taglist_bygroup = std::vector(); nlocalele = 0; for (int gbit : group_bits) { - std::vector taglist_local; + std::vector taglist_local_group; for (int i = 0; i < nlocal; i++) { if (mask[i] & gbit) { - taglist_local.push_back(tag[i]); + taglist_local_group.push_back(tag[i]); nlocalele++; } } // gather from all cpus for this group - int gnum_local = taglist_local.size(); + int gnum_local = taglist_local_group.size(); MPI_Allgather(&gnum_local, 1, MPI_INT, recvcounts, 1, MPI_INT, world); displs[0] = 0; for (int i = 1; i < nprocs; i++) { displs[i] = displs[i - 1] + recvcounts[i - 1]; } int const gnum = displs[nprocs - 1] + recvcounts[nprocs - 1]; std::vector taglist_all(gnum); - MPI_Allgatherv(&taglist_local.front(), gnum_local, MPI_LMP_TAGINT, &taglist_all.front(), + MPI_Allgatherv(&taglist_local_group.front(), gnum_local, MPI_LMP_TAGINT, &taglist_all.front(), recvcounts, displs, MPI_LMP_TAGINT, world); std::sort(taglist_all.begin(), taglist_all.end()); for (tagint t : taglist_all) taglist_bygroup.push_back(t); @@ -656,8 +680,6 @@ void FixElectrodeConp::setup_pre_exchange() // create_taglist tag_to_iele.insert(std::pair(taglist[i], i)); } - nlocalele_outdated = 1; // force regather - // group_idx allows mapping a vector that is sorted by taglist to being // ordered by taglist_bygroup group_idx = std::vector(taglist_bygroup.size()); @@ -668,10 +690,10 @@ void FixElectrodeConp::setup_pre_exchange() // create_taglist // if memory_usage > 0.5 GiB, warn with expected usage double mem_needed = memory_usage(); mem_needed /= (1024 * 1024 * 1024); // convert to GiB - if (mem_needed > 0.5) + if (mem_needed > 0.5 && comm->me == 0) error->warning(FLERR, fmt::format("Please ensure there is sufficient memory for fix electrode " - "(anticipated usage is {:.1f} per proc)", + "(anticipated usage is at least {:.1f} GiB per proc)", mem_needed)); } @@ -688,13 +710,15 @@ void FixElectrodeConp::pre_reverse(int eflag, int /*vflag*/) { gausscorr(eflag, true); self_energy(eflag); - potential_energy(eflag); + //potential_energy(eflag); // not always part of the energy, depending on ensemble, therefore + // removed } /* ---------------------------------------------------------------------- */ void FixElectrodeConp::compute_sd_vectors() { + assert(algo == Algo::MATRIX_INV); for (int g = 0; g < num_of_groups; g++) { for (int j = 0; j < ngroup; j++) { if (iele_to_group[j] == g) { @@ -708,6 +732,7 @@ void FixElectrodeConp::compute_sd_vectors() void FixElectrodeConp::compute_sd_vectors_ffield() { + assert(algo == Algo::MATRIX_INV); double **x = atom->x; int *mask = atom->mask; tagint *tag = atom->tag; @@ -756,6 +781,7 @@ int FixElectrodeConp::get_top_group() void FixElectrodeConp::update_charges() { + n_call++; MPI_Barrier(world); double start = MPI_Wtime(); if (atom->nmax > nmax) { @@ -764,92 +790,214 @@ void FixElectrodeConp::update_charges() memory->create(potential_i, nmax, "FixElectrode:potential_i"); } - std::fill(sb_charges.begin(), sb_charges.end(), 0.); double *q = atom->q; - int *mask = atom->mask; - tagint *tag = atom->tag; - int const nlocal = atom->nlocal; - int const nall = nlocal + atom->nghost; - memset(potential_i, 0, atom->nmax * sizeof(double)); - ele_vector->compute_vector(potential_i); - if (force->newton_pair) comm->reverse_comm(this); - buffer_and_gather(potential_i, potential_iele); - MPI_Barrier(world); + gather_list_iele(); pre_update(); - MPI_Barrier(world); - double mult_start = MPI_Wtime(); - for (int i_iele = 0; i_iele < nlocalele; i_iele++) { - double q_tmp = 0; - int const iele = list_iele[i_iele]; - double *_noalias caprow = capacitance[iele]; - for (int j = 0; j < ngroup; j++) { q_tmp -= caprow[j] * potential_iele[j]; } - buf_iele[i_iele] = q_tmp; - sb_charges[iele_to_group[iele]] += q_tmp; + accel_interface->intel_pack_buffers(); // update buffers for pppmintel to compute potential + auto q_local = std::vector(nlocalele, 0.); + if (algo == Algo::MATRIX_INV) { + std::fill(sb_charges.begin(), sb_charges.end(), 0.); + memset(potential_i, 0, atom->nmax * sizeof(double)); + elyt_vector->compute_vector(potential_i); + if (force->newton_pair) comm->reverse_comm(this); + buffer_and_gather(potential_i, potential_iele); + MPI_Barrier(world); + double mult_start = MPI_Wtime(); + for (int i_iele = 0; i_iele < nlocalele; i_iele++) { + double q_tmp = 0; + int const iele = list_iele[i_iele]; + double *_noalias caprow = capacitance[iele]; + for (int j = 0; j < ngroup; j++) { q_tmp -= caprow[j] * potential_iele[j]; } + q_local[i_iele] = q_tmp; + sb_charges[iele_to_group[iele]] += q_tmp; + } + MPI_Allreduce(MPI_IN_PLACE, &sb_charges.front(), num_of_groups, MPI_DOUBLE, MPI_SUM, world); + update_psi(); // use for equal-style and conq + for (int g = 0; g < num_of_groups; g++) + for (int j = 0; j < nlocalele; j++) q_local[j] += sd_vectors[g][list_iele[j]] * group_psi[g]; + MPI_Barrier(world); + mult_time += MPI_Wtime() - mult_start; + } else if (algo == Algo::MATRIX_CG || algo == Algo::CG) { // conjugate gradient algorithm + update_psi(); // update group_psi if equal-style + auto b = gather_elevec_local(elyt_vector); + for (int i = 0; i < nlocalele; i++) { + b[i] -= evscale * group_psi[iele_to_group_local[i]]; + q_local[i] = q[atom->map(taglist_local[i])]; // pre-condition with current charges + } + q_local = constraint_correction(q_local); + MPI_Barrier(world); + double mult_start = MPI_Wtime(); + auto a = ele_ele_interaction(q_local); + MPI_Barrier(world); + mult_time += MPI_Wtime() - mult_start; + auto r = add_nlocalele(b, a); + auto d = constraint_projection(r); + double dot_old = dot_nlocalele(r, d); + double delta = dot_old; + for (int k = 0; k < ngroup && delta > cg_threshold; k++, n_cg_step++) { + MPI_Barrier(world); + double mult_start_loop = MPI_Wtime(); + auto y = ele_ele_interaction(d); + MPI_Barrier(world); + mult_time += MPI_Wtime() - mult_start_loop; + double alpha = dot_old / -dot_nlocalele(d, y); + q_local = add_nlocalele(q_local, scale_vector(alpha, d)); + // prepare next step + if ((k + 1) % 20 == 0) { + // avoid shifting residual. This rarely happens. + q_local = constraint_correction(q_local); + a = ele_ele_interaction(q_local); + r = add_nlocalele(b, a); + } else { + r = add_nlocalele(r, scale_vector(alpha, y)); + } + auto p = constraint_projection(r); + double dot_new = dot_nlocalele(r, p); + d = add_nlocalele(p, scale_vector(dot_new / dot_old, d)); + delta = dot_nlocalele(r, d); + dot_old = dot_new; + } + recompute_potential(b, q_local); + if (delta > cg_threshold && comm->me == 0) error->warning(FLERR, "CG threshold not reached"); + } else { + error->all(FLERR, "This algorithm is not implemented, yet"); } - gather_elevec(charge_iele); - MPI_Allreduce(MPI_IN_PLACE, &sb_charges.front(), num_of_groups, MPI_DOUBLE, MPI_SUM, world); - - update_setvars(QSB); - update_psi(); // use for equal-style and conq - update_setvars(V); // push psi into 'fix_modify set' vars - - for (int g = 0; g < num_of_groups; g++) - for (int j = 0; j < ngroup; j++) { charge_iele[j] += sd_vectors[g][j] * group_psi[g]; } - - for (int i = 0; i < nall; i++) { - if (!(groupbit & mask[i])) continue; - int const iele = tag_to_iele[tag[i]]; - q[i] = charge_iele[iele]; - } - - MPI_Barrier(world); - mult_time += MPI_Wtime() - mult_start; + set_charges(q_local); update_time += MPI_Wtime() - start; accel_interface->intel_pack_buffers(); } +std::vector FixElectrodeConp::ele_ele_interaction(std::vector q_local) +{ + assert(q_local.size() == nlocalele); + assert(algo == Algo::CG || algo == Algo::MATRIX_CG); + if (algo == Algo::CG) { + set_charges(q_local); + return gather_elevec_local(elec_vector); + } else { + return times_elastance(gather_ngroup(q_local)); + } +} + +/* ---------------------------------------------------------------------- */ + +void FixElectrodeConp::set_charges(std::vector q_local) +{ + assert(q_local.size() == nlocalele); + double *q = atom->q; + for (int i = 0; i < nlocalele; i++) q[atom->map(taglist_local[i])] = q_local[i]; + comm->forward_comm(this); + accel_interface->intel_pack_buffers(); +} + +/* ---------------------------------------------------------------------- */ + +std::vector FixElectrodeConp::gather_elevec_local(ElectrodeVector *vec) +{ + memset(potential_i, 0, atom->nmax * sizeof(double)); + vec->compute_vector(potential_i); + if (force->newton_pair) comm->reverse_comm(this); + auto a = std::vector(nlocalele, 0.); + for (int i = 0; i < nlocalele; i++) a[i] = potential_i[atom->map(taglist_local[i])]; + return a; +} + +/* ---------------------------------------------------------------------- */ + +std::vector FixElectrodeConp::gather_ngroup(std::vector x_local) +{ + auto x = std::vector(ngroup, 0.); + for (int i = 0; i < nlocalele; i++) { + int const iele = list_iele[i]; + x[iele] = x_local[i]; + } + MPI_Allreduce(MPI_IN_PLACE, &x.front(), ngroup, MPI_DOUBLE, MPI_SUM, world); + return x; +} + +/* ---------------------------------------------------------------------- + ensure total electrode charge is 0 if symm +------------------------------------------------------------------------- */ + +std::vector FixElectrodeConp::constraint_correction(std::vector x) +{ + return constraint_projection(x); +} + +/* ---------------------------------------------------------------------- + project into direction that conserves total charge (cf. Gingrich master thesis) +------------------------------------------------------------------------- */ + +std::vector FixElectrodeConp::constraint_projection(std::vector x) +{ + if (symm) { + double sum = 0.; + for (double xi : x) sum += xi; + MPI_Allreduce(MPI_IN_PLACE, &sum, 1, MPI_DOUBLE, MPI_SUM, world); + sum /= ngroup; + for (double &xi : x) xi -= sum; + } + return x; +} + +/* ---------------------------------------------------------------------- */ + +std::vector FixElectrodeConp::scale_vector(double alpha, std::vector x) +{ + for (double &xi : x) xi *= alpha; + return x; +} + +/* ---------------------------------------------------------------------- */ + +std::vector FixElectrodeConp::add_nlocalele(std::vector a, std::vector b) +{ + assert(a.size() == nlocalele && b.size() == nlocalele); + for (int i = 0; i < nlocalele; i++) a[i] += b[i]; + return a; +} + +/* ---------------------------------------------------------------------- */ + +double FixElectrodeConp::dot_nlocalele(std::vector a, std::vector b) +{ + assert(a.size() == nlocalele && b.size() == nlocalele); + double out = 0.; + for (int i = 0; i < nlocalele; i++) out += a[i] * b[i]; + MPI_Allreduce(MPI_IN_PLACE, &out, 1, MPI_DOUBLE, MPI_SUM, world); + return out; +} + +/* ---------------------------------------------------------------------- */ + +std::vector FixElectrodeConp::times_elastance(std::vector x) +{ + assert(x.size() == ngroup); + auto out = std::vector(nlocalele, 0.); + for (int i = 0; i < nlocalele; i++) { + double *_noalias row = elastance[list_iele[i]]; + double oi = 0; + for (int j = 0; j < ngroup; j++) oi += row[j] * x[j]; + out[i] = oi; + } + return out; +} + /* ---------------------------------------------------------------------- */ void FixElectrodeConp::update_psi() { for (int g = 0; g < num_of_groups; g++) { - if (group_psi_var_styles[g] == CONST) continue; + if (group_psi_var_styles[g] == VarStyle::CONST) continue; group_psi[g] = input->variable->compute_equal(group_psi_var_ids[g]); } } /* ---------------------------------------------------------------------- */ -void FixElectrodeConp::update_setvars(int vtype) -{ - int num_of_vars = static_cast(setvars_groups.size()); - for (int v = 0; v < num_of_vars; v++) { - if (vtype != setvars_types[v]) continue; - switch (vtype) { - case V: - input->variable->internal_set(setvars_vars[v], group_psi[setvars_groups[v]]); - break; - case QSB: - input->variable->internal_set(setvars_vars[v], sb_charges[setvars_groups[v]]); - break; - case MC: { - int groupi = setvars_groups[v] / num_of_groups; - int groupj = setvars_groups[v] % num_of_groups; - input->variable->internal_set(setvars_vars[v], macro_capacitance[groupi][groupj]); - } break; - case ME: { - int groupi = setvars_groups[v] / num_of_groups; - int groupj = setvars_groups[v] % num_of_groups; - input->variable->internal_set(setvars_vars[v], macro_elastance[groupi][groupj]); - } - } - } -} - -/* ---------------------------------------------------------------------- */ - void FixElectrodeConp::compute_macro_matrices() { + assert(algo == Algo::MATRIX_INV); macro_capacitance = std::vector>(num_of_groups, std::vector(num_of_groups)); for (int g = 0; g < num_of_groups; g++) { @@ -865,13 +1013,13 @@ void FixElectrodeConp::compute_macro_matrices() macro_elastance = std::vector>(num_of_groups, std::vector(num_of_groups)); - // TODO: does determinant ever = 0 if !symm? what to do then? if (num_of_groups == 1) { macro_elastance[0][0] = 1 / macro_capacitance[0][0]; } else if (num_of_groups == 2) { - double detinv = 1 / - (macro_capacitance[0][0] * macro_capacitance[1][1] - - macro_capacitance[0][1] * macro_capacitance[1][0]); + double const det = macro_capacitance[0][0] * macro_capacitance[1][1] - + macro_capacitance[0][1] * macro_capacitance[1][0]; + if (fabs(det) < SMALL) error->all(FLERR, "ELECTRODE macro matrix inversion failed!"); + double const detinv = 1 / det; macro_elastance[0][0] = macro_capacitance[1][1] * detinv; macro_elastance[1][1] = macro_capacitance[0][0] * detinv; macro_elastance[0][1] = -macro_capacitance[0][1] * detinv; @@ -894,7 +1042,7 @@ void FixElectrodeConp::compute_macro_matrices() int info_rf, info_ri; dgetrf_(&m, &n, &tmp.front(), &lda, &ipiv.front(), &info_rf); dgetri_(&n, &tmp.front(), &lda, &ipiv.front(), &work.front(), &lwork, &info_ri); - if (info_rf != 0 || info_ri != 0) error->all(FLERR, "CONP macro matrix inversion failed!"); + if (info_rf != 0 || info_ri != 0) error->all(FLERR, "ELECTRODE macro matrix inversion failed!"); for (int i = 0; i < num_of_groups; i++) { for (int j = 0; j < num_of_groups; j++) { int idx = i * num_of_groups + j; @@ -902,17 +1050,15 @@ void FixElectrodeConp::compute_macro_matrices() } } } - - update_setvars(MC); - update_setvars(ME); } /* ---------------------------------------------------------------------- */ double FixElectrodeConp::compute_scalar() { - return potential_energy(0); + return potential_energy(); } + /* ---------------------------------------------------------------------- */ double FixElectrodeConp::compute_vector(int i) @@ -922,24 +1068,32 @@ double FixElectrodeConp::compute_vector(int i) /* ---------------------------------------------------------------------- */ -double FixElectrodeConp::potential_energy(int eflag) +double FixElectrodeConp::compute_array(int i, int j) +{ + if (j == 0) + return sb_charges[i]; + else if (j <= num_of_groups) + return macro_capacitance[i][j - 1]; + else if (j <= 2 * num_of_groups) + return macro_elastance[i][j - num_of_groups - 1]; + else + return 0.; // avoid -Wreturn-type warning +} + +/* ---------------------------------------------------------------------- */ + +double FixElectrodeConp::potential_energy() { // corrections to energy due to potential psi double const qqrd2e = force->qqrd2e; int const nlocal = atom->nlocal; int *mask = atom->mask; - tagint *tag = atom->tag; double *q = atom->q; double energy = 0; - for (int i = 0; i < nlocal; i++) { + for (int i = 0, iele = 0; i < nlocal; i++) { if (groupbit & mask[i]) { - int const i_iele = tag_to_iele[tag[i]]; - double e = -qqrd2e * q[i] * group_psi[iele_to_group[i_iele]] * evscale; - energy += e; - if (eflag) { - force->pair->ev_tally(i, i, nlocal, force->newton_pair, 0., e, 0, 0, 0, - 0); // 0 evdwl, 0 fpair, 0 delxyz - } + energy -= qqrd2e * q[i] * group_psi[iele_to_group_local[iele]] * evscale; + iele++; } } MPI_Allreduce(MPI_IN_PLACE, &energy, 1, MPI_DOUBLE, MPI_SUM, world); @@ -1054,30 +1208,36 @@ double FixElectrodeConp::gausscorr(int eflag, bool fflag) FixElectrodeConp::~FixElectrodeConp() { - if (timer_flag && (comm->me == 0)) { + if (comm->me == 0) { try { - utils::logmesg(lmp, fmt::format("Multiplication time: {:.4g} s\n", mult_time)); - utils::logmesg(lmp, fmt::format("Update time: {:.4g} s\n", update_time)); + if (timer_flag) { + utils::logmesg(lmp, fmt::format("Multiplication time: {:.4g} s\n", mult_time)); + utils::logmesg(lmp, fmt::format("Update time: {:.4g} s\n", update_time)); + } + if (algo == Algo::CG || algo == Algo::MATRIX_CG) + utils::logmesg( + lmp, + fmt::format("Average conjugate gradient steps: {:.4g}\n", n_cg_step * 1. / n_call)); } catch (std::exception &) { } } if (!modify->get_fix_by_id(id)) // avoid segfault if derived fixes' ctor throws err atom->delete_callback(id, Atom::GROW); // atomvec track local electrode atoms - delete[] recvcounts; - delete[] displs; - memory->destroy(iele_gathered); - memory->destroy(buf_gathered); + if (matrix_algo) { + delete[] recvcounts; + delete[] displs; + memory->destroy(iele_gathered); + memory->destroy(buf_gathered); + memory->destroy(potential_iele); + } memory->destroy(potential_i); - memory->destroy(potential_iele); - memory->destroy(charge_iele); - if (!(read_mat || read_inv)) delete array_compute; - delete ele_vector; - memory->destroy(capacitance); - delete accel_interface; - if (f_inv) fclose(f_inv); - if (f_mat) fclose(f_mat); - if (f_vec) fclose(f_vec); + delete elyt_vector; + if (need_elec_vector) delete elec_vector; + if (algo == Algo::MATRIX_INV) + memory->destroy(capacitance); + else if (matrix_algo) + memory->destroy(elastance); } /* ---------------------------------------------------------------------- */ @@ -1116,7 +1276,8 @@ void FixElectrodeConp::read_from_file(const std::string &input_file, double **ar std::vector tags; try { TextFileReader reader(input_file, filetype); - reader.set_bufsize(ngroup * 20 + 4); + int bufsize = ngroup * 20 + 4; + reader.set_bufsize(bufsize > 100 ? bufsize : 100); // get line with tags auto values = reader.next_values(ngroup); @@ -1157,6 +1318,25 @@ void FixElectrodeConp::read_from_file(const std::string &input_file, double **ar void FixElectrodeConp::request_etypes_neighlists() { int const ntypes = atom->ntypes; + // construct etypes + int *mask = atom->mask; + int *type = atom->type; + auto elec = std::vector(ntypes, 0); + auto elyt = std::vector(ntypes, 0); + for (int i = 0; i < atom->nlocal; i++) { + if (mask[i] & groupbit) + elec[type[i] - 1] += 1; + else + elyt[type[i] - 1] += 1; + } + MPI_Allreduce(MPI_IN_PLACE, &elec.front(), ntypes, MPI_INT, MPI_SUM, world); + MPI_Allreduce(MPI_IN_PLACE, &elyt.front(), ntypes, MPI_INT, MPI_SUM, world); + etypes.clear(); + for (int i = 0; i < ntypes; i++) { + if (!elec[i] == !elyt[i]) error->all(FLERR, "Types overlap, cannot use etypes keyword"); + if (elec[i]) etypes.push_back(i + 1); + } + // construct skip arrays int *iskip_mat = new int[ntypes + 1]; int *iskip_vec = new int[ntypes + 1]; int **ijskip_mat; @@ -1182,11 +1362,16 @@ void FixElectrodeConp::request_etypes_neighlists() } } - if (!(read_inv || read_mat)) { + if (need_array_compute) { auto matReq = neighbor->add_request(this, NeighConst::REQ_OCCASIONAL); matReq->set_skip(iskip_mat, ijskip_mat); matReq->set_id(1); if (intelflag) matReq->enable_intel(); + } else if (need_elec_vector) { + auto matReq = neighbor->add_request(this); + matReq->set_skip(iskip_mat, ijskip_mat); + matReq->set_id(1); + if (intelflag) matReq->enable_intel(); } else { delete[] iskip_mat; memory->destroy(ijskip_mat); @@ -1224,26 +1409,40 @@ void FixElectrodeConp::gather_list_iele() int *mask = atom->mask; tagint *tag = atom->tag; int const nlocal = atom->nlocal; - list_iele.clear(); - list_iele.reserve(nlocalele); - for (int i = 0; i < nlocal; i++) { - if (mask[i] & groupbit) list_iele.push_back(tag_to_iele[tag[i]]); + if (matrix_algo) { + list_iele.clear(); + list_iele.reserve(nlocalele); } + taglist_local.clear(); + iele_to_group_local.clear(); + for (int i = 0, iele = 0; i < nlocal; i++) { + if (mask[i] & groupbit) { + tagint const t = tag[i]; + if (matrix_algo) list_iele.push_back(tag_to_iele[t]); + taglist_local.push_back(t); + for (int g = 0; g < num_of_groups; g++) + if (mask[i] & group_bits[g]) iele_to_group_local.push_back(g); + iele++; + } + } + nlocalele = static_cast(taglist_local.size()); // just for safety + assert(iele_to_group_local.size() == nlocalele); - nlocalele = static_cast(list_iele.size()); // just for safety + if (matrix_algo) { + MPI_Allgather(&nlocalele, 1, MPI_INT, recvcounts, 1, MPI_INT, world); + displs[0] = 0; + int const nprocs = comm->nprocs; + for (int i = 1; i < nprocs; i++) { displs[i] = displs[i - 1] + recvcounts[i - 1]; } - MPI_Allgather(&nlocalele, 1, MPI_INT, recvcounts, 1, MPI_INT, world); - displs[0] = 0; - int const nprocs = comm->nprocs; - for (int i = 1; i < nprocs; i++) { displs[i] = displs[i - 1] + recvcounts[i - 1]; } - - MPI_Allgatherv(&list_iele[0], nlocalele, MPI_INT, iele_gathered, recvcounts, displs, MPI_INT, - world); + MPI_Allgatherv(&list_iele[0], nlocalele, MPI_INT, iele_gathered, recvcounts, displs, MPI_INT, + world); + } nlocalele_outdated = 0; } void FixElectrodeConp::gather_elevec(double *elevec) { + assert(matrix_algo); MPI_Allgatherv(&buf_iele[0], nlocalele, MPI_DOUBLE, buf_gathered, recvcounts, displs, MPI_DOUBLE, world); @@ -1252,13 +1451,11 @@ void FixElectrodeConp::gather_elevec(double *elevec) void FixElectrodeConp::buffer_and_gather(double *ivec, double *elevec) { - gather_list_iele(); - + assert(matrix_algo); buf_iele.reserve(nlocalele); // avoid unexpected reallocs for (int i_iele = 0; i_iele < nlocalele; i_iele++) { buf_iele[i_iele] = ivec[atom->map(taglist[list_iele[i_iele]])]; } - gather_elevec(elevec); } @@ -1268,16 +1465,25 @@ double FixElectrodeConp::memory_usage() int const nmax = atom->nmax; double bytes = 0.0; bytes += nmax * (sizeof(double)); // potential_i - bytes += ngroup * - (sizeof(int) + 3 * sizeof(double)); // iele_gathered, buf_gathered, pot / charge_iele - bytes += ngroup * ngroup * sizeof(double); // capacitance - bytes += nprocs * (2 * sizeof(int)); // displs, recvcounts - bytes += list_iele.capacity() * sizeof(int); - bytes += buf_iele.capacity() * sizeof(double); + if (matrix_algo) { + bytes += ngroup * (sizeof(int) + 2 * sizeof(double)); // iele_gathered, buf_gathered, pot + bytes += ngroup * ngroup * sizeof(double); // capacitance or elastance + bytes += list_iele.capacity() * sizeof(int); + bytes += buf_iele.capacity() * sizeof(double); + bytes += nprocs * (2 * sizeof(int)); // displs, recvcounts + bytes += (tag_to_iele.size() * (sizeof(int) + sizeof(void *)) + // data list + tag_to_iele.bucket_count() * (sizeof(void *) + sizeof(size_t))); // bucket index + bytes += taglist.capacity() * sizeof(tagint); + bytes += iele_to_group.capacity() * sizeof(int); + } + bytes += taglist_local.capacity() * sizeof(tagint); + bytes += iele_to_group_local.capacity() * sizeof(int); return bytes; } +/* ---------------------------------------------------------------------- */ + int FixElectrodeConp::pack_reverse_comm(int n, int first, double *buf) { int m = 0; @@ -1287,7 +1493,30 @@ int FixElectrodeConp::pack_reverse_comm(int n, int first, double *buf) return m; } +/* ---------------------------------------------------------------------- */ + void FixElectrodeConp::unpack_reverse_comm(int n, int *list, double *buf) { for (int i = 0; i < n; i++) { potential_i[list[i]] += buf[i]; } } + +/* ---------------------------------------------------------------------- */ + +int FixElectrodeConp::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/, + int * /*pbc*/) +{ + int m = 0; + for (int i = 0; i < n; i++) { + int const j = list[i]; + buf[m++] = atom->q[j]; + } + return m; +} + +/* ---------------------------------------------------------------------- */ + +void FixElectrodeConp::unpack_forward_comm(int n, int first, double *buf) +{ + int const last = first + n; + for (int i = first, m = 0; i < last; i++) atom->q[i] = buf[m++]; +} diff --git a/src/ELECTRODE/fix_electrode_conp.h b/src/ELECTRODE/fix_electrode_conp.h index c461920b90..42b0e5f52b 100644 --- a/src/ELECTRODE/fix_electrode_conp.h +++ b/src/ELECTRODE/fix_electrode_conp.h @@ -31,11 +31,13 @@ FixStyle(electrode/conp, FixElectrodeConp); #include #include +#include #include namespace LAMMPS_NS { class FixElectrodeConp : public Fix { + public: FixElectrodeConp(class LAMMPS *, int, char **); ~FixElectrodeConp() override; @@ -47,6 +49,7 @@ class FixElectrodeConp : public Fix { void pre_reverse(int, int) override; double compute_scalar() override; double compute_vector(int) override; + double compute_array(int, int) override; int modify_param(int, char **) override; int modify_param(const std::string &); void init() override; @@ -60,54 +63,64 @@ class FixElectrodeConp : public Fix { int pack_reverse_comm(int, int, double *) override; void unpack_reverse_comm(int, int *, double *) override; + int pack_forward_comm(int, int *, double *, int, int *) override; + void unpack_forward_comm(int, int, double *) override; protected: + enum class Algo { MATRIX_INV, MATRIX_CG, CG }; + enum class VarStyle { CONST, EQUAL }; virtual void update_psi(); virtual void pre_update(){}; + virtual void recompute_potential(std::vector, std::vector){}; + virtual std::vector constraint_projection(std::vector); + virtual std::vector constraint_correction(std::vector); virtual void compute_macro_matrices(); + std::vector ele_ele_interaction(std::vector); std::vector group_psi; std::vector group_bits; + std::vector groups; int num_of_groups; bigint ngroup; + double evscale; std::vector> sd_vectors; std::vector sb_charges; - std::vector group_psi_var_ids, group_psi_var_styles; + std::vector group_psi_var_ids; + std::vector group_psi_var_styles; std::vector group_psi_var_names; - bool symm; // symmetrize elastance for charge neutrality - std::vector> macro_elastance; // used by conq + std::vector iele_to_group_local; + bool symm; // symmetrize elastance for charge neutrality + Algo algo; + std::vector> macro_elastance; // used by conq std::vector> macro_capacitance; // used by thermo double thermo_temp, thermo_time; // used by electrode/thermo only int thermo_init; // initializer for rng in electrode/thermo bool ffield; // possibly tweak electrode/conq's version std::string fixname; // used by electrode/ffield to set up internal efield bool intelflag; - ElectrodeAccelInterface *accel_interface; // used by /intel + std::unique_ptr accel_interface; // used by /intel private: - FILE *f_inv, *f_mat, *f_vec; // files for capacitance, eleastance and vector + std::string output_file_inv, output_file_mat, output_file_vec; std::string input_file_inv, input_file_mat; - class ElectrodeMatrix *array_compute; - class ElectrodeVector *ele_vector; - std::vector groups; - double **capacitance; - bool read_inv, read_mat; - double eta; + class ElectrodeVector *elyt_vector, *elec_vector; + double **capacitance, **elastance; + bool read_inv, read_mat, write_inv, write_mat, write_vec; + bool matrix_algo, need_array_compute, need_elec_vector; + double eta, cg_threshold; double update_time, mult_time; + long n_cg_step, n_call; void create_taglist(); void invert(); void symmetrize(); double gausscorr(int, bool); void update_charges(); - double potential_energy(int); + double potential_energy(); double self_energy(int); void write_to_file(FILE *, const std::vector &, const std::vector> &); void read_from_file(const std::string &input_file, double **, const std::string &); void compute_sd_vectors(); void compute_sd_vectors_ffield(); - std::vector setvars_types, setvars_groups, setvars_vars; - void update_setvars(int); int groupnum_from_name(char *); - double evscale; class Pair *pair; class NeighList *mat_neighlist, *vec_neighlist; std::vector etypes; @@ -119,12 +132,21 @@ class FixElectrodeConp : public Fix { bool tfflag; bool timer_flag; std::map tf_types; + // cg + std::vector scale_vector(double, std::vector); + std::vector add_nlocalele(std::vector, std::vector); + double dot_nlocalele(std::vector, std::vector); + std::vector times_elastance(std::vector); + std::vector gather_ngroup(std::vector); + std::vector gather_elevec_local(ElectrodeVector *); + void set_charges(std::vector); // fix-specific electrode ID storage system: - std::vector taglist; // global list: all tags in combined electrode group - std::vector taglist_bygroup; // taglist sorted by group - std::vector group_idx; // permutation taglist<->taglist_bygroup + std::vector taglist; // global list: all tags in combined electrode group + std::vector taglist_local; + std::vector taglist_bygroup; // taglist sorted by group + std::vector group_idx; // permutation taglist<->taglist_bygroup std::unordered_map tag_to_iele; // inverse of taglist: std::vector iele_to_group; // tag_to_iele[taglist[iele]] = iele @@ -138,7 +160,6 @@ class FixElectrodeConp : public Fix { double *buf_gathered; // buffer for MPIgathered buf_iele (NOT YET iele-ordered) double *potential_i; // potentials, i-indexed (0 for non-electrode atoms) double *potential_iele; // potentials ordered by iele - double *charge_iele; // charges ordered by iele void gather_list_iele(); // build iele_gathered void gather_elevec(double *); // gather buf_iele and rearrange into iele-order diff --git a/src/ELECTRODE/fix_electrode_conq.cpp b/src/ELECTRODE/fix_electrode_conq.cpp index d7f4f58be1..0d3d1d2aaf 100644 --- a/src/ELECTRODE/fix_electrode_conq.cpp +++ b/src/ELECTRODE/fix_electrode_conq.cpp @@ -17,44 +17,108 @@ #include "fix_electrode_conq.h" +#include "comm.h" #include "error.h" #include "fix_electrode_conp.h" +#include "group.h" #include "input.h" #include "variable.h" using namespace LAMMPS_NS; -#define SMALL 0.00001 - -enum { CONST, EQUAL }; - -// 0 1 2 3 4 -// fix fxupdate group1 electrode/conp pot1 eta couple group2 pot2 FixElectrodeConq::FixElectrodeConq(LAMMPS *lmp, int narg, char **arg) : FixElectrodeConp(lmp, narg, arg) { // copy const-style values across because update_psi will change group_psi group_q = group_psi; - if (symm) { error->all(FLERR, "Keyword symm on not allowed in electrode/conq"); } + if (symm) { + if (num_of_groups == 1) + error->all(FLERR, "Keyword symm on not allowed in electrode/conq with only one electrode"); + if (comm->me == 0) + error->warning(FLERR, + "Fix electrode/conq with keyword symm ignores the charge setting for the last " + "electrode listed"); + if (algo != Algo::MATRIX_INV) { + double last_q = 0.; + for (int g = 0; g < num_of_groups - 1; g++) last_q -= group_q[g]; + group_q.back() = last_q; // needed for CG algos + } + } } void FixElectrodeConq::update_psi() { - // don't need MPI_Barrier because always preceded by MPI_Allreduce - for (int g = 0; g < num_of_groups; g++) { - if (group_psi_var_styles[g] == CONST) continue; + int const numsymm = num_of_groups - ((symm) ? 