diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index 69aff2d72d..8c5b69b260 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -504,7 +504,10 @@ if(PKG_LATTE) URL https://github.com/lanl/LATTE/archive/v1.2.1.tar.gz URL_MD5 85ac414fdada2d04619c8f936344df14 SOURCE_SUBDIR cmake - CMAKE_ARGS -DCMAKE_INSTALL_PREFIX= ${CMAKE_REQUEST_PIC} -DBLAS_LIBRARIES=${BLAS_LIBRARIES} -DLAPACK_LIBRARIES=${LAPACK_LIBRARIES} + CMAKE_ARGS -DCMAKE_INSTALL_PREFIX= ${CMAKE_REQUEST_PIC} + -DBLAS_LIBRARIES=${BLAS_LIBRARIES} -DLAPACK_LIBRARIES=${LAPACK_LIBRARIES} + -DCMAKE_Fortran_COMPILER=${CMAKE_Fortran_COMPILER} -DCMAKE_Fortran_FLAGS=${CMAKE_Fortran_FLAGS} + -DCMAKE_Fortran_FLAGS_${BTYPE}=${CMAKE_Fortran_FLAGS_${BTYPE}} -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE} ) ExternalProject_get_property(latte_build INSTALL_DIR) set(LATTE_LIBRARIES ${INSTALL_DIR}/${CMAKE_INSTALL_LIBDIR}/liblatte.a) @@ -1124,9 +1127,6 @@ if(PKG_OPT) endif() if(PKG_USER-INTEL) - if(LAMMPS_SIZES STREQUAL BIGBIG) - message(FATAL_ERROR "The USER-INTEL Package is not compatible with -DLAMMPS_BIGBIG") - endif() add_definitions(-DLMP_USER_INTEL) set(INTEL_ARCH "cpu" CACHE STRING "Architectures used by USER-INTEL (cpu or knl)") @@ -1220,8 +1220,7 @@ if(PKG_USER-INTEL) ${USER-INTEL_SOURCES_DIR}/fix_nh_intel.cpp ${USER-INTEL_SOURCES_DIR}/intel_buffers.cpp ${USER-INTEL_SOURCES_DIR}/nbin_intel.cpp - ${USER-INTEL_SOURCES_DIR}/npair_intel.cpp - ${USER-INTEL_SOURCES_DIR}/verlet_lrt_intel.cpp) + ${USER-INTEL_SOURCES_DIR}/npair_intel.cpp) set_property(GLOBAL PROPERTY "USER-INTEL_SOURCES" "${USER-INTEL_SOURCES}") @@ -1230,9 +1229,12 @@ if(PKG_USER-INTEL) RegisterNBinStyle(${USER-INTEL_SOURCES_DIR}/nbin_intel.h) RegisterNPairStyle(${USER-INTEL_SOURCES_DIR}/npair_intel.h) RegisterFixStyle(${USER-INTEL_SOURCES_DIR}/fix_intel.h) - RegisterIntegrateStyle(${USER-INTEL_SOURCES_DIR}/verlet_lrt_intel.h) get_property(USER-INTEL_SOURCES GLOBAL PROPERTY USER-INTEL_SOURCES) + if(PKG_KSPACE) + list(APPEND USER-INTEL_SOURCES ${USER-INTEL_SOURCES_DIR}/verlet_lrt_intel.cpp) + RegisterIntegrateStyle(${USER-INTEL_SOURCES_DIR}/verlet_lrt_intel.h) + endif() list(APPEND LIB_SOURCES ${USER-INTEL_SOURCES}) include_directories(${USER-INTEL_SOURCES_DIR}) @@ -1370,7 +1372,15 @@ if(PKG_GPU) set(OCL_COMMON_HEADERS ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_preprocessor.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_aux_fun1.h) file(GLOB GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cu) - list(REMOVE_ITEM GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne.cu ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne_lj.cu) + list(REMOVE_ITEM GPU_LIB_CU + ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne.cu + ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne_lj.cu + ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_re_squared.cu + ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_re_squared_lj.cu + ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff.cu + ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_zbl.cu + ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_mod.cu + ) foreach(GPU_KERNEL ${GPU_LIB_CU}) get_filename_component(basename ${GPU_KERNEL} NAME_WE) @@ -1381,7 +1391,21 @@ if(PKG_GPU) GenerateOpenCLHeader(gayberne ${CMAKE_CURRENT_BINARY_DIR}/gpu/gayberne_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_ellipsoid_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne.cu) GenerateOpenCLHeader(gayberne_lj ${CMAKE_CURRENT_BINARY_DIR}/gpu/gayberne_lj_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_ellipsoid_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne_lj.cu) - list(APPEND GPU_LIB_SOURCES ${CMAKE_CURRENT_BINARY_DIR}/gpu/gayberne_cl.h ${CMAKE_CURRENT_BINARY_DIR}/gpu/gayberne_lj_cl.h) + GenerateOpenCLHeader(re_squared ${CMAKE_CURRENT_BINARY_DIR}/gpu/re_squared_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_ellipsoid_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_re_squared.cu) + GenerateOpenCLHeader(re_squared_lj ${CMAKE_CURRENT_BINARY_DIR}/gpu/re_squared_lj_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_ellipsoid_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_re_squared_lj.cu) + GenerateOpenCLHeader(tersoff ${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff.cu) + GenerateOpenCLHeader(tersoff_zbl ${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_zbl_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_zbl_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_zbl.cu) + GenerateOpenCLHeader(tersoff_mod ${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_mod_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_mod_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_mod.cu) + + list(APPEND GPU_LIB_SOURCES + ${CMAKE_CURRENT_BINARY_DIR}/gpu/gayberne_cl.h + ${CMAKE_CURRENT_BINARY_DIR}/gpu/gayberne_lj_cl.h + ${CMAKE_CURRENT_BINARY_DIR}/gpu/re_squared_cl.h + ${CMAKE_CURRENT_BINARY_DIR}/gpu/re_squared_lj_cl.h + ${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_cl.h + ${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_zbl_cl.h + ${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_mod_cl.h + ) add_library(gpu STATIC ${GPU_LIB_SOURCES}) target_link_libraries(gpu ${OpenCL_LIBRARIES}) diff --git a/cmake/Modules/OpenCLUtils.cmake b/cmake/Modules/OpenCLUtils.cmake index 5c147a685c..a9441ce518 100644 --- a/cmake/Modules/OpenCLUtils.cmake +++ b/cmake/Modules/OpenCLUtils.cmake @@ -6,7 +6,7 @@ function(GenerateOpenCLHeader varname outfile files) foreach(IDX RANGE 2 ${ARG_END}) list(GET ARGV ${IDX} filename) file(READ ${filename} content) - string(REGEX REPLACE "\\s*//[^\n]*\n" "" content "${content}") + string(REGEX REPLACE "\\s*//[^\n]*\n" "\n" content "${content}") string(REGEX REPLACE "\\\\" "\\\\\\\\" content "${content}") string(REGEX REPLACE "\"" "\\\\\"" content "${content}") string(REGEX REPLACE "([^\n]+)\n" "\"\\1\\\\n\"\n" content "${content}") diff --git a/cmake/README.md b/cmake/README.md index a635f3e06d..c11326f9d5 100644 --- a/cmake/README.md +++ b/cmake/README.md @@ -211,7 +211,7 @@ cmake -C ../cmake/presets/all_on.cmake -C ../cmake/presets/nolib.cmake -D PKG_GP - + CMAKE_VERBOSE_MAKEFILE Enable verbose output from Makefile builds (useful for debugging), the same can be achived by adding `VERBOSE=1` to the `make` call.
diff --git a/doc/lammps.1 b/doc/lammps.1 index 4686198fef..ac23e7abf8 100644 --- a/doc/lammps.1 +++ b/doc/lammps.1 @@ -1,4 +1,4 @@ -.TH LAMMPS "11 April 2019" "2019-04-11" +.TH LAMMPS "15 May 2019" "2019-05-15" .SH NAME .B LAMMPS \- Molecular Dynamics Simulator. diff --git a/doc/src/Commands_all.txt b/doc/src/Commands_all.txt index 66c348ee30..58ca148555 100644 --- a/doc/src/Commands_all.txt +++ b/doc/src/Commands_all.txt @@ -83,6 +83,7 @@ An alphabetic list of all general LAMMPS commands. "molecule"_molecule.html, "ndx2group"_group2ndx.html, "neb"_neb.html, +"neb/spin"_neb_spin.html, "neigh_modify"_neigh_modify.html, "neighbor"_neighbor.html, "newton"_newton.html, diff --git a/doc/src/Commands_category.txt b/doc/src/Commands_category.txt index 134dae82bb..14a328b227 100644 --- a/doc/src/Commands_category.txt +++ b/doc/src/Commands_category.txt @@ -116,6 +116,7 @@ Actions: "minimize"_minimize.html, "neb"_neb.html, +"neb_spin"_neb_spin.html, "prd"_prd.html, "rerun"_rerun.html, "run"_run.html, diff --git a/doc/src/Commands_fix.txt b/doc/src/Commands_fix.txt index 14de1d06dd..d2d781d4b2 100644 --- a/doc/src/Commands_fix.txt +++ b/doc/src/Commands_fix.txt @@ -107,6 +107,7 @@ OPT. "mvv/edpd"_fix_mvv_dpd.html, "mvv/tdpd"_fix_mvv_dpd.html, "neb"_fix_neb.html, +"neb_spin"_fix_neb_spin.html, "nph (ko)"_fix_nh.html, "nph/asphere (o)"_fix_nph_asphere.html, "nph/body"_fix_nph_body.html, diff --git a/doc/src/Commands_pair.txt b/doc/src/Commands_pair.txt index e887f0178a..e9925b0e0b 100644 --- a/doc/src/Commands_pair.txt +++ b/doc/src/Commands_pair.txt @@ -80,6 +80,8 @@ OPT. "dpd/fdt/energy (k)"_pair_dpd_fdt.html, "dpd/tstat (go)"_pair_dpd.html, "dsmc"_pair_dsmc.html, +"e3b"_pair_e3b.html, +"drip"_pair_drip.html, "eam (gikot)"_pair_eam.html, "eam/alloy (gikot)"_pair_eam.html, "eam/cd (o)"_pair_eam.html, diff --git a/doc/src/Eqs/e3b.jpg b/doc/src/Eqs/e3b.jpg new file mode 100644 index 0000000000..d3b07da409 Binary files /dev/null and b/doc/src/Eqs/e3b.jpg differ diff --git a/doc/src/Eqs/e3b.tex b/doc/src/Eqs/e3b.tex new file mode 100644 index 0000000000..550538bf35 --- /dev/null +++ b/doc/src/Eqs/e3b.tex @@ -0,0 +1,15 @@ +\documentclass[12pt]{article} +\usepackage{amsmath} +\begin{document} + +\begin{align*} +E =& E_2 \sum_{i,j}e^{-k_2 r_{ij}} + E_A \sum_{\substack{i,j,k,\ell \\\in \textrm{type A}}} f(r_{ij})f(r_{k\ell}) + E_B \sum_{\substack{i,j,k,\ell \\\in \textrm{type B}}} f(r_{ij})f(r_{k\ell}) + E_C \sum_{\substack{i,j,k,\ell \\\in \textrm{type C}}} f(r_{ij})f(r_{k\ell}) \\ +f(r) =& e^{-k_3 r}s(r) \\ +s(r) =& \begin{cases} + 1 & rR_f\\ +\end{cases} +\end{align*} + +\end{document} diff --git a/doc/src/Eqs/fix_spin_cubic.jpg b/doc/src/Eqs/fix_spin_cubic.jpg new file mode 100644 index 0000000000..871641111c Binary files /dev/null and b/doc/src/Eqs/fix_spin_cubic.jpg differ diff --git a/doc/src/Eqs/fix_spin_cubic.tex b/doc/src/Eqs/fix_spin_cubic.tex new file mode 100644 index 0000000000..9c402294d7 --- /dev/null +++ b/doc/src/Eqs/fix_spin_cubic.tex @@ -0,0 +1,21 @@ +\documentclass[preview]{standalone} +\usepackage{varwidth} +\usepackage[utf8x]{inputenc} +\usepackage{amsmath,amssymb,amsthm,bm} +\begin{document} +\begin{varwidth}{50in} + \begin{equation} + \bm{H}_{cubic} = -\sum_{{ i}=1}^{N} K_{1} + \Big[ + \left(\vec{s}_{i} \cdot \vec{n1} \right)^2 + \left(\vec{s}_{i} \cdot \vec{n2} \right)^2 + + \left(\vec{s}_{i} \cdot \vec{n2} \right)^2 + \left(\vec{s}_{i} \cdot \vec{n3} \right)^2 + + \left(\vec{s}_{i} \cdot \vec{n1} \right)^2 + \left(\vec{s}_{i} \cdot \vec{n3} \right)^2 \Big] + +K_{2}^{(c)} \left(\vec{s}_{i} \cdot \vec{n1} \right)^2 + \left(\vec{s}_{i} \cdot \vec{n2} \right)^2 + \left(\vec{s}_{i} \cdot \vec{n3} \right)^2 \nonumber + \end{equation} +\end{varwidth} +\end{document} diff --git a/doc/src/Eqs/neb_spin_angle.jpg b/doc/src/Eqs/neb_spin_angle.jpg new file mode 100644 index 0000000000..b7021c4f62 Binary files /dev/null and b/doc/src/Eqs/neb_spin_angle.jpg differ diff --git a/doc/src/Eqs/neb_spin_angle.tex b/doc/src/Eqs/neb_spin_angle.tex new file mode 100644 index 0000000000..03b133cd77 --- /dev/null +++ b/doc/src/Eqs/neb_spin_angle.tex @@ -0,0 +1,15 @@ +\documentclass[preview]{standalone} +\usepackage{varwidth} +\usepackage[utf8x]{inputenc} +\usepackage{amsmath, amssymb, graphics, setspace} + +\begin{document} +\begin{varwidth}{50in} + \begin{equation} + \omega_i^{\nu} = + (\nu - 1) \Delta \omega_i + {\rm ~~and~~} \Delta \omega_i = \frac{\omega_i}{Q-1} + , \nonumber + \end{equation} +\end{varwidth} +\end{document} diff --git a/doc/src/Eqs/neb_spin_k.jpg b/doc/src/Eqs/neb_spin_k.jpg new file mode 100644 index 0000000000..add309694f Binary files /dev/null and b/doc/src/Eqs/neb_spin_k.jpg differ diff --git a/doc/src/Eqs/neb_spin_k.tex b/doc/src/Eqs/neb_spin_k.tex new file mode 100644 index 0000000000..f0ce8e180e --- /dev/null +++ b/doc/src/Eqs/neb_spin_k.tex @@ -0,0 +1,16 @@ +\documentclass[preview]{standalone} +\usepackage{varwidth} +\usepackage[utf8x]{inputenc} +\usepackage{amsmath, amssymb, graphics, setspace} + +\begin{document} +\begin{varwidth}{50in} + \begin{equation} + \vec{k}_i = + \frac{\vec{m}_i^I \times \vec{m}_i^F}{\left|\vec{m}_i^I + \times \vec{m}_i^F\right|} + %&{\rm ~if~}& \vec{m}_i^I \times \vec{m}_i^F + , \nonumber + \end{equation} +\end{varwidth} +\end{document} diff --git a/doc/src/Eqs/neb_spin_rodrigues_formula.jpg b/doc/src/Eqs/neb_spin_rodrigues_formula.jpg new file mode 100644 index 0000000000..66070f7bc5 Binary files /dev/null and b/doc/src/Eqs/neb_spin_rodrigues_formula.jpg differ diff --git a/doc/src/Eqs/neb_spin_rodrigues_formula.tex b/doc/src/Eqs/neb_spin_rodrigues_formula.tex new file mode 100644 index 0000000000..4a8347cd79 --- /dev/null +++ b/doc/src/Eqs/neb_spin_rodrigues_formula.tex @@ -0,0 +1,16 @@ +\documentclass[preview]{standalone} +\usepackage{varwidth} +\usepackage[utf8x]{inputenc} +\usepackage{amsmath, amssymb, graphics, setspace} + +\begin{document} +\begin{varwidth}{50in} + \begin{equation} + \vec{m}_i^{\nu} = \vec{m}_i^{I} \cos(\omega_i^{\nu}) + + (\vec{k}_i \times \vec{m}_i^{I}) \sin(\omega_i^{\nu}) + + (1.0-\cos(\omega_i^{\nu})) \vec{k}_i (\vec{k}_i\cdot + \vec{m}_i^{I}) + , \nonumber + \end{equation} +\end{varwidth} +\end{document} diff --git a/doc/src/Eqs/pair_drip.jpg b/doc/src/Eqs/pair_drip.jpg new file mode 100644 index 0000000000..a94b4141b0 Binary files /dev/null and b/doc/src/Eqs/pair_drip.jpg differ diff --git a/doc/src/Eqs/pair_drip.tex b/doc/src/Eqs/pair_drip.tex new file mode 100644 index 0000000000..079a2cdf84 --- /dev/null +++ b/doc/src/Eqs/pair_drip.tex @@ -0,0 +1,14 @@ +\documentclass[12pt]{article} +\usepackage{amsmath} +\usepackage{bm} + +\begin{document} + +\begin{eqnarray*} +E &=& \frac{1}{2} \sum_{i} \sum_{j\notin\text{layer}\,i} \phi_{ij} \\\phi_{ij} &=& f_\text{c}(x_r) \left[ e^{-\lambda(r_{ij} - z_0 )} \left[C+f(\rho_{ij})+ g(\rho_{ij}, \{\alpha_{ij}^{(m)}\}) \right]- A\left (\frac{z_0}{r_{ij}} \right)^6 \right] \\ +\end{eqnarray*} + + + + +\end{document} \ No newline at end of file diff --git a/doc/src/Eqs/pair_mdf-6.jpg b/doc/src/Eqs/pair_mdf-6.jpg index 54a08b25d6..60bd7e3a9e 100644 Binary files a/doc/src/Eqs/pair_mdf-6.jpg and b/doc/src/Eqs/pair_mdf-6.jpg differ diff --git a/doc/src/Eqs/pair_mdf-6.tex b/doc/src/Eqs/pair_mdf-6.tex index 9f25e09bc7..b80f6f69b5 100644 --- a/doc/src/Eqs/pair_mdf-6.tex +++ b/doc/src/Eqs/pair_mdf-6.tex @@ -1,9 +1,9 @@ \documentclass[12pt]{article} - +\pagestyle{empty} \begin{document} $$ - E(r) = \frac{A}{r^{12}} - \frac{A}{r^{6}} + E(r) = \frac{A}{r^{12}} - \frac{B}{r^{6}} $$ \end{document} diff --git a/doc/src/Examples.txt b/doc/src/Examples.txt index e26e6abd99..daf9966155 100644 --- a/doc/src/Examples.txt +++ b/doc/src/Examples.txt @@ -11,7 +11,7 @@ Section"_Tools.html :c Example scripts :h3 The LAMMPS distribution includes an examples sub-directory with many -sample problems. Many are 2d models that run quickly are are +sample problems. Many are 2d models that run quickly and are straightforward to visualize, requiring at most a couple of minutes to run on a desktop machine. Each problem has an input script (in.*) and produces a log file (log.*) when it runs. Some use a data file diff --git a/doc/src/Howto_bioFF.txt b/doc/src/Howto_bioFF.txt index b6995920ae..d238e4024f 100644 --- a/doc/src/Howto_bioFF.txt +++ b/doc/src/Howto_bioFF.txt @@ -56,7 +56,7 @@ COMPASS is a general force field for atomistic simulation of common organic molecules, inorganic small molecules, and polymers which was developed using ab initio and empirical parameterization techniques. See the "Tools"_Tools.html doc page for the msi2lmp tool for creating -LAMMPS template input and data files from BIOVIA’s Materials Studio +LAMMPS template input and data files from BIOVIA's Materials Studio files. Please note that the msi2lmp tool is very old and largely unmaintained, so it does not support all features of Materials Studio provided force field files, especially additions during the last decade. @@ -129,7 +129,7 @@ Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998). Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995). :link(howto-Sun) -[(Sun)] Sun, J. Phys. Chem. B, 102, 7338–7364 (1998). +[(Sun)] Sun, J. Phys. Chem. B, 102, 7338-7364 (1998). :link(howto-Mayo) [(Mayo)] Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909 diff --git a/doc/src/Howto_diffusion.txt b/doc/src/Howto_diffusion.txt index 6c920c9bc3..6b6eaf72ec 100644 --- a/doc/src/Howto_diffusion.txt +++ b/doc/src/Howto_diffusion.txt @@ -29,3 +29,5 @@ diffusion coefficient. The instantaneous VACF values can be accumulated in a vector via the "fix vector"_fix_vector.html command, and time integrated via the "variable trap"_variable.html function, and thus extract D. + +:line diff --git a/doc/src/Howto_drude2.txt b/doc/src/Howto_drude2.txt index afb528eb4a..376ecb0292 100644 --- a/doc/src/Howto_drude2.txt +++ b/doc/src/Howto_drude2.txt @@ -274,7 +274,7 @@ crash. Even without reaching this extreme case, the correlation between nearby dipoles on the same molecule may be exaggerated. Often, special bond relations prevent bonded neighboring atoms to see the charge of each other's DP, so that the problem does not always appear. -It is possible to use screened dipole dipole interactions by using the +It is possible to use screened dipole-dipole interactions by using the "{pair_style thole}"_pair_thole.html. This is implemented as a correction to the Coulomb pair_styles, which dampens at short distance the interactions between the charges representing the induced dipoles. diff --git a/doc/src/Howto_replica.txt b/doc/src/Howto_replica.txt index 29d1aa02fd..505967c1b8 100644 --- a/doc/src/Howto_replica.txt +++ b/doc/src/Howto_replica.txt @@ -17,6 +17,7 @@ periodically. These are the relevant commands: "neb"_neb.html for nudged elastic band calculations +"neb_spin"_neb_spin.html for magnetic nudged elastic band calculations "prd"_prd.html for parallel replica dynamics "tad"_tad.html for temperature accelerated dynamics "temper"_temper.html for parallel tempering diff --git a/doc/src/Howto_spins.txt b/doc/src/Howto_spins.txt index 7f16883487..80b2a54fe4 100644 --- a/doc/src/Howto_spins.txt +++ b/doc/src/Howto_spins.txt @@ -10,7 +10,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c Magnetic spins :h3 The magnetic spin simulations are enabled by the SPIN package, whose -implementation is detailed in "Tranchida"_#Tranchida7. +implementation is detailed in "Tranchida"_#Tranchida. The model represents the simulation of atomic magnetic spins coupled to lattice vibrations. The dynamics of those magnetic spins can be used @@ -36,13 +36,28 @@ A Langevin thermostat can be applied to those magnetic spins using "fix langevin/spin"_fix_langevin_spin.html. Typically, this thermostat can be coupled to another Langevin thermostat applied to the atoms using "fix langevin"_fix_langevin.html in order to simulate -thermostatted spin-lattice system. +thermostatted spin-lattice systems. The magnetic Gilbert damping can also be applied using "fix langevin/spin"_fix_langevin_spin.html. It allows to either dissipate the thermal energy of the Langevin thermostat, or to perform a relaxation of the magnetic configuration toward an equilibrium state. +The command "fix setforce/spin"_fix_setforce.html allows to set the +components of the magnetic precession vectors (while erasing and +replacing the previously computed magnetic precession vectors on +the atom). +This command can be used to freeze the magnetic moment of certain +atoms in the simulation by zeroing their precession vector. + +The command "fix nve/spin"_fix_nve_spin.html can be used to +perform a symplectic integration of the combined dynamics of spins +and atomic motions. + +The minimization style "min/spin"_min_spin.html can be applied +to the spins to perform a minimization of the spin configuration. + + All the computed magnetic properties can be output by two main commands. The first one is "compute spin"_compute_spin.html, that enables to evaluate magnetic averaged quantities, such as the total @@ -54,6 +69,6 @@ magnetic spin, or the magnetic force acting on this spin. :line -:link(Tranchida7) +:link(Tranchida) [(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson, -arXiv preprint arXiv:1801.10233, (2018). +Journal of Computational Physics, 372, 406-425, (2018). diff --git a/doc/src/Install_git.txt b/doc/src/Install_git.txt index bae5bef94f..19decde516 100644 --- a/doc/src/Install_git.txt +++ b/doc/src/Install_git.txt @@ -52,7 +52,7 @@ as if you unpacked a current LAMMPS tarball, with the exception, that the HTML documentation files are not included. They can be fetched from the LAMMPS website by typing "make fetch" in the doc directory. Or they can be generated from the content provided in doc/src by -typing "make html" from the the doc directory. +typing "make html" from the doc directory. After initial cloning, as bug fixes and new features are added to LAMMPS, as listed on "this page"_Errors_bugs.html, you can stay diff --git a/doc/src/Install_svn.txt b/doc/src/Install_svn.txt index 84a46865f3..b701c0b04d 100644 --- a/doc/src/Install_svn.txt +++ b/doc/src/Install_svn.txt @@ -40,7 +40,7 @@ as if you unpacked a current LAMMPS tarball, with the exception, that the HTML documentation files are not included. They can be fetched from the LAMMPS website by typing "make fetch" in the doc directory. Or they can be generated from the content provided in doc/src by -typing "make html" from the the doc directory. +typing "make html" from the doc directory. After initial checkout, as bug fixes and new features are added to LAMMPS, as listed on "this page"_Errors_bugs.html, you can stay diff --git a/doc/src/Manual.txt b/doc/src/Manual.txt index e36e4063c9..396155cc45 100644 --- a/doc/src/Manual.txt +++ b/doc/src/Manual.txt @@ -1,7 +1,7 @@ LAMMPS Users Manual - + @@ -21,7 +21,7 @@ :line LAMMPS Documentation :c,h1 -29 Mar 2019 version :c,h2 +15 May 2019 version :c,h2 "What is a LAMMPS version?"