1 : 0); + bool symm_update_back = false; + for (int g = 0; g < numsymm; g++) { + if (group_psi_var_styles[g] == VarStyle::CONST) continue; group_q[g] = input->variable->compute_equal(group_psi_var_ids[g]); + symm_update_back = true; } - - std::vector group_remainder_q(num_of_groups); - for (int g = 0; g < num_of_groups; g++) { group_remainder_q[g] = group_q[g] - sb_charges[g]; } - - for (int g = 0; g < num_of_groups; g++) { - double vtmp = 0; - for (int h = 0; h < num_of_groups; h++) { - vtmp += macro_elastance[g][h] * group_remainder_q[h]; + if (algo == Algo::MATRIX_INV) { + std::vector group_remainder_q(num_of_groups, 0.); + for (int g = 0; g < numsymm; g++) { group_remainder_q[g] = group_q[g] - sb_charges[g]; } + for (int g = 0; g < num_of_groups; g++) { + double vtmp = 0; + for (int h = 0; h < num_of_groups; h++) { + vtmp += macro_elastance[g][h] * group_remainder_q[h]; + } + group_psi[g] = vtmp; } - group_psi[g] = vtmp; + } else { + if (symm && symm_update_back) { // needed for CG algos + double last_q = 0.; + for (int g = 0; g < num_of_groups - 1; g++) last_q -= group_q[g]; + group_q.back() = last_q; + } + for (double &g : group_psi) g = 0; } } + +/* ---------------------------------------------------------------------- + Correct charge of each electrode to target charge by adding a homogeneous charge +------------------------------------------------------------------------- */ + +std::vector FixElectrodeConq::constraint_correction(std::vector x) +{ + int const n = x.size(); + auto sums = std::vector(num_of_groups, 0); + for (int i = 0; i < n; i++) sums[iele_to_group_local[i]] += x[i]; + MPI_Allreduce(MPI_IN_PLACE, &sums.front(), num_of_groups, MPI_DOUBLE, MPI_SUM, world); + for (int g = 0; g < num_of_groups; g++) { + sums[g] -= group_q[g]; + sums[g] /= group->count(groups[g]); + } + for (int i = 0; i < n; i++) x[i] -= sums[iele_to_group_local[i]]; + return x; +} + +/* ---------------------------------------------------------------------- + Project into direction that conserves charge of each electrode (cf. M. Shariff (1995)) +------------------------------------------------------------------------- */ + +std::vector FixElectrodeConq::constraint_projection(std::vector x) +{ + int const n = x.size(); + auto sums = std::vector(num_of_groups, 0); + for (int i = 0; i < n; i++) sums[iele_to_group_local[i]] += x[i]; + MPI_Allreduce(MPI_IN_PLACE, &sums.front(), num_of_groups, MPI_DOUBLE, MPI_SUM, world); + for (int g = 0; g < num_of_groups; g++) sums[g] /= group->count(groups[g]); + for (int i = 0; i < n; i++) x[i] -= sums[iele_to_group_local[i]]; + return x; +} + +/* ---------------------------------------------------------------------- + Recompute group potential as average for output if using cg algo +------------------------------------------------------------------------- */ + +void FixElectrodeConq::recompute_potential(std::vector b, std::vector q_local) +{ + int const n = b.size(); + auto a = ele_ele_interaction(q_local); + auto psi_sums = std::vector(num_of_groups, 0); + for (int i = 0; i < n; i++) { psi_sums[iele_to_group_local[i]] += (a[i] + b[i]) / evscale; } + MPI_Allreduce(MPI_IN_PLACE, &psi_sums.front(), num_of_groups, MPI_DOUBLE, MPI_SUM, world); + for (int g = 0; g < num_of_groups; g++) group_psi[g] = psi_sums[g] / group->count(groups[g]); +} diff --git a/src/ELECTRODE/fix_electrode_conq.h b/src/ELECTRODE/fix_electrode_conq.h index f2bb763f7a..221ec2beff 100644 --- a/src/ELECTRODE/fix_electrode_conq.h +++ b/src/ELECTRODE/fix_electrode_conq.h @@ -34,6 +34,9 @@ class FixElectrodeConq : public FixElectrodeConp { public: FixElectrodeConq(class LAMMPS *, int, char **); void update_psi() override; + void recompute_potential(std::vector, std::vector) override; + std::vector constraint_projection(std::vector) override; + std::vector constraint_correction(std::vector) override; private: std::vector group_q; diff --git a/src/ELECTRODE/fix_electrode_thermo.cpp b/src/ELECTRODE/fix_electrode_thermo.cpp index c1f401527b..3bdf446f53 100644 --- a/src/ELECTRODE/fix_electrode_thermo.cpp +++ b/src/ELECTRODE/fix_electrode_thermo.cpp @@ -31,8 +31,6 @@ using namespace LAMMPS_NS; #define NUM_GROUPS 2 #define SMALL 0.00001 -enum { CONST, EQUAL }; - /* ----------------------------------------------------------------------- */ // 0 1 2 3 4 @@ -44,11 +42,11 @@ FixElectrodeThermo::FixElectrodeThermo(LAMMPS *lmp, int narg, char **arg) : error->all(FLERR, "Number of electrodes != two in electrode/thermo"); if (group_psi_var_styles[0] != group_psi_var_styles[1]) error->all(FLERR, "Potentials in electrode/thermo must have same style"); - if (symm) error->all(FLERR, "Keyword symm on not allowed in electrode/thermo"); + if (algo != Algo::MATRIX_INV) error->all(FLERR, "Algorithm not allowed in electrode/thermo"); if (thermo_time < SMALL) error->all(FLERR, "Keyword temp not set or zero in electrode/thermo"); thermo_random = new RanMars(lmp, thermo_init); - if (group_psi_var_styles[0] == CONST) delta_psi_0 = group_psi[1] - group_psi[0]; + if (group_psi_var_styles[0] == VarStyle::CONST) delta_psi_0 = group_psi[1] - group_psi[0]; } /* ----------------------------------------------------------------------- */ @@ -63,9 +61,12 @@ FixElectrodeThermo::~FixElectrodeThermo() void FixElectrodeThermo::compute_macro_matrices() { FixElectrodeConp::compute_macro_matrices(); - vac_cap = (macro_capacitance[0][0] * macro_capacitance[1][1] - - macro_capacitance[0][1] * macro_capacitance[0][1]) / - (macro_capacitance[0][0] + macro_capacitance[1][1] + 2 * macro_capacitance[0][1]); + if (symm) + vac_cap = macro_capacitance[0][0]; + else + vac_cap = (macro_capacitance[0][0] * macro_capacitance[1][1] - + macro_capacitance[0][1] * macro_capacitance[0][1]) / + (macro_capacitance[0][0] + macro_capacitance[1][1] + 2 * macro_capacitance[0][1]); } /* ----------------------------------------------------------------------- */ @@ -92,18 +93,15 @@ void FixElectrodeThermo::update_psi() double const dt = update->dt; // group_q_eff is charge that corresponds to potential after previous step - double group_q_eff[NUM_GROUPS] = {0., 0.}; - for (int g = 0; g < NUM_GROUPS; g++) { group_q_eff[g] = group_q_old[g] - sb_charges[g]; } - double group_psi_old[NUM_GROUPS] = {0., 0.}; - for (int g = 0; g < NUM_GROUPS; g++) { - double vtmp = 0; - for (int h = 0; h < NUM_GROUPS; h++) { vtmp += macro_elastance[g][h] * group_q_eff[h]; } - group_psi_old[g] = vtmp; - } + double const group_q_eff[NUM_GROUPS] = {group_q_old[0] - sb_charges[0], + (symm) ? 0. : group_q_old[1] - sb_charges[1]}; + double const group_psi_old[NUM_GROUPS] = { + macro_elastance[0][0] * group_q_eff[0] + macro_elastance[0][1] * group_q_eff[1], + macro_elastance[1][0] * group_q_eff[0] + macro_elastance[1][1] * group_q_eff[1]}; double const delta_psi = group_psi_old[1] - group_psi_old[0]; // target potential difference from input parameters - if (group_psi_var_styles[0] != CONST) { + if (group_psi_var_styles[0] != VarStyle::CONST) { delta_psi_0 = input->variable->compute_equal(group_psi_var_ids[1]) - input->variable->compute_equal(group_psi_var_ids[0]); } @@ -114,11 +112,10 @@ void FixElectrodeThermo::update_psi() thermo_random->gaussian(); double const group_remainder_q[NUM_GROUPS] = {-delta_charge - sb_charges[0], - delta_charge - sb_charges[1]}; + (symm) ? 0. : delta_charge - sb_charges[1]}; - for (int g = 0; g < NUM_GROUPS; g++) { - double vtmp = 0; - for (int h = 0; h < NUM_GROUPS; h++) { vtmp += macro_elastance[g][h] * group_remainder_q[h]; } - group_psi[g] = vtmp; - } + group_psi[0] = + macro_elastance[0][0] * group_remainder_q[0] + macro_elastance[0][1] * group_remainder_q[1]; + group_psi[1] = + macro_elastance[1][0] * group_remainder_q[0] + macro_elastance[1][1] * group_remainder_q[1]; } diff --git a/src/ELECTRODE/pppm_electrode.cpp b/src/ELECTRODE/pppm_electrode.cpp index e620983081..7418a052e6 100644 --- a/src/ELECTRODE/pppm_electrode.cpp +++ b/src/ELECTRODE/pppm_electrode.cpp @@ -20,7 +20,7 @@ #include "angle.h" #include "atom.h" #include "bond.h" -#include "boundary_correction.h" +#include "citeme.h" #include "comm.h" #include "domain.h" #include "error.h" @@ -62,11 +62,26 @@ enum { FORWARD_IK, FORWARD_AD, FORWARD_IK_PERATOM, FORWARD_AD_PERATOM }; #define ONEF 1.0 #endif +static const char cite_pppm_electrode[] = + "kspace_style pppm/electrode command:\n\n" + "@article{Ahrens2021,\n" + "author = {Ahrens-Iwers, Ludwig J.V. and Mei{\\ss}ner, Robert H.},\n" + "doi = {10.1063/5.0063381},\n" + "title = {{Constant potential simulations on a mesh}},\n" + "journal = {Journal of Chemical Physics},\n" + "year = {2021}\n" + "volume = {155},\n" + "pages = {104104},\n" + "}\n"; + /* ---------------------------------------------------------------------- */ PPPMElectrode::PPPMElectrode(LAMMPS *lmp) : - PPPM(lmp), electrolyte_density_brick(nullptr), electrolyte_density_fft(nullptr) + PPPM(lmp), electrolyte_density_brick(nullptr), electrolyte_density_fft(nullptr), + boundcorr(nullptr) { + if (lmp->citeme) lmp->citeme->add(cite_pppm_electrode); + group_group_enable = 0; electrolyte_density_brick = nullptr; electrolyte_density_fft = nullptr; @@ -83,7 +98,6 @@ PPPMElectrode::~PPPMElectrode() if (copymode) return; deallocate(); - delete boundcorr; if (peratom_allocate_flag) deallocate_peratom(); if (group_allocate_flag) deallocate_groups(); memory->destroy(part2grid); @@ -304,8 +318,6 @@ void PPPMElectrode::setup() double zprd_slab = zprd * slab_volfactor; volume = xprd_wire * yprd_wire * zprd_slab; - boundcorr->setup(xprd_wire, yprd_wire, zprd_slab); - delxinv = nx_pppm / xprd_wire; delyinv = ny_pppm / yprd_wire; delzinv = nz_pppm / zprd_slab; @@ -319,7 +331,7 @@ void PPPMElectrode::setup() // fkx,fky,fkz for my FFT grid pts for (i = nxlo_fft; i <= nxhi_fft; i++) { - int per = i - nx_pppm * (2 * i / nx_pppm); // TODO int division intentional? + int per = i - nx_pppm * (2 * i / nx_pppm); fkx[i] = unitkx * per; } @@ -431,13 +443,12 @@ void PPPMElectrode::compute(int eflag, int vflag) // return if there are no charges - // if (qsqsum == 0.0) return; TODO move back in - start_compute(); - if (compute_vector_called) { - // electrolyte_density_brick is filled, so we can - // grab only electrode atoms + if (compute_vector_called && last_invert_source) { + // electrolyte_density_brick is filled, so we can grab only electrode atoms. + // Does not work for direct cg algorithm because electrode charges change after compute_vector. + // Therefore, only when last_invert_source true. // TODO: this is dangerous now that compute_vector's interface has been // changed since a compute could call an arbitrary source, needs tightening make_rho_in_brick(last_source_grpbit, density_brick, !last_invert_source); @@ -467,9 +478,6 @@ void PPPMElectrode::compute(int eflag, int vflag) // also performs per-atom calculations via poisson_peratom() poisson(); - // cout << "###" << endl - //<< "POISSON ENERGY: " << energy * 0.5 * volume << endl - //<< "###" << endl; // all procs communicate E-field values // to fill ghost cells surrounding their 3d bricks @@ -548,7 +556,7 @@ void PPPMElectrode::compute(int eflag, int vflag) } } - boundcorr->compute_corr(qsum, slab_volfactor, eflag_atom, eflag_global, energy, eatom); + boundcorr->compute_corr(qsum, eflag_atom, eflag_global, energy, eatom); compute_vector_called = false; } @@ -661,11 +669,12 @@ void PPPMElectrode::project_psi(double *vec, int sensor_grpbit) void PPPMElectrode::compute_matrix(bigint *imat, double **matrix, bool timer_flag) { - // TODO replace compute with required setup - compute(1, 0); + compute(1, 0); // make sure density bricks etc. are set up - // fft green's function k -> r - std::vector greens_real((std::size_t) nz_pppm * ny_pppm * nx_pppm, 0.0); + // fft green's function k -> r (double) + double *greens_real; + memory->create(greens_real, nz_pppm * ny_pppm * nx_pppm, "pppm/electrode:greens_real"); + memset(greens_real, 0, (std::size_t)nz_pppm * (std::size_t)ny_pppm * (std::size_t)nx_pppm * sizeof(double)); for (int i = 0, n = 0; i < nfft; i++) { work2[n++] = greensfn[i]; work2[n++] = ZEROF; @@ -677,13 +686,14 @@ void PPPMElectrode::compute_matrix(bigint *imat, double **matrix, bool timer_fla greens_real[ny_pppm * nx_pppm * k + nx_pppm * j + i] = work2[n]; n += 2; } - MPI_Allreduce(MPI_IN_PLACE, &greens_real.front(), nz_pppm * ny_pppm * nx_pppm, MPI_DOUBLE, - MPI_SUM, world); + MPI_Allreduce(MPI_IN_PLACE, greens_real, nz_pppm * ny_pppm * nx_pppm, MPI_DOUBLE, MPI_SUM, world); int const nlocal = atom->nlocal; int nmat = std::count_if(&imat[0], &imat[nlocal], [](int x) { return x >= 0; }); MPI_Allreduce(MPI_IN_PLACE, &nmat, 1, MPI_INT, MPI_SUM, world); + + // gather x_ele double **x_ele; memory->create(x_ele, nmat, 3, "pppm/electrode:x_ele"); memset(&(x_ele[0][0]), 0, nmat * 3 * sizeof(double)); @@ -699,14 +709,14 @@ void PPPMElectrode::compute_matrix(bigint *imat, double **matrix, bool timer_fla one_step_multiplication(imat, greens_real, x_ele, matrix, nmat, timer_flag); else two_step_multiplication(imat, greens_real, x_ele, matrix, nmat, timer_flag); + memory->destroy(greens_real); memory->destroy(x_ele); } /* ----------------------------------------------------------------------*/ -void PPPMElectrode::one_step_multiplication(bigint *imat, const std::vector &greens_real, - double **x_ele, double **matrix, int const nmat, - bool timer_flag) +void PPPMElectrode::one_step_multiplication(bigint *imat, double *greens_real, double **x_ele, + double **matrix, int const nmat, bool timer_flag) { // map green's function in real space from mesh to particle positions // with matrix multiplication 'W^T G W' in one steps. Uses less memory than @@ -718,11 +728,19 @@ void PPPMElectrode::one_step_multiplication(bigint *imat, const std::vector>> rho1d_j( - nlocal, std::vector>(3, std::vector(order, 0))); + std::vector j_list; for (int j = 0; j < nlocal; j++) { int jpos = imat[j]; if (jpos < 0) continue; + j_list.push_back(j); + } + int const nj_local = j_list.size(); + + FFT_SCALAR ***rho1d_j; + memory->create(rho1d_j, nj_local, 3, order, "pppm/electrode:rho1d_j"); + + for (int jlist_pos = 0; jlist_pos < nj_local; jlist_pos++) { + int j = j_list[jlist_pos]; int njx = part2grid[j][0]; int njy = part2grid[j][1]; int njz = part2grid[j][2]; @@ -731,7 +749,7 @@ void PPPMElectrode::one_step_multiplication(bigint *imat, const std::vectorcreate(amesh, order6, "pppm/electrode:amesh"); for (int ipos = 0; ipos < nmat; ipos++) { double *_noalias xi_ele = x_ele[ipos]; // new calculation for nx, ny, nz because part2grid available for nlocal, @@ -750,44 +772,48 @@ void PPPMElectrode::one_step_multiplication(bigint *imat, const std::vectordestroy(amesh); + memory->destroy(rho1d_j); MPI_Barrier(world); if (timer_flag && (comm->me == 0)) utils::logmesg(lmp, fmt::format("Single step time: {:.4g} s\n", MPI_Wtime() - step1_time)); @@ -795,9 +821,38 @@ void PPPMElectrode::one_step_multiplication(bigint *imat, const std::vector &greens_real, - double **x_ele, double **matrix, int const nmat, - bool timer_flag) +void PPPMElectrode::build_amesh(const int dx, // = njx - nix + const int dy, // = njy - niy + const int dz, // = njz - niz + double *amesh, double *const greens_real) +{ + auto fmod = [](int x, int n) { // fast unsigned mod + int r = abs(x); + while (r >= n) r -= n; + return r; + }; + int ind_amesh = 0; + + for (int iz = 0; iz < order; iz++) + for (int jz = 0; jz < order; jz++) { + int const mz = fmod(dz + jz - iz, nz_pppm) * nx_pppm * ny_pppm; + for (int iy = 0; iy < order; iy++) + for (int jy = 0; jy < order; jy++) { + int const my = fmod(dy + jy - iy, ny_pppm) * nx_pppm; + for (int ix = 0; ix < order; ix++) + for (int jx = 0; jx < order; jx++) { + int const mx = fmod(dx + jx - ix, nx_pppm); + amesh[ind_amesh] = greens_real[mz + my + mx]; + ind_amesh++; + } + } + } +} + +/* ----------------------------------------------------------------------*/ + +void PPPMElectrode::two_step_multiplication(bigint *imat, double *greens_real, double **x_ele, + double **matrix, int const nmat, bool timer_flag) { // map green's function in real space from mesh to particle positions // with matrix multiplication 'W^T G W' in two steps. gw is result of @@ -809,7 +864,16 @@ void PPPMElectrode::two_step_multiplication(bigint *imat, const std::vector> gw(nmat, std::vector(nxyz, 0.)); + + double **gw; + memory->create(gw, nmat, nxyz, "pppm/electrode:gw"); + memset(&(gw[0][0]), 0, (std::size_t)nmat * (std::size_t)nxyz * sizeof(double)); + + auto fmod = [](int x, int n) { // fast unsigned mod + int r = abs(x); + while (r >= n) r -= n; + return r; + }; // loops over weights of electrode atoms and weights of complete grid // (nx,ny,nz) = global coords of grid pt to "lower left" of charge @@ -826,21 +890,21 @@ void PPPMElectrode::two_step_multiplication(bigint *imat, const std::vectorx; for (int i = 0; i < nlocal; i++) { @@ -890,6 +956,7 @@ void PPPMElectrode::two_step_multiplication(bigint *imat, const std::vectordestroy(gw); if (timer_flag && (comm->me == 0)) utils::logmesg(lmp, fmt::format("step 2 time: {:.4g} s\n", MPI_Wtime() - step2_time)); } @@ -1045,6 +1112,7 @@ void PPPMElectrode::deallocate() memory->destroy(gc_buf1); memory->destroy(gc_buf2); + if (boundcorr != nullptr) delete boundcorr; memory->destroy3d_offset(electrolyte_density_brick, nzlo_out, nylo_out, nxlo_out); memory->destroy(electrolyte_density_fft); diff --git a/src/ELECTRODE/pppm_electrode.h b/src/ELECTRODE/pppm_electrode.h index 58cc66eaa0..1eda1d78b8 100644 --- a/src/ELECTRODE/pppm_electrode.h +++ b/src/ELECTRODE/pppm_electrode.h @@ -93,10 +93,9 @@ class PPPMElectrode : public PPPM, public ElectrodeKSpace { void start_compute(); void make_rho_in_brick(int, FFT_SCALAR ***, bool); void project_psi(double *, int); - void one_step_multiplication(bigint *, const std::vector &, double **, double **, - int const, bool); - void two_step_multiplication(bigint *, const std::vector &, double **, double **, - int const, bool); + void one_step_multiplication(bigint *, double *, double **, double **, int const, bool); + void two_step_multiplication(bigint *, double *, double **, double **, int const, bool); + void build_amesh(int, int, int, double *, double *); bool compute_vector_called; }; diff --git a/src/ELECTRODE/slab_2d.cpp b/src/ELECTRODE/slab_2d.cpp index 509b3061e3..dac6001f9b 100644 --- a/src/ELECTRODE/slab_2d.cpp +++ b/src/ELECTRODE/slab_2d.cpp @@ -20,6 +20,8 @@ #include "atom.h" #include "comm.h" #include "domain.h" +#include "force.h" +#include "kspace.h" #include "math_const.h" #include "memory.h" @@ -32,13 +34,14 @@ using namespace MathConst; ------------------------------------------------------------------------- */ Slab2d::Slab2d(LAMMPS *lmp) : BoundaryCorrection(lmp){}; -void Slab2d::compute_corr(double /*qsum*/, double /*slab_volfactor*/, int eflag_atom, - int eflag_global, double &energy, double *eatom) +void Slab2d::compute_corr(double /*qsum*/, int eflag_atom, int eflag_global, double &energy, + double *eatom) { double *q = atom->q; double **x = atom->x; double **f = atom->f; int nlocal = atom->nlocal; + double const g_ewald = force->kspace->g_ewald; bigint natoms = atom->natoms; std::vector z = std::vector(nlocal); @@ -53,7 +56,9 @@ void Slab2d::compute_corr(double /*qsum*/, double /*slab_volfactor*/, int eflag_ &displs.front(), MPI_DOUBLE, world); const double g_ewald_inv = 1.0 / g_ewald; - const double qscale = qqrd2e * scale; + double const scale = 1.0; + const double qscale = force->qqrd2e * scale; + double const area = domain->xprd * domain->yprd; const double ffact = qscale * MY_2PI / area; const double efact = qscale * MY_PIS / area; double e_keq0 = 0; @@ -70,7 +75,7 @@ void Slab2d::compute_corr(double /*qsum*/, double /*slab_volfactor*/, int eflag_ } // per-atom energy; see eq. (20) in metalwalls ewald doc - if (eflag_atom) eatom[i] -= efact * q[i] * pot_ij; // TODO check if 0.5 factor + if (eflag_atom) eatom[i] -= efact * q[i] * pot_ij; if (eflag_global) e_keq0 -= q[i] * pot_ij; } if (eflag_global) { @@ -105,6 +110,8 @@ void Slab2d::vector_corr(double *vec, int sensor_grpbit, int source_grpbit, bool &recvcounts.front(), &displs.front(), MPI_DOUBLE, world); MPI_Allgatherv(&q_local.front(), n_electrolyte_local, MPI_DOUBLE, &q_all.front(), &recvcounts.front(), &displs.front(), MPI_DOUBLE, world); + double const g_ewald = force->kspace->g_ewald; + double const area = domain->xprd * domain->yprd; double const prefac = 2 * MY_PIS / area; for (int i = 0; i < nlocal; i++) { if (!(mask[i] & sensor_grpbit)) continue; @@ -148,8 +155,10 @@ void Slab2d::matrix_corr(bigint *imat, double **matrix) MPI_Allgatherv(&nprd_local.front(), ngrouplocal, MPI_DOUBLE, &nprd_all.front(), &recvcounts.front(), &displs.front(), MPI_DOUBLE, world); + double const g_ewald = force->kspace->g_ewald; const double g_ewald_inv = 1.0 / g_ewald; const double g_ewald_sq = g_ewald * g_ewald; + double const area = domain->xprd * domain->yprd; const double prefac = 2.0 * MY_PIS / area; std::vector jmat = gather_jmat(imat); for (int i = 0; i < nlocal; i++) { diff --git a/src/ELECTRODE/slab_2d.h b/src/ELECTRODE/slab_2d.h index 53bf57329d..544602cfab 100644 --- a/src/ELECTRODE/slab_2d.h +++ b/src/ELECTRODE/slab_2d.h @@ -27,7 +27,7 @@ class Slab2d : public BoundaryCorrection { Slab2d(LAMMPS *); void vector_corr(double *, int, int, bool) override; void matrix_corr(bigint *, double **) override; - void compute_corr(double, double, int, int, double &, double *) override; + void compute_corr(double, int, int, double &, double *) override; void setup(double); }; diff --git a/src/ELECTRODE/slab_dipole.cpp b/src/ELECTRODE/slab_dipole.cpp index d4f339750d..773d2a6bd6 100644 --- a/src/ELECTRODE/slab_dipole.cpp +++ b/src/ELECTRODE/slab_dipole.cpp @@ -20,6 +20,8 @@ #include "atom.h" #include "comm.h" #include "domain.h" +#include "force.h" +#include "kspace.h" #include "math_const.h" using namespace LAMMPS_NS; @@ -37,13 +39,14 @@ using namespace MathConst; */ SlabDipole::SlabDipole(LAMMPS *lmp) : BoundaryCorrection(lmp){}; -void SlabDipole::compute_corr(double qsum, double slab_volfactor, int eflag_atom, int eflag_global, - double &energy, double *eatom) +void SlabDipole::compute_corr(double qsum, int eflag_atom, int eflag_global, double &energy, + double *eatom) { // compute local contribution to global dipole moment + double const volume = get_volume(); double *q = atom->q; double **x = atom->x; - double zprd_slab = domain->zprd * slab_volfactor; + double zprd_slab = domain->zprd * force->kspace->slab_volfactor; int nlocal = atom->nlocal; double dipole = 0.0; for (int i = 0; i < nlocal; i++) dipole += q[i] * x[i][2]; @@ -67,7 +70,8 @@ void SlabDipole::compute_corr(double qsum, double slab_volfactor, int eflag_atom double const e_slabcorr = MY_2PI * (dipole_all * dipole_all - qsum * dipole_r2 - qsum * qsum * zprd_slab * zprd_slab / 12.0) / volume; - double const qscale = qqrd2e * scale; + double const scale = 1.0; + double const qscale = force->qqrd2e * scale; if (eflag_global) energy += qscale * e_slabcorr; // per-atom energy @@ -87,6 +91,7 @@ void SlabDipole::compute_corr(double qsum, double slab_volfactor, int eflag_atom void SlabDipole::vector_corr(double *vec, int sensor_grpbit, int source_grpbit, bool invert_source) { + double const volume = get_volume(); int const nlocal = atom->nlocal; double **x = atom->x; double *q = atom->q; @@ -104,6 +109,7 @@ void SlabDipole::vector_corr(double *vec, int sensor_grpbit, int source_grpbit, void SlabDipole::matrix_corr(bigint *imat, double **matrix) { + double const volume = get_volume(); int nlocal = atom->nlocal; double **x = atom->x; @@ -138,5 +144,4 @@ void SlabDipole::matrix_corr(bigint *imat, double **matrix) if (imat[i] != jmat[j]) matrix[jmat[j]][imat[i]] += aij; } } - // TODO add ELC corrections, needs sum over all kpoints but not (0,0) } diff --git a/src/ELECTRODE/slab_dipole.h b/src/ELECTRODE/slab_dipole.h index 677f71dd50..baa5fb5a4b 100644 --- a/src/ELECTRODE/slab_dipole.h +++ b/src/ELECTRODE/slab_dipole.h @@ -27,7 +27,7 @@ class SlabDipole : public BoundaryCorrection { SlabDipole(LAMMPS *); void vector_corr(double *, int, int, bool); void matrix_corr(bigint *, double **); - void compute_corr(double, double, int, int, double &, double *); + void compute_corr(double, int, int, double &, double *); void setup(double); }; diff --git a/src/ELECTRODE/wire_dipole.cpp b/src/ELECTRODE/wire_dipole.cpp index c113693d55..fc9cbc7014 100644 --- a/src/ELECTRODE/wire_dipole.cpp +++ b/src/ELECTRODE/wire_dipole.cpp @@ -20,6 +20,7 @@ #include "atom.h" #include "comm.h" #include "domain.h" +#include "force.h" #include "math_const.h" using namespace LAMMPS_NS; @@ -34,9 +35,10 @@ using namespace MathConst; */ WireDipole::WireDipole(LAMMPS *lmp) : BoundaryCorrection(lmp){}; -void WireDipole::compute_corr(double /*qsum*/, double /*slab_volfactor*/, int eflag_atom, - int eflag_global, double &energy, double *eatom) +void WireDipole::compute_corr(double /*qsum*/, int eflag_atom, int eflag_global, double &energy, + double *eatom) { + double const volume = get_volume(); double *q = atom->q; double **x = atom->x; int nlocal = atom->nlocal; @@ -72,7 +74,8 @@ void WireDipole::compute_corr(double /*qsum*/, double /*slab_volfactor*/, int ef // compute corrections const double e_wirecorr = MY_PI * (xdipole_all * xdipole_all + ydipole_all * ydipole_all) / volume; - const double qscale = qqrd2e * scale; + double const scale = 1.0; + const double qscale = force->qqrd2e * scale; if (eflag_global) energy += qscale * e_wirecorr; // per-atom energy @@ -94,6 +97,7 @@ void WireDipole::compute_corr(double /*qsum*/, double /*slab_volfactor*/, int ef void WireDipole::vector_corr(double *vec, int sensor_grpbit, int source_grpbit, bool invert_source) { + double const volume = get_volume(); int const nlocal = atom->nlocal; double **x = atom->x; double *q = atom->q; @@ -113,6 +117,7 @@ void WireDipole::vector_corr(double *vec, int sensor_grpbit, int source_grpbit, void WireDipole::matrix_corr(bigint *imat, double **matrix) { + double const volume = get_volume(); int nlocal = atom->nlocal; double **x = atom->x; diff --git a/src/ELECTRODE/wire_dipole.h b/src/ELECTRODE/wire_dipole.h index 70f596c0e8..649913cd13 100644 --- a/src/ELECTRODE/wire_dipole.h +++ b/src/ELECTRODE/wire_dipole.h @@ -27,7 +27,7 @@ class WireDipole : public BoundaryCorrection { WireDipole(LAMMPS *); void vector_corr(double *, int, int, bool); void matrix_corr(bigint *, double **); - void compute_corr(double, double, int, int, double &, double *); + void compute_corr(double, int, int, double &, double *); void setup(double); }; diff --git a/src/GPU/Install.sh b/src/GPU/Install.sh index 1768ec024f..d28e6260f8 100755 --- a/src/GPU/Install.sh +++ b/src/GPU/Install.sh @@ -176,7 +176,7 @@ if (test $1 = 1) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*gpu.