_Manual_version.html diff --git a/doc/src/PDF/colvars-refman-lammps.pdf b/doc/src/PDF/colvars-refman-lammps.pdf index 07d8254475..6194424212 100644 Binary files a/doc/src/PDF/colvars-refman-lammps.pdf and b/doc/src/PDF/colvars-refman-lammps.pdf differ diff --git a/doc/src/Packages_details.txt b/doc/src/Packages_details.txt index 0ab1b5e4fd..4f9bcc1910 100644 --- a/doc/src/Packages_details.txt +++ b/doc/src/Packages_details.txt @@ -706,7 +706,7 @@ PERI package :link(PKG-PERI),h4 An atom style, several pair styles which implement different Peridynamics materials models, and several computes which calculate -diagnostics. Peridynamics is a a particle-based meshless continuum +diagnostics. Peridynamics is a particle-based meshless continuum model. [Authors:] The original package was created by Mike Parks (Sandia). @@ -905,7 +905,7 @@ SPIN package :link(PKG-SPIN),h4 Model atomic magnetic spins classically, coupled to atoms moving in the usual manner via MD. Various pair, fix, and compute styles. -[Author:] Julian Tranchida (Sandia). +[Author:] Julien Tranchida (Sandia). [Supporting info:] @@ -918,6 +918,7 @@ src/SPIN: filenames -> commands "fix nve/spin"_fix_nve_spin.html "fix precession/spin"_fix_precession_spin.html "compute spin"_compute_spin.html +"neb/spin"_neb_spin.html examples/SPIN :ul :line @@ -1228,7 +1229,7 @@ isothermal, isoenergetic, isobaric and isenthalpic conditions are included. These enable long timesteps via the Shardlow splitting algorithm. -[Authors:] Jim Larentzos (ARL), Tim Mattox (Engility Corp), and and John +[Authors:] Jim Larentzos (ARL), Tim Mattox (Engility Corp), and John Brennan (ARL). [Supporting info:] @@ -1536,7 +1537,7 @@ USER-MESO package :link(PKG-USER-MESO),h4 [Contents:] -Several extensions of the the dissipative particle dynamics (DPD) +Several extensions of the dissipative particle dynamics (DPD) method. Specifically, energy-conserving DPD (eDPD) that can model non-isothermal processes, many-body DPD (mDPD) for simulating vapor-liquid coexistence, and transport DPD (tDPD) for modeling diff --git a/doc/src/Python_library.txt b/doc/src/Python_library.txt index e76af83962..d9ddbe0cbb 100644 --- a/doc/src/Python_library.txt +++ b/doc/src/Python_library.txt @@ -180,7 +180,7 @@ doubles is returned, one value per atom, which you can use via normal Python subscripting. The values will be zero for atoms not in the specified group. -The get_thermo() method returns returns the current value of a thermo +The get_thermo() method returns the current value of a thermo keyword as a float. The get_natoms() method returns the total number of atoms in the diff --git a/doc/src/Run_options.txt b/doc/src/Run_options.txt index 1c3cb60c5f..87b272a866 100644 --- a/doc/src/Run_options.txt +++ b/doc/src/Run_options.txt @@ -242,7 +242,7 @@ processors. Running with multiple partitions can be useful for running "multi-replica simulations"_Howto_replica.html, where each replica -runs on on one or a few processors. Note that with MPI installed on a +runs on one or a few processors. Note that with MPI installed on a machine (e.g. your desktop), you can run on more (virtual) processors than you have physical processors. diff --git a/doc/src/Run_output.txt b/doc/src/Run_output.txt index 7d5a9e6ae6..70eecff20d 100644 --- a/doc/src/Run_output.txt +++ b/doc/src/Run_output.txt @@ -93,7 +93,7 @@ monitor thread utilization and load balance is provided. A new {Thread timings} section is also added, which lists the time spent in reducing the per-thread data elements to the storage for non-threaded computation. These thread timings are measured for the first MPI rank -only and and thus, because the breakdown for MPI tasks can change from +only and thus, because the breakdown for MPI tasks can change from MPI rank to MPI rank, this breakdown can be very different for individual ranks. Here is an example output for this section: diff --git a/doc/src/Tools.txt b/doc/src/Tools.txt index af9fd4298c..eb7b6d81b8 100644 --- a/doc/src/Tools.txt +++ b/doc/src/Tools.txt @@ -77,6 +77,7 @@ Post-processing tools :h3 "python"_#pythontools, "reax"_#reax_tool, "smd"_#smd, +"spin"_#spin, "xmgrace"_#xmgrace :tb(c=6,ea=c,a=l) Miscellaneous tools :h3 @@ -511,6 +512,20 @@ Ernst Mach Institute in Germany (georg.ganzenmueller at emi.fhg.de). :line +spin tool :h4,link(spin) + +The spin sub-directory contains a C file interpolate.c which can +be compiled and used to perform a cubic polynomial interpolation of +the MEP following a GNEB calculation. + +See the README file in tools/spin/interpolate_gneb for more details. + +This tool was written by the SPIN package author, Julien +Tranchida at Sandia National Labs (jtranch at sandia.gov, and by Aleksei +Ivanov, at University of Iceland (ali5 at hi.is). + +:line + vim tool :h4,link(vim) The files in the tools/vim directory are add-ons to the VIM editor diff --git a/doc/src/commands_list.txt b/doc/src/commands_list.txt index 6f90d9c93a..cf716df9ac 100644 --- a/doc/src/commands_list.txt +++ b/doc/src/commands_list.txt @@ -67,6 +67,7 @@ Commands :h1 minimize molecule neb + neb_spin neigh_modify neighbor newton diff --git a/doc/src/compute_chunk_atom.txt b/doc/src/compute_chunk_atom.txt index b924f90da8..c6dfddbd55 100644 --- a/doc/src/compute_chunk_atom.txt +++ b/doc/src/compute_chunk_atom.txt @@ -468,7 +468,7 @@ property/chunk"_compute_property_chunk.html command. NOTE: The compression operation requires global communication across all processors to share their chunk ID values. It can require large memory on every processor to store them, even after they are -compressed, if there are are a large number of unique chunk IDs with +compressed, if there are a large number of unique chunk IDs with atoms assigned to them. It uses a STL map to find unique chunk IDs and store them in sorted order. Each time an atom is assigned a compressed chunk ID, it must access the STL map. All of this means diff --git a/doc/src/compute_chunk_spread_atom.txt b/doc/src/compute_chunk_spread_atom.txt index 5f65900a49..4afb62683e 100644 --- a/doc/src/compute_chunk_spread_atom.txt +++ b/doc/src/compute_chunk_spread_atom.txt @@ -49,7 +49,7 @@ For inputs that are computes, they must be a compute that calculates per-chunk values. These are computes whose style names end in "/chunk". -For inputs that are fixes, they should be a a fix that calculates +For inputs that are fixes, they should be a fix that calculates per-chunk values. For example, "fix ave/chunk"_fix_ave_chunk.html or "fix ave/time"_fix_ave_time.html (assuming it is time-averaging per-chunk data). diff --git a/doc/src/compute_voronoi_atom.txt b/doc/src/compute_voronoi_atom.txt index d01f4df712..4d7bd56838 100644 --- a/doc/src/compute_voronoi_atom.txt +++ b/doc/src/compute_voronoi_atom.txt @@ -96,7 +96,7 @@ group. The argument {maxedge} of the this keyword is the largest number of edges on a single Voronoi cell face expected to occur in the sample. This keyword adds the generation of a global vector with {maxedge}+1 entries. The last entry in the vector contains the number of -faces with with more than {maxedge} edges. Since the polygon with the +faces with more than {maxedge} edges. Since the polygon with the smallest amount of edges is a triangle, entries 1 and 2 of the vector will always be zero. diff --git a/doc/src/dihedral_spherical.txt b/doc/src/dihedral_spherical.txt index 61949174df..62ba6cf9e5 100644 --- a/doc/src/dihedral_spherical.txt +++ b/doc/src/dihedral_spherical.txt @@ -47,7 +47,7 @@ division by sin(74.4)*sin(48.1) (the minima positions for theta1 and theta2). The following coefficients must be defined for each dihedral type via the "dihedral_coeff"_dihedral_coeff.html command as in the example above, or in -the Dihedral Coeffs section of a data file file read by the +the Dihedral Coeffs section of a data file read by the "read_data"_read_data.html command: n (integer >= 1) diff --git a/doc/src/dihedral_table_cut.txt b/doc/src/dihedral_table_cut.txt index 6f3f6edbcc..b72f34e36e 100644 --- a/doc/src/dihedral_table_cut.txt +++ b/doc/src/dihedral_table_cut.txt @@ -174,7 +174,7 @@ radians instead of degrees. (Note: This changes the way the forces are scaled in the 4th column of the data file.) The optional "CHECKU" keyword is followed by a filename. This allows -the user to save all of the the {Ntable} different entries in the +the user to save all of the {Ntable} different entries in the interpolated energy table to a file to make sure that the interpolated function agrees with the user's expectations. (Note: You can temporarily increase the {Ntable} parameter to a high value for this diff --git a/doc/src/dump.txt b/doc/src/dump.txt index a776ff70fc..ff1b2dc3a6 100644 --- a/doc/src/dump.txt +++ b/doc/src/dump.txt @@ -21,7 +21,7 @@ dump ID group-ID style N file args :pre ID = user-assigned name for the dump :ulb,l group-ID = ID of the group of atoms to be dumped :l -style = {atom} or {atom/gz} or {atom/mpiio} or {cfg} or {cfg/gz} or {cfg/mpiio} or {custom} or {custom/gz} or {custom/mpiio} or {dcd} or {h5md} or {image} or or {local} or {molfile} or {movie} or {netcdf} or {netcdf/mpiio} or {vtk} or {xtc} or {xyz} or {xyz/gz} or {xyz/mpiio} :l +style = {atom} or {atom/gz} or {atom/mpiio} or {cfg} or {cfg/gz} or {cfg/mpiio} or {custom} or {custom/gz} or {custom/mpiio} or {dcd} or {h5md} or {image} or {local} or {molfile} or {movie} or {netcdf} or {netcdf/mpiio} or {vtk} or {xtc} or {xyz} or {xyz/gz} or {xyz/mpiio} :l N = dump every this many timesteps :l file = name of file to write dump info to :l args = list of arguments for a particular style :l @@ -196,7 +196,7 @@ For post-processing purposes the {atom}, {local}, and {custom} text files are self-describing in the following sense. The dimensions of the simulation box are included in each snapshot. -For an orthogonal simulation box this information is is formatted as: +For an orthogonal simulation box this information is formatted as: ITEM: BOX BOUNDS xx yy zz xlo xhi @@ -619,7 +619,7 @@ should be replaced by the actual name of the variable that has been defined previously in the input script. Only an atom-style variable can be