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*gpu.*$/d' ../Makefile.package.settings # multiline form needed for BSD sed on Macs sed -i -e '4 i \ include ..\/..\/lib\/gpu\/Makefile.lammps @@ -191,7 +191,7 @@ elif (test $1 = 0) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*gpu.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*gpu.*$/d' ../Makefile.package.settings fi fi diff --git a/src/H5MD/Install.sh b/src/H5MD/Install.sh index 1070afaa96..ee442d80bc 100755 --- a/src/H5MD/Install.sh +++ b/src/H5MD/Install.sh @@ -45,7 +45,7 @@ if (test $1 = 1) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*h5md.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*h5md.*$/d' ../Makefile.package.settings # multiline form needed for BSD sed on Macs sed -i -e '4 i \ include ..\/..\/lib\/h5md\/Makefile.lammps @@ -60,7 +60,7 @@ elif (test $1 = 0) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*h5md.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*h5md.*$/d' ../Makefile.package.settings fi fi diff --git a/src/INTEL/electrode_accel_intel.h b/src/INTEL/electrode_accel_intel.h index 38b0fe9661..eba6bc0157 100644 --- a/src/INTEL/electrode_accel_intel.h +++ b/src/INTEL/electrode_accel_intel.h @@ -23,8 +23,8 @@ namespace LAMMPS_NS { class ElectrodeAccelIntel : public ElectrodeAccelInterface { public: ElectrodeAccelIntel(class LAMMPS *lmp); - void intel_find_fix(); - void intel_pack_buffers(); + void intel_find_fix() override; + void intel_pack_buffers() override; private: class FixIntel *fix; diff --git a/src/INTEL/fix_electrode_conp_intel.h b/src/INTEL/fix_electrode_conp_intel.h index e2dff685ad..920cdcb89a 100644 --- a/src/INTEL/fix_electrode_conp_intel.h +++ b/src/INTEL/fix_electrode_conp_intel.h @@ -36,8 +36,7 @@ class FixElectrodeConpIntel : public FixElectrodeConp { FixElectrodeConpIntel(class LAMMPS *lmp, int narg, char **arg) : FixElectrodeConp(lmp, narg, arg) { intelflag = true; - delete accel_interface; - accel_interface = new ElectrodeAccelIntel(lmp); + accel_interface = std::unique_ptr(new ElectrodeAccelIntel(lmp)); } }; diff --git a/src/INTEL/fix_electrode_conq_intel.h b/src/INTEL/fix_electrode_conq_intel.h index 8b4f41b694..2bc04a72fc 100644 --- a/src/INTEL/fix_electrode_conq_intel.h +++ b/src/INTEL/fix_electrode_conq_intel.h @@ -36,8 +36,7 @@ class FixElectrodeConqIntel : public FixElectrodeConq { FixElectrodeConqIntel(class LAMMPS *lmp, int narg, char **arg) : FixElectrodeConq(lmp, narg, arg) { intelflag = true; - delete accel_interface; - accel_interface = new ElectrodeAccelIntel(lmp); + accel_interface = std::unique_ptr(new ElectrodeAccelIntel(lmp)); } }; diff --git a/src/INTEL/fix_electrode_thermo_intel.h b/src/INTEL/fix_electrode_thermo_intel.h index 4d4ea6b374..de6d5fa29c 100644 --- a/src/INTEL/fix_electrode_thermo_intel.h +++ b/src/INTEL/fix_electrode_thermo_intel.h @@ -37,8 +37,7 @@ class FixElectrodeThermoIntel : public FixElectrodeThermo { FixElectrodeThermo(lmp, narg, arg) { intelflag = true; - delete accel_interface; - accel_interface = new ElectrodeAccelIntel(lmp); + accel_interface = std::unique_ptr(new ElectrodeAccelIntel(lmp)); } }; diff --git a/src/INTEL/pppm_electrode_intel.cpp b/src/INTEL/pppm_electrode_intel.cpp index bf1f9715e4..7a15f1d8a6 100644 --- a/src/INTEL/pppm_electrode_intel.cpp +++ b/src/INTEL/pppm_electrode_intel.cpp @@ -23,6 +23,7 @@ #include "angle.h" #include "atom.h" #include "bond.h" +#include "citeme.h" #include "comm.h" #include "domain.h" #include "error.h" @@ -65,10 +66,24 @@ enum : bool { ELECTRODE = true, ELECTROLYTE = false }; #define ONEF 1.0 #endif +static const char cite_pppm_electrode[] = + "kspace_style pppm/electrode command:\n\n" + "@article{Ahrens2021,\n" + "author = {Ahrens-Iwers, Ludwig J.V. and Mei{\\ss}ner, Robert H.},\n" + "doi = {10.1063/5.0063381},\n" + "title = {{Constant potential simulations on a mesh}},\n" + "journal = {Journal of Chemical Physics},\n" + "year = {2021}\n" + "volume = {155},\n" + "pages = {104104},\n" + "}\n"; + PPPMElectrodeIntel::PPPMElectrodeIntel(LAMMPS *lmp) : PPPMIntel(lmp), ElectrodeKSpace(), electrolyte_density_brick(nullptr), - electrolyte_density_fft(nullptr) + electrolyte_density_fft(nullptr), boundcorr(nullptr) { + if (lmp->citeme) lmp->citeme->add(cite_pppm_electrode); + group_group_enable = 0; electrolyte_density_brick = nullptr; electrolyte_density_fft = nullptr; @@ -83,7 +98,6 @@ PPPMElectrodeIntel::~PPPMElectrodeIntel() memory->destroy(electrolyte_density_fft); if ((differentiation_flag != 1) && !peratom_allocate_flag) memory->destroy3d_offset(u_brick, nzlo_out, nylo_out, nxlo_out); - delete boundcorr; } void PPPMElectrodeIntel::init() @@ -156,7 +170,6 @@ void PPPMElectrodeIntel::setup() prd[0] /= wire_volfactor; prd[1] /= wire_volfactor; - boundcorr->setup(xprd_wire, yprd_wire, zprd_slab); } void PPPMElectrodeIntel::compute(int eflag, int vflag) @@ -272,7 +285,7 @@ void PPPMElectrodeIntel::compute(int eflag, int vflag) slabflag = 0; // bypass compute_second's slabcorr() PPPMIntel::compute_second(eflag, vflag); slabflag = tempslabflag; - boundcorr->compute_corr(qsum, slab_volfactor, eflag_atom, eflag_global, energy, eatom); + boundcorr->compute_corr(qsum, eflag_atom, eflag_global, energy, eatom); compute_vector_called = false; } @@ -505,7 +518,9 @@ void PPPMElectrodeIntel::compute_matrix(bigint *imat, double **matrix, bool time compute(1, 0); // fft green's function k -> r - vector greens_real(nz_pppm * ny_pppm * nx_pppm, 0.); + double *greens_real; + memory->create(greens_real, nz_pppm * ny_pppm * nx_pppm, "pppm/electrode:greens_real"); + memset(greens_real, 0, nz_pppm * ny_pppm * nx_pppm * sizeof(double)); for (int i = 0, n = 0; i < nfft; i++) { work2[n++] = greensfn[i]; work2[n++] = ZEROF; @@ -517,8 +532,7 @@ void PPPMElectrodeIntel::compute_matrix(bigint *imat, double **matrix, bool time greens_real[ny_pppm * nx_pppm * k + nx_pppm * j + i] = work2[n]; n += 2; } - MPI_Allreduce(MPI_IN_PLACE, &greens_real.front(), nz_pppm * ny_pppm * nx_pppm, MPI_DOUBLE, - MPI_SUM, world); + MPI_Allreduce(MPI_IN_PLACE, greens_real, nz_pppm * ny_pppm * nx_pppm, MPI_DOUBLE, MPI_SUM, world); int const nlocal = atom->nlocal; int nmat = std::count_if(&imat[0], &imat[nlocal], [](int x) { return x >= 0; @@ -539,47 +553,50 @@ void PPPMElectrodeIntel::compute_matrix(bigint *imat, double **matrix, bool time one_step_multiplication(imat, greens_real, x_ele, matrix, nmat, timer_flag); else two_step_multiplication(imat, greens_real, x_ele, matrix, nmat, timer_flag); + memory->destroy(greens_real); memory->destroy(x_ele); } /* ----------------------------------------------------------------------*/ -void PPPMElectrodeIntel::one_step_multiplication(bigint *imat, vector greens_real, - double **x_ele, double **matrix, int const nmat, - bool timer_flag) +void PPPMElectrodeIntel::one_step_multiplication(bigint *imat, double *greens_real, double **x_ele, + double **matrix, int const nmat, bool timer_flag) { // map green's function in real space from mesh to particle positions // with matrix multiplication 'W^T G W' in one steps. Uses less memory than // two_step_multiplication // int const nlocal = atom->nlocal; - // double **x = atom->x; + double **x = atom->x; MPI_Barrier(world); double step1_time = MPI_Wtime(); // precalculate rho_1d for local electrode - vector>> rho1d_j(nlocal, - vector>(3, vector(order, 0))); - - _alignvar(FFT_SCALAR rho[3][INTEL_P3M_ALIGNED_MAXORDER], 64) = {0}; - + std::vector j_list; for (int j = 0; j < nlocal; j++) { int jpos = imat[j]; if (jpos < 0) continue; - double *_noalias xj = x_ele[jpos]; + j_list.push_back(j); + } + int const nj_local = j_list.size(); + + FFT_SCALAR ***rho1d_j; + memory->create(rho1d_j, nj_local, 3, order, "pppm/electrode:rho1d_j"); + + _alignvar(FFT_SCALAR rho[3][INTEL_P3M_ALIGNED_MAXORDER], 64) = {0}; + + for (int jlist_pos = 0; jlist_pos < nj_local; jlist_pos++) { + int j = j_list[jlist_pos]; int njx = part2grid[j][0]; int njy = part2grid[j][1]; int njz = part2grid[j][2]; - FFT_SCALAR djx = njx + shiftone - (xj[0] - boxlo[0]) * delxinv; - FFT_SCALAR djy = njy + shiftone - (xj[1] - boxlo[1]) * delyinv; - FFT_SCALAR djz = njz + shiftone - (xj[2] - boxlo[2]) * delzinv; + FFT_SCALAR const djx = njx + shiftone - (x[j][0] - boxlo[0]) * delxinv; + FFT_SCALAR const djy = njy + shiftone - (x[j][1] - boxlo[1]) * delyinv; + FFT_SCALAR const djz = njz + shiftone - (x[j][2] - boxlo[2]) * delzinv; if (_use_table) { - djx = djx * half_rho_scale + half_rho_scale_plus; - int idx = djx; - djy = djy * half_rho_scale + half_rho_scale_plus; - int idy = djy; - djz = djz * half_rho_scale + half_rho_scale_plus; - int idz = djz; + int idx = (int) (djx * half_rho_scale + half_rho_scale_plus); + int idy = (int) (djy * half_rho_scale + half_rho_scale_plus); + int idz = (int) (djz * half_rho_scale + half_rho_scale_plus); #if defined(LMP_SIMD_COMPILER) #pragma simd #endif @@ -607,7 +624,7 @@ void PPPMElectrodeIntel::one_step_multiplication(bigint *imat, vector gr } } for (int dim = 0; dim < 3; dim++) { - for (int oi = 0; oi < order; oi++) { rho1d_j[j][dim][oi] = (double) rho[dim][oi]; } + for (int oi = 0; oi < order; oi++) { rho1d_j[jlist_pos][dim][oi] = rho[dim][oi]; } } } @@ -615,6 +632,9 @@ void PPPMElectrodeIntel::one_step_multiplication(bigint *imat, vector gr // (nx,ny,nz) = global coords of grid pt to "lower left" of charge // (dx,dy,dz) = distance to "lower left" grid pt // (mx,my,mz) = global coords of moving stencil pt + int const order2 = INTEL_P3M_ALIGNED_MAXORDER * INTEL_P3M_ALIGNED_MAXORDER; + int const order6 = order2 * order2 * order2; + _alignvar(double amesh[order6], 64) = {0}; for (int ipos = 0; ipos < nmat; ipos++) { double *_noalias xi_ele = x_ele[ipos]; // new calculation for nx, ny, nz because part2grid available for nlocal, @@ -626,12 +646,9 @@ void PPPMElectrodeIntel::one_step_multiplication(bigint *imat, vector gr FFT_SCALAR diy = niy + shiftone - (xi_ele[1] - boxlo[1]) * delyinv; FFT_SCALAR diz = niz + shiftone - (xi_ele[2] - boxlo[2]) * delzinv; if (_use_table) { - dix = dix * half_rho_scale + half_rho_scale_plus; - int idx = dix; - diy = diy * half_rho_scale + half_rho_scale_plus; - int idy = diy; - diz = diz * half_rho_scale + half_rho_scale_plus; - int idz = diz; + int idx = (int) (dix * half_rho_scale + half_rho_scale_plus); + int idy = (int) (diy * half_rho_scale + half_rho_scale_plus); + int idz = (int) (diz * half_rho_scale + half_rho_scale_plus); #if defined(LMP_SIMD_COMPILER) #pragma simd #endif @@ -658,54 +675,85 @@ void PPPMElectrodeIntel::one_step_multiplication(bigint *imat, vector gr rho[2][k - nlower] = r3; } } - for (int j = 0; j < nlocal; j++) { + int njx = -1; + int njy = -1; + int njz = -1; // force initial build_amesh + for (int jlist_pos = 0; jlist_pos < nj_local; jlist_pos++) { + int j = j_list[jlist_pos]; int jpos = imat[j]; - if (jpos < 0) continue; + if ((ipos < jpos) == !((ipos - jpos) % 2)) continue; double aij = 0.; - int njx = part2grid[j][0]; - int njy = part2grid[j][1]; - int njz = part2grid[j][2]; - for (int ni = nlower; ni <= nupper; ni++) { - double iz0 = rho[2][ni - nlower]; - int miz = ni + niz; - for (int mi = nlower; mi <= nupper; mi++) { - double iy0 = iz0 * rho[1][mi - nlower]; - int miy = mi + niy; - for (int li = nlower; li <= nupper; li++) { - int mix = li + nix; - double const ix0 = iy0 * rho[0][li - nlower]; - for (int nj = nlower; nj <= nupper; nj++) { - double jz0 = rho1d_j[j][2][nj - nlower]; - int mjz = nj + njz; - int mz = abs(mjz - miz) % nz_pppm; - for (int mj = nlower; mj <= nupper; mj++) { - double jy0 = jz0 * rho1d_j[j][1][mj - nlower]; - int mjy = mj + njy; - int my = abs(mjy - miy) % ny_pppm; - for (int lj = nlower; lj <= nupper; lj++) { - int mjx = lj + njx; - int mx = abs(mjx - mix) % nx_pppm; - double const jx0 = jy0 * rho1d_j[j][0][lj - nlower]; - aij += ix0 * jx0 * greens_real[mz * nx_pppm * ny_pppm + my * nx_pppm + mx]; + if (njx != part2grid[j][0] || njy != part2grid[j][1] || njz != part2grid[j][2]) { + njx = part2grid[j][0]; + njy = part2grid[j][1]; + njz = part2grid[j][2]; + build_amesh(njx - nix, njy - niy, njz - niz, amesh, greens_real); + } + int ind_amesh = 0; + for (int ni = 0; ni < order; ni++) { + FFT_SCALAR const iz0 = rho[2][ni]; + for (int nj = 0; nj < order; nj++) { + FFT_SCALAR const jz0 = rho1d_j[jlist_pos][2][nj]; + for (int mi = 0; mi < order; mi++) { + FFT_SCALAR const iy0 = iz0 * rho[1][mi]; + for (int mj = 0; mj < order; mj++) { + FFT_SCALAR const jy0 = jz0 * rho1d_j[jlist_pos][1][mj]; + for (int li = 0; li < order; li++) { + FFT_SCALAR const ix0 = iy0 * rho[0][li]; + double aij_xscan = 0.; + for (int lj = 0; lj < order; lj++) { + aij_xscan += amesh[ind_amesh] * rho1d_j[jlist_pos][0][lj]; + ind_amesh++; } + aij += (double) ix0 * jy0 * aij_xscan; } } } } } matrix[ipos][jpos] += aij / volume; + if (ipos != jpos) matrix[jpos][ipos] += aij / volume; } } MPI_Barrier(world); + memory->destroy(rho1d_j); if (timer_flag && (comm->me == 0)) utils::logmesg(lmp, fmt::format("Single step time: {:.4g} s\n", MPI_Wtime() - step1_time)); } /* ----------------------------------------------------------------------*/ -void PPPMElectrodeIntel::two_step_multiplication(bigint *imat, vector greens_real, - double **x_ele, double **matrix, int const nmat, - bool timer_flag) +void PPPMElectrodeIntel::build_amesh(const int dx, // = njx - nix + const int dy, // = njy - niy + const int dz, // = njz - niz + double *amesh, double *const greens_real) +{ + auto fmod = [](int x, int n) { // fast unsigned mod + int r = abs(x); + while (r >= n) r -= n; + return r; + }; + int ind_amesh = 0; + + for (int iz = 0; iz < order; iz++) + for (int jz = 0; jz < order; jz++) { + int const mz = fmod(dz + jz - iz, nz_pppm) * nx_pppm * ny_pppm; + for (int iy = 0; iy < order; iy++) + for (int jy = 0; jy < order; jy++) { + int const my = fmod(dy + jy - iy, ny_pppm) * nx_pppm; + for (int ix = 0; ix < order; ix++) + for (int jx = 0; jx < order; jx++) { + int const mx = fmod(dx + jx - ix, nx_pppm); + amesh[ind_amesh] = greens_real[mz + my + mx]; + ind_amesh++; + } + } + } +} +/* ----------------------------------------------------------------------*/ + +void PPPMElectrodeIntel::two_step_multiplication(bigint *imat, double *greens_real, double **x_ele, + double **matrix, int const nmat, bool timer_flag) { // map green's function in real space from mesh to particle positions // with matrix multiplication 'W^T G W' in two steps. gw is result of @@ -1099,6 +1147,7 @@ void PPPMElectrodeIntel::allocate_peratom() void PPPMElectrodeIntel::deallocate() { + if (boundcorr != nullptr) delete boundcorr; // duplicated to always deallocate u_brick memory->destroy3d_offset(density_brick, nzlo_out, nylo_out, nxlo_out); memory->destroy3d_offset(u_brick, nzlo_out, nylo_out, nxlo_out); diff --git a/src/INTEL/pppm_electrode_intel.h b/src/INTEL/pppm_electrode_intel.h index e0e21af43f..8277aa9a82 100644 --- a/src/INTEL/pppm_electrode_intel.h +++ b/src/INTEL/pppm_electrode_intel.h @@ -89,10 +89,9 @@ class PPPMElectrodeIntel : public PPPMIntel, public ElectrodeKSpace { project_psi(buffers, vec, sensor_grpbit); } - void one_step_multiplication(bigint *, std::vector, double **, double **, int const, - bool); - void two_step_multiplication(bigint *, std::vector, double **, double **, int const, - bool); + void one_step_multiplication(bigint *, double *, double **, double **, int const, bool); + void two_step_multiplication(bigint *, double *, double **, double **, int const, bool); + void build_amesh(int, int, int, double *, double *); bool compute_vector_called; }; diff --git a/src/KIM/Install.sh b/src/KIM/Install.sh index 7ddb9c8227..533f4f997a 100755 --- a/src/KIM/Install.sh +++ b/src/KIM/Install.sh @@ -44,7 +44,7 @@ if (test $1 = 1) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*kim.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*kim.*$/d' ../Makefile.package.settings # multiline form needed for BSD sed on Macs sed -i -e '4 i \ include ..\/..\/lib\/kim\/Makefile.lammps @@ -58,7 +58,7 @@ elif (test $1 = 0) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*kim.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*kim.*$/d' ../Makefile.package.settings fi fi diff --git a/src/KOKKOS/Install.sh b/src/KOKKOS/Install.sh index 3c1f2dce1d..04859aedf1 100755 --- a/src/KOKKOS/Install.sh +++ b/src/KOKKOS/Install.sh @@ -374,7 +374,7 @@ if (test $1 = 1) then if (test -e ../Makefile.package.settings) then sed -i -e '/CXX\ =\ \$(CC)/d' ../Makefile.package.settings - sed -i -e '/^include.*kokkos.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*kokkos.*$/d' ../Makefile.package.settings # multiline form needed for BSD sed on Macs sed -i -e '4 i \ CXX = $(CC) @@ -401,7 +401,7 @@ elif (test $1 = 0) then if (test -e ../Makefile.package.settings) then sed -i -e '/CXX\ =\ \$(CC)/d' ../Makefile.package.settings - sed -i -e '/^include.*kokkos.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*kokkos.*$/d' ../Makefile.package.settings fi fi diff --git a/src/KOKKOS/min_linesearch_kokkos.cpp b/src/KOKKOS/min_linesearch_kokkos.cpp index 101502d023..920e06f70c 100644 --- a/src/KOKKOS/min_linesearch_kokkos.cpp +++ b/src/KOKKOS/min_linesearch_kokkos.cpp @@ -376,11 +376,15 @@ double MinLineSearchKokkos::alpha_step(double alpha, int resetflag) }); } + atomKK->modified(Device,X_MASK); + // step forward along h if (alpha > 0.0) { if (nextra_global) modify->min_step(alpha,hextra); + atomKK->sync(Device,X_MASK); // positions can be modified by fix box/relax + // local variables for lambda capture auto l_xvec = xvec; diff --git a/src/LATTE/Install.sh b/src/LATTE/Install.sh index 73f8bc24cb..4d895ca434 100755 --- a/src/LATTE/Install.sh +++ b/src/LATTE/Install.sh @@ -47,7 +47,7 @@ if (test $1 = 1) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*latte.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*latte.*$/d' ../Makefile.package.settings # multiline form needed for BSD sed on Macs sed -i -e '4 i \ include ..\/..\/lib\/latte\/Makefile.lammps @@ -61,7 +61,7 @@ elif (test $1 = 0) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*latte.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*latte.*$/d' ../Makefile.package.settings fi fi diff --git a/src/MACHDYN/Install.sh b/src/MACHDYN/Install.sh index bf18c332f3..604f53f8b1 100755 --- a/src/MACHDYN/Install.sh +++ b/src/MACHDYN/Install.sh @@ -45,7 +45,7 @@ if (test $1 = 1) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*machdyn.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*machdyn.*$/d' ../Makefile.package.settings # multiline form needed for BSD sed on Macs sed -i -e '4 i \ include ..\/..\/lib\/machdyn\/Makefile.lammps @@ -59,7 +59,7 @@ elif (test $1 = 0) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*machdyn.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*machdyn.*$/d' ../Makefile.package.settings fi fi diff --git a/src/MDI/Install.sh b/src/MDI/Install.sh index bc19162a17..804e66be5e 100755 --- a/src/MDI/Install.sh +++ b/src/MDI/Install.sh @@ -49,7 +49,7 @@ if (test $1 = 1) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*mdi.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*mdi.*$/d' ../Makefile.package.settings # multiline form needed for BSD sed on Macs sed -i -e '4 i \ include ..\/..\/lib\/mdi\/Makefile.lammps @@ -65,7 +65,7 @@ elif (test $1 = 0) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*mdi.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*mdi.*$/d' ../Makefile.package.settings fi fi diff --git a/src/MESONT/Install.sh b/src/MESONT/Install.sh index 6e51bfae64..09e6c03dde 100644 --- a/src/MESONT/Install.sh +++ b/src/MESONT/Install.sh @@ -47,7 +47,7 @@ if (test $1 = 1) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*mesont.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*mesont.*$/d' ../Makefile.package.settings # multiline form needed for BSD sed on Macs sed -i -e '4 i \ include ..\/..\/lib\/mesont\/Makefile.lammps @@ -61,7 +61,7 @@ elif (test $1 = 0) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*mesont.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*mesont.*$/d' ../Makefile.package.settings fi fi diff --git a/src/ML-HDNNP/Install.sh b/src/ML-HDNNP/Install.sh index 74e5f1b91e..f343f38851 100644 --- a/src/ML-HDNNP/Install.sh +++ b/src/ML-HDNNP/Install.sh @@ -46,7 +46,7 @@ if (test $1 = 1) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*hdnnp.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*hdnnp.*$/d' ../Makefile.package.settings # multiline form needed for BSD sed on Macs sed -i -e '4 i \ include ..\/..\/lib\/hdnnp\/Makefile.lammps @@ -60,7 +60,7 @@ elif (test $1 = 0) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*hdnnp.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*hdnnp.*$/d' ../Makefile.package.settings fi fi diff --git a/src/ML-IAP/Install.sh b/src/ML-IAP/Install.sh index 27c9b19b01..18812c6026 100755 --- a/src/ML-IAP/Install.sh +++ b/src/ML-IAP/Install.sh @@ -52,7 +52,7 @@ if (test $1 = 1) then sed -i -e 's|^PKG_INC =[ \t]*|&-DMLIAP_PYTHON |' ../Makefile.package fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*python.*mliap_python.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*python.*mliap_python.*$/d' ../Makefile.package.settings # multiline form needed for BSD sed on Macs sed -i -e '4 i \ include ..\/..\/lib\/python\/Makefile.mliap_python @@ -68,7 +68,7 @@ elif (test $1 = 0) then fi rm -f ../mliap_model_python_couple.cpp ../mliap_model_python_couple.h \ ../mliap_unified_couple.cpp ../mliap_unified_couple.h - sed -i -e '/^include.*python.*mliap_python.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*python.*mliap_python.*$/d' ../Makefile.package.settings elif (test $1 = 2) then if (type cythonize > /dev/null 2>&1 && test -e ../python_impl.cpp) then @@ -77,12 +77,12 @@ elif (test $1 = 2) then fi rm -f ../mliap_model_python_couple.cpp ../mliap_model_python_couple.h \ ../mliap_unified_couple.cpp ../mliap_unified_couple.h - sed -i -e '/^include.*python.*mliap_python.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*python.*mliap_python.*$/d' ../Makefile.package.settings if (test -e ../Makefile.package) then sed -i -e 's|^PKG_INC =[ \t]*|&-DMLIAP_PYTHON |' ../Makefile.package fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*python.*mliap_python.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*python.*mliap_python.*$/d' ../Makefile.package.settings # multiline form needed for BSD sed on Macs sed -i -e '4 i \ include ..\/..\/lib\/python\/Makefile.mliap_python diff --git a/src/ML-PACE/Install.sh b/src/ML-PACE/Install.sh index c099ddd2c4..c0a0958424 100644 --- a/src/ML-PACE/Install.sh +++ b/src/ML-PACE/Install.sh @@ -44,7 +44,7 @@ if (test $1 = 1) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*pace.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*pace.*$/d' ../Makefile.package.settings # multiline form needed for BSD sed on Macs sed -i -e '4 i \ include ..\/..\/lib\/pace\/Makefile.lammps @@ -58,7 +58,7 @@ elif (test $1 = 0) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*pace.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*pace.*$/d' ../Makefile.package.settings fi fi diff --git a/src/ML-POD/Install.sh b/src/ML-POD/Install.sh new file mode 100755 index 0000000000..a62887e1b3 --- /dev/null +++ b/src/ML-POD/Install.sh @@ -0,0 +1,59 @@ +# Install/unInstall package files in LAMMPS +# mode = 0/1/2 for uninstall/install/update + +mode=$1 + +# enforce using portable C locale +LC_ALL=C +export LC_ALL + +# arg1 = file, arg2 = file it depends on + +action () { + if (test $mode = 0) then + rm -f ../$1 + elif (! cmp -s $1 ../$1) then + if (test -z "$2" || test -e ../$2) then + cp $1 .. + if (test $mode = 2) then + echo " updating src/$1" + fi + fi + elif (test -n "$2") then + if (test ! -e ../$2) then + rm -f ../$1 + fi + fi +} + +# all package files with no dependencies + +for file in *.cpp *.h; do + test -f ${file} && action $file +done + +if (test $1 = 1) then + if (test -e ../Makefile.package) then + sed -i -e 's/[^ \t]*mlpod[^ \t]* //g' ../Makefile.package + sed -i -e 's|^PKG_PATH =[ \t]*|&-L../../lib/mlpod |' ../Makefile.package + sed -i -e 's|^PKG_LIB =[ \t]*|&-lmlpod |' ../Makefile.package + sed -i -e 's|^PKG_SYSPATH =[ \t]*|&$(mlpod_SYSPATH) |' ../Makefile.package + sed -i -e 's|^PKG_SYSLIB =[ \t]*|&$(mlpod_SYSLIB) |' ../Makefile.package + fi + if (test -e ../Makefile.package.settings) then + sed -i -e '/^[ \t]*include.*mlpod.*$/d' ../Makefile.package.settings + # multiline form needed for BSD sed on Macs + sed -i -e '4 i \ +include ..\/..\/lib\/mlpod\/Makefile.lammps +' ../Makefile.package.settings + fi + +elif (test $1 = 0) then + if (test -e ../Makefile.package) then + sed -i -e 's/[^ \t]*mlpod[^ \t]* //g' ../Makefile.package + fi + if (test -e ../Makefile.package.settings) then + sed -i -e '/^[ \t]*include.*mlpod.