referenced, since it is the only style that generates per-atom values. Variables of style {atom} can reference individual atom -attributes, per-atom atom attributes, thermodynamic keywords, or +attributes, per-atom attributes, thermodynamic keywords, or invoke other computes, fixes, or variables when they are evaluated, so this is a very general means of creating quantities to output to a dump file. diff --git a/doc/src/dump_modify.txt b/doc/src/dump_modify.txt index 9a35956055..6be0d26463 100644 --- a/doc/src/dump_modify.txt +++ b/doc/src/dump_modify.txt @@ -310,7 +310,7 @@ NOTE: Atom and molecule IDs are stored internally as 4-byte or 8-byte signed integers, depending on how LAMMPS was compiled. When specifying the {format int} option you can use a "%d"-style format identifier in the format string and LAMMPS will convert this to the -corresponding 8-byte form it it is needed when outputting those +corresponding 8-byte form if it is needed when outputting those values. However, when specifying the {line} option or {format M string} option for those values, you should specify a format string appropriate for an 8-byte signed integer, e.g. one with "%ld", if diff --git a/doc/src/fix.txt b/doc/src/fix.txt index c424e56074..294802c4fa 100644 --- a/doc/src/fix.txt +++ b/doc/src/fix.txt @@ -321,20 +321,16 @@ accelerated styles exist. "restrain"_fix_restrain.html - constrain a bond, angle, dihedral "rhok"_fix_rhok.html - "rigid"_fix_rigid.html - constrain one or more clusters of atoms to move as a rigid body with NVE integration -"rigid/nph"_fix_rigid.html - constrain one or more clusters of atoms to move as a rigid body with NPH integration -"rigid/nph/small"_fix_rigid.html - -"rigid/npt"_fix_rigid.html - constrain one or more clusters of atoms to move as a rigid body with NPT integration -"rigid/npt/small"_fix_rigid.html - -"rigid/nve"_fix_rigid.html - constrain one or more clusters of atoms to move as a rigid body with alternate NVE integration -"rigid/nve/small"_fix_rigid.html - -"rigid/nvt"_fix_rigid.html - constrain one or more clusters of atoms to move as a rigid body with NVT integration -"rigid/nvt/small"_fix_rigid.html - -"rigid/small"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with NVE integration -"rigid/small/nph"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with NPH integration -"rigid/small/npt"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with NPT integration -"rigid/small/nve"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with alternate NVE integration -"rigid/small/nvt"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with NVT integration "rigid/meso"_fix_rigid_meso.html - constrain clusters of mesoscopic SPH/SDPD particles to move as a rigid body +"rigid/nph"_fix_rigid.html - constrain one or more clusters of atoms to move as a rigid body with NPH integration +"rigid/nph/small"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with NPH integration +"rigid/npt"_fix_rigid.html - constrain one or more clusters of atoms to move as a rigid body with NPT integration +"rigid/npt/small"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with NPT integration +"rigid/nve"_fix_rigid.html - constrain one or more clusters of atoms to move as a rigid body with alternate NVE integration +"rigid/nve/small"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with alternate NVE integration +"rigid/nvt"_fix_rigid.html - constrain one or more clusters of atoms to move as a rigid body with NVT integration +"rigid/nvt/small"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with NVT integration +"rigid/small"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with NVE integration "rx"_fix_rx.html - "saed/vtk"_fix_saed_vtk.html - "setforce"_fix_setforce.html - set the force on each atom diff --git a/doc/src/fix_ave_chunk.txt b/doc/src/fix_ave_chunk.txt index 4e036367e2..a8bdef0425 100644 --- a/doc/src/fix_ave_chunk.txt +++ b/doc/src/fix_ave_chunk.txt @@ -361,7 +361,7 @@ computes that calculate a temperature to see which ones implement a bias. The {adof} and {cdof} keywords define the values used in the degree of -freedom (DOF) formula described above for for temperature calculation +freedom (DOF) formula described above for temperature calculation for each chunk. They are only used when the {temp} value is calculated. They can be used to calculate a more appropriate temperature for some kinds of chunks. Here are 3 examples: diff --git a/doc/src/fix_colvars.txt b/doc/src/fix_colvars.txt index d9eb9ac5aa..304273d451 100644 --- a/doc/src/fix_colvars.txt +++ b/doc/src/fix_colvars.txt @@ -98,6 +98,16 @@ fix to add the energy change from the biasing force added by the fix to the system's potential energy as part of "thermodynamic output"_thermo_style.html. +The {fix_modify configfile } option allows to add settings +from an additional config file to the colvars module. This option can +only be used, after the system has been initialized with a "run"_run.html +command. + +The {fix_modify config } option allows to add settings +from inline strings. Those have to fit on a single line when enclosed +in a pair of double quotes ("), or can span multiple lines when bracketed +by a pair of triple double quotes (""", like