*$/d' ../Makefile.package.settings + fi +fi + diff --git a/src/ML-POD/fitpod_command.cpp b/src/ML-POD/fitpod_command.cpp new file mode 100644 index 0000000000..c78f5eec76 --- /dev/null +++ b/src/ML-POD/fitpod_command.cpp @@ -0,0 +1,1826 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/ Sandia National Laboratories + LAMMPS development team: developers@lammps.org + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing authors: Ngoc Cuong Nguyen (MIT) and Andrew Rohskopf (SNL) +------------------------------------------------------------------------- */ + +#include "fitpod_command.h" + +#include "mlpod.h" + +#include "atom.h" +#include "comm.h" +#include "error.h" +#include "force.h" +#include "math_const.h" +#include "math_special.h" +#include "memory.h" +#include "modify.h" +#include "neigh_list.h" +#include "neighbor.h" +#include "pair.h" +#include "tokenizer.h" +#include "update.h" + +#include +#include +#include +#include +#include + +using namespace LAMMPS_NS; +using MathSpecial::powint; + +#define MAXLINE 1024 + +static constexpr double SMALL = 1.0e-10; + +FitPOD::FitPOD(LAMMPS *_lmp) : Command(_lmp), podptr(nullptr) +{ +} + +void FitPOD::command(int narg, char **arg) +{ + if (narg < 2) utils::missing_cmd_args(FLERR, "fitpod", error); + + std::string pod_file = std::string(arg[0]); // pod input file + std::string data_file = std::string(arg[1]); // data input file + std::string coeff_file; // coefficient input file + + if (narg > 2) + coeff_file = std::string(arg[2]); // coefficient input file + else + coeff_file = ""; + + podptr = new MLPOD(lmp, pod_file, coeff_file); + read_data_files(data_file, podptr->pod.species); + + if ((int) traindata.data_path.size() > 1) + allocate_memory(traindata); + else if ((int) testdata.data_path.size() > 1) + allocate_memory(testdata); + + // get POD coefficients from an input file + + if (coeff_file != "") podArrayCopy(desc.c, podptr->pod.coeff, podptr->pod.nd); + + // compute POD coefficients using least-squares method + + least_squares_fit(traindata); + + // calculate errors for the training data set + + if ((traindata.training_analysis) && ((int) traindata.data_path.size() > 1) ) + error_analysis(traindata, desc.c); + + // calculate errors for the test data set + + if ((testdata.test_analysis) && ((int) testdata.data_path.size() > 1) && (testdata.data_path != traindata.data_path)) + error_analysis(testdata, desc.c); + + // calculate energy and force for the training data set + + if ((traindata.training_calculation) && ((int) traindata.data_path.size() > 1) ) + energyforce_calculation(traindata, desc.c); + + // calculate energy and force for the test data set + + if ((testdata.test_calculation) && ((int) testdata.data_path.size() > 1) && (testdata.data_path != traindata.data_path) ) + energyforce_calculation(testdata, desc.c); + + // deallocate training data + + if ((int) traindata.data_path.size() > 1){ + memory->destroy(traindata.lattice); + memory->destroy(traindata.energy); + memory->destroy(traindata.stress); + memory->destroy(traindata.position); + memory->destroy(traindata.force); + memory->destroy(traindata.atomtype); + } + + // deallocate testing data + + if ((int) testdata.data_path.size() > 1 && (testdata.data_path != traindata.data_path)){ + memory->destroy(testdata.lattice); + memory->destroy(testdata.energy); + memory->destroy(testdata.stress); + memory->destroy(testdata.position); + memory->destroy(testdata.force); + memory->destroy(testdata.atomtype); + } + + // deallocate descriptors + + memory->destroy(desc.gd); + memory->destroy(desc.gdd); + memory->destroy(desc.A); + memory->destroy(desc.b); + memory->destroy(desc.c); + memory->destroy(desc.tmpint); + + // deallocate neighbor data + + memory->destroy(nb.alist); + memory->destroy(nb.pairnum); + memory->destroy(nb.pairnum_cumsum); + memory->destroy(nb.pairlist); + memory->destroy(nb.y); + delete podptr; +} + +/* ---------------------------------------------------------------------- */ + +int FitPOD::read_data_file(double *fitting_weights, std::string &file_format, + std::string &file_extension, std::string &test_path, + std::string &training_path, std::string &filenametag, + const std::string &data_file) +{ + int precision = 8; + + std::string datafilename = data_file; + FILE *fpdata; + if (comm->me == 0) { + + fpdata = utils::open_potential(datafilename,lmp,nullptr); + if (fpdata == nullptr) + error->one(FLERR,"Cannot open training data file {}: ", datafilename, utils::getsyserror()); + } + + // loop through lines of training data file and parse keywords + + char line[MAXLINE],*ptr; + int eof = 0; + while (true) { + if (comm->me == 0) { + ptr = fgets(line,MAXLINE,fpdata); + if (ptr == nullptr) { + eof = 1; + fclose(fpdata); + } + } + MPI_Bcast(&eof,1,MPI_INT,0,world); + if (eof) break; + MPI_Bcast(line,MAXLINE,MPI_CHAR,0,world); + + // words = ptrs to all words in line + // strip single and double quotes from words + + std::vector words; + try { + words = Tokenizer(utils::trim_comment(line),"\"' \t\n\r\f").as_vector(); + } catch (TokenizerException &) { + // ignore + } + + if (words.size() == 0) continue; + + auto keywd = words[0]; + + if (words.size() != 2) + error->one(FLERR,"Improper POD file.", utils::getsyserror()); + + // settings for fitting weights + + if (keywd == "fitting_weight_energy") fitting_weights[0] = utils::numeric(FLERR,words[1],false,lmp); + if (keywd == "fitting_weight_force") fitting_weights[1] = utils::numeric(FLERR,words[1],false,lmp); + if (keywd == "fitting_weight_stress") fitting_weights[2] = utils::numeric(FLERR,words[1],false,lmp); + if (keywd == "error_analysis_for_training_data_set") fitting_weights[3] = utils::numeric(FLERR,words[1],false,lmp); + if (keywd == "error_analysis_for_test_data_set") fitting_weights[4] = utils::numeric(FLERR,words[1],false,lmp); + if (keywd == "energy_force_calculation_for_training_data_set") fitting_weights[5] = utils::numeric(FLERR,words[1],false,lmp); + if (keywd == "energy_force_calculation_for_test_data_set") fitting_weights[6] = utils::numeric(FLERR,words[1],false,lmp); + if (keywd == "fraction_training_data_set") fitting_weights[7] = utils::numeric(FLERR,words[1],false,lmp); + if (keywd == "fraction_test_data_set") fitting_weights[8] = utils::numeric(FLERR,words[1],false,lmp); + if (keywd == "randomize_training_data_set") fitting_weights[9] = utils::numeric(FLERR,words[1],false,lmp); + if (keywd == "randomize_test_data_set") fitting_weights[10] = utils::numeric(FLERR,words[1],false,lmp); + if (keywd == "fitting_regularization_parameter") fitting_weights[11] = utils::numeric(FLERR,words[1],false,lmp); + if (keywd == "precision_for_pod_coefficients") precision = utils::inumeric(FLERR,words[1],false,lmp); + + // other settings + + if (keywd == "file_format") file_format = words[1]; + if (keywd == "file_extension") file_extension = words[1]; + if (keywd == "path_to_training_data_set") training_path = words[1]; + if (keywd == "path_to_test_data_set") test_path = words[1]; + if (keywd == "basename_for_output_files") filenametag = words[1]; + } + + if (comm->me == 0) { + utils::logmesg(lmp, "**************** Begin of Data File ****************\n"); + utils::logmesg(lmp, "file format: {}\n", file_format); + utils::logmesg(lmp, "file extension: {}\n", file_extension); + utils::logmesg(lmp, "path to training data set: {}\n", training_path); + utils::logmesg(lmp, "path to test data set: {}\n", test_path); + utils::logmesg(lmp, "training fraction: {}\n", fitting_weights[7]); + utils::logmesg(lmp, "test fraction: {}\n", fitting_weights[8]); + utils::logmesg(lmp, "randomize training data set: {}\n", fitting_weights[9]); + utils::logmesg(lmp, "randomize test data set: {}\n", fitting_weights[10]); + utils::logmesg(lmp, "error analysis for training data set: {}\n", fitting_weights[3]); + utils::logmesg(lmp, "error analysis for test data set: {}\n", fitting_weights[4]); + utils::logmesg(lmp, "energy/force calculation for training data set: {}\n", fitting_weights[5]); + utils::logmesg(lmp, "energy/force calculation for test data set: {}\n", fitting_weights[6]); + utils::logmesg(lmp, "fitting weight for energy: {}\n", fitting_weights[0]); + utils::logmesg(lmp, "fitting weight for force: {}\n", fitting_weights[1]); + utils::logmesg(lmp, "fitting weight for stress: {}\n", fitting_weights[2]); + utils::logmesg(lmp, "fitting regularization parameter: {}\n", fitting_weights[11]); + utils::logmesg(lmp, "**************** End of Data File ****************\n"); + } + + return precision; +} + +void FitPOD::get_exyz_files(std::vector& files, const std::string &datapath, + const std::string &extension) +{ + auto allfiles = platform::list_directory(datapath); + std::sort(allfiles.begin(), allfiles.end()); + for (const auto &fname : allfiles) { + if (utils::strmatch(fname, fmt::format(".*\\.{}$", extension))) + files.push_back(datapath + platform::filepathsep + fname); + } +} + +int FitPOD::get_number_atom_exyz(std::vector& num_atom, int& num_atom_sum, std::string file) +{ + std::string filename = file; + FILE *fp; + if (comm->me == 0) { + fp = utils::open_potential(filename,lmp,nullptr); + if (fp == nullptr) + error->one(FLERR,"Cannot open POD coefficient file {}: ", filename, utils::getsyserror()); + } + + char line[MAXLINE],*ptr; + int eof = 0; + int num_configs = 0; + num_atom_sum = 0; + + // loop over all lines of this xyz file and extract number of atoms and number of configs + + while (true) { + if (comm->me == 0) { + ptr = fgets(line,MAXLINE,fp); + if (ptr == nullptr) { + eof = 1; + fclose(fp); + } + } + MPI_Bcast(&eof,1,MPI_INT,0,world); + if (eof) break; + MPI_Bcast(line,MAXLINE,MPI_CHAR,0,world); + + // words = ptrs to all words in line + // strip single and double quotes from words + + std::vector words; + try { + words = Tokenizer(utils::trim_comment(line),"\"' \t\n\r\f").as_vector(); + } catch (TokenizerException &) { + // ignore + } + + if (words.size() == 0) continue; + + int natom; + if (words.size() == 1) { + natom = utils::inumeric(FLERR,words[0],false,lmp); + num_atom.push_back(natom); + num_configs += 1; + num_atom_sum += natom; + } + } + return num_configs; +} + +int FitPOD::get_number_atoms(std::vector& num_atom, std::vector &num_atom_sum, std::vector& num_config, std::vector training_files) +{ + int nfiles = training_files.size(); // number of files + int d, n; + + for (int i=0; i species) +{ + + std::string filename = file; + FILE *fp; + if (comm->me == 0) { + fp = utils::open_potential(filename,lmp,nullptr); + if (fp == nullptr) + error->one(FLERR,"Cannot open POD coefficient file {}: ", filename, utils::getsyserror()); + } + + char line[MAXLINE],*ptr; + int eof = 0; + int cfi = 0; + int nat = 0; + int ns = species.size(); + + // loop over all lines of this xyz file and extract training data + + while (true) { + if (comm->me == 0) { + ptr = fgets(line,MAXLINE,fp); + if (ptr == nullptr) { + eof = 1; + fclose(fp); + } + } + MPI_Bcast(&eof,1,MPI_INT,0,world); + if (eof) break; + MPI_Bcast(line,MAXLINE,MPI_CHAR,0,world); + + // words = ptrs to all words in line + // strip single and double quotes from words + + std::vector words; + try { + words = Tokenizer(utils::trim_comment(line),"\"' \t\n\r\f").as_vector(); + } catch (TokenizerException &) { + // ignore + } + + if (words.size() == 0) continue; + + ValueTokenizer text(utils::trim_comment(line),"\"' \t\n\r\f"); + if (text.contains("attice")) { + + // find the word containing "lattice" + + auto it = std::find_if(words.begin(), words.end(), [](const std::string& str) { return str.find("attice") != std::string::npos; }); + + // get index of element from iterator + + int index = std::distance(words.begin(), it); + + if (words[index].find("=") != std::string::npos) { + + // lattice numbers start at index + 1 + + for (int k = 0; k < 9; k++) { + lattice[k + 9*cfi] = utils::numeric(FLERR,words[index+1+k],false,lmp); + } + } else { + + // lattice numbers start at index + 2 + + for (int k = 0; k < 9; k++) { + lattice[k + 9*cfi] = utils::numeric(FLERR,words[index+2+k],false,lmp); + } + } + + // find the word containing "energy" + + it = std::find_if(words.begin(), words.end(), [](const std::string& str) { return str.find("nergy") != std::string::npos; }); + + // get index of element from iterator + + index = std::distance(words.begin(), it); + + if (words[index].find("=") != std::string::npos) { + + // energy is after "=" inside this string + + std::size_t found = words[index].find("="); + energy[cfi] = utils::numeric(FLERR,words[index].substr(found+1),false,lmp); + } else { + + // energy is at index + 2 + + energy[cfi] = utils::numeric(FLERR,words[index+2],false,lmp); + + } + + // find the word containing "stress" + + it = std::find_if(words.begin(), words.end(), [](const std::string& str) { return str.find("tress") != std::string::npos; }); + + // get index of element from iterator + + index = std::distance(words.begin(), it); + + if (words[index].find("=") != std::string::npos) { + + // stress numbers start at index + 1 + + for (int k = 0; k < 9; k++) { + stress[k + 9*cfi] = utils::numeric(FLERR,words[index+1+k],false,lmp); + } + } else { + + // lattice numbers start at index + 2 + + for (int k = 0; k < 9; k++) { + stress[k + 9*cfi] = utils::numeric(FLERR,words[index+2+k],false,lmp); + } + } + + cfi += 1; + + } + + // loop over atoms + + else if (words.size() > 1) { + + for (int ii = 0; ii < ns; ii++) + if (species[ii] == words[0]) + atomtype[nat] = ii+1; + + for (int k = 0; k < 6; k++) { + if (k <= 2) pos[k + 3*nat] = utils::numeric(FLERR,words[1+k],false,lmp); + if (k > 2 ) forces[k-3 + 3*nat] = utils::numeric(FLERR,words[1+k],false,lmp); + } + nat += 1; + } + } +} + +void FitPOD::get_data(datastruct &data, std::vector species) +{ + get_exyz_files(data.data_files, data.data_path, data.file_extension); + data.num_atom_sum = get_number_atoms(data.num_atom, data.num_atom_each_file, data.num_config, data.data_files); + data.num_config_sum = data.num_atom.size(); + size_t maxname = 9; + for (auto fname : data.data_files) maxname = MAX(maxname,fname.size()); + maxname -= data.data_path.size()+1; + const std::string sepline(maxname+46, '-'); + if (comm->me == 0) + utils::logmesg(lmp, "{}\n {:^{}} | number of configurations | number of atoms\n{}\n", + sepline, "data file", maxname, sepline); + int i = 0; + for (const auto &fname : data.data_files) { + std::string filename = fname.substr(data.data_path.size()+1); + data.filenames.push_back(filename); + if (comm->me == 0) + utils::logmesg(lmp, " {:<{}} | {:>10} | {:>8}\n", + filename, maxname, data.num_config[i], data.num_atom_each_file[i]); + ++i; + } + if (comm->me == 0) { + utils::logmesg(lmp, "{}\n", sepline); + utils::logmesg(lmp, "number of files: {}\n", data.data_files.size()); + utils::logmesg(lmp, "number of configurations in all files: {}\n", data.num_config_sum); + utils::logmesg(lmp, "number of atoms in all files: {}\n", data.num_atom_sum); + } + + if (data.data_files.size() < 1) error->all(FLERR, "Cannot fit potential without data files"); + + int n = data.num_config_sum; + memory->create(data.lattice, 9*n, "fitpod:lattice"); + memory->create(data.stress, 9*n, "fitpod:stress"); + memory->create(data.energy, n, "fitpod:energy"); + n = data.num_atom_sum; + memory->create(data.position, 3*n, "fitpod:position"); + memory->create(data.force, 3*n, "fitpod:force"); + memory->create(data.atomtype, n, "fitpod:atomtype"); + + int nfiles = data.data_files.size(); // number of files + int nconfigs = 0; + int natoms = 0; + for (int i=0; ime == 0) { + utils::logmesg(lmp, "minimum number of atoms: {}\n", data.num_atom_min); + utils::logmesg(lmp, "maximum number of atoms: {}\n", data.num_atom_max); + } +} + +std::vector FitPOD::linspace(int start_in, int end_in, int num_in) +{ + + std::vector linspaced; + + double start = static_cast(start_in); + double end = static_cast(end_in); + double num = static_cast(num_in); + + int elm; + + if (num == 0) { return linspaced; } + if (num == 1) + { + elm = (int) std::round(start); + linspaced.push_back(elm); + return linspaced; + } + + double delta = (end - start) / (num - 1); + + for(int i=0; i < num-1; ++i) + { + elm = (int) std::round(start + delta * i); + linspaced.push_back(elm); + } + + elm = (int) std::round(end); + linspaced.push_back(elm); + + return linspaced; +} + +std::vector FitPOD::shuffle(int start_in, int end_in, int num_in) +{ + int sz = end_in - start_in + 1; + std::vector myvector(sz); + + for (int i = 0; i shuffle_vec(num_in); + for (int i = 0; i FitPOD::select(int n, double fraction, int randomize) +{ + std::vector selected; + + int m = (int) std::round(n*fraction); + m = MAX(m, 1); + + selected = (randomize==1) ? shuffle(1, n, m) : linspace(1, n, m); + + return selected; +} + +void FitPOD::select_data(datastruct &newdata, datastruct data) +{ + double fraction = data.fraction; + int randomize = data.randomize; + + if (comm->me == 0) { + if (randomize==1) + utils::logmesg(lmp, "Select {} fraction of the data set at random using shuffle\n", data.fraction); + else + utils::logmesg(lmp, "Select {} fraction of the data set deterministically using linspace\n", data.fraction); + } + + int nfiles = data.data_files.size(); // number of files + std::vector> selected(nfiles); + + newdata.num_config.resize(nfiles); + newdata.num_config_cumsum.resize(nfiles+1); + newdata.num_atom_each_file.resize(nfiles); + + for (int file = 0; file < nfiles; file++) { + int nconfigs = data.num_config[file]; + selected[file] = select(nconfigs, fraction, randomize); + int ns = (int) selected[file].size(); // number of selected configurations + + newdata.num_config[file] = ns; + int num_atom_sum = 0; + for (int ii=0; ii < ns; ii++) { // loop over each selected configuration in a file + int ci = data.num_config_cumsum[file] + selected[file][ii] - 1; + int natom = data.num_atom[ci]; + newdata.num_atom.push_back(natom); + num_atom_sum += natom; + } + newdata.num_atom_each_file[file] = num_atom_sum; + } + int len = newdata.num_atom.size(); + newdata.num_atom_min = podArrayMin(&newdata.num_atom[0], len); + newdata.num_atom_max = podArrayMax(&newdata.num_atom[0], len); + newdata.num_atom_cumsum.resize(len+1); + podCumsum(&newdata.num_atom_cumsum[0], &newdata.num_atom[0], len+1); + newdata.num_atom_sum = newdata.num_atom_cumsum[len]; + podCumsum(&newdata.num_config_cumsum[0], &newdata.num_config[0], nfiles+1); + newdata.num_config_sum = newdata.num_atom.size(); + + int n = data.num_config_sum; + memory->create(newdata.lattice, 9*n, "fitpod:newdata_lattice"); + memory->create(newdata.stress, 9*n, "fitpod:newdata_stress"); + memory->create(newdata.energy, n, "fitpod:newdata_energy"); + n = data.num_atom_sum; + memory->create(newdata.position, 3*n, "fitpod:newdata_position"); + memory->create(newdata.force, 3*n, "fitpod:newdata_force"); + memory->create(newdata.atomtype, n, "fitpod:newdata_atomtype"); + + int cn = 0; + int dim = 3; + for (int file = 0; file < nfiles; file++) { + int ns = (int) selected[file].size(); // number of selected configurations + for (int ii=0; ii < ns; ii++) { // loop over each selected configuration in a file + int ci = data.num_config_cumsum[file] + selected[file][ii] - 1; + int natom = data.num_atom[ci]; + int natom_cumsum = data.num_atom_cumsum[ci]; + + int natomnew = newdata.num_atom[cn]; + int natomnew_cumsum = newdata.num_atom_cumsum[cn]; + + if (natom != natomnew) + error->all(FLERR,"number of atoms in the new data set must be the same as that in the old data set."); + + int *atomtype = &data.atomtype[natom_cumsum]; + double *position = &data.position[dim*natom_cumsum]; + double *force = &data.force[dim*natom_cumsum]; + + newdata.energy[cn] = data.energy[ci]; + for (int j=0; j<9; j++) { + newdata.stress[j+9*cn] = data.stress[j+9*ci]; + newdata.lattice[j+9*cn] = data.lattice[j+9*ci]; + } + + for (int na=0; name == 0) + utils::logmesg(lmp, "{:-<{}}\n {:^{}} | # configs (selected) | # atoms (selected) " + "| # configs (original) | # atoms (original)\n{:-<{}}\n", + "", maxname+90, "data_file", maxname, "", maxname+90); + for (int i=0; i< (int) newdata.data_files.size(); i++) { + std::string filename = newdata.data_files[i].substr(newdata.data_path.size()+1,newdata.data_files[i].size()); + newdata.filenames.push_back(filename.c_str()); + if (comm->me == 0) + utils::logmesg(lmp, " {:<{}} | {:>8} | {:>8} | {:>8} | {:>8}\n", + newdata.filenames[i], maxname, newdata.num_config[i], newdata.num_atom_each_file[i], + data.num_config[i], data.num_atom_each_file[i]); + } + if (comm->me == 0) { + utils::logmesg(lmp, "{:-<{}}\nnumber of files: {}\n", "", maxname+90, newdata.data_files.size()); + utils::logmesg(lmp, "number of configurations in all files (selected and original): {} and {}\n", newdata.num_config_sum, data.num_config_sum); + utils::logmesg(lmp, "number of atoms in all files (selected and original: {} and {}\n", newdata.num_atom_sum, data.num_atom_sum); + } +} + +void FitPOD::read_data_files(std::string data_file, std::vector species) +{ + datastruct data; + + // read data input file to datastruct + + data.precision = read_data_file(data.fitting_weights, data.file_format, data.file_extension, + testdata.data_path, data.data_path, data.filenametag, data_file); + + data.training_analysis = (int) data.fitting_weights[3]; + data.test_analysis = (int) data.fitting_weights[4]; + data.training_calculation = (int) data.fitting_weights[5]; + data.test_calculation = (int) data.fitting_weights[6]; + data.fraction = data.fitting_weights[7]; + data.randomize = (int) data.fitting_weights[9]; + + data.copydatainfo(traindata); + + if (data.fraction >= 1.0) { + if (comm->me == 0) + utils::logmesg(lmp, "**************** Begin of Training Data Set ****************\n"); + if (traindata.data_path.size() > 1) + get_data(traindata, species); + else + error->all(FLERR,"data set is not found"); + if (comm->me == 0) + utils::logmesg(lmp, "**************** End of Training Data Set ****************\n"); + } else { + if (comm->me == 0) + utils::logmesg(lmp, "**************** Begin of Training Data Set ****************\n"); + if (data.data_path.size() > 1) + get_data(data, species); + else + error->all(FLERR,"data set is not found"); + if (comm->me == 0) + utils::logmesg(lmp, "**************** End of Training Data Set ****************\n"); + + if (comm->me == 0) + utils::logmesg(lmp, "**************** Begin of Select Training Data Set ****************\n"); + select_data(traindata, data); + if (comm->me == 0) + utils::logmesg(lmp, "**************** End of Select Training Data Set ****************\n"); + + memory->destroy(data.lattice); + memory->destroy(data.energy); + memory->destroy(data.stress); + memory->destroy(data.position); + memory->destroy(data.force); + memory->destroy(data.atomtype); + } + + if (((int) testdata.data_path.size() > 1) && (testdata.data_path != traindata.data_path)) { + testdata.training = 0; + testdata.file_format = traindata.file_format; + testdata.file_extension = traindata.file_extension; + testdata.training_analysis = traindata.training_analysis; + testdata.test_analysis = traindata.test_analysis; + testdata.training_calculation = traindata.training_calculation; + testdata.test_calculation = traindata.test_calculation; + testdata.fraction = traindata.fitting_weights[8]; + testdata.randomize = (int) traindata.fitting_weights[10]; + if (comm->me == 0) + utils::logmesg(lmp, "**************** Begin of Test Data Set ****************\n"); + get_data(testdata, species); + if (comm->me == 0) + utils::logmesg(lmp, "**************** End of Test Data Set ****************\n"); + } + else { + testdata.data_path = traindata.data_path; + } +} + +int FitPOD::latticecoords(double *y, int *alist, double *x, double *a1, double *a2, double *a3, double rcut, int *pbc, int nx) +{ + int m=0, n=0, p=0; + if (pbc[0] == 1) m = (int) ceil(rcut/a1[0]); + if (pbc[1] == 1) n = (int) ceil(rcut/a2[1]); + if (pbc[2] == 1) p = (int) ceil(rcut/a3[2]); + + // index for the center lattice + + int ind = m + (2*m+1)*(n) + (2*m+1)*(2*n+1)*(p); + + // number of lattices + + int nl = (2*m+1)*(2*n+1)*(2*p+1); + + for (int j=0; j<3*nx; j++) + y[j] = x[j]; + int q = nx; + + for (int i = 0; i < (2*p+1); i++) + for (int j = 0; j < (2*n+1); j++) + for (int k = 0; k < (2*m+1); k++) { + int ii = k + (2*m+1)*j + (2*m+1)*(2*n+1)*i; + if (ii != ind) { + double x0 = a1[0]*(k - m) + a2[0]*(j - n) + a3[0]*(i - p); + double x1 = a1[1]*(k - m) + a2[1]*(j - n) + a3[1]*(i - p); + double x2 = a1[2]*(k - m) + a2[2]*(j - n) + a3[2]*(i - p); + for (int jj=0; jj SMALL) && (rijsq <= rcutsq)) { + inc += 1; + neighlist[k] = j; + k += 1; + } + } + numneigh[i] = inc; + } + return k; +} + +int FitPOD::podfullneighborlist(double *y, int *alist, int *neighlist, int *numneigh, int *numneighsum, + double *x, double *a1, double *a2, double *a3, double rcut, int *pbc, int nx) +{ + double rcutsq = rcut*rcut; + int dim = 3, nl = 0, nn = 0; + + // number of lattices + + nl = latticecoords(y, alist, x, a1, a2, a3, rcut, pbc, nx); + int N = nx*nl; + + // total number of neighbors + + nn = podneighborlist(neighlist, numneigh, y, rcutsq, nx, N, dim); + + podCumsum(numneighsum, numneigh, nx+1); + + return nn; +} + +void FitPOD::allocate_memory(const datastruct &data) +{ + int nd = podptr->pod.nd; + memory->create(desc.gd, nd, "fitpod:desc_gd"); + memory->create(desc.A, nd*nd, "fitpod:desc_A"); + memory->create(desc.b, nd, "fitpod:desc_b"); + memory->create(desc.c, nd, "fitpod:desc_c"); + podArraySetValue(desc.A, 0.0, nd*nd); + podArraySetValue(desc.b, 0.0, nd); + podArraySetValue(desc.c, 0.0, nd); + + int dim = 3; + int natom_max = data.num_atom_max; + int nd1 = podptr->pod.nd1; + int nd2 = podptr->pod.nd2; + int nd3 = podptr->pod.nd3; + int nd4 = podptr->pod.nd4; + int nelements = podptr->pod.nelements; + int nbesselpars = podptr->pod.nbesselpars; + int nrbf2 = podptr->pod.nbf2; + int nabf3 = podptr->pod.nabf3; + int nrbf3 = podptr->pod.nrbf3; + int *pdegree2 = podptr->pod.twobody; + int *pdegree3 = podptr->pod.threebody; + int *pbc = podptr->pod.pbc; + double rcut = podptr->pod.rcut; + + int Nj=0, Nij=0; + int m=0, n=0, p=0, nl=0, ny=0, na=0, np=0; + + for (int ci=0; ci<(int) data.num_atom.size(); ci++) + { + int natom = data.num_atom[ci]; + double *lattice = &data.lattice[9*ci]; + double *a1 = &lattice[0]; + double *a2 = &lattice[3]; + double *a3 = &lattice[6]; + if (pbc[0] == 1) m = (int) ceil(rcut/a1[0]); + if (pbc[1] == 1) n = (int) ceil(rcut/a2[1]); + if (pbc[2] == 1) p = (int) ceil(rcut/a3[2]); + + // number of lattices + + nl = (2*m+1)*(2*n+1)*(2*p+1); + ny = MAX(ny,dim*natom*nl); + na = MAX(na, natom*nl); + np = MAX(np, natom*natom*nl); + } + + memory->create(nb.y, ny, "fitpod:nb_y"); + memory->create(nb.alist, na, "fitpod:nb_alist"); + memory->create(nb.pairnum, natom_max, "fitpod:nb_pairnum"); + memory->create(nb.pairnum_cumsum, natom_max+1, "fitpod:nb_pairnum_cumsum"); + memory->create(nb.pairlist, np, "fitpod:nb_pairlist"); + + nb.natom_max = natom_max; + nb.sze = nelements*nelements; + nb.sza = na; + nb.szy = ny; + nb.szp = np; + + if (comm->me == 0) + utils::logmesg(lmp,"**************** Begin of Memory Allocation ****************\n"); + + int szd = 0, szi=0, szsnap=0; + for (int ci=0; ci<(int) data.num_atom.size(); ci++) + { + int natom = data.num_atom[ci]; + int natom_cumsum = data.num_atom_cumsum[ci]; + double *x = &data.position[dim*natom_cumsum]; + double *lattice = &data.lattice[9*ci]; + double *a1 = &lattice[0]; + double *a2 = &lattice[3]; + double *a3 = &lattice[6]; + + Nij = podfullneighborlist(nb.y, nb.alist, nb.pairlist, nb.pairnum, nb.pairnum_cumsum, x, a1, a2, a3, rcut, pbc, natom); + + int ns2 = pdegree2[0]*nbesselpars + pdegree2[1]; + int ns3 = pdegree3[0]*nbesselpars + pdegree3[1]; + + int szd1 = 3*Nij+ (1+dim)*Nij*MAX(nrbf2+ns2,nrbf3+ns3) + (nabf3+1)*7; + int szi1 = 6*Nij + 2*natom+1 + (Nj-1)*Nj; + szd = MAX(szd, szd1); + szi = MAX(szi, szi1); + + if (podptr->sna.twojmax>0) { + szd1 = 0; + szd1 += Nij*dim; // rij + szd1 += MAX(2*podptr->sna.idxu_max*Nij, 2*podptr->sna.idxz_max*podptr->sna.ndoubles*natom); // (Ur, Ui) and (Zr, Zi) + szd1 += 2*podptr->sna.idxu_max*dim*Nij; // dUr, dUi + szd1 += MAX(podptr->sna.idxb_max*podptr->sna.ntriples*dim*Nij, 2*podptr->sna.idxu_max*podptr->sna.nelements*natom); // dblist and (Utotr, Utoti) + szsnap = MAX(szsnap, szd1); + } + } + + szd = MAX(szsnap, szd); + szd = MAX(natom_max*(nd1+nd2+nd3+nd4) + szd, dim*natom_max*(nd-nd1-nd2-nd3-nd4)); + szd = dim*natom_max*(nd1+nd2+nd3+nd4) + szd; + + // gdd includes linear descriptors derivatives, quadratic descriptors derivatives and temporary memory + + memory->create(desc.gdd, szd, "fitpod:desc_gdd"); + memory->create(desc.tmpint, szi, "fitpod:desc_tmpint"); + desc.szd = szd; + desc.szi = szi; + + if (comm->me == 0) { + utils::logmesg(lmp, "maximum number of atoms in periodic domain: {}\n", natom_max); + utils::logmesg(lmp, "maximum number of atoms in extended domain: {}\n", nb.sza); + utils::logmesg(lmp, "maximum number of neighbors in extended domain: {}\n", nb.szp); + utils::logmesg(lmp, "size of double memory: {}\n", szd); + utils::logmesg(lmp, "size of int memory: {}\n", szi); + utils::logmesg(lmp, "size of descriptor matrix: {} x {}\n", nd, nd); + utils::logmesg(lmp, "**************** End of Memory Allocation ****************\n"); + } +} + +void FitPOD::linear_descriptors(const datastruct &data, int ci) +{ + int dim = 3; + int nd1 = podptr->pod.nd1; + int nd2 = podptr->pod.nd2; + int nd3 = podptr->pod.nd3; + int nd4 = podptr->pod.nd4; + int nd1234 = nd1+nd2+nd3+nd4; + int *pbc = podptr->pod.pbc; + double rcut = podptr->pod.rcut; + + int natom = data.num_atom[ci]; + int natom_cumsum = data.num_atom_cumsum[ci]; + int *atomtype = &data.atomtype[natom_cumsum]; + double *position = &data.position[dim*natom_cumsum]; + double *lattice = &data.lattice[9*ci]; + double *a1 = &lattice[0]; + double *a2 = &lattice[3]; + double *a3 = &lattice[6]; + + // neighbor list + int Nij = podfullneighborlist(nb.y, nb.alist, nb.pairlist, nb.pairnum, nb.pairnum_cumsum, + position, a1, a2, a3, rcut, pbc, natom); + + int *tmpint = &desc.tmpint[0]; + double *tmpmem = &desc.gdd[dim*natom*nd1234+natom*nd1234]; + podptr->linear_descriptors(desc.gd, desc.gdd, nb.y, tmpmem, atomtype, nb.alist, + nb.pairlist, nb.pairnum, nb.pairnum_cumsum, tmpint, natom, Nij); + +} + +void FitPOD::quadratic_descriptors(const datastruct &data, int ci) +{ + int dim = 3; + int natom = data.num_atom[ci]; + int nd1 = podptr->pod.nd1; + int nd2 = podptr->pod.nd2; + int nd3 = podptr->pod.nd3; + int nd4 = podptr->pod.nd4; + int nd22 = podptr->pod.nd22; + int nd23 = podptr->pod.nd23; + int nd24 = podptr->pod.nd24; + int nd33 = podptr->pod.nd33; + int nd34 = podptr->pod.nd34; + int nd44 = podptr->pod.nd44; + int nd123 = nd1+nd2+nd3; + int nd1234 = nd1+nd2+nd3+nd4; + + double *fatom2 = &desc.gdd[dim*natom*(nd1)]; + double *fatom3 = &desc.gdd[dim*natom*(nd1+nd2)]; + double *fatom4 = &desc.gdd[dim*natom*(nd123)]; + + // global descriptors for four-body quadratic22 potential + + if (nd22 > 0) { + int nq2 = podptr->pod.quadratic22[0]*podptr->pod.nc2; + podptr->quadratic_descriptors(&desc.gd[nd1234], &desc.gdd[dim*natom*nd1234], + &desc.gd[nd1], fatom2, nq2, dim*natom); + } + + // global descriptors for four-body quadratic23 potential + + if (nd23 > 0) { + int nq2 = podptr->pod.quadratic23[0]*podptr->pod.nc2; + int nq3 = podptr->pod.quadratic23[1]*podptr->pod.nc3; + podptr->quadratic_descriptors(&desc.gd[nd1234+nd22], &desc.gdd[dim*natom*(nd1234+nd22)], + &desc.gd[nd1], &desc.gd[nd1+nd2], fatom2, fatom3, nq2, nq3, dim*natom); + } + + // global descriptors for five-body quadratic24 potential + + if (nd24 > 0) { + int nq2 = podptr->pod.quadratic24[0]*podptr->pod.nc2; + int nq4 = podptr->pod.quadratic24[1]*podptr->pod.nc4; + podptr->quadratic_descriptors(&desc.gd[nd1234+nd22+nd23], &desc.gdd[dim*natom*(nd1234+nd22+nd23)], + &desc.gd[nd1], &desc.gd[nd1+nd2+nd3], fatom2, fatom4, nq2, nq4, dim*natom); + } + + // global descriptors for five-body quadratic33 potential + + if (nd33 > 0) { + int nq3 = podptr->pod.quadratic33[0]*podptr->pod.nc3; + podptr->quadratic_descriptors(&desc.gd[nd1234+nd22+nd23+nd24], &desc.gdd[dim*natom*(nd1234+nd22+nd23+nd24)], + &desc.gd[nd1+nd2], fatom3, nq3, dim*natom); + } + + // global descriptors for six-body quadratic34 potential + + if (nd34 > 0) { + int nq3 = podptr->pod.quadratic34[0]*podptr->pod.nc3; + int nq4 = podptr->pod.quadratic34[1]*podptr->pod.nc4; + podptr->quadratic_descriptors(&desc.gd[nd1234+nd22+nd23+nd24+nd33], &desc.gdd[dim*natom*(nd1234+nd22+nd23+nd24+nd33)], + &desc.gd[nd1+nd2], &desc.gd[nd1+nd2+nd3], fatom3, fatom4, nq3, nq4, dim*natom); + } + + // global descriptors for seven-body quadratic44 potential + + if (nd44 > 0) { + int nq4 = podptr->pod.quadratic44[0]*podptr->pod.nc4; + podptr->quadratic_descriptors(&desc.gd[nd1234+nd22+nd23+nd24+nd33+nd34], &desc.gdd[dim*natom*(nd1234+nd22+nd23+nd24+nd33+nd34)], + &desc.gd[nd1+nd2+nd3], fatom4, nq4, dim*natom); + } + + // normalize quadratic descriptors + + for (int i=0; i<(nd22+nd23+nd24+nd33+nd34+nd44); i++) + desc.gd[nd1234+i] = desc.gd[nd1234+i]/(natom); + + for (int i=0; ipod.nd1; + int nd2 = podptr->pod.nd2; + int nd3 = podptr->pod.nd3; + int nd4 = podptr->pod.nd4; + int nd22 = podptr->pod.nd22; + int nd23 = podptr->pod.nd23; + int nd24 = podptr->pod.nd24; + int nd33 = podptr->pod.nd33; + int nd34 = podptr->pod.nd34; + int nd44 = podptr->pod.nd44; + int nd234 = podptr->pod.nd234; + int nd333 = podptr->pod.nd333; + int nd444 = podptr->pod.nd444; + int nd123 = nd1+nd2+nd3; + int nd1234 = nd1+nd2+nd3+nd4; + + // global descriptors for seven-body cubic234 potential + if (nd234 > 0) { + int nq2 = podptr->pod.cubic234[0]*podptr->pod.nc2; + int nq3 = podptr->pod.cubic234[1]*podptr->pod.nc3; + int nq4 = podptr->pod.cubic234[2]*podptr->pod.nc4; + int np3 = nd1234+nd22+nd23+nd24+nd33+nd34+nd44; + double *eatom2 = &desc.gd[nd1]; + double *eatom3 = &desc.gd[nd1+nd2]; + double *eatom4 = &desc.gd[nd123]; + double *fatom2 = &desc.gdd[dim*natom*(nd1)]; + double *fatom3 = &desc.gdd[dim*natom*(nd1+nd2)]; + double *fatom4 = &desc.gdd[dim*natom*(nd123)]; + podptr->cubic_descriptors(&desc.gd[np3], &desc.gdd[dim*natom*np3], + eatom2, eatom3, eatom4, fatom2, fatom3, fatom4, nq2, nq3, nq4, dim*natom); + } + + // global descriptors for seven-body cubic333 potential + + if (nd333 > 0) { + int nq3 = podptr->pod.cubic333[0]*podptr->pod.nc3; + int np3 = nd1234+nd22+nd23+nd24+nd33+nd34+nd44+nd234; + double *eatom3 = &desc.gd[nd1+nd2]; + double *fatom3 = &desc.gdd[dim*natom*(nd1+nd2)]; + podptr->cubic_descriptors(&desc.gd[np3], &desc.gdd[dim*natom*np3], + eatom3, fatom3, nq3, dim*natom); + } + + // global descriptors for ten-body cubic444 potential + + if (nd444 > 0) { + int nq4 = podptr->pod.cubic444[0]*podptr->pod.nc4; + int np4 = nd1234+nd22+nd23+nd24+nd33+nd34+nd44+nd234+nd333; + double *eatom4 = &desc.gd[nd123]; + double *fatom4 = &desc.gdd[dim*natom*(nd123)]; + podptr->cubic_descriptors(&desc.gd[np4], &desc.gdd[dim*natom*(np4)], + eatom4, fatom4, nq4, dim*natom); + } + + // normalize cubic descriptors + int nd = podptr->pod.nd; + for (int i=(nd1234+nd22+nd23+nd24+nd33+nd34+nd44); ipod.nd; + int nforce = dim*natom; + + // compute energy weight and force weight + + double normconst = 1.0; + if (data.normalizeenergy==1) normconst = 1.0/natom; + double we = data.fitting_weights[0]; + double wf = data.fitting_weights[1]; + double we2 = (we*we)*(normconst*normconst); + double wf2 = (wf*wf); + + // get energy and force from the training data set + + double energy = data.energy[ci]; + double *force = &data.force[dim*natom_cumsum]; + + // least-square matrix for all descriptors: A = A + (we*we)*(gd^T * gd) + + podKron(desc.A, desc.gd, desc.gd, we2, nd, nd); + + // least-square matrix for all descriptors derivatives: A = A + (wf*wf) * (gdd^T * gdd) + + char cht = 'T'; + char chn = 'N'; + double one = 1.0; + int inc1 = 1; + DGEMM(&cht, &chn, &nd, &nd, &nforce, &wf2, desc.gdd, &nforce, desc.gdd, &nforce, &one, desc.A, &nd); + + // least-square vector for all descriptors: b = b + (we*we*energy)*gd + + double wee = we2*energy; + for (int i = 0; i< nd; i++) + desc.b[i] += wee*desc.gd[i]; + + // least-square vector for all descriptors derivatives: b = b + (wf*wf) * (gdd^T * f) + + DGEMV(&cht, &nforce, &nd, &wf2, desc.gdd, &nforce, force, &inc1, &one, desc.b, &inc1); + +} + +void FitPOD::least_squares_fit(const datastruct &data) +{ + if (comm->me == 0) + utils::logmesg(lmp, "**************** Begin of Least-Squares Fitting ****************\n"); + + // loop over each configuration in the training data set + + for (int ci=0; ci < (int) data.num_atom.size(); ci++) { + + if ((ci % 100)==0) { + if (comm->me == 0) + utils::logmesg(lmp, "Configuration: # {}\n", ci+1); + } + + if ((ci % comm->nprocs) == comm->me) { + + // compute linear POD descriptors + + linear_descriptors(data, ci); + + // compute quadratic POD descriptors + + quadratic_descriptors(data, ci); + + // compute cubic POD descriptors + + cubic_descriptors(data, ci); + + // assemble the least-squares linear system + + least_squares_matrix(data, ci); + } + } + + int nd = podptr->pod.nd; + + MPI_Allreduce(MPI_IN_PLACE, desc.b, nd, MPI_DOUBLE, MPI_SUM, world); + MPI_Allreduce(MPI_IN_PLACE, desc.A, nd*nd, MPI_DOUBLE, MPI_SUM, world); + + if (comm->me == 0) { + + // symmetrize A + + for (int i = 0; i fabs(desc.b[i])) ? maxb : fabs(desc.b[i]); + + maxb = 1.0/maxb; + for (int i = 0; ime == 0) { // save coefficients into a text file + std::string filename = data.filenametag + "_coefficients" + ".pod"; + FILE *fp = fopen(filename.c_str(), "w"); + + fmt::print(fp, "POD_coefficients: {}\n", nd); + for (int count = 0; count < nd; count++) { + fmt::print(fp, "{:<10.{}f}\n", desc.c[count], data.precision); + } + fclose(fp); + utils::logmesg(lmp, "**************** End of Least-Squares Fitting ****************\n"); + } +} + +double FitPOD::energyforce_calculation(double *force, double *coeff, const datastruct &data, int ci) +{ + int dim = 3; + int *pbc = podptr->pod.pbc; + double rcut = podptr->pod.rcut; + int nd1234 = podptr->pod.nd1 + podptr->pod.nd2 + podptr->pod.nd3 + podptr->pod.nd4; + + int natom = data.num_atom[ci]; + int natom_cumsum2 = data.num_atom_cumsum[ci]; + int *atomtype = &data.atomtype[natom_cumsum2]; + double *position = &data.position[dim*natom_cumsum2]; + double *lattice = &data.lattice[9*ci]; + double *a1 = &lattice[0]; + double *a2 = &lattice[3]; + double *a3 = &lattice[6]; + + // neighbor list + + int Nij = podfullneighborlist(nb.y, nb.alist, nb.pairlist, nb.pairnum, nb.pairnum_cumsum, + position, a1, a2, a3, rcut, pbc, natom); + + double *tmpmem = &desc.gdd[0]; + int *tmpint = &desc.tmpint[0]; + double *rij = &tmpmem[0]; // 3*Nij + int *ai = &tmpint[0]; // Nij + int *aj = &tmpint[Nij]; // Nij + int *ti = &tmpint[2*Nij]; // Nij + int *tj = &tmpint[3*Nij]; // Nij + int *idxi = &tmpint[4*Nij]; // Nij + podptr->podNeighPairs(rij, nb.y, idxi, ai, aj, ti, tj, nb.pairnum_cumsum, atomtype, nb.pairlist, nb.alist, natom); + + double *effectivecoeff = &tmpmem[3*Nij]; // 3*Nij + podArraySetValue(effectivecoeff, 0.0, nd1234); + + double energy = podptr->energyforce_calculation(force, coeff, effectivecoeff, desc.gd, rij, + &tmpmem[3*Nij+nd1234], nb.pairnum_cumsum, atomtype, idxi, ai, aj, ti, tj, natom, Nij); + + return energy; +} + +void FitPOD::print_analysis(const datastruct &data, double *outarray, double *errors) +{ + int nfiles = data.data_files.size(); // number of files + int lm = 10; + for (int i = 0; i < nfiles; i++) + lm = MAX(lm, (int) data.filenames[i].size()); + lm = lm + 2; + + std::string filename_errors = fmt::format("{}_{}_errors.pod", data.filenametag, data.training ? "training" : "test"); + std::string filename_analysis = fmt::format("{}_{}_analysis.pod", data.filenametag, data.training ? "training" : "test"); + + FILE *fp_errors = nullptr; + FILE *fp_analysis = nullptr; + fp_errors = fopen(filename_errors.c_str(), "w"); + fp_analysis = fopen(filename_analysis.c_str(), "w"); + + std::string mystr = fmt::format("**************** Begin of Error Analysis for the {} Data Set ****************\n", + data.training ? "Training" : "Test"); + + utils::logmesg(lmp, mystr); + fmt::print(fp_errors, mystr); + + std::string sa(lm+80,'-'); + sa += '\n'; + std::string sb = fmt::format(" {:^{}} | # configs | # atoms | MAE energy | RMSE energy | MAE force | RMSE force\n", + "File", lm); + utils::logmesg(lmp, sa + sb + sa); + fmt::print(fp_errors, sa + sb + sa); + + int ci=0, m=8, nc=0, nf=0; + for (int file = 0; file < nfiles; file++) { + fmt::print(fp_analysis, "# {}\n", data.filenames[file]); + fmt::print(fp_analysis, " config # atoms energy DFT energy energy error " + " force DFT force force error\n"); + + int nforceall = 0; + int nconfigs = data.num_config[file]; + nc += nconfigs; + for (int ii=0; ii < nconfigs; ii++) { // loop over each configuration in a file + fmt::print(fp_analysis, "{:6} {:8} ", outarray[m*ci], outarray[1 + m*ci]); + for(int count = 2; count < m; count ++) + fmt::print(fp_analysis, "{:<15.10} ", outarray[count + m*ci]); + fmt::print(fp_analysis, "\n"); + + nforceall += 3*data.num_atom[ci]; + ci += 1; + } + nf += nforceall; + + int q = file+1; + auto s = fmt::format("{:<{}} {:>10} {:>11} {:<10.6f} {:<10.6f} {:<10.6f} {:<10.6f}\n", + data.filenames[file], lm, nconfigs, nforceall/3, + errors[0 + 4*q], errors[1 + 4*q], errors[2 + 4*q], errors[3 + 4*q]); + utils::logmesg(lmp, s); + fmt::print(fp_errors, s); + } + utils::logmesg(lmp, sa); + fmt::print(fp_errors, sa); + + auto s = fmt::format("{:<{}} {:>10} {:>11} {:<10.6f} {:<10.6f} {:<10.6f} {:<10.6f}\n", + "All files", lm, nc, nf/3, errors[0], errors[1], errors[2], errors[3]); + utils::logmesg(lmp, s + sa); + fmt::print(fp_errors, "{}", s + sa); + + mystr = fmt::format("**************** End of Error Analysis for the {} Data Set ****************\n", + data.training ? "Training" : "Test"); + + utils::logmesg(lmp, mystr); + fmt::print(fp_errors, mystr); + + fclose(fp_errors); + fclose(fp_analysis); +} + +void FitPOD::error_analysis(const datastruct &data, double *coeff) +{ + int dim = 3; + double energy; + std::vector force(dim*data.num_atom_max); + + int nfiles = data.data_files.size(); // number of files + int num_configs = data.num_atom.size(); // number of configurations in all files + + int m = 8; + std::vector outarray(m*num_configs); + for (int i=0; i ssrarray(num_configs); + for (int i=0; i errors(4*(nfiles+1)); + for (int i=0; i<4*(nfiles+1); i++) + errors[i] = 0.0; + + int nd1 = podptr->pod.nd1; + int nd2 = podptr->pod.nd2; + int nd3 = podptr->pod.nd3; + int nd4 = podptr->pod.nd4; + int nd22 = podptr->pod.nd22; + int nd23 = podptr->pod.nd23; + int nd24 = podptr->pod.nd24; + int nd33 = podptr->pod.nd33; + int nd34 = podptr->pod.nd34; + int nd44 = podptr->pod.nd44; + int nd1234 = nd1+nd2+nd3+nd4; + int nd = podptr->pod.nd; + + std::vector newcoeff(nd); + for (int j=0; jme == 0) + utils::logmesg(lmp, "**************** Begin of Error Calculation ****************\n"); + + int ci = 0; // configuration counter + for (int file = 0; file < nfiles; file++) { // loop over each file in the training data set + + int nconfigs = data.num_config[file]; + for (int ii=0; ii < nconfigs; ii++) { // loop over each configuration in a file + + if ((ci % 100)==0) { + if (comm->me == 0) + utils::logmesg(lmp, "Configuration: # {}\n", ci+1); + } + + if ((ci % comm->nprocs) == comm->me) { + int natom = data.num_atom[ci]; + int nforce = dim*natom; + + for (int j=nd1234; j<(nd1234+nd22+nd23+nd24+nd33+nd34+nd44); j++) + newcoeff[j] = coeff[j]/(natom); + + for (int j=(nd1234+nd22+nd23+nd24+nd33+nd34+nd44); jme == 0) { + utils::logmesg(lmp, "**************** End of Error Calculation ****************\n"); + print_analysis(data, outarray.data(), errors.data()); + } +} + +void FitPOD::energyforce_calculation(const datastruct &data, double *coeff) +{ + int dim = 3; + double energy; + std::vector force(1+dim*data.num_atom_max); + + int nfiles = data.data_files.size(); // number of files + + if (comm->me == 0) + utils::logmesg(lmp, "**************** Begin of Energy/Force Calculation ****************\n"); + + int ci = 0; // configuration counter + for (int file = 0; file < nfiles; file++) { // loop over each file in the data set + + int nconfigs = data.num_config[file]; + for (int ii=0; ii < nconfigs; ii++) { // loop over each configuration in a file + if ((ci % 100)==0) { + if (comm->me == 0) utils::logmesg(lmp, "Configuration: # {}\n", ci+1); + } + + int natom = data.num_atom[ci]; + int nforce = dim*natom; + + if ((ci % comm->nprocs) == comm->me) { + energy = energyforce_calculation(force.data()+1, coeff, data, ci); + + // save energy and force into a binary file + + force[0] = energy; + std::string filename = "energyforce_config" + std::to_string(ci+1) + ".bin"; + + FILE *fp = fopen(filename.c_str(), "wb"); + + fwrite( reinterpret_cast( force.data() ), sizeof(double) * (1 + nforce), 1, fp); + + fclose(fp); + } + ci += 1; + } + } + if (comm->me == 0) + utils::logmesg(lmp, "**************** End of Energy/Force Calculation ****************\n"); +} + +void FitPOD::print_matrix(const char *desc, int m, int n, double **a, int /*lda*/ ) +{ + int i, j; + printf( "\n %s\n", desc ); + + for( i = 0; i < m; i++ ) + { + for( j = 0; j < n; j++ ) printf( " %6.12f", a[j][i] ); + printf( "\n" ); + } +} + +void FitPOD::print_matrix(const char *desc, int m, int n, double *a, int lda ) +{ + int i, j; + printf( "\n %s\n", desc ); + + for( i = 0; i < m; i++ ) + { + for( j = 0; j < n; j++ ) printf( " %6.12f", a[i+j*lda] ); + printf( "\n" ); + } +} + +void FitPOD::print_matrix(const char *desc, int m, int n, int *a, int lda) +{ + int i, j; + printf( "\n %s\n", desc ); + + for( i = 0; i < m; i++ ) + { + for( j = 0; j < n; j++ ) printf( " %d", a[i+j*lda] ); + printf( "\n" ); + } +} + +void FitPOD::podArrayFill(int* output, int start, int length) +{ + for (int j = 0; j < length; ++j) + output[j] = start + j; +} + +double FitPOD::podArraySum(double *a, int n) +{ + double e = a[0]; + for (int i=1; ib) + b = a[i]; + return b; +} + +int FitPOD::podArrayMin(int *a, int n) +{ + int b = a[0]; + for (int i=1; ib) + b = a[i]; + return b; +} + +void FitPOD::podKron(double *C, double *A, double *B, double alpha, int M1, int M2) +{ + int M = M1*M2; + for (int idx=0; idx data_files; + std::vector filenames; + std::string filenametag = "pod"; + + std::vector num_atom; + std::vector num_atom_cumsum; + std::vector num_atom_each_file; + std::vector num_config; + std::vector num_config_cumsum; + int num_atom_sum; + int num_atom_min; + int num_atom_max; + int num_config_sum; + + double *lattice; + double *energy; + double *stress; + double *position; + double *force; + int *atomtype; + + int training = 1; + int normalizeenergy = 1; + int training_analysis = 1; + int test_analysis = 1; + int training_calculation = 0; + int test_calculation = 0; + int randomize = 1; + int precision = 8; + double fraction = 1.0; + + double fitting_weights[12] = {100.0, 1.0, 0.0, 1, 1, 0, 0, 1, 1, 1, 1, 1e-10}; + + void copydatainfo(datastruct &data) { + data.data_path = data_path; + data.file_format = file_format; + data.file_extension = file_extension; + data.data_files = data_files; + data.filenametag = filenametag; + data.filenames = filenames; + data.training_analysis = training_analysis; + data.test_analysis = test_analysis; + data.training_calculation = training_calculation; + data.test_calculation = test_calculation; + data.fraction = fraction; + data.randomize = randomize; + data.precision = precision; + data.training = training; + data.normalizeenergy = normalizeenergy; + for (int i = 0; i < 12; i++) + data.fitting_weights[i] = fitting_weights[i]; + } + }; + + struct neighborstruct { + int *alist; + int *pairnum; + int *pairnum_cumsum; + int *pairlist; + double *y; + + int natom; + int nalist; + int natom_max; + int sze; + int sza; + int szy; + int szp; + }; + + struct descriptorstruct { + double *gd; // global descriptors + double *gdd; // derivatives of global descriptors and peratom descriptors + double *A; // least-square matrix for all descriptors + double *b; // least-square vector for all descriptors + double *c; // coefficents of descriptors + int *tmpint; + int szd; + int szi; + }; + + datastruct traindata; + datastruct testdata; + descriptorstruct desc; + neighborstruct nb; + class MLPOD *podptr; + + // functions for collecting/collating arrays + + void print_matrix(const char *desc, int m, int n, int *a, int lda); + void print_matrix(const char *desc, int m, int n, double *a, int lda); + void print_matrix(const char *desc, int m, int n, double **a, int lda); + void podCumsum(int *output, int *input, int length); + double podArrayNorm(double *a, int n); + double podArrayErrorNorm(double *a, double *b, int n); + void podArraySetValue(double *y, double a, int n); + void podArrayCopy(double *y, double *x, int n); + void podArrayFill(int *output, int start, int length); + double podArrayMin(double *a, int n); + double podArrayMax(double *a, int n); + double podArraySum(double *a, int n); + int podArrayMin(int *a, int n); + int podArrayMax(int *a, int n); + void podKron(double *C, double *A, double *B, double alpha, int M1, int M2); + void rotation_matrix(double *Rmat, double alpha, double beta, double gamma); + void triclinic_lattice_conversion(double *a, double *b, double *c, double *A, double *B, + double *C); + void matrix33_multiplication(double *xrot, double *Rmat, double *x, int natom); + void matrix33_inverse(double *invA, double *A1, double *A2, double *A3); + + // functions for reading input files and fitting + + + int read_data_file(double *fitting_weights, std::string &file_format, std::string &file_extension, + std::string &test_path, std::string &training_path, std::string &filenametag, const std::string &data_file); + void get_exyz_files(std::vector &, const std::string &, const std::string &); + int get_number_atom_exyz(std::vector& num_atom, int& num_atom_sum, std::string file); + int get_number_atoms(std::vector& num_atom, std::vector &num_atom_sum, std::vector& num_config, std::vector training_files); + void read_exyz_file(double *lattice, double *stress, double *energy, double *pos, double *forces, + int *atomtype, std::string file, std::vector species); + void get_data(datastruct &data, std::vector species); + std::vector linspace(int start_in, int end_in, int num_in); + std::vector shuffle(int start_in, int end_in, int num_in); + std::vector select(int n, double fraction, int randomize); + void select_data(datastruct &newdata, datastruct data); + void read_data_files(std::string data_file, std::vector species); + int latticecoords(double *y, int *alist, double *x, double *a1, double *a2, double *a3, double rcut, int *pbc, int nx); + int podneighborlist(int *neighlist, int *numneigh, double *r, double rcutsq, int nx, int N, int dim); + int podfullneighborlist(double *y, int *alist, int *neighlist, int *numneigh, int *numneighsum, + double *x, double *a1, double *a2, double *a3, double rcut, int *pbc, int nx); + void allocate_memory(const datastruct &data); + void linear_descriptors(const datastruct &data, int ci); + void quadratic_descriptors(const datastruct &data, int ci); + void cubic_descriptors(const datastruct &data, int ci); + void least_squares_matrix(const datastruct &data, int ci); + void least_squares_fit(const datastruct &data); + void print_analysis(const datastruct &data, double *outarray, double *errors); + void error_analysis(const datastruct &data, double *coeff); + double energyforce_calculation(double *force, double *coeff, const datastruct &data, int ci); + void energyforce_calculation(const datastruct &data, double *coeff); +}; + +} // namespace LAMMPS_NS + +#endif +#endif + diff --git a/src/ML-POD/mlpod.cpp b/src/ML-POD/mlpod.cpp new file mode 100644 index 0000000000..859b269375 --- /dev/null +++ b/src/ML-POD/mlpod.cpp @@ -0,0 +1,3698 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/ Sandia National Laboratories + LAMMPS development team: developers@lammps.org + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing authors: Ngoc Cuong Nguyen (MIT) and Andrew Rohskopf (SNL) +------------------------------------------------------------------------- */ + +// POD header file + +#include "mlpod.h" + +// LAMMPS header files + +#include "comm.h" +#include "error.h" +#include "math_const.h" +#include "math_special.h" +#include "memory.h" +#include "tokenizer.h" + +#include + +using namespace LAMMPS_NS; +using MathConst::MY_PI; +using MathSpecial::cube; +using MathSpecial::powint; + +#define MAXLINE 1024 + +MLPOD::podstruct::podstruct() : + twobody{5, 10, 10}, threebody{4, 8, 8, 5}, fourbody{0, 0, 0, 0}, pbc(nullptr), + elemindex(nullptr), quadratic22{0, 0}, quadratic23{0, 0}, quadratic24{0, 0}, quadratic33{0, 0}, + quadratic34{0, 0}, quadratic44{0, 0}, cubic234{0, 0, 0}, cubic333{0, 0, 0}, cubic444{0, 0, 0}, + besselparams(nullptr), coeff(nullptr), Phi2(nullptr), Phi3(nullptr), Phi4(nullptr), + Lambda2(nullptr), Lambda3(nullptr), Lambda4(nullptr) +{ +} + +MLPOD::podstruct::~podstruct() +{ + delete[] pbc; + delete[] elemindex; + delete[] besselparams; +} + +MLPOD::MLPOD(LAMMPS *_lmp, const std::string &pod_file, const std::string &coeff_file) : + Pointers(_lmp) +{ + // read pod input file to podstruct + + read_pod(pod_file); + + // read pod coefficient file to podstruct + + if (coeff_file != "") read_coeff_file(coeff_file); + + if (pod.snaptwojmax > 0) InitSnap(); +} + +MLPOD::~MLPOD() +{ + // deallocate pod arrays + + memory->destroy(pod.coeff); + if (pod.ns2 > 0) { + memory->destroy(pod.Phi2); + memory->destroy(pod.Lambda2); + } + if (pod.ns3 > 0) { + memory->destroy(pod.Phi3); + memory->destroy(pod.Lambda3); + } + if (pod.ns4 > 0) { + memory->destroy(pod.Phi4); + memory->destroy(pod.Lambda4); + } + + // deallocate snap arrays if used + + if (pod.snaptwojmax > 0) { + memory->destroy(sna.map); + memory->destroy(sna.idx_max); + memory->destroy(sna.idxz); + memory->destroy(sna.idxb); + memory->destroy(sna.idxb_block); + memory->destroy(sna.idxu_block); + memory->destroy(sna.idxz_block); + memory->destroy(sna.idxcg_block); + memory->destroy(sna.rootpqarray); + memory->destroy(sna.cglist); + memory->destroy(sna.fac); + memory->destroy(sna.bzero); + memory->destroy(sna.wjelem); + memory->destroy(sna.radelem); + memory->destroy(sna.rcutsq); + } +} + +// clang-format off + +void MLPOD::podMatMul(double *c, double *a, double *b, int r1, int c1, int c2) +{ + int i, j, k; + + for(j = 0; j < c2; j++) + for(i = 0; i < r1; i++) + c[i + r1*j] = 0.0; + + for(j = 0; j < c2; j++) + for(i = 0; i < r1; i++) + for(k = 0; k < c1; k++) + c[i + r1*j] += a[i + r1*k] * b[k + c1*j]; +} + +void MLPOD::podArrayFill(int* output, int start, int length) +{ + for (int j = 0; j < length; ++j) + output[j] = start + j; +} + +void MLPOD::podArraySetValue(double *y, double a, int n) +{ + for (int i=0; icreate(xij, N, "pod:xij"); + memory->create(S, N*ns, "pod:S"); + memory->create(Q, N*ns, "pod:Q"); + memory->create(A, ns*ns, "pod:A"); + memory->create(b, ns, "pod:ns"); + + for (int i=0; i= max(1,3*N-1) + int info = 1; // = 0: successful exit + std::vector work(ns*ns); + DSYEV(&chv, &chu, &ns, A, &ns, b, work.data(), &lwork, &info); + + // order eigenvalues and eigenvectors from largest to smallest + + for (int j=0; jdestroy(xij); + memory->destroy(S); + memory->destroy(A); + memory->destroy(b); + memory->destroy(Q); +} + +void MLPOD::read_pod(const std::string &pod_file) +{ + pod.nbesselpars = 3; + delete[] pod.besselparams; + pod.besselparams = new double[3]; + delete[] pod.pbc; + pod.pbc = new int[3]; + + pod.besselparams[0] = 0.0; + pod.besselparams[1] = 2.0; + pod.besselparams[2] = 4.0; + + pod.nelements = 0; + pod.onebody = 1; + pod.besseldegree = 3; + pod.inversedegree = 6; + pod.quadraticpod = 0; + pod.rin = 0.5; + pod.rcut = 4.6; + + pod.snaptwojmax = 0; + pod.snapchemflag = 0; + pod.snaprfac0 = 0.99363; + + sna.twojmax = 0; + sna.ntypes = 0; + + std::string podfilename = pod_file; + FILE *fppod; + if (comm->me == 0) { + + fppod = utils::open_potential(podfilename,lmp,nullptr); + if (fppod == nullptr) + error->one(FLERR,"Cannot open POD coefficient file {}: ", + podfilename, utils::getsyserror()); + } + + // loop through lines of POD file and parse keywords + + char line[MAXLINE],*ptr; + int eof = 0; + while (true) { + if (comm->me == 0) { + ptr = fgets(line,MAXLINE,fppod); + if (ptr == nullptr) { + eof = 1; + fclose(fppod); + } + } + MPI_Bcast(&eof,1,MPI_INT,0,world); + if (eof) break; + MPI_Bcast(line,MAXLINE,MPI_CHAR,0,world); + + // words = ptrs to all words in line + // strip single and double quotes from words + + std::vector words; + try { + words = Tokenizer(utils::trim_comment(line),"\"' \t\n\r\f").as_vector(); + } catch (TokenizerException &) { + // ignore + } + + if (words.size() == 0) continue; + + auto keywd = words[0]; + + if (keywd == "species") { + pod.nelements = words.size()-1; + for (int ielem = 1; ielem <= pod.nelements; ielem++) { + pod.species.push_back(words[ielem]); + } + } + + if (keywd == "pbc") { + if (words.size() != 4) + error->one(FLERR,"Improper POD file.", utils::getsyserror()); + pod.pbc[0] = utils::inumeric(FLERR,words[1],false,lmp); + pod.pbc[1] = utils::inumeric(FLERR,words[2],false,lmp); + pod.pbc[2] = utils::inumeric(FLERR,words[3],false,lmp); + } + + if ((keywd != "#") && (keywd != "species") && (keywd != "pbc")) { + + if (words.size() != 2) + error->one(FLERR,"Improper POD file.", utils::getsyserror()); + + if (keywd == "rin") pod.rin = utils::numeric(FLERR,words[1],false,lmp); + if (keywd == "rcut") pod.rcut = utils::numeric(FLERR,words[1],false,lmp); + if (keywd == "bessel_scaling_parameter1") + pod.besselparams[0] = utils::numeric(FLERR,words[1],false,lmp); + if (keywd == "bessel_scaling_parameter2") + pod.besselparams[1] = utils::numeric(FLERR,words[1],false,lmp); + if (keywd == "bessel_scaling_parameter3") + pod.besselparams[2] = utils::numeric(FLERR,words[1],false,lmp); + if (keywd == "bessel_polynomial_degree") + pod.besseldegree = utils::inumeric(FLERR,words[1],false,lmp); + if (keywd == "inverse_polynomial_degree") + pod.inversedegree = utils::inumeric(FLERR,words[1],false,lmp); + if (keywd == "onebody") pod.onebody = utils::inumeric(FLERR,words[1],false,lmp); + if (keywd == "twobody_bessel_polynomial_degree") + pod.twobody[0] = utils::inumeric(FLERR,words[1],false,lmp); + if (keywd == "twobody_inverse_polynomial_degree") + pod.twobody[1] = utils::inumeric(FLERR,words[1],false,lmp); + if (keywd == "twobody_number_radial_basis_functions") + pod.twobody[2] = utils::inumeric(FLERR,words[1],false,lmp); + if (keywd == "threebody_bessel_polynomial_degree") + pod.threebody[0] = utils::inumeric(FLERR,words[1],false,lmp); + if (keywd == "threebody_inverse_polynomial_degree") + pod.threebody[1] = utils::inumeric(FLERR,words[1],false,lmp); + if (keywd == "threebody_number_radial_basis_functions") + pod.threebody[2] = utils::inumeric(FLERR,words[1],false,lmp); + if (keywd == "threebody_number_angular_basis_functions") + pod.threebody[3] = utils::inumeric(FLERR,words[1],false,lmp)-1; + if (keywd == "fourbody_bessel_polynomial_degree") + pod.fourbody[0] = utils::inumeric(FLERR,words[1],false,lmp); + if (keywd == "fourbody_inverse_polynomial_degree") + pod.fourbody[1] = utils::inumeric(FLERR,words[1],false,lmp); + if (keywd == "fourbody_number_radial_basis_functions") + pod.fourbody[2] = utils::inumeric(FLERR,words[1],false,lmp); + if (keywd == "fourbody_snap_twojmax") + pod.snaptwojmax = utils::inumeric(FLERR,words[1],false,lmp); + if (keywd == "fourbody_snap_chemflag") + pod.snapchemflag = utils::inumeric(FLERR,words[1],false,lmp); + if (keywd == "fourbody_snap_rfac0") + pod.snaprfac0 = utils::numeric(FLERR,words[1],false,lmp); + if (keywd == "fourbody_snap_neighbor_weight1") + pod.snapelementweight[0] = utils::numeric(FLERR,words[1],false,lmp); + if (keywd == "fourbody_snap_neighbor_weight2") + pod.snapelementweight[1] = utils::numeric(FLERR,words[1],false,lmp); + if (keywd == "fourbody_snap_neighbor_weight3") + pod.snapelementweight[2] = utils::numeric(FLERR,words[1],false,lmp); + if (keywd == "fourbody_snap_neighbor_weight4") + pod.snapelementweight[3] = utils::numeric(FLERR,words[1],false,lmp); + if (keywd == "fourbody_snap_neighbor_weight5") + pod.snapelementweight[4] = utils::numeric(FLERR,words[1],false,lmp); + if (keywd == "quadratic_pod_potential") + pod.quadraticpod = utils::inumeric(FLERR,words[1],false,lmp); + if (keywd == "quadratic22_number_twobody_basis_functions") + pod.quadratic22[0] = utils::inumeric(FLERR,words[1],false,lmp); + if (keywd == "quadratic22_number_twobody_basis_functions") + pod.quadratic22[1] = utils::inumeric(FLERR,words[1],false,lmp); + if (keywd == "quadratic23_number_twobody_basis_functions") + pod.quadratic23[0] = utils::inumeric(FLERR,words[1],false,lmp); + if (keywd == "quadratic23_number_threebody_basis_functions") + pod.quadratic23[1] = utils::inumeric(FLERR,words[1],false,lmp); + if (keywd == "quadratic24_number_twobody_basis_functions") + pod.quadratic24[0] = utils::inumeric(FLERR,words[1],false,lmp); + if (keywd == "quadratic24_number_fourbody_basis_functions") + pod.quadratic24[1] = utils::inumeric(FLERR,words[1],false,lmp); + if (keywd == "quadratic33_number_threebody_basis_functions") + pod.quadratic33[0] = utils::inumeric(FLERR,words[1],false,lmp); + if (keywd == "quadratic33_number_threebody_basis_functions") + pod.quadratic33[1] = utils::inumeric(FLERR,words[1],false,lmp); + if (keywd == "quadratic34_number_threebody_basis_functions") + pod.quadratic34[0] = utils::inumeric(FLERR,words[1],false,lmp); + if (keywd == "quadratic34_number_fourbody_basis_functions") + pod.quadratic34[1] = utils::inumeric(FLERR,words[1],false,lmp); + if (keywd == "quadratic44_number_fourbody_basis_functions") + pod.quadratic44[0] = utils::inumeric(FLERR,words[1],false,lmp); + if (keywd == "quadratic44_number_fourbody_basis_functions") + pod.quadratic44[1] = utils::inumeric(FLERR,words[1],false,lmp); + if (keywd == "cubic234_number_twobody_basis_functions") + pod.cubic234[0] = utils::inumeric(FLERR,words[1],false,lmp); + if (keywd == "cubic234_number_threebody_basis_functions") + pod.cubic234[1] = utils::inumeric(FLERR,words[1],false,lmp); + if (keywd == "cubic234_number_fourbody_basis_functions") + pod.cubic234[2] = utils::inumeric(FLERR,words[1],false,lmp); + if (keywd == "cubic333_number_threebody_basis_functions") + pod.cubic333[0] = utils::inumeric(FLERR,words[1],false,lmp); + if (keywd == "cubic444_number_fourbody_basis_functions") + pod.cubic444[0] = utils::inumeric(FLERR,words[1],false,lmp); + } + } + + pod.twobody[0] = pod.besseldegree; + pod.twobody[1] = pod.inversedegree; + pod.threebody[0] = pod.besseldegree; + pod.threebody[1] = pod.inversedegree; + + // number of snapshots + + pod.ns2 = pod.nbesselpars*pod.twobody[0] + pod.twobody[1]; + pod.ns3 = pod.nbesselpars*pod.threebody[0] + pod.threebody[1]; + pod.ns4 = pod.nbesselpars*pod.fourbody[0] + pod.fourbody[1]; + + for (int i = 0; i < pod.nbesselpars; i++) + if (fabs(pod.besselparams[i]) < 1e-3) pod.besselparams[i] = 1e-3; + + // allocate memory for eigenvectors and eigenvalues + + if (pod.ns2 > 0) { + memory->create(pod.Phi2, pod.ns2*pod.ns2, "pod:pod_Phi2"); + memory->create(pod.Lambda2, pod.ns2, "pod:pod_Lambda2"); + } + if (pod.ns3 > 0) { + memory->create(pod.Phi3, pod.ns3*pod.ns3, "pod:pod_Phi3"); + memory->create(pod.Lambda3, pod.ns3, "pod:pod_Lambda3"); + } + if (pod.ns4 > 0) { + memory->create(pod.Phi4, pod.ns4*pod.ns4, "pod:pod_Phi4"); + memory->create(pod.Lambda4, pod.ns4, "pod:pod_Lambda4"); + } + + if (pod.ns2 > 0) { + podeigenvaluedecomposition(pod.Phi2, pod.Lambda2, pod.besselparams, pod.rin, pod.rcut, + pod.twobody[0], pod.twobody[1], pod.nbesselpars, 2000); + +// /* Print eigenvalues */ +// print_matrix( "Eigenvalues for two-body potential:", 1, pod.ns2, pod.Lambda2, 1 ); +// +// /* Print eigenvectors */ +// print_matrix( "Eigenvectors for two-body potential:", pod.ns2, pod.ns2, pod.Phi2, pod.ns2); + } + if (pod.ns3 > 0) { + podeigenvaluedecomposition(pod.Phi3, pod.Lambda3, pod.besselparams, pod.rin, pod.rcut, + pod.threebody[0], pod.threebody[1], pod.nbesselpars, 2000); + } + if (pod.ns4 > 0) { + podeigenvaluedecomposition(pod.Phi4, pod.Lambda4, pod.besselparams, pod.rin, pod.rcut, + pod.fourbody[0], pod.fourbody[1], pod.nbesselpars, 2000); + } + + // number of chemical combinations + + pod.nc2 = pod.nelements*(pod.nelements+1)/2; + pod.nc3 = pod.nelements*pod.nelements*(pod.nelements+1)/2; + pod.nc4 = pod.snapchemflag ? pod.nelements*pod.nelements*pod.nelements*pod.nelements : pod.nelements; + + // number of basis functions and descriptors for one-body potential + + if (pod.onebody==1) { + pod.nbf1 = 1; + pod.nd1 = pod.nelements; + } else { + pod.nbf1 = 0; + pod.nd1 = 0; + } + + // number of basis functions and descriptors for two-body potential + + pod.nbf2 = pod.twobody[2]; + pod.nd2 = pod.nbf2*pod.nc2; + + // number of basis functions and descriptors for three-body potential + + pod.nrbf3 = pod.threebody[2]; + pod.nabf3 = pod.threebody[3]; + pod.nbf3 = pod.nrbf3*(1 + pod.nabf3); + pod.nd3 = pod.nbf3*pod.nc3; + + // number of basis functions and descriptors for four-body potential + + int twojmax = pod.snaptwojmax; + int idxb_count = 0; + if (twojmax > 0) { + for(int j1 = 0; j1 <= twojmax; j1++) + for(int j2 = 0; j2 <= j1; j2++) + for(int j = j1 - j2; j <= MIN(twojmax, j1 + j2); j += 2) + if (j >= j1) idxb_count++; + } + pod.nbf4 = idxb_count; + pod.nd4 = pod.nbf4*pod.nc4; + + if (pod.quadraticpod==1) { + pod.quadratic23[0] = pod.nbf2; + pod.quadratic23[1] = pod.nbf3; + } + + pod.quadratic22[0] = MIN(pod.quadratic22[0], pod.nbf2); + pod.quadratic22[1] = MIN(pod.quadratic22[1], pod.nbf2); + pod.quadratic23[0] = MIN(pod.quadratic23[0], pod.nbf2); + pod.quadratic23[1] = MIN(pod.quadratic23[1], pod.nbf3); + pod.quadratic24[0] = MIN(pod.quadratic24[0], pod.nbf2); + pod.quadratic24[1] = MIN(pod.quadratic24[1], pod.nbf4); + pod.quadratic33[0] = MIN(pod.quadratic33[0], pod.nbf3); + pod.quadratic33[1] = MIN(pod.quadratic33[1], pod.nbf3); + pod.quadratic34[0] = MIN(pod.quadratic34[0], pod.nbf3); + pod.quadratic34[1] = MIN(pod.quadratic34[1], pod.nbf4); + pod.quadratic44[0] = MIN(pod.quadratic44[0], pod.nbf4); + pod.quadratic44[1] = MIN(pod.quadratic44[1], pod.nbf4); + + pod.cubic234[0] = MIN(pod.cubic234[0], pod.nbf2); + pod.cubic234[1] = MIN(pod.cubic234[1], pod.nbf3); + pod.cubic234[2] = MIN(pod.cubic234[2], pod.nbf4); + pod.cubic333[0] = MIN(pod.cubic333[0], pod.nbf3); + pod.cubic333[1] = MIN(pod.cubic333[0], pod.nbf3); + pod.cubic333[2] = MIN(pod.cubic333[0], pod.nbf3); + pod.cubic444[0] = MIN(pod.cubic444[0], pod.nbf4); + pod.cubic444[1] = MIN(pod.cubic444[0], pod.nbf4); + pod.cubic444[2] = MIN(pod.cubic444[0], pod.nbf4); + + // number of descriptors for quadratic POD potentials + + pod.nd22 = pod.quadratic22[0]*pod.quadratic22[1]*pod.nc2*pod.nc2; + pod.nd23 = pod.quadratic23[0]*pod.quadratic23[1]*pod.nc2*pod.nc3; + pod.nd24 = pod.quadratic24[0]*pod.quadratic24[1]*pod.nc2*pod.nc4; + pod.nd33 = pod.quadratic33[0]*pod.quadratic33[1]*pod.nc3*pod.nc3; + pod.nd34 = pod.quadratic34[0]*pod.quadratic34[1]*pod.nc3*pod.nc4; + pod.nd44 = pod.quadratic44[0]*pod.quadratic44[1]*pod.nc4*pod.nc4; + + int nq; + nq = pod.quadratic22[0]*pod.nc2; pod.nd22 = nq*(nq+1)/2; + nq = pod.quadratic33[0]*pod.nc3; pod.nd33 = nq*(nq+1)/2; + nq = pod.quadratic44[0]*pod.nc4; pod.nd44 = nq*(nq+1)/2; + + // number of descriptors for cubic POD potentials + + pod.nd234 = pod.cubic234[0]*pod.cubic234[1]*pod.cubic234[2]*pod.nc2*pod.nc3*pod.nc4; + nq = pod.cubic333[0]*pod.nc3; pod.nd333 = nq*(nq+1)*(nq+2)/6; + nq = pod.cubic444[0]*pod.nc4; pod.nd444 = nq*(nq+1)*(nq+2)/6; + + // total number of descriptors for all POD potentials + + pod.nd = pod.nd1 + pod.nd2 + pod.nd3 + pod.nd4 + pod.nd22 + pod.nd23 + pod.nd24 + + pod.nd33 + pod.nd34 + pod.nd44 + pod.nd234 + pod.nd333 + pod.nd444; + pod.nd1234 = pod.nd1 + pod.nd2 + pod.nd3 + pod.nd4; + + int nelements = pod.nelements; + delete[] pod.elemindex; + pod.elemindex = new int[nelements*nelements]; + + int k = 1; + for (int i=0; i < nelements; i++) { + for (int j=i; j < nelements; j++) { + pod.elemindex[i + nelements*j] = k; + pod.elemindex[j + nelements*i] = k; + k += 1; + } + } + + if (comm->me == 0) { + utils::logmesg(lmp, "**************** Begin of POD Potentials ****************\n"); + utils::logmesg(lmp, "species: "); + for (int i=0; ime == 0) { + + fpcoeff = utils::open_potential(coefffilename,lmp,nullptr); + if (fpcoeff == nullptr) + error->one(FLERR,"Cannot open POD coefficient file {}: ", + coefffilename, utils::getsyserror()); + } + + // check format for first line of file + + char line[MAXLINE],*ptr; + int eof = 0; + int nwords = 0; + while (nwords == 0) { + if (comm->me == 0) { + ptr = fgets(line,MAXLINE,fpcoeff); + if (ptr == nullptr) { + eof = 1; + fclose(fpcoeff); + } + } + MPI_Bcast(&eof,1,MPI_INT,0,world); + if (eof) break; + MPI_Bcast(line,MAXLINE,MPI_CHAR,0,world); + + // strip comment, skip line if blank + + nwords = utils::count_words(utils::trim_comment(line)); + } + + if (nwords != 2) + error->all(FLERR,"Incorrect format in POD coefficient file"); + + // strip single and double quotes from words + + int ncoeffall; + std::string tmp_str; + try { + ValueTokenizer words(utils::trim_comment(line),"\"' \t\n\r\f"); + tmp_str = words.next_string(); + ncoeffall = words.next_int(); + } catch (TokenizerException &e) { + error->all(FLERR,"Incorrect format in POD coefficient file: {}", e.what()); + } + + // loop over single block of coefficients and insert values in pod.coeff + + memory->create(pod.coeff, ncoeffall, "pod:pod_coeff"); + + for (int icoeff = 0; icoeff < ncoeffall; icoeff++) { + if (comm->me == 0) { + ptr = fgets(line,MAXLINE,fpcoeff); + if (ptr == nullptr) { + eof = 1; + fclose(fpcoeff); + } + } + + MPI_Bcast(&eof,1,MPI_INT,0,world); + if (eof) + error->all(FLERR,"Incorrect format in POD coefficient file"); + MPI_Bcast(line,MAXLINE,MPI_CHAR,0,world); + + try { + ValueTokenizer coeff(utils::trim_comment(line)); + if (coeff.count() != 1) + error->all(FLERR,"Incorrect format in POD coefficient file"); + + pod.coeff[icoeff] = coeff.next_double(); + } catch (TokenizerException &e) { + error->all(FLERR,"Incorrect format in POD coefficient file: {}", e.what()); + } + } + if (comm->me == 0) { + if (!eof) fclose(fpcoeff); + } +} + +/*********************************************************************************************************/ + +void MLPOD::linear_descriptors(double *gd, double *efatom, double *y, double *tmpmem, + int *atomtype, int *alist, int *pairlist, int * /*pairnum*/, + int *pairnumsum, int *tmpint, int natom, int Nij) +{ + int dim = 3; + int nelements = pod.nelements; + int nbesselpars = pod.nbesselpars; + int nrbf2 = pod.nbf2; + int nabf3 = pod.nabf3; + int nrbf3 = pod.nrbf3; + int nd1 = pod.nd1; + int nd2 = pod.nd2; + int nd3 = pod.nd3; + int nd4 = pod.nd4; + int nd1234 = nd1+nd2+nd3+nd4; + int *pdegree2 = pod.twobody; + int *elemindex = pod.elemindex; + double rin = pod.rin; + double rcut = pod.rcut; + double *Phi2 = pod.Phi2; + double *besselparams = pod.besselparams; + + double *fatom1 = &efatom[0]; + double *fatom2 = &efatom[dim*natom*(nd1)]; + double *fatom3 = &efatom[dim*natom*(nd1+nd2)]; + double *fatom4 = &efatom[dim*natom*(nd1+nd2+nd3)]; + double *eatom1 = &efatom[dim*natom*(nd1+nd2+nd3+nd4)]; + double *eatom2 = &efatom[dim*natom*(nd1+nd2+nd3+nd4)+natom*nd1]; + double *eatom3 = &efatom[dim*natom*(nd1+nd2+nd3+nd4)+natom*(nd1+nd2)]; + double *eatom4 = &efatom[dim*natom*(nd1+nd2+nd3+nd4)+natom*(nd1+nd2+nd3)]; + + podArraySetValue(fatom1, 0.0, (1+dim)*natom*(nd1+nd2+nd3+nd4)); + + double *rij = &tmpmem[0]; // 3*Nij + int *ai = &tmpint[0]; // Nij + int *aj = &tmpint[Nij]; // Nij + int *ti = &tmpint[2*Nij]; // Nij + int *tj = &tmpint[3*Nij]; // Nij + podNeighPairs(rij, y, ai, aj, ti, tj, pairlist, pairnumsum, atomtype, + alist, natom, dim); + + // peratom descriptors for one-body, two-body, and three-body linear potentials + + poddesc(eatom1, fatom1, eatom2, fatom2, eatom3, fatom3, rij, Phi2, besselparams, + &tmpmem[3*Nij], rin, rcut, pairnumsum, atomtype, ai, aj, ti, tj, elemindex, pdegree2, + nbesselpars, nrbf2, nrbf3, nabf3, nelements, Nij, natom); + + if (pod.snaptwojmax > 0) + snapdesc(eatom4, fatom4, rij, &tmpmem[3*Nij], atomtype, ai, aj, ti, tj, natom, Nij); + + // global descriptors for one-body, two-body, three-body, and four-bodt linear potentials + + podArraySetValue(tmpmem, 1.0, natom); + + char cht = 'T'; + double one = 1.0, zero = 0.0; + int inc1 = 1; + DGEMV(&cht, &natom, &nd1234, &one, eatom1, &natom, tmpmem, &inc1, &zero, gd, &inc1); +} + +void MLPOD::quadratic_descriptors(double* d23, double *dd23, double* d2, double *d3, double* dd2, double *dd3, + int M2, int M3, int N) +{ + for (int m3 = 0; m3 0) energy += quadratic_coefficients(c2, d2, coeff22, pod.quadratic22, nc2); + + // calculate energy for quadratic23 potential + + if (nd23 > 0) energy += quadratic_coefficients(c2, c3, d2, d3, coeff23, pod.quadratic23, nc2, nc3); + + // calculate energy for quadratic24 potential + + if (nd24 > 0) energy += quadratic_coefficients(c2, c4, d2, d4, coeff24, pod.quadratic24, nc2, nc4); + + // calculate energy for quadratic33 potential + + if (nd33 > 0) energy += quadratic_coefficients(c3, d3, coeff33, pod.quadratic33, nc3); + + // calculate energy for quadratic34 potential + + if (nd34 > 0) energy += quadratic_coefficients(c3, c4, d3, d4, coeff34, pod.quadratic34, nc3, nc4); + + // calculate energy for quadratic44 potential + + if (nd44 > 0) energy += quadratic_coefficients(c4, d4, coeff44, pod.quadratic44, nc4); + + // calculate energy for cubic234 potential + + if (nd234 > 0) energy += cubic_coefficients(c2, c3, c4, d2, d3, d4, coeff234, pod.cubic234, nc2, nc3, nc4); + + // calculate energy for cubic333 potential + + if (nd333 > 0) energy += cubic_coefficients(c3, d3, coeff333, pod.cubic333, nc3); + + // calculate energy for cubic444 potential + + if (nd444 > 0) energy += cubic_coefficients(c4, d4, coeff444, pod.cubic444, nc4); + + // calculate effective POD coefficients + + for (int i=0; i< nd1234; i++) c1[i] += coeff[i]; + + // calculate force = gdd * c1 + + char chn = 'N'; + double one = 1.0, zero = 0.0; + int inc1 = 1; + DGEMV(&chn, &nforce, &nd1234, &one, gdd, &nforce, c1, &inc1, &zero, force, &inc1); + + return energy; +} + +double MLPOD::energyforce_calculation(double *force, double *gd, double *gdd, double *coeff, double *y, + int *atomtype, int *alist, int *pairlist, int *pairnum, int *pairnumsum, int *tmpint, int natom, int Nij) +{ + int dim = 3; + int nd1234 = pod.nd1+pod.nd2+pod.nd3+pod.nd4; + double *tmpmem = &gdd[dim*natom*nd1234+natom*nd1234]; + + // calculate POD and SNAP descriptors and their derivatives + + linear_descriptors(gd, gdd, y, tmpmem, atomtype, alist, + pairlist, pairnum, pairnumsum, tmpint, natom, Nij); + + // calculate energy and force + + double energy = 0.0; + energy = calculate_energyforce(force, gd, gdd, coeff, &gdd[dim*natom*nd1234], natom); + + return energy; +} + +void MLPOD::podNeighPairs(double *xij, double *x, int *ai, int *aj, int *ti, int *tj, + int *pairlist, int *pairnumsum, int *atomtype, int *alist, int inum, int dim) +{ + for (int ii=0; ii j) + ik = lk + s; + k = aj[ik]; // atom k + typek = tj[ik] - 1; + xik1 = yij[0+dim*ik]; // xk - xi + xik2 = yij[1+dim*ik]; // xk - xi + xik3 = yij[2+dim*ik]; // xk - xi + riksq = xik1*xik1 + xik2*xik2 + xik3*xik3; + rik = sqrt(riksq); + + xdot = xij1*xik1 + xij2*xik2 + xij3*xik3; + costhe = xdot/(rij*rik); + costhe = costhe > 1.0 ? 1.0 : costhe; + costhe = costhe < -1.0 ? -1.0 : costhe; + xdot = costhe*(rij*rik); + + sinthe = sqrt(1.0 - costhe*costhe); + sinthe = sinthe > 1e-12 ? sinthe : 1e-12; + theta = acos(costhe); + dtheta = -1.0/sinthe; + + tm1 = 1.0/(rij*rijsq*rik); + tm2 = 1.0/(rij*riksq*rik); + dct1 = (xik1*rijsq - xij1*xdot)*tm1; + dct2 = (xik2*rijsq - xij2*xdot)*tm1; + dct3 = (xik3*rijsq - xij3*xdot)*tm1; + dct4 = (xij1*riksq - xik1*xdot)*tm2; + dct5 = (xij2*riksq - xik2*xdot)*tm2; + dct6 = (xij3*riksq - xik3*xdot)*tm2; + + for (int p=0; p = j1) idxb_count++; + + int idxb_max = idxb_count; + idx_max[2] = idxb_max; + + idxb_count = 0; + for(int j1 = 0; j1 <= twojmax; j1++) + for(int j2 = 0; j2 <= j1; j2++) + for(int j = j1 - j2; j <= MIN(twojmax, j1 + j2); j += 2) + if (j >= j1) { + idxb[idxb_count*3 + 0] = j1; + idxb[idxb_count*3 + 1] = j2; + idxb[idxb_count*3 + 2] = j; + idxb_count++; + } + + idxb_count = 0; + for(int j1 = 0; j1 <= twojmax; j1++) + for(int j2 = 0; j2 <= j1; j2++) + for(int j = j1 - j2; j <= MIN(twojmax, j1 + j2); j += 2) { + if (j >= j1) { + idxb_block[j + j2*jdim + j1*jdim*jdim] = idxb_count; + idxb_count++; + } + } + + // index list for zlist + + int idxz_count = 0; + + for(int j1 = 0; j1 <= twojmax; j1++) + for(int j2 = 0; j2 <= j1; j2++) + for(int j = j1 - j2; j <= MIN(twojmax, j1 + j2); j += 2) + for (int mb = 0; 2*mb <= j; mb++) + for (int ma = 0; ma <= j; ma++) + idxz_count++; + + int idxz_max = idxz_count; + idx_max[3] = idxz_max; + + idxz_count = 0; + for(int j1 = 0; j1 <= twojmax; j1++) + for(int j2 = 0; j2 <= j1; j2++) + for(int j = j1 - j2; j <= MIN(twojmax, j1 + j2); j += 2) { + idxz_block[j + j2*jdim + j1*jdim*jdim] = idxz_count; + + for (int mb = 0; 2*mb <= j; mb++) + for (int ma = 0; ma <= j; ma++) { + + idxz[idxz_count*10 + 0] = j1; + idxz[idxz_count*10 + 1] = j2; + idxz[idxz_count*10 + 2] = j; + idxz[idxz_count*10 + 3] = MAX(0, (2 * ma - j - j2 + j1) / 2); + idxz[idxz_count*10 + 4] = (2 * ma - j - (2 * idxz[idxz_count*10 + 3] - j1) + j2) / 2; + idxz[idxz_count*10 + 5] = MIN(j1, (2 * ma - j + j2 + j1) / 2) - idxz[idxz_count*10 + 3] + 1; + idxz[idxz_count*10 + 6] = MAX(0, (2 * mb - j - j2 + j1) / 2); + idxz[idxz_count*10 + 7] = (2 * mb - j - (2 * idxz[idxz_count*10 + 6] - j1) + j2) / 2; + idxz[idxz_count*10 + 8] = MIN(j1, (2 * mb - j + j2 + j1) / 2) - idxz[idxz_count*10 + 6] + 1; + + const int jju = idxu_block[j] + (j+1)*mb + ma; + idxz[idxz_count*10 + 9] = jju; + + idxz_count++; + } + } +}; + +void snapInitRootpqArray(double *rootpqarray, int twojmax) +{ + int jdim = twojmax + 1; + for (int p = 1; p <= twojmax; p++) + for (int q = 1; q <= twojmax; q++) + rootpqarray[p*jdim + q] = sqrt(((double) p)/q); +}; + +double snapDeltacg(double *factorial, int j1, int j2, int j) +{ + double sfaccg = factorial[(j1 + j2 + j) / 2 + 1]; + return sqrt(factorial[(j1 + j2 - j) / 2] * + factorial[(j1 - j2 + j) / 2] * + factorial[(-j1 + j2 + j) / 2] / sfaccg); +}; + +void snapInitClebschGordan(double *cglist, double *factorial, int twojmax) +{ + double sum,dcg,sfaccg; + int m, aa2, bb2, cc2; + int ifac; + + int idxcg_count = 0; + for(int j1 = 0; j1 <= twojmax; j1++) + for(int j2 = 0; j2 <= j1; j2++) + for(int j = j1 - j2; j <= MIN(twojmax, j1 + j2); j += 2) { + for (int m1 = 0; m1 <= j1; m1++) { + aa2 = 2 * m1 - j1; + + for (int m2 = 0; m2 <= j2; m2++) { + + bb2 = 2 * m2 - j2; + m = (aa2 + bb2 + j) / 2; + + if(m < 0 || m > j) { + cglist[idxcg_count] = 0.0; + idxcg_count++; + continue; + } + + sum = 0.0; + + for (int z = MAX(0, MAX(-(j - j2 + aa2) + / 2, -(j - j1 - bb2) / 2)); + z <= MIN((j1 + j2 - j) / 2, + MIN((j1 - aa2) / 2, (j2 + bb2) / 2)); + z++) { + ifac = z % 2 ? -1 : 1; + sum += ifac / + (factorial[z] * + factorial[(j1 + j2 - j) / 2 - z] * + factorial[(j1 - aa2) / 2 - z] * + factorial[(j2 + bb2) / 2 - z] * + factorial[(j - j2 + aa2) / 2 + z] * + factorial[(j - j1 - bb2) / 2 + z]); + } + + cc2 = 2 * m - j; + dcg = snapDeltacg(factorial, j1, j2, j); + sfaccg = sqrt(factorial[(j1 + aa2) / 2] * + factorial[(j1 - aa2) / 2] * + factorial[(j2 + bb2) / 2] * + factorial[(j2 - bb2) / 2] * + factorial[(j + cc2) / 2] * + factorial[(j - cc2) / 2] * + (j + 1)); + + cglist[idxcg_count] = sum * dcg * sfaccg; + idxcg_count++; + } + } + } +} + +void snapInitSna(double *rootpqarray, double *cglist, double *factorial, int *idx_max, int *idxz, + int *idxz_block, int *idxb, int *idxb_block, int *idxu_block, int *idxcg_block, int twojmax) +{ + snapBuildIndexList(idx_max, idxz, idxz_block, idxb, + idxb_block, idxu_block, idxcg_block, twojmax); + + snapInitRootpqArray(rootpqarray, twojmax); + snapInitClebschGordan(cglist, factorial, twojmax); +} + +void MLPOD::snapSetup(int twojmax, int ntypes) +{ + sna.twojmax = twojmax; + sna.ntypes = ntypes; + + int jdim = twojmax + 1; + int jdimpq = twojmax + 2; + + memory->create(sna.map, ntypes+1, "pod:sna_map"); + memory->create(sna.idxcg_block, jdim*jdim*jdim, "pod:sna_idxcg_block"); + memory->create(sna.idxz_block, jdim*jdim*jdim, "pod:sna_idxz_block"); + memory->create(sna.idxb_block, jdim*jdim*jdim, "pod:sna_idxb_block"); + memory->create(sna.idxu_block, jdim, "pod:sna_idxu_block"); + memory->create(sna.idx_max, 5, "pod:sna_idx_max"); + + int idxb_count = 0; + for(int j1 = 0; j1 <= twojmax; j1++) + for(int j2 = 0; j2 <= j1; j2++) + for(int j = j1 - j2; j <= MIN(twojmax, j1 + j2); j += 2) + if (j >= j1) idxb_count++; + + int idxz_count = 0; + for(int j1 = 0; j1 <= twojmax; j1++) + for(int j2 = 0; j2 <= j1; j2++) + for(int j = j1 - j2; j <= MIN(twojmax, j1 + j2); j += 2) + for (int mb = 0; 2*mb <= j; mb++) + for (int ma = 0; ma <= j; ma++) + idxz_count++; + + int idxcg_count = 0; + for(int j1 = 0; j1 <= twojmax; j1++) + for(int j2 = 0; j2 <= j1; j2++) + for(int j = j1 - j2; j <= MIN(twojmax, j1 + j2); j += 2) { + for (int m1 = 0; m1 <= j1; m1++) + for (int m2 = 0; m2 <= j2; m2++) + idxcg_count++; + } + + memory->create(sna.idxz, idxz_count*10, "pod:sna_idxz"); + memory->create(sna.idxb, idxb_count*3, "pod:sna_idxb"); + memory->create(sna.rcutsq, (ntypes+1)*(ntypes+1), "pod:sna_rcutsq"); + memory->create(sna.radelem, ntypes+1, "pod:sna_radelem"); + memory->create(sna.wjelem, ntypes+1, "pod:sna_wjelem"); + memory->create(sna.rootpqarray, jdimpq*jdimpq, "pod:sna_rootpqarray"); + memory->create(sna.cglist, idxcg_count, "pod:sna_cglist"); + memory->create(sna.bzero, jdim, "pod:sna_bzero"); + memory->create(sna.fac, 168, "pod:sna_fac"); + + for (int i=0; i rcutij) { + sfac = 0.0; + dsfac = 0.0; + } + else { + double rcutfac0 = MY_PI / (rcutij - rmin0); + sfac = 0.5 * (cos((r - rmin0) * rcutfac0) + 1.0); + dsfac = -0.5 * sin((r - rmin0) * rcutfac0) * rcutfac0; + } + } + sfac *= wjelem[tj[ij]]; + dsfac *= wjelem[tj[ij]]; + + double r0inv, dr0invdr; + 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]; + double rootpq; + int jdim = twojmax + 1; + + r0inv = 1.0 / sqrt(r * r + z0 * z0); + a_r = r0inv * z0; + a_i = -r0inv * z; + b_r = r0inv * y; + b_i = -r0inv * x; + + dr0invdr = -cube(r0inv) * (r + z0 * dz0dr); + + dr0inv[0] = dr0invdr * ux; + dr0inv[1] = dr0invdr * uy; + dr0inv[2] = dr0invdr * uz; + + dz0[0] = dz0dr * ux; + dz0[1] = dz0dr * uy; + dz0[2] = dz0dr * uz; + + for (int k = 0; k < 3; k++) { + da_r[k] = dz0[k] * r0inv + z0 * dr0inv[k]; + da_i[k] = -z * dr0inv[k]; + } + da_i[2] += -r0inv; + + for (int k = 0; k < 3; k++) { + db_r[k] = y * dr0inv[k]; + db_i[k] = -x * dr0inv[k]; + } + db_i[0] += -r0inv; + db_r[1] += r0inv; + + Sr[ij+0*ijnum] = 1.0; + Si[ij+0*ijnum] = 0.0; + Srx[ij+0*ijnum] = 0.0; + Six[ij+0*ijnum] = 0.0; + Sry[ij+0*ijnum] = 0.0; + Siy[ij+0*ijnum] = 0.0; + Srz[ij+0*ijnum] = 0.0; + Siz[ij+0*ijnum] = 0.0; + for (int j = 1; j <= twojmax; j++) { + int jju = idxu_block[j]; + int jjup = idxu_block[j-1]; + + // fill in left side of matrix layer from previous layer + + for (int mb = 0; 2*mb <= j; mb++) { + Sr[ij+jju*ijnum] = 0.0; + Si[ij+jju*ijnum] = 0.0; + Srx[ij+jju*ijnum] = 0.0; + Six[ij+jju*ijnum] = 0.0; + Sry[ij+jju*ijnum] = 0.0; + Siy[ij+jju*ijnum] = 0.0; + Srz[ij+jju*ijnum] = 0.0; + Siz[ij+jju*ijnum] = 0.0; + for (int ma = 0; ma < j; ma++) { + rootpq = rootpqarray[(j - ma)*jdim + (j - mb)]; + int njju = ij+jju*ijnum; + int njju1 = ij+(jju+1)*ijnum; + int njjup = ij+jjup*ijnum; + double u_r = Sr[njjup]; + double u_i = Si[njjup]; + double ux_r = Srx[njjup]; + double ux_i = Six[njjup]; + double uy_r = Sry[njjup]; + double uy_i = Siy[njjup]; + double uz_r = Srz[njjup]; + double uz_i = Siz[njjup]; + + Sr[njju] += rootpq * (a_r * u_r + a_i * u_i); + Si[njju] += rootpq * (a_r * u_i - a_i * u_r); + Srx[njju] += rootpq * (da_r[0] * u_r + da_i[0] * u_i + a_r * ux_r + a_i * ux_i); + Six[njju] += rootpq * (da_r[0] * u_i - da_i[0] * u_r + a_r * ux_i - a_i * ux_r); + Sry[njju] += rootpq * (da_r[1] * u_r + da_i[1] * u_i + a_r * uy_r + a_i * uy_i); + Siy[njju] += rootpq * (da_r[1] * u_i - da_i[1] * u_r + a_r * uy_i - a_i * uy_r); + Srz[njju] += rootpq * (da_r[2] * u_r + da_i[2] * u_i + a_r * uz_r + a_i * uz_i); + Siz[njju] += rootpq * (da_r[2] * u_i - da_i[2] * u_r + a_r * uz_i - a_i * uz_r); + + rootpq = rootpqarray[(ma + 1)*jdim + (j - mb)]; + Sr[njju1] = -rootpq * (b_r * u_r + b_i * u_i); + Si[njju1] = -rootpq * (b_r * u_i - b_i * u_r); + Srx[njju1] = -rootpq * (db_r[0] * u_r + db_i[0] * u_i + b_r * ux_r + b_i * ux_i); + Six[njju1] = -rootpq * (db_r[0] * u_i - db_i[0] * u_r + b_r * ux_i - b_i * ux_r); + Sry[njju1] = -rootpq * (db_r[1] * u_r + db_i[1] * u_i + b_r * uy_r + b_i * uy_i); + Siy[njju1] = -rootpq * (db_r[1] * u_i - db_i[1] * u_r + b_r * uy_i - b_i * uy_r); + Srz[njju1] = -rootpq * (db_r[2] * u_r + db_i[2] * u_i + b_r * uz_r + b_i * uz_i); + Siz[njju1] = -rootpq * (db_r[2] * u_i - db_i[2] * u_r + b_r * uz_i - b_i * uz_r); + jju++; + jjup++; + } + jju++; + } + + jju = idxu_block[j]; + jjup = jju+(j+1)*(j+1)-1; + int mbpar = 1; + for (int mb = 0; 2*mb <= j; mb++) { + int mapar = mbpar; + for (int ma = 0; ma <= j; ma++) { + int njju = ij+jju*ijnum; + int njjup = ij+jjup*ijnum; + if (mapar == 1) { + Sr[njjup] = Sr[njju]; + Si[njjup] = -Si[njju]; + if (j%2==1 && mb==(j/2)) { + Srx[njjup] = Srx[njju]; + Six[njjup] = -Six[njju]; + Sry[njjup] = Sry[njju]; + Siy[njjup] = -Siy[njju]; + Srz[njjup] = Srz[njju]; + Siz[njjup] = -Siz[njju]; + } + } else { + Sr[njjup] = -Sr[njju]; + Si[njjup] = Si[njju]; + if (j%2==1 && mb==(j/2)) { + Srx[njjup] = -Srx[njju]; + Six[njjup] = Six[njju]; + Sry[njjup] = -Sry[njju]; + Siy[njjup] = Siy[njju]; + Srz[njjup] = -Srz[njju]; + Siz[njjup] = Siz[njju]; + } + } + mapar = -mapar; + jju++; + jjup--; + } + mbpar = -mbpar; + } + } + + 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++) { + int ijk = ij+jju*ijnum; + Srx[ijk] = dsfac * Sr[ijk] * ux + sfac * Srx[ijk]; + Six[ijk] = dsfac * Si[ijk] * ux + sfac * Six[ijk]; + Sry[ijk] = dsfac * Sr[ijk] * uy + sfac * Sry[ijk]; + Siy[ijk] = dsfac * Si[ijk] * uy + sfac * Siy[ijk]; + Srz[ijk] = dsfac * Sr[ijk] * uz + sfac * Srz[ijk]; + Siz[ijk] = dsfac * Si[ijk] * uz + sfac * Siz[ijk]; + jju++; + } + } + + for (int k=0; k 1e-20) { + rij[ninside*3 + 0] = delx; + rij[ninside*3 + 1] = dely; + rij[ninside*3 + 2] = delz; + idxi[ninside] = ii; + ai[ninside] = gi; + aj[ninside] = gj; + ti[ninside] = itype; + tj[ninside] = atomtype[gj]; + ninside++; + pairnumsum[ii+1] += 1; + } + } + } + + pairnumsum[0] = 0; + for (int ii=0; ii j) + ik = lk + s; + typek = tj[ik] - 1; + xik1 = yij[0+dim*ik]; // xk - xi + xik2 = yij[1+dim*ik]; // xk - xi + xik3 = yij[2+dim*ik]; // xk - xi s + riksq = xik1*xik1 + xik2*xik2 + xik3*xik3; + rik = sqrt(riksq); + + xdot = xij1*xik1 + xij2*xik2 + xij3*xik3; + costhe = xdot/(rij*rik); + costhe = costhe > 1.0 ? 1.0 : costhe; + costhe = costhe < -1.0 ? -1.0 : costhe; + theta = acos(costhe); + + for (int p=0; p rcutij) { + sfac = 0.0; + } + else { + double rcutfac0 = MY_PI / (rcutij - rmin0); + sfac = 0.5 * (cos((r - rmin0) * rcutfac0) + 1.0); + } + } + sfac *= wjelem[tj[ij]]; + + double r0inv; + double a_r, a_i, b_r, b_i; + double rootpq; + int jdim = twojmax + 1; + + r0inv = 1.0 / sqrt(r * r + z0 * z0); + a_r = r0inv * z0; + a_i = -r0inv * z; + b_r = r0inv * y; + b_i = -r0inv * x; + + Sr[ij+0*ijnum] = 1.0; + Si[ij+0*ijnum] = 0.0; + for (int j = 1; j <= twojmax; j++) { + int jju = idxu_block[j]; + int jjup = idxu_block[j-1]; + + // fill in left side of matrix layer from previous layer + + for (int mb = 0; 2*mb <= j; mb++) { + Sr[ij+jju*ijnum] = 0.0; + Si[ij+jju*ijnum] = 0.0; + for (int ma = 0; ma < j; ma++) { + rootpq = rootpqarray[(j - ma)*jdim + (j - mb)]; + int njju = ij+jju*ijnum; + int njju1 = ij+(jju+1)*ijnum; + int njjup = ij+jjup*ijnum; + double u_r = Sr[njjup]; + double u_i = Si[njjup]; + + Sr[njju] += rootpq * (a_r * u_r + a_i * u_i); + Si[njju] += rootpq * (a_r * u_i - a_i * u_r); + + rootpq = rootpqarray[(ma + 1)*jdim + (j - mb)]; + Sr[njju1] = -rootpq * (b_r * u_r + b_i * u_i); + Si[njju1] = -rootpq * (b_r * u_i - b_i * u_r); + jju++; + jjup++; + } + jju++; + } + + jju = idxu_block[j]; + jjup = jju+(j+1)*(j+1)-1; + int mbpar = 1; + for (int mb = 0; 2*mb <= j; mb++) { + int mapar = mbpar; + for (int ma = 0; ma <= j; ma++) { + int njju = ij+jju*ijnum; + int njjup = ij+jjup*ijnum; + if (mapar == 1) { + Sr[njjup] = Sr[njju]; + Si[njjup] = -Si[njju]; + } else { + Sr[njjup] = -Sr[njju]; + Si[njjup] = Si[njju]; + } + mapar = -mapar; + jju++; + jjup--; + } + mbpar = -mbpar; + } + } + + for (int k=0; k 0) + snapdesc_ij(eatom4, rij, tmpmem, atomtype, idxi, ti, tj, natom, Nij); + + // global descriptors for one-body, two-body, three-body, and four-bodt linear potentials + + podArraySetValue(tmpmem, 1.0, natom); + + char cht = 'T'; + double one = 1.0; + int inc1 = 1; + DGEMV(&cht, &natom, &nd1234, &one, eatom1, &natom, tmpmem, &inc1, &one, gd, &inc1); +} + +double MLPOD::calculate_energy(double *effectivecoeff, double *gd, double *coeff) +{ + int nd1 = pod.nd1; + int nd2 = pod.nd2; + int nd3 = pod.nd3; + int nd4 = pod.nd4; + int nd1234 = nd1+nd2+nd3+nd4; + int nd22 = pod.nd22; + int nd23 = pod.nd23; + int nd24 = pod.nd24; + int nd33 = pod.nd33; + int nd34 = pod.nd34; + int nd44 = pod.nd44; + int nd234 = pod.nd234; + int nd333 = pod.nd333; + int nd444 = pod.nd444; + int nc2 = pod.nc2; + int nc3 = pod.nc3; + int nc4 = pod.nc4; + + // two-body, three-body, and four-body descriptors + + double *d2 = &gd[nd1]; + double *d3 = &gd[nd1+nd2]; + double *d4 = &gd[nd1+nd2+nd3]; + + // quadratic and cubic POD coefficients + + double *coeff22 = &coeff[nd1234]; + double *coeff23 = &coeff[nd1234+nd22]; + double *coeff24 = &coeff[nd1234+nd22+nd23]; + double *coeff33 = &coeff[nd1234+nd22+nd23+nd24]; + double *coeff34 = &coeff[nd1234+nd22+nd23+nd24+nd33]; + double *coeff44 = &coeff[nd1234+nd22+nd23+nd24+nd33+nd34]; + double *coeff234 = &coeff[nd1234+nd22+nd23+nd24+nd33+nd34+nd44]; + double *coeff333 = &coeff[nd1234+nd22+nd23+nd24+nd33+nd34+nd44+nd234]; + double *coeff444 = &coeff[nd1234+nd22+nd23+nd24+nd33+nd34+nd44+nd234+nd333]; + + // calculate energy for linear potentials + + double energy = 0.0; + for (int i=0; i< nd1234; i++) { + effectivecoeff[i] = 0.0; + energy += coeff[i]*gd[i]; + } + + // effective POD coefficients for calculating force + + double *c2 = &effectivecoeff[nd1]; + double *c3 = &effectivecoeff[nd1+nd2]; + double *c4 = &effectivecoeff[nd1+nd2+nd3]; + + // calculate energy for quadratic22 potential + + if (nd22 > 0) energy += quadratic_coefficients(c2, d2, coeff22, pod.quadratic22, nc2); + + // calculate energy for quadratic23 potential + + if (nd23 > 0) energy += quadratic_coefficients(c2, c3, d2, d3, coeff23, pod.quadratic23, nc2, nc3); + + // calculate energy for quadratic24 potential + + if (nd24 > 0) energy += quadratic_coefficients(c2, c4, d2, d4, coeff24, pod.quadratic24, nc2, nc4); + + // calculate energy for quadratic33 potential + + if (nd33 > 0) energy += quadratic_coefficients(c3, d3, coeff33, pod.quadratic33, nc3); + + // calculate energy for quadratic34 potential + + if (nd34 > 0) energy += quadratic_coefficients(c3, c4, d3, d4, coeff34, pod.quadratic34, nc3, nc4); + + // calculate energy for quadratic44 potential + + if (nd44 > 0) energy += quadratic_coefficients(c4, d4, coeff44, pod.quadratic44, nc4); + + // calculate energy for cubic234 potential + + if (nd234 > 0) energy += cubic_coefficients(c2, c3, c4, d2, d3, d4, coeff234, pod.cubic234, nc2, nc3, nc4); + + // calculate energy for cubic333 potential + + if (nd333 > 0) energy += cubic_coefficients(c3, d3, coeff333, pod.cubic333, nc3); + + // calculate energy for cubic444 potential + + if (nd444 > 0) energy += cubic_coefficients(c4, d4, coeff444, pod.cubic444, nc4); + + // calculate effective POD coefficients + + for (int i=0; i< nd1234; i++) effectivecoeff[i] += coeff[i]; + + return energy; +} + +double MLPOD::calculate_energy(double *energycoeff, double *forcecoeff, double *gd, + double *gdall, double *coeff) +{ + int nd1 = pod.nd1; + int nd2 = pod.nd2; + int nd3 = pod.nd3; + int nd4 = pod.nd4; + int nd1234 = nd1+nd2+nd3+nd4; + int nd22 = pod.nd22; + int nd23 = pod.nd23; + int nd24 = pod.nd24; + int nd33 = pod.nd33; + int nd34 = pod.nd34; + int nd44 = pod.nd44; + int nd234 = pod.nd234; + int nd333 = pod.nd333; + int nd444 = pod.nd444; + int nc2 = pod.nc2; + int nc3 = pod.nc3; + int nc4 = pod.nc4; + + // quadratic and cubic POD coefficients + + double *coeff22 = &coeff[nd1234]; + double *coeff23 = &coeff[nd1234+nd22]; + double *coeff24 = &coeff[nd1234+nd22+nd23]; + double *coeff33 = &coeff[nd1234+nd22+nd23+nd24]; + double *coeff34 = &coeff[nd1234+nd22+nd23+nd24+nd33]; + double *coeff44 = &coeff[nd1234+nd22+nd23+nd24+nd33+nd34]; + double *coeff234 = &coeff[nd1234+nd22+nd23+nd24+nd33+nd34+nd44]; + double *coeff333 = &coeff[nd1234+nd22+nd23+nd24+nd33+nd34+nd44+nd234]; + double *coeff444 = &coeff[nd1234+nd22+nd23+nd24+nd33+nd34+nd44+nd234+nd333]; + + // sum global descriptors over all MPI ranks + + MPI_Allreduce(gd, gdall, nd1234, MPI_DOUBLE, MPI_SUM, world); + + for (int i=0; i< nd1234; i++) { + energycoeff[i] = 0.0; + forcecoeff[i] = 0.0; + } + + // effective POD coefficients for calculating force + + double *c2 = &forcecoeff[nd1]; + double *c3 = &forcecoeff[nd1+nd2]; + double *c4 = &forcecoeff[nd1+nd2+nd3]; + + // effective POD coefficients for calculating energy + + double *ce2 = &energycoeff[nd1]; + double *ce3 = &energycoeff[nd1+nd2]; + double *ce4 = &energycoeff[nd1+nd2+nd3]; + + // two-body, three-body, and four-body descriptors + + double *d2 = &gdall[nd1]; + double *d3 = &gdall[nd1+nd2]; + double *d4 = &gdall[nd1+nd2+nd3]; + + // calculate energy for quadratic22 potential + + if (nd22 > 0) quadratic_coefficients(ce2, c2, d2, coeff22, pod.quadratic22, nc2); + + // calculate energy for quadratic23 potential + + if (nd23 > 0) quadratic_coefficients(ce2, ce3, c2, c3, d2, d3, coeff23, pod.quadratic23, nc2, nc3); + + // calculate energy for quadratic24 potential + + if (nd24 > 0) quadratic_coefficients(ce2, ce4, c2, c4, d2, d4, coeff24, pod.quadratic24, nc2, nc4); + + // calculate energy for quadratic33 potential + + if (nd33 > 0) quadratic_coefficients(ce3, c3, d3, coeff33, pod.quadratic33, nc3); + + // calculate energy for quadratic34 potential + + if (nd34 > 0) quadratic_coefficients(ce3, ce4, c3, c4, d3, d4, coeff34, pod.quadratic34, nc3, nc4); + + // calculate energy for quadratic44 potential + + if (nd44 > 0) quadratic_coefficients(ce4, c4, d4, coeff44, pod.quadratic44, nc4); + + // calculate energy for cubic234 potential + + if (nd234 > 0) cubic_coefficients(ce2, ce3, ce4, c2, c3, c4, d2, d3, d4, coeff234, pod.cubic234, nc2, nc3, nc4); + + // calculate energy for cubic333 potential + + if (nd333 > 0) cubic_coefficients(ce3, c3, d3, coeff333, pod.cubic333, nc3); + + // calculate energy for cubic444 potential + + if (nd444 > 0) cubic_coefficients(ce4, c4, d4, coeff444, pod.cubic444, nc4); + + // calculate effective POD coefficients + + for (int i=0; i< nd1234; i++) { + energycoeff[i] += coeff[i]; + forcecoeff[i] += coeff[i]; + } + + // calculate energy + + double energy = 0.0; + for (int i=0; i< nd1234; i++) + energy += energycoeff[i]*gd[i]; + + return energy; +} + +void MLPOD::pod2body_force(double *force, double *fij, double *coeff2, int *ai, int *aj, int *ti, + int *tj, int *elemindex, int nelements, int nbf, int /*natom*/, int N) +{ + int nelements2 = nelements*(nelements+1)/2; + for (int n=0; n j) + ik = lk + s; + k = aj[ik]; // atom k + typek = tj[ik] - 1; + xik1 = yij[0+dim*ik]; // xk - xi + xik2 = yij[1+dim*ik]; // xk - xi + xik3 = yij[2+dim*ik]; // xk - xi s + riksq = xik1*xik1 + xik2*xik2 + xik3*xik3; + rik = sqrt(riksq); + + xdot = xij1*xik1 + xij2*xik2 + xij3*xik3; + costhe = xdot/(rij*rik); + costhe = costhe > 1.0 ? 1.0 : costhe; + costhe = costhe < -1.0 ? -1.0 : costhe; + xdot = costhe*(rij*rik); + + sinthe = sqrt(1.0 - costhe*costhe); + sinthe = sinthe > 1e-12 ? sinthe : 1e-12; + theta = acos(costhe); + dtheta = -1.0/sinthe; + + tm1 = 1.0/(rij*rijsq*rik); + tm2 = 1.0/(rij*riksq*rik); + dct1 = (xik1*rijsq - xij1*xdot)*tm1; + dct2 = (xik2*rijsq - xij2*xdot)*tm1; + dct3 = (xik3*rijsq - xij3*xdot)*tm1; + dct4 = (xij1*riksq - xik1*xdot)*tm2; + dct5 = (xij2*riksq - xik2*xdot)*tm2; + dct6 = (xij3*riksq - xik3*xdot)*tm2; + + for (int p=0; p 0) + pod4body_force(force, rij, coeff4, tmpmem, atomtype, idxi, ai, aj, ti, tj, natom, Nij); +} + +double MLPOD::energyforce_calculation(double *force, double *podcoeff, double *effectivecoeff, double *gd, double *rij, + double *tmpmem, int *pairnumsum, int *atomtype, int *idxi, int *ai, int *aj, int *ti, int *tj, int natom, int Nij) +{ + int nd1234 = pod.nd1+pod.nd2+pod.nd3+pod.nd4; + double *eatom = &tmpmem[0]; + + podArraySetValue(gd, 0.0, nd1234); + linear_descriptors_ij(gd, eatom, rij, &tmpmem[natom*nd1234], pairnumsum, atomtype, idxi, ti, tj, natom, Nij); + + // Need to do MPI_Allreduce on gd for parallel + + double energy = calculate_energy(effectivecoeff, gd, podcoeff); + + podArraySetValue(force, 0.0, 3*natom); + + calculate_force(force, effectivecoeff, rij, tmpmem, pairnumsum, atomtype, idxi, ai, aj, ti, tj, natom, Nij); + + return energy; +} + + +void MLPOD::pod2body_force(double **force, double *fij, double *coeff2, int *ai, int *aj, int *ti, + int *tj, int *elemindex, int nelements, int nbf, int /*natom*/, int N) +{ + int nelements2 = nelements*(nelements+1)/2; + for (int n=0; n j) + ik = lk + s; + k = aj[ik]; // atom k + typek = tj[ik] - 1; + xik1 = yij[0+dim*ik]; // xk - xi + xik2 = yij[1+dim*ik]; // xk - xi + xik3 = yij[2+dim*ik]; // xk - xi s + riksq = xik1*xik1 + xik2*xik2 + xik3*xik3; + rik = sqrt(riksq); + + xdot = xij1*xik1 + xij2*xik2 + xij3*xik3; + costhe = xdot/(rij*rik); + costhe = costhe > 1.0 ? 1.0 : costhe; + costhe = costhe < -1.0 ? -1.0 : costhe; + xdot = costhe*(rij*rik); + + sinthe = pow(1.0 - costhe*costhe, 0.5); + sinthe = sinthe > 1e-12 ? sinthe : 1e-12; + theta = acos(costhe); + dtheta = -1.0/sinthe; + + tm1 = 1.0/(rij*rijsq*rik); + tm2 = 1.0/(rij*riksq*rik); + dct1 = (xik1*rijsq - xij1*xdot)*tm1; + dct2 = (xik2*rijsq - xij2*xdot)*tm1; + dct3 = (xik3*rijsq - xij3*xdot)*tm1; + dct4 = (xij1*riksq - xik1*xdot)*tm2; + dct5 = (xij2*riksq - xik2*xdot)*tm2; + dct6 = (xij3*riksq - xik3*xdot)*tm2; + + for (int p=0; p 0) + pod4body_force(force, rij, coeff4, tmpmem, atomtype, idxi, ai, aj, ti, tj, natom, Nij); +} diff --git a/src/ML-POD/mlpod.h b/src/ML-POD/mlpod.h new file mode 100644 index 0000000000..54e75988be --- /dev/null +++ b/src/ML-POD/mlpod.h @@ -0,0 +1,308 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/ Sandia National Laboratories + LAMMPS development team: developers@lammps.org + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifndef LMP_MLPOD_H +#define LMP_MLPOD_H + +#include "pointers.h" + +#define DDOT ddot_ +#define DGEMV dgemv_ +#define DGEMM dgemm_ +#define DGETRF dgetrf_ +#define DGETRI dgetri_ +#define DSYEV dsyev_ +#define DPOSV dposv_ + +extern "C" { +double DDOT(int *, double *, int *, double *, int *); +void DGEMV(char *, int *, int *, double *, double *, int *, double *, int *, double *, double *, + int *); +void DGEMM(char *, char *, int *, int *, int *, double *, double *, int *, double *, int *, + double *, double *, int *); +void DGETRF(int *, int *, double *, int *, int *, int *); +void DGETRI(int *, double *, int *, int *, double *, int *, int *); +void DSYEV(char *, char *, int *, double *, int *, double *, double *, int *, int *); +void DPOSV(char *, int *, int *, double *, int *, double *, int *, int *); +} + +namespace LAMMPS_NS { + +class MLPOD : protected Pointers { + + private: + // functions for reading input files + + void read_pod(const std::string &pod_file); + void read_coeff_file(const std::string &coeff_file); + + // functions for calculating/collating POD descriptors/coefficients for energies + + void podradialbasis(double *rbf, double *drbf, double *xij, double *besselparams, double rin, + double rmax, int besseldegree, int inversedegree, int nbesselpars, int N); + void pod1body(double *eatom, double *fatom, int *atomtype, int nelements, int natom); + void podtally2b(double *eatom, double *fatom, double *eij, double *fij, int *ai, int *aj, int *ti, + int *tj, int *elemindex, int nelements, int nbf, int natom, int N); + void pod3body(double *eatom, double *fatom, double *rij, double *e2ij, double *f2ij, + double *tmpmem, int *elemindex, int *pairnumsum, int *ai, int *aj, int *ti, int *tj, + int nrbf, int nabf, int nelements, int natom, int Nij); + void poddesc(double *eatom1, double *fatom1, double *eatom2, double *fatom2, double *eatom3, + double *fatom3, double *rij, double *Phi, double *besselparams, double *tmpmem, + double rin, double rcut, int *pairnumsum, int *atomtype, int *ai, int *aj, int *ti, + int *tj, int *elemindex, int *pdegree, int nbesselpars, int nrbf2, int nrbf3, + int nabf, int nelements, int Nij, int natom); + double quadratic_coefficients(double *c2, double *c3, double *d2, double *d3, double *coeff23, + int *quadratic, int nc2, int nc3); + double quadratic_coefficients(double *c3, double *d3, double *coeff33, int *quadratic, int nc3); + double cubic_coefficients(double *c2, double *c3, double *c4, double *d2, double *d3, double *d4, + double *coeff234, int *cubic, int nc2, int nc3, int nc4); + double cubic_coefficients(double *c3, double *d3, double *coeff333, int *cubic, int nc3); + double quadratic_coefficients(double *ce2, double *ce3, double *c2, double *c3, double *d2, + double *d3, double *coeff23, int *quadratic, int nc2, int nc3); + double quadratic_coefficients(double *ce3, double *c3, double *d3, double *coeff33, + int *quadratic, int nc3); + double cubic_coefficients(double *ce2, double *ce3, double *ce4, double *c2, double *c3, + double *c4, double *d2, double *d3, double *d4, double *coeff234, + int *cubic, int nc2, int nc3, int nc4); + double cubic_coefficients(double *ce3, double *c3, double *d3, double *coeff333, int *cubic, + int nc3); + + // functions for calculating/collating SNAP descriptors/coefficients for energies + + void snapSetup(int twojmax, int ntypes); + void InitSnap(); + void snapComputeUlist(double *Sr, double *Si, double *dSr, double *dSi, double *rootpqarray, + double *rij, double *wjelem, double *radelem, double rmin0, double rfac0, + double rcutfac, int *idxu_block, int *ti, int *tj, int twojmax, + int idxu_max, int ijnum, int switch_flag); + void snapZeroUarraytot2(double *Stotr, double *Stoti, double wself, int *idxu_block, int *type, + int *map, int *ai, int wselfall_flag, int chemflag, int idxu_max, + int nelements, int twojmax, int inum); + void snapAddUarraytot(double *Stotr, double *Stoti, double *Sr, double *Si, int *map, int *ai, + int *tj, int idxu_max, int inum, int ijnum, int chemflag); + void snapComputeZi2(double *zlist_r, double *zlist_i, double *Stotr, double *Stoti, + double *cglist, int *idxz, int *idxu_block, int *idxcg_block, int twojmax, + int idxu_max, int idxz_max, int nelements, int bnorm_flag, int inum); + void snapComputeBi1(double *blist, double *zlist_r, double *zlist_i, double *Stotr, double *Stoti, + int *idxb, int *idxu_block, int *idxz_block, int twojmax, int idxb_max, + int idxu_max, int idxz_max, int nelements, int inum); + void snapComputeDbidrj(double *dblist, double *zlist_r, double *zlist_i, double *dulist_r, + double *dulist_i, int *idxb, int *idxu_block, int *idxz_block, int *map, + int *ai, int *tj, int twojmax, int idxb_max, int idxu_max, int idxz_max, + int nelements, int bnorm_flag, int chemflag, int inum, int ijnum); + void snapdesc(double *blist, double *bd, double *rij, double *tmpmem, int *atomtype, int *ai, + int *aj, int *ti, int *tj, int natom, int Nij); + + // functions for calculating/collating POD descriptors/coefficients for forces + + void podradialbasis(double *rbf, double *xij, double *besselparams, double rin, double rmax, + int besseldegree, int inversedegree, int nbesselpars, int N); + void pod1body(double *eatom, int *atomtype, int nelements, int natom); + void podtally2b(double *eatom, double *eij, int *ai, int *ti, int *tj, int *elemindex, + int nelements, int nbf, int natom, int N); + void pod3body(double *eatom, double *yij, double *e2ij, double *tmpmem, int *elemindex, + int *pairnumsum, int *ai, int *ti, int *tj, int nrbf, int nabf, int nelements, + int natom, int Nij); + void poddesc_ij(double *eatom1, double *eatom2, double *eatom3, double *rij, double *Phi, + double *besselparams, double *tmpmem, double rin, double rcut, int *pairnumsum, + int *atomtype, int *ai, int *ti, int *tj, int *elemindex, int *pdegree, + int nbesselpars, int nrbf2, int nrbf3, int nabf, int nelements, int Nij, + int natom); + void snapComputeUij(double *Sr, double *Si, double *rootpqarray, double *rij, double *wjelem, + double *radelem, double rmin0, double rfac0, double rcutfac, int *idxu_block, + int *ti, int *tj, int twojmax, int idxu_max, int ijnum, int switch_flag); + void snapdesc_ij(double *blist, double *rij, double *tmpmem, int *atomtype, int *ai, int *ti, + int *tj, int natom, int Nij); + void pod2body_force(double *force, double *fij, double *coeff2, int *ai, int *aj, int *ti, + int *tj, int *elemindex, int nelements, int nbf, int natom, int Nij); + void pod3body_force(double *force, double *yij, double *e2ij, double *f2ij, double *coeff3, + double *tmpmem, int *elemindex, int *pairnumsum, int *ai, int *aj, int *ti, + int *tj, int nrbf, int nabf, int nelements, int natom, int Nij); + void snapTallyForce(double *force, double *dbdr, double *coeff4, int *ai, int *aj, int *ti, + int ijnum, int ncoeff, int ntype); + void pod4body_force(double *force, double *rij, double *coeff4, double *tmpmem, int *atomtype, + int *idxi, int *ai, int *aj, int *ti, int *tj, int natom, int Nij); + void pod2body_force(double **force, double *fij, double *coeff2, int *ai, int *aj, int *ti, + int *tj, int *elemindex, int nelements, int nbf, int natom, int Nij); + void pod3body_force(double **force, double *yij, double *e2ij, double *f2ij, double *coeff3, + double *tmpmem, int *elemindex, int *pairnumsum, int *ai, int *aj, int *ti, + int *tj, int nrbf, int nabf, int nelements, int natom, int Nij); + void snapTallyForce(double **force, double *dbdr, double *coeff4, int *ai, int *aj, int *ti, + int ijnum, int ncoeff, int ntype); + void pod4body_force(double **force, double *rij, double *coeff4, double *tmpmem, int *atomtype, + int *idxi, int *ai, int *aj, int *ti, int *tj, int natom, int Nij); + + // eigenproblem functions + + void podeigenvaluedecomposition(double *Phi, double *Lambda, double *besselparams, double rin, + double rcut, int besseldegree, int inversedegree, int nbesselpars, + int N); + + public: + MLPOD(LAMMPS *, const std::string &pod_file, const std::string &coeff_file); + + MLPOD(LAMMPS *lmp) : Pointers(lmp){}; + ~MLPOD() override; + + struct podstruct { + podstruct(); + virtual ~podstruct(); + + std::vector species; + int twobody[3]; + int threebody[4]; + int fourbody[4]; + int *pbc; + int *elemindex; + + int quadratic22[2]; + int quadratic23[2]; + int quadratic24[2]; + int quadratic33[2]; + int quadratic34[2]; + int quadratic44[2]; + int cubic234[3]; + int cubic333[3]; + int cubic444[3]; + int nelements; + int onebody; + int besseldegree; + int inversedegree; + + int quadraticpod; + + double rin; + double rcut; + double *besselparams; + double *coeff; + double *Phi2, *Phi3, *Phi4, *Lambda2, *Lambda3, *Lambda4; + + // variables declaring number of snapshots, descriptors, and combinations + + int nbesselpars = 3; + int ns2, ns3, + ns4; // number of snapshots for radial basis functions for linear POD potentials + int nc2, nc3, nc4; // number of chemical combinations for linear POD potentials + int nbf1, nbf2, nbf3, nbf4; // number of basis functions for linear POD potentials + int nd1, nd2, nd3, nd4; // number of descriptors for linear POD potentials + int nd22, nd23, nd24, nd33, nd34, nd44; // number of descriptors for quadratic POD potentials + int nd234, nd333, nd444; // number of descriptors for cubic POD potentials + int nrbf3, nabf3, nrbf4, nabf4; + int nd, nd1234; + + int snaptwojmax; // also used to tell if SNAP is used when allocating/deallocating + int snapchemflag; + double snaprfac0; + double snapelementradius[10]; + double snapelementweight[10]; + }; + + struct snastruct { + int twojmax; + int ncoeff; + int idxb_max; + int idxu_max; + int idxz_max; + int idxcg_max; + int ntypes; + int nelements; + int ndoubles; // number of multi-element pairs + int ntriples; // number of multi-element triplets + int bnormflag; + int chemflag; + int switchflag; + int bzeroflag; + int wselfallflag; + + double wself; + double rmin0; + double rfac0; + double rcutfac; + double rcutmax; + + int *map; // map types to [0,nelements) + int *idx_max; + int *idxz; + int *idxz_block; + int *idxb; + int *idxb_block; + int *idxu_block; + int *idxcg_block; + + double *rcutsq; + double *radelem; + double *wjelem; + double *bzero; + double *fac; + double *rootpqarray; + double *cglist; + }; + + podstruct pod; + snastruct sna; + + // functions for collecting/collating arrays + + void podMatMul(double *c, double *a, double *b, int r1, int c1, int c2); + void podArraySetValue(double *y, double a, int n); + void podArrayCopy(double *y, double *x, int n); + void podArrayFill(int *output, int start, int length); + + // functions for calculating energy and force descriptors + + void podNeighPairs(double *xij, double *x, int *ai, int *aj, int *ti, int *tj, int *pairlist, + int *pairnumsum, int *atomtype, int *alist, int inum, int dim); + void linear_descriptors(double *gd, double *efatom, double *y, double *tmpmem, int *atomtype, + int *alist, int *pairlist, int *pairnum, int *pairnumsum, int *tmpint, + int natom, int Nij); + void quadratic_descriptors(double *d23, double *dd23, double *d2, double *d3, double *dd2, + double *dd3, int M2, int M3, int N); + void quadratic_descriptors(double *d33, double *dd33, double *d3, double *dd3, int M3, int N); + void cubic_descriptors(double *d234, double *dd234, double *d2, double *d3, double *d4, + double *dd2, double *dd3, double *dd4, int M2, int M3, int M4, int N); + void cubic_descriptors(double *d333, double *Dd333, double *d3, double *Dd3, int M3, int N); + double calculate_energyforce(double *force, double *gd, double *gdd, double *coeff, double *tmp, + int natom); + double energyforce_calculation(double *f, double *gd, double *gdd, double *coeff, double *y, + int *atomtype, int *alist, int *pairlist, int *pairnum, + int *pairnumsum, int *tmpint, int natom, int Nij); + + // functions for calculating energies and forces + + void podNeighPairs(double *rij, double *x, int *idxi, int *ai, int *aj, int *ti, int *tj, + int *pairnumsum, int *atomtype, int *jlist, int *alist, int inum); + int lammpsNeighPairs(double *rij, double **x, double rcutsq, int *idxi, int *ai, int *aj, int *ti, + int *tj, int *pairnumsum, int *atomtype, int *numneigh, int *ilist, + int **jlist, int inum); + void linear_descriptors_ij(double *gd, double *eatom, double *rij, double *tmpmem, + int *pairnumsum, int *atomtype, int *ai, int *ti, int *tj, int natom, + int Nij); + double calculate_energy(double *effectivecoeff, double *gd, double *coeff); + double calculate_energy(double *energycoeff, double *forcecoeff, double *gd, double *gdall, + double *coeff); + void calculate_force(double *force, double *effectivecoeff, double *rij, double *tmpmem, + int *pairnumsum, int *atomtype, int *idxi, int *ai, int *aj, int *ti, + int *tj, int natom, int Nij); + void calculate_force(double **force, double *effectivecoeff, double *rij, double *tmpmem, + int *pairnumsum, int *atomtype, int *idxi, int *ai, int *aj, int *ti, + int *tj, int natom, int Nij); + double energyforce_calculation(double *force, double *podcoeff, double *effectivecoeff, + double *gd, double *rij, double *tmpmem, int *pairnumsum, + int *atomtype, int *idxi, int *ai, int *aj, int *ti, int *tj, + int natom, int Nij); + +}; + +} // namespace LAMMPS_NS + +#endif diff --git a/src/ML-POD/pair_pod.cpp b/src/ML-POD/pair_pod.cpp new file mode 100644 index 0000000000..aaf8f730a4 --- /dev/null +++ b/src/ML-POD/pair_pod.cpp @@ -0,0 +1,335 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/ Sandia National Laboratories + LAMMPS development team: developers@lammps.org + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing authors: Ngoc Cuong Nguyen (MIT) and Andrew Rohskopf (SNL) +------------------------------------------------------------------------- */ + +#include "pair_pod.h" + +#include "mlpod.h" + +#include "atom.h" +#include "comm.h" +#include "error.h" +#include "force.h" +#include "math_const.h" +#include "memory.h" +#include "neigh_list.h" +#include "neighbor.h" +#include "tokenizer.h" + +#include +#include + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +PairPOD::PairPOD(LAMMPS *lmp) : + Pair(lmp), gd(nullptr), gdall(nullptr), podcoeff(nullptr), newpodcoeff(nullptr), + energycoeff(nullptr), forcecoeff(nullptr), podptr(nullptr), tmpmem(nullptr), typeai(nullptr), + numneighsum(nullptr), rij(nullptr), idxi(nullptr), ai(nullptr), aj(nullptr), ti(nullptr), + tj(nullptr) +{ + single_enable = 0; + restartinfo = 0; + one_coeff = 1; + manybody_flag = 1; + centroidstressflag = CENTROID_NOTAVAIL; + peratom_warn = true; + + dim = 3; + nablockmax = 0; + nij = 0; + nijmax = 0; + szd = 0; +} + +/* ---------------------------------------------------------------------- */ + +PairPOD::~PairPOD() +{ + free_tempmemory(); + memory->destroy(podcoeff); + memory->destroy(newpodcoeff); + memory->destroy(gd); + memory->destroy(gdall); + memory->destroy(energycoeff); + memory->destroy(forcecoeff); + + delete podptr; + + if (allocated) { + memory->destroy(setflag); + memory->destroy(cutsq); + } +} + +void PairPOD::compute(int eflag, int vflag) +{ + ev_init(eflag, vflag); + + // we must enforce using F dot r, since we have no energy or stress tally calls. + vflag_fdotr = 1; + + if (peratom_warn && (vflag_atom || eflag_atom)) { + peratom_warn = false; + if (comm->me == 0) + error->warning(FLERR, "Pair style pod does not support per-atom energies or stresses"); + } + + double **x = atom->x; + double **f = atom->f; + int **firstneigh = list->firstneigh; + int *numneigh = list->numneigh; + int *type = atom->type; + int *ilist = list->ilist; + int inum = list->inum; + + // initialize global descriptors to zero + + int nd1234 = podptr->pod.nd1234; + podptr->podArraySetValue(gd, 0.0, nd1234); + + for (int ii = 0; ii < inum; ii++) { + int i = ilist[ii]; + int jnum = numneigh[i]; + + // allocate temporary memory + + if (nijmax < jnum) { + nijmax = MAX(nijmax, jnum); + nablockmax = 1; + free_tempmemory(); + estimate_tempmemory(); + allocate_tempmemory(); + } + + // get neighbor pairs for atom i + + lammpsNeighPairs(x, firstneigh, type, map, numneigh, i); + + // compute global POD descriptors for atom i + + podptr->linear_descriptors_ij(gd, tmpmem, rij, &tmpmem[nd1234], numneighsum, typeai, idxi, ti, + tj, 1, nij); + } + + int nd22 = podptr->pod.nd22; + int nd23 = podptr->pod.nd23; + int nd24 = podptr->pod.nd24; + int nd33 = podptr->pod.nd33; + int nd34 = podptr->pod.nd34; + int nd44 = podptr->pod.nd44; + int nd = podptr->pod.nd; + bigint natom = atom->natoms; + + for (int j = nd1234; j < (nd1234 + nd22 + nd23 + nd24 + nd33 + nd34 + nd44); j++) + newpodcoeff[j] = podcoeff[j] / (natom); + + for (int j = (nd1234 + nd22 + nd23 + nd24 + nd33 + nd34 + nd44); j < nd; j++) + newpodcoeff[j] = podcoeff[j] / (natom * natom); + + // compute energy and effective coefficients + eng_vdwl = podptr->calculate_energy(energycoeff, forcecoeff, gd, gdall, newpodcoeff); + + for (int ii = 0; ii < inum; ii++) { + int i = ilist[ii]; + + // get neighbor pairs for atom i + + lammpsNeighPairs(x, firstneigh, type, map, numneigh, i); + + // compute atomic force for atom i + + podptr->calculate_force(f, forcecoeff, rij, tmpmem, numneighsum, typeai, idxi, ai, aj, ti, tj, + 1, nij); + } + + if (vflag_fdotr) virial_fdotr_compute(); +} + +/* ---------------------------------------------------------------------- + global settings +------------------------------------------------------------------------- */ + +void PairPOD::settings(int narg, char ** /* arg */) +{ + if (narg > 0) error->all(FLERR, "Pair style pod accepts no arguments"); +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more type pairs +------------------------------------------------------------------------- */ + +void PairPOD::coeff(int narg, char **arg) +{ + const int np1 = atom->ntypes + 1; + memory->destroy(setflag); + memory->destroy(cutsq); + memory->create(setflag, np1, np1, "pair:setflag"); + memory->create(cutsq, np1, np1, "pair:cutsq"); + delete[] map; + map = new int[np1]; + allocated = 1; + + if (narg < 4) utils::missing_cmd_args(FLERR, "pair_coeff", error); + map_element2type(narg - 4, arg + 4); + + std::string pod_file = std::string(arg[2]); // pod input file + std::string coeff_file = std::string(arg[3]); // coefficient input file + + delete podptr; + podptr = new MLPOD(lmp, pod_file, coeff_file); + + if (coeff_file != "") { + memory->destroy(podcoeff); + memory->destroy(newpodcoeff); + memory->destroy(energycoeff); + memory->destroy(forcecoeff); + memory->destroy(gd); + memory->destroy(gdall); + memory->create(podcoeff, podptr->pod.nd, "pair:podcoeff"); + memory->create(newpodcoeff, podptr->pod.nd, "pair:newpodcoeff"); + memory->create(energycoeff, podptr->pod.nd1234, "pair:energycoeff"); + memory->create(forcecoeff, podptr->pod.nd1234, "pair:forcecoeff"); + memory->create(gd, podptr->pod.nd1234, "pair:gd"); + memory->create(gdall, podptr->pod.nd1234, "pair:gdall"); + podptr->podArrayCopy(podcoeff, podptr->pod.coeff, podptr->pod.nd); + podptr->podArrayCopy(newpodcoeff, podptr->pod.coeff, podptr->pod.nd); + } + + for (int ii = 0; ii < np1; ii++) + for (int jj = 0; jj < np1; jj++) cutsq[ii][jj] = podptr->pod.rcut * podptr->pod.rcut; +} + +/* ---------------------------------------------------------------------- + init specific to this pair style +------------------------------------------------------------------------- */ + +void PairPOD::init_style() +{ + if (force->newton_pair == 0) error->all(FLERR, "Pair style pod requires newton pair on"); + + // need a full neighbor list + + neighbor->add_request(this, NeighConst::REQ_FULL); + + // reset flag to print warning about per-atom energies or stresses + peratom_warn = true; +} + +/* ---------------------------------------------------------------------- + init for one type pair i,j and corresponding j,i +------------------------------------------------------------------------- */ + +double PairPOD::init_one(int i, int j) +{ + if (setflag[i][j] == 0) error->all(FLERR, "All pair coeffs are not set"); + return podptr->pod.rcut; +} + +/* ---------------------------------------------------------------------- + memory usage +------------------------------------------------------------------------- */ + +double PairPOD::memory_usage() +{ + double bytes = Pair::memory_usage(); + return bytes; +} + +void PairPOD::free_tempmemory() +{ + memory->destroy(rij); + memory->destroy(idxi); + memory->destroy(ai); + memory->destroy(aj); + memory->destroy(ti); + memory->destroy(tj); + memory->destroy(numneighsum); + memory->destroy(typeai); + memory->destroy(tmpmem); +} + +void PairPOD::allocate_tempmemory() +{ + memory->create(rij, dim * nijmax, "pair:rij"); + memory->create(idxi, nijmax, "pair:idxi"); + memory->create(ai, nijmax, "pair:ai"); + memory->create(aj, nijmax, "pair:aj"); + memory->create(ti, nijmax, "pair:ti"); + memory->create(tj, nijmax, "pair:tj"); + memory->create(numneighsum, nablockmax + 1, "pair:numneighsum"); + memory->create(typeai, nablockmax, "pair:typeai"); + memory->create(tmpmem, szd, "pair:tmpmem"); +} + +void PairPOD::estimate_tempmemory() +{ + int nrbf2 = podptr->pod.nbf2; + int nabf3 = podptr->pod.nabf3; + int nrbf3 = podptr->pod.nrbf3; + int ns2 = podptr->pod.ns2; + int ns3 = podptr->pod.ns3; + + szd = dim * nijmax + (1 + dim) * nijmax * MAX(nrbf2 + ns2, nrbf3 + ns3) + (nabf3 + 1) * 7; + int szsnap = 0; + if (podptr->sna.twojmax > 0) { + szsnap += nijmax * dim; + szsnap += MAX(2 * podptr->sna.idxu_max * nijmax, + 2 * podptr->sna.idxz_max * podptr->sna.ndoubles * + nablockmax); // (Ur, Ui) and (Zr, Zi) + szsnap += 2 * podptr->sna.idxu_max * dim * nijmax; // dUr, dUi + szsnap += MAX(podptr->sna.idxb_max * podptr->sna.ntriples * dim * nijmax, + 2 * podptr->sna.idxu_max * podptr->sna.nelements * + nablockmax); // dblist and (Utotr, Utoti) + } + + szd = MAX(szsnap, szd); + szd = nablockmax * (podptr->pod.nd1234) + szd; +} + +void PairPOD::lammpsNeighPairs(double **x, int **firstneigh, int *atomtypes, int *map, + int *numneigh, int gi) +{ + + double rcutsq = podptr->pod.rcut * podptr->pod.rcut; + + nij = 0; + int itype = map[atomtypes[gi]] + 1; + int m = numneigh[gi]; + typeai[0] = itype; + for (int l = 0; l < m; l++) { // loop over each atom around atom i + int gj = firstneigh[gi][l]; // atom j + double delx = x[gj][0] - x[gi][0]; // xj - xi + double dely = x[gj][1] - x[gi][1]; // xj - xi + double delz = x[gj][2] - x[gi][2]; // xj - xi + double rsq = delx * delx + dely * dely + delz * delz; + if (rsq < rcutsq && rsq > 1e-20) { + rij[nij * 3 + 0] = delx; + rij[nij * 3 + 1] = dely; + rij[nij * 3 + 2] = delz; + idxi[nij] = 0; + ai[nij] = gi; + aj[nij] = gj; + ti[nij] = itype; + tj[nij] = map[atomtypes[gj]] + 1; + nij++; + } + } + + numneighsum[0] = 0; + numneighsum[1] = nij; +} diff --git a/src/ML-POD/pair_pod.h b/src/ML-POD/pair_pod.h new file mode 100644 index 0000000000..62b6e99f3b --- /dev/null +++ b/src/ML-POD/pair_pod.h @@ -0,0 +1,81 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/ Sandia National Laboratories + LAMMPS development team: developers@lammps.org + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef PAIR_CLASS +// clang-format off +PairStyle(pod,PairPOD); +// clang-format on +#else + +#ifndef LMP_PAIR_POD_H +#define LMP_PAIR_POD_H + +#include "pair.h" + +namespace LAMMPS_NS { + +class PairPOD : public Pair { + public: + PairPOD(class LAMMPS *); + ~PairPOD() override; + void compute(int, int) override; + + void settings(int, char **) override; + void coeff(int, char **) override; + void init_style() override; + double init_one(int, int) override; + double memory_usage() override; + + int dim; // typically 3 + + double *gd; // global linear descriptors + double *gdall; // global linear descriptors summed over all MPI ranks + double *podcoeff; // POD coefficients + double *newpodcoeff; // normalized POD coefficients + double *energycoeff; // energy coefficients + double *forcecoeff; // force coefficients + + void estimate_tempmemory(); + void free_tempmemory(); + void allocate_tempmemory(); + + void lammpsNeighPairs(double **x, int **firstneigh, int *atomtype, int *map, int *numneigh, + int i); + + protected: + int nablockmax; // maximum number of atoms per computation block + int nij; // number of atom pairs + int nijmax; // maximum number of atom pairs + int szd; // size of tmpmem + + class MLPOD *podptr; + + // temporary arrays for computation blocks + + double *tmpmem; // temporary memory + int *typeai; // types of atoms I only + int *numneighsum; // cumulative sum for an array of numbers of neighbors + double *rij; // (xj - xi) for all pairs (I, J) + int *idxi; // storing linear indices for all pairs (I, J) + int *ai; // IDs of atoms I for all pairs (I, J) + int *aj; // IDs of atoms J for all pairs (I, J) + int *ti; // types of atoms I for all pairs (I, J) + int *tj; // types of atoms J for all pairs (I, J) + + bool peratom_warn; // print warning about missing per-atom energies or stresses +}; + +} // namespace LAMMPS_NS + +#endif +#endif diff --git a/src/ML-QUIP/Install.sh b/src/ML-QUIP/Install.sh index 20174e664a..03f93c14b8 100755 --- a/src/ML-QUIP/Install.sh +++ b/src/ML-QUIP/Install.sh @@ -44,7 +44,7 @@ if (test $1 = 1) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*quip.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*quip.*$/d' ../Makefile.package.settings # multiline form needed for BSD sed on Macs sed -i -e '4 i \ include ..\/..\/lib\/quip\/Makefile.lammps\ @@ -58,7 +58,7 @@ elif (test $1 = 0) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*quip.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*quip.*$/d' ../Makefile.package.settings fi fi diff --git a/src/MOLECULE/angle_table.cpp b/src/MOLECULE/angle_table.cpp index 4a89591612..03027700a6 100644 --- a/src/MOLECULE/angle_table.cpp +++ b/src/MOLECULE/angle_table.cpp @@ -405,6 +405,9 @@ void AngleTable::read_table(Table *tb, char *file, char *keyword) reader.skip_line(); for (int i = 0; i < tb->ninput; i++) { line = reader.next_line(); + if (!line) + error->one(FLERR, "Data missing when parsing angle table '{}' line {} of {}.", keyword, i + 1, + tb->ninput); try { ValueTokenizer values(line); values.next_int(); diff --git a/src/MOLECULE/bond_table.cpp b/src/MOLECULE/bond_table.cpp index 0b9cde32e1..5978d63561 100644 --- a/src/MOLECULE/bond_table.cpp +++ b/src/MOLECULE/bond_table.cpp @@ -330,6 +330,9 @@ void BondTable::read_table(Table *tb, char *file, char *keyword) reader.skip_line(); for (int i = 0; i < tb->ninput; i++) { line = reader.next_line(); + if (!line) + error->one(FLERR, "Data missing when parsing bond table '{}' line {} of {}.", keyword, i + 1, + tb->ninput); try { ValueTokenizer values(line); values.next_int(); diff --git a/src/MOLECULE/dihedral_table.cpp b/src/MOLECULE/dihedral_table.cpp index 4ad2a57a46..070d0a6972 100644 --- a/src/MOLECULE/dihedral_table.cpp +++ b/src/MOLECULE/dihedral_table.cpp @@ -1021,6 +1021,9 @@ void DihedralTable::read_table(Table *tb, char *file, char *keyword) for (int i = 0; i < tb->ninput; i++) { line = reader.next_line(); + if (!line) + error->one(FLERR, "Data missing when parsing dihedral table '{}' line {} of {}.", + keyword, i + 1, tb->ninput); try { ValueTokenizer values(line); if (tb->f_unspecified) { diff --git a/src/MOLFILE/Install.sh b/src/MOLFILE/Install.sh index 85885f66b9..3ae4357ade 100755 --- a/src/MOLFILE/Install.sh +++ b/src/MOLFILE/Install.sh @@ -44,7 +44,7 @@ if (test $1 = 1) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*molfile.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*molfile.*$/d' ../Makefile.package.settings # multiline form needed for BSD sed on Macs sed -i -e '4 i \ include ..\/..\/lib\/molfile\/Makefile.lammps @@ -58,7 +58,7 @@ elif (test $1 = 0) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*molfile.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*molfile.*$/d' ../Makefile.package.settings fi fi diff --git a/src/MSCG/Install.sh b/src/MSCG/Install.sh index 353403c7da..67f0f837ce 100755 --- a/src/MSCG/Install.sh +++ b/src/MSCG/Install.sh @@ -43,7 +43,7 @@ if (test $1 = 1) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*mscg.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*mscg.*$/d' ../Makefile.package.settings # multiline form needed for BSD sed on Macs sed -i -e '4 i \ include ..\/..\/lib\/mscg\/Makefile.lammps @@ -57,7 +57,7 @@ elif (test $1 = 0) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*mscg.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*mscg.*$/d' ../Makefile.package.settings fi fi diff --git a/src/Makefile b/src/Makefile index 923cc535fd..6f3ece5376 100644 --- a/src/Makefile +++ b/src/Makefile @@ -55,7 +55,7 @@ PACKAGE = \ awpmd \ bocs \ body \ - bpm \ + bpm \ brownian \ cg-dna \ cg-spica \ @@ -99,6 +99,7 @@ PACKAGE = \ misc \ ml-hdnnp \ ml-pace \ + ml-pod \ ml-quip \ ml-rann \ ml-snap \ @@ -228,6 +229,7 @@ PACKLIB = \ molfile \ netcdf \ ml-pace \ + ml-pod \ plumed \ qmmm \ ml-quip \ @@ -238,7 +240,7 @@ PACKLIB = \ PACKSYS = compress latboltz mpiio python -PACKINT = atc awpmd colvars electrode gpu kokkos mesont poems +PACKINT = atc awpmd colvars electrode gpu kokkos mesont ml-pod poems PACKEXT = \ adios \ diff --git a/src/NETCDF/Install.sh b/src/NETCDF/Install.sh index 4d21f0f894..8c70d84fd8 100755 --- a/src/NETCDF/Install.sh +++ b/src/NETCDF/Install.sh @@ -42,7 +42,7 @@ if (test $1 = 1) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*netcdf.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*netcdf.*$/d' ../Makefile.package.settings # multiline form needed for BSD sed on Macs sed -i -e '4 i \ include ..\/..\/lib\/netcdf\/Makefile.lammps @@ -57,7 +57,7 @@ elif (test $1 = 0) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*netcdf.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*netcdf.*$/d' ../Makefile.package.settings fi fi diff --git a/src/PLUGIN/Install.sh b/src/PLUGIN/Install.sh index 0df642193e..86de36d7df 100755 --- a/src/PLUGIN/Install.sh +++ b/src/PLUGIN/Install.sh @@ -44,7 +44,7 @@ if (test $1 = 1) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*plugin.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*plugin.*$/d' ../Makefile.package.settings # multiline form needed for BSD sed on Macs sed -i -e '4 i \ include ..\/..\/lib\/plugin\/Makefile.lammps @@ -58,7 +58,7 @@ elif (test $1 = 0) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*plugin.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*plugin.*$/d' ../Makefile.package.settings fi fi diff --git a/src/PLUMED/Install.sh b/src/PLUMED/Install.sh index f879d42feb..500a55ec77 100755 --- a/src/PLUMED/Install.sh +++ b/src/PLUMED/Install.sh @@ -45,7 +45,7 @@ if (test $1 = 1) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*plumed.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*plumed.*$/d' ../Makefile.package.settings # multiline form needed for BSD sed on Macs sed -i -e '4 i \ include ..\/..\/lib\/plumed\/Makefile.lammps @@ -59,7 +59,7 @@ elif (test $1 = 0) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*plumed.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*plumed.*$/d' ../Makefile.package.settings fi fi diff --git a/src/POEMS/Install.sh b/src/POEMS/Install.sh index be407d76f0..37f8404738 100755 --- a/src/POEMS/Install.sh +++ b/src/POEMS/Install.sh @@ -44,7 +44,7 @@ if (test $1 = 1) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*poems.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*poems.*$/d' ../Makefile.package.settings # multiline form needed for BSD sed on Macs sed -i -e '4 i \ include ..\/..\/lib\/poems\/Makefile.lammps @@ -58,7 +58,7 @@ elif (test $1 = 0) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*poems.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*poems.*$/d' ../Makefile.package.settings fi fi diff --git a/src/PYTHON/Install.sh b/src/PYTHON/Install.sh index 8c394d43ad..b23cf574f8 100755 --- a/src/PYTHON/Install.sh +++ b/src/PYTHON/Install.sh @@ -50,7 +50,7 @@ if (test $1 = 1) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*python.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*python.*$/d' ../Makefile.package.settings # multiline form needed for BSD sed on Macs sed -i -e '4 i \ include ..\/..\/lib\/python\/Makefile.lammps @@ -65,7 +65,7 @@ elif (test $1 = 0) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*python.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*python.*$/d' ../Makefile.package.settings fi fi diff --git a/src/QMMM/Install.sh b/src/QMMM/Install.sh index 4bede66d80..0c9643b84e 100755 --- a/src/QMMM/Install.sh +++ b/src/QMMM/Install.sh @@ -47,7 +47,7 @@ if (test $1 = 1) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*qmmm.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*qmmm.*$/d' ../Makefile.package.settings # multiline form needed for BSD sed on Macs sed -i -e '4 i \ include ..\/..\/lib\/qmmm\/Makefile.lammps @@ -62,7 +62,7 @@ elif (test $1 = 0) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*qmmm.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*qmmm.*$/d' ../Makefile.package.settings fi fi diff --git a/src/VORONOI/Install.sh b/src/VORONOI/Install.sh index 6373506b19..c7f897e5e6 100755 --- a/src/VORONOI/Install.sh +++ b/src/VORONOI/Install.sh @@ -48,7 +48,7 @@ if (test $1 = 1) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*voronoi.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*voronoi.*$/d' ../Makefile.package.settings # multiline form needed for BSD sed on Macs sed -i -e '4 i \ include ..\/..\/lib\/voronoi\/Makefile.lammps @@ -63,7 +63,7 @@ elif (test $1 = 0) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*voronoi.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*voronoi.*$/d' ../Makefile.package.settings fi fi diff --git a/src/VTK/Install.sh b/src/VTK/Install.sh index 3749242fb2..fda4287d51 100755 --- a/src/VTK/Install.sh +++ b/src/VTK/Install.sh @@ -43,7 +43,7 @@ if (test $1 = 1) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*vtk.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*vtk.*$/d' ../Makefile.package.settings # multiline form needed for BSD sed on Macs sed -i -e '4 i \ include ..\/..\/lib\/vtk\/Makefile.lammps @@ -58,7 +58,7 @@ elif (test $1 = 0) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*vtk.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*vtk.*$/d' ../Makefile.package.settings fi fi diff --git a/src/pair_table.cpp b/src/pair_table.cpp index e8a7530d6b..3e293cb414 100644 --- a/src/pair_table.cpp +++ b/src/pair_table.cpp @@ -398,6 +398,9 @@ void PairTable::read_table(Table *tb, char *file, char *keyword) reader.skip_line(); for (int i = 0; i < tb->ninput; i++) { line = reader.next_line(); + if (!line) + error->one(FLERR, "Data missing when parsing pair table '{}' line {} of {}.", keyword, i + 1, + tb->ninput); try { ValueTokenizer values(line); values.next_int(); diff --git a/src/reset_atoms_id.cpp b/src/reset_atoms_id.cpp index 26685f1972..c0fce95326 100644 --- a/src/reset_atoms_id.cpp +++ b/src/reset_atoms_id.cpp @@ -43,7 +43,9 @@ static int compare_coords(const int, const int, void *); /* ---------------------------------------------------------------------- */ -ResetAtomsID::ResetAtomsID(LAMMPS *lmp) : Command(lmp) {} +ResetAtomsID::ResetAtomsID(LAMMPS *lmp) : Command(lmp) { + binlo = binhi = -1; +} /* ---------------------------------------------------------------------- */ @@ -480,6 +482,9 @@ int ResetAtomsID::sort_bins(int n, char *inbuf, int &flag, int *&proclist, char bigint binlo = rptr->binlo; bigint binhi = rptr->binhi; + if ((binlo < 0) || (binhi < 0)) + error->one(FLERR, "Called sort_bins without previous setup of bins"); + // nbins = my subset of bins from binlo to binhi-1 // initialize linked lists of my Rvous atoms in each bin diff --git a/unittest/force-styles/test_pair_style.cpp b/unittest/force-styles/test_pair_style.cpp index de1ea26d54..385525c90b 100644 --- a/unittest/force-styles/test_pair_style.cpp +++ b/unittest/force-styles/test_pair_style.cpp @@ -379,8 +379,9 @@ TEST(PairStyle, plain) EXPECT_FP_LE_WITH_EPS(pair->eng_vdwl, test_config.run_vdwl, epsilon); EXPECT_FP_LE_WITH_EPS(pair->eng_coul, test_config.run_coul, epsilon); // skip comparing per-atom energy with total energy for "kim" and "in.conp" - if (std::string("kim") != lmp->force->pair_style && - std::string("in.conp") != test_config.input_file) + if ((std::string("kim") != lmp->force->pair_style) && + (std::string("pod") != lmp->force->pair_style) && + (std::string("in.conp") != test_config.input_file)) EXPECT_FP_LE_WITH_EPS((pair->eng_vdwl + pair->eng_coul), energy, epsilon); if (print_stats) std::cerr << "run_energy stats, newton on: " << stats << std::endl; diff --git a/unittest/force-styles/tests/kspace-ewald_conp_charge.yaml b/unittest/force-styles/tests/kspace-ewald_conp_charge.yaml index 1a2a1db2f4..73fb252226 100644 --- a/unittest/force-styles/tests/kspace-ewald_conp_charge.yaml +++ b/unittest/force-styles/tests/kspace-ewald_conp_charge.yaml @@ -1,6 +1,7 @@ --- -lammps_version: 24 Dec 2020 -date_generated: Fri Nov 5 00:12:57 202 +lammps_version: 23 Jun 2022 +tags: generated +date_generated: Wed Sep 21 13:52:53 2022 epsilon: 1e-12 skip_tests: gpu kokkos_omp omp prerequisites: ! | @@ -23,101 +24,101 @@ pair_coeff: ! | extract: ! "" natoms: 44 init_vdwl: 0 -init_coul: -9.72959727118154 +init_coul: 2.215589572896434 init_stress: ! |2- 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 init_forces: ! |2 - 1 2.0780648532794574e-04 1.9949672015209092e-03 3.1005914149473983e+00 - 2 -1.6777235182686229e-02 2.1481432256291342e-03 3.0881659196467974e+00 - 3 6.0082164895560364e-04 5.1573260226633706e-03 3.1029192412328546e+00 - 4 -1.6728974802490627e-02 6.1174723156885305e-03 3.0909324782862337e+00 - 5 4.2029366155132364e-02 -2.3455526736195550e-03 -1.5659617577954639e+00 - 6 5.5635790919204925e-02 -2.4542947062522690e-03 -1.5693827709331338e+00 - 7 4.2014920784252015e-02 -7.5287470219124282e-04 -1.5671265392163825e+00 - 8 5.5808767852333477e-02 -9.9105389808567764e-04 -1.5707104957299394e+00 - 9 -5.0959878750421531e-02 -2.3630298689785432e-03 -1.5769250181497103e+00 - 10 -3.3526564930579102e-02 -2.3802275431283235e-03 -1.5617801011657177e+00 - 11 -5.1236396351794382e-02 -4.9531100598977304e-04 -1.5779995894034007e+00 - 12 -3.3740693032952136e-02 -1.0210406243571671e-03 -1.5630986537874154e+00 - 13 -1.1437102611352990e-03 -4.6454866413028723e-05 5.4282837980149275e-03 - 14 2.3914999373115440e-03 -1.6478680244651225e-04 2.9802178734319302e-02 - 15 3.9287193302652881e-05 -2.5715673267285195e-05 2.8944525105129492e-03 - 16 2.0458480716482371e-03 -1.2119161321908680e-04 3.3689550843809465e-02 - 17 -2.7146073277767458e-03 -8.2376243258224945e-04 2.6564130941474605e-02 - 18 1.3669692885198122e-03 -4.2357196145490015e-04 3.2396141113926726e-02 - 19 3.0143371860819919e-04 -8.6218593339584197e-04 2.6284521141350690e-02 - 20 1.1542435168435086e-03 -2.7252318260839162e-04 3.4237916528138131e-02 - 21 -1.2350056952573586e-03 4.8655691135364389e-04 5.9284283442393787e-03 - 22 2.3656743884722833e-03 9.6575340844312564e-04 2.9811074931784812e-02 - 23 4.6754986244969928e-05 3.0149464050351158e-04 3.4630785686112402e-03 - 24 2.0301227080749681e-03 6.3879578068684975e-04 3.3653437189053448e-02 - 25 -2.3656211013513085e-03 -8.0454594828768345e-04 2.8476980555362921e-02 - 26 1.1566723797446984e-03 -3.9614599888570650e-04 3.2873323713155919e-02 - 27 2.8784994028036509e-04 -8.3661697184444985e-04 2.8317655886021299e-02 - 28 9.3882364605486616e-04 -2.3327601777843430e-04 3.4334676606415655e-02 - 29 -4.7969977052125280e-04 -1.2933334305372763e-04 -1.2336987392568074e-02 - 30 6.4733118786855018e-05 -1.3190918849005555e-04 -1.2737933567178899e-02 - 31 2.4269094157913960e-04 -1.3093943526788605e-04 -1.2136133260084996e-02 - 32 1.7452552740941009e-04 -1.1792779046242482e-04 -1.4181538324619818e-02 - 33 -3.8366266481516418e-04 -7.1061854758754935e-05 -1.3699106365426129e-02 - 34 2.8849004082561659e-05 -5.7838605310673273e-05 -1.3764181266896892e-02 - 35 2.2648059665862354e-04 -7.2851385190898286e-05 -1.3537361892926624e-02 - 36 1.2929221129083783e-04 -4.2862960950054417e-05 -1.4926105930886916e-02 - 37 -4.7698025941706373e-04 2.9971529466656685e-04 -1.2393604822896297e-02 - 38 6.4231095731185554e-05 2.7548977518459893e-04 -1.2789498345723030e-02 - 39 2.4169204779864371e-04 3.0552093685810432e-04 -1.2193908285665970e-02 - 40 1.7324998349441787e-04 2.2898000918153319e-04 -1.4225267020837271e-02 - 41 -3.4345772150395259e-04 -9.8012060153888811e-05 -1.4482722052972288e-02 - 42 2.0345466940577996e-05 -8.5250083485344193e-05 -1.4497101004472081e-02 - 43 2.0917627239293082e-04 -1.0051271468149260e-04 -1.4335313646556430e-02 - 44 1.1456796622437166e-04 -6.7553675788590515e-05 -1.5543196158603997e-02 + 1 2.0780648532795694e-04 1.9949672015209204e-03 3.1005914149473996e+00 + 2 -1.6777235182686288e-02 2.1481432256290419e-03 3.0881659196467988e+00 + 3 6.0082164895554737e-04 5.1573260226633801e-03 3.1029192412328555e+00 + 4 -1.6728974802490675e-02 6.1174723156886242e-03 3.0909324782862346e+00 + 5 4.2029366155132378e-02 -2.3455526736195693e-03 -1.5659617577954634e+00 + 6 5.5635790919204904e-02 -2.4542947062522369e-03 -1.5693827709331334e+00 + 7 4.2014920784252008e-02 -7.5287470219125008e-04 -1.5671265392163820e+00 + 8 5.5808767852333470e-02 -9.9105389808573120e-04 -1.5707104957299389e+00 + 9 -5.0959878750421551e-02 -2.3630298689785601e-03 -1.5769250181497101e+00 + 10 -3.3526564930579039e-02 -2.3802275431282884e-03 -1.5617801011657175e+00 + 11 -5.1236396351794389e-02 -4.9531100598979201e-04 -1.5779995894034005e+00 + 12 -3.3740693032952060e-02 -1.0210406243572182e-03 -1.5630986537874150e+00 + 13 -1.1437102611353016e-03 -4.6454866413029015e-05 5.4282837980149448e-03 + 14 2.3914999373115431e-03 -1.6478680244651469e-04 2.9802178734319239e-02 + 15 3.9287193302652786e-05 -2.5715673267285659e-05 2.8944525105129479e-03 + 16 2.0458480716482328e-03 -1.2119161321908735e-04 3.3689550843809452e-02 + 17 -2.7146073277767471e-03 -8.2376243258224663e-04 2.6564130941474612e-02 + 18 1.3669692885198135e-03 -4.2357196145489820e-04 3.2396141113926739e-02 + 19 3.0143371860819995e-04 -8.6218593339583785e-04 2.6284521141350669e-02 + 20 1.1542435168435056e-03 -2.7252318260838826e-04 3.4237916528138110e-02 + 21 -1.2350056952573553e-03 4.8655691135364269e-04 5.9284283442393631e-03 + 22 2.3656743884722890e-03 9.6575340844312705e-04 2.9811074931784823e-02 + 23 4.6754986244969657e-05 3.0149464050350903e-04 3.4630785686112129e-03 + 24 2.0301227080749633e-03 6.3879578068684812e-04 3.3653437189053413e-02 + 25 -2.3656211013513076e-03 -8.0454594828768334e-04 2.8476980555362911e-02 + 26 1.1566723797447039e-03 -3.9614599888570504e-04 3.2873323713155905e-02 + 27 2.8784994028036400e-04 -8.3661697184444898e-04 2.8317655886021253e-02 + 28 9.3882364605486020e-04 -2.3327601777843495e-04 3.4334676606415648e-02 + 29 -4.7969977052124917e-04 -1.2933334305373028e-04 -1.2336987392568071e-02 + 30 6.4733118786851766e-05 -1.3190918849005797e-04 -1.2737933567178844e-02 + 31 2.4269094157913586e-04 -1.3093943526788584e-04 -1.2136133260085013e-02 + 32 1.7452552740941527e-04 -1.1792779046242341e-04 -1.4181538324619835e-02 + 33 -3.8366266481516803e-04 -7.1061854758754556e-05 -1.3699106365426135e-02 + 34 2.8849004082563746e-05 -5.7838605310673531e-05 -1.3764181266896890e-02 + 35 2.2648059665862587e-04 -7.2851385190891320e-05 -1.3537361892926607e-02 + 36 1.2929221129083645e-04 -4.2862960950045859e-05 -1.4926105930886896e-02 + 37 -4.7698025941707008e-04 2.9971529466656788e-04 -1.2393604822896313e-02 + 38 6.4231095731188766e-05 2.7548977518460050e-04 -1.2789498345723021e-02 + 39 2.4169204779864826e-04 3.0552093685810269e-04 -1.2193908285665961e-02 + 40 1.7324998349441456e-04 2.2898000918153004e-04 -1.4225267020837207e-02 + 41 -3.4345772150395188e-04 -9.8012060153887415e-05 -1.4482722052972283e-02 + 42 2.0345466940577010e-05 -8.5250083485342566e-05 -1.4497101004472062e-02 + 43 2.0917627239292995e-04 -1.0051271468149899e-04 -1.4335313646556430e-02 + 44 1.1456796622437295e-04 -6.7553675788598551e-05 -1.5543196158604005e-02 run_vdwl: 0 -run_coul: -29.2317829589917 +run_coul: 6.662694629990089 run_stress: ! |2- 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 run_forces: ! |2 - 1 2.4590612609440857e-04 1.9614041218568765e-03 3.0874291949281156e+00 - 2 -1.6646393233505169e-02 2.1136941574791466e-03 3.0751132981100078e+00 - 3 6.3535217476582122e-04 5.1012487117746679e-03 3.0897301317927286e+00 - 4 -1.6598677148313316e-02 6.0535154567108096e-03 3.0778495346381414e+00 - 5 4.2257888534897002e-02 -2.3028533365964912e-03 -1.5593100596807519e+00 - 6 5.5690508027606674e-02 -2.4104721624763751e-03 -1.5626897542440841e+00 - 7 4.2243973130370163e-02 -7.6153220413262529e-04 -1.5604618260035836e+00 - 8 5.5862703939049151e-02 -9.9825803703213855e-04 -1.5640031014325451e+00 - 9 -5.1059409954744270e-02 -2.3195553026588225e-03 -1.5701677851024036e+00 - 10 -3.3824298857146974e-02 -2.3375522139359138e-03 -1.5551647619109399e+00 - 11 -5.1334079184640349e-02 -5.0583705005138380e-04 -1.5712298444761110e+00 - 12 -3.4037363466305995e-02 -1.0275978089057552e-03 -1.5564691026885338e+00 - 13 -1.1767076011504490e-03 -4.7681963272732622e-05 5.6177800544716184e-03 - 14 2.3826294437743313e-03 -1.6349140124449456e-04 2.9836275824428979e-02 - 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"" +input_file: in.manybody +pair_style: pod +pair_coeff: ! | + * * Ta_param.pod Ta_coeff.pod Ta Ta Ta Ta Ta Ta Ta Ta +extract: ! 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7.7871977254688995e-01 + 62 -7.4381007616019534e+00 6.1448378054475778e+00 -4.6683183548425067e+00 + 63 5.5682593755810563e+00 -7.3119820285913608e+00 -2.0100166481798887e-01 + 64 6.5075012240147911e+00 6.2545959336473818e+00 1.4555696233577285e+01 +... diff --git a/unittest/force-styles/tests/mol-pair-coul_slater_long.yaml b/unittest/force-styles/tests/mol-pair-coul_slater_long.yaml index 52efdaa52d..ba11503a2c 100644 --- a/unittest/force-styles/tests/mol-pair-coul_slater_long.yaml +++ b/unittest/force-styles/tests/mol-pair-coul_slater_long.yaml @@ -6,6 +6,7 @@ skip_tests: prerequisites: ! | atom full pair coul/slater/long + kspace ewald pre_commands: ! "" post_commands: ! | pair_modify mix arithmetic