python embedded documentation). + This fix computes a global scalar which can be accessed by various "output commands"_Howto_output.html. The scalar is the cumulative energy change due to this fix. The scalar value calculated by this diff --git a/doc/src/fix_halt.txt b/doc/src/fix_halt.txt index 87ad97accf..8e85dc7ea5 100644 --- a/doc/src/fix_halt.txt +++ b/doc/src/fix_halt.txt @@ -113,12 +113,11 @@ state of the system, e.g. via a "write_dump"_write_dump.html or "write_restart"_write_restart.html command. If its value is {continue}, the behavior is the same as for {soft}, -except subsequent subsequent "run"_run.html or -"minimize"_minimize.html commands are executed. This allows your -script to remedy the condition that triggered the halt, if necessary. -Note that you may wish use the "unfix"_unfix.html command on the fix -halt ID, so that the same condition is not immediately triggered in a -subsequent run. +except subsequent "run"_run.html or "minimize"_minimize.html commands +are executed. This allows your script to remedy the condition that +triggered the halt, if necessary. Note that you may wish use the +"unfix"_unfix.html command on the fix halt ID, so that the same +condition is not immediately triggered in a subsequent run. The optional {message} keyword determines whether a message is printed to the screen and logfile when the halt condition is triggered. If diff --git a/doc/src/fix_hyper_global.txt b/doc/src/fix_hyper_global.txt index 81404ac6a2..bfe8203b50 100644 --- a/doc/src/fix_hyper_global.txt +++ b/doc/src/fix_hyper_global.txt @@ -188,7 +188,7 @@ No information about this fix is written to "binary restart files"_restart.html. The "fix_modify"_fix_modify.html {energy} option is supported by this -fix to add the energy of the bias potential to the the system's +fix to add the energy of the bias potential to the system's potential energy as part of "thermodynamic output"_thermo_style.html. This fix computes a global scalar and global vector of length 12, which diff --git a/doc/src/fix_hyper_local.txt b/doc/src/fix_hyper_local.txt index 185fa8f20b..d3bbb3849d 100644 --- a/doc/src/fix_hyper_local.txt +++ b/doc/src/fix_hyper_local.txt @@ -301,7 +301,7 @@ No information about this fix is written to "binary restart files"_restart.html. The "fix_modify"_fix_modify.html {energy} option is supported by this -fix to add the energy of the bias potential to the the system's +fix to add the energy of the bias potential to the system's potential energy as part of "thermodynamic output"_thermo_style.html. This fix computes a global scalar and global vector of length 21, @@ -322,13 +322,13 @@ vector stores the following quantities: 9 = fraction of biased bonds with negative strain during this run 10 = average bias coeff for all bonds during this run (unitless) 11 = min bias coeff for any bond during this run (unitless) -12 = max bias coeff for any bond during this run (unitless) +12 = max bias coeff for any bond during this run (unitless) :ul 13 = max drift distance of any bond atom during this run (distance units) 14 = max distance from proc subbox of any ghost atom with maxstrain < qfactor during this run (distance units) 15 = max distance outside my box of any ghost atom with any maxstrain during this run (distance units) 16 = count of ghost atoms that could not be found on reneighbor steps during this run -17 = count of bias overlaps (< Dcut) found during this run +17 = count of bias overlaps (< Dcut) found during this run :ul 18 = cumulative hyper time since fix created (time units) 19 = cumulative count of event timesteps since fix created diff --git a/doc/src/fix_langevin_spin.txt b/doc/src/fix_langevin_spin.txt index ddd3a0319b..e4065adad5 100644 --- a/doc/src/fix_langevin_spin.txt +++ b/doc/src/fix_langevin_spin.txt @@ -99,4 +99,4 @@ integration fix (e.g. {fix nve/spin}). :link(Tranchida2) [(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson, -Journal of Computational Physics, (2018). +Journal of Computational Physics, 372, 406-425, (2018). diff --git a/doc/src/fix_neb.txt b/doc/src/fix_neb.txt index 410ab3d4d1..87292bb5cd 100644 --- a/doc/src/fix_neb.txt +++ b/doc/src/fix_neb.txt @@ -97,7 +97,7 @@ Note that in this case the specified {Kspring} is in force/distance units. With a value of {ideal}, the spring force is computed as suggested in -"(WeinenE)"_#WeinenE : +"(WeinanE)"_#WeinanE : Fnudge_parallel = -{Kspring} * (RD-RDideal) / (2 * meanDist) :pre @@ -224,8 +224,8 @@ specified (no inter-replica force on the end replicas). [(Henkelman2)] Henkelman, Uberuaga, Jonsson, J Chem Phys, 113, 9901-9904 (2000). -:link(WeinenE) -[(WeinenE)] E, Ren, Vanden-Eijnden, Phys Rev B, 66, 052301 (2002). +:link(WeinanE) +[(WeinanE)] E, Ren, Vanden-Eijnden, Phys Rev B, 66, 052301 (2002). :link(Jonsson) [(Jonsson)] Jonsson, Mills and Jacobsen, in Classical and Quantum diff --git a/doc/src/fix_neb_spin.txt b/doc/src/fix_neb_spin.txt new file mode 100644 index 0000000000..89420f451c --- /dev/null +++ b/doc/src/fix_neb_spin.txt @@ -0,0 +1,76 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +fix neb/spin command :h3 + +[Syntax:] + +fix ID group-ID neb/spin Kspring :pre + +ID, group-ID are documented in "fix"_fix.html command :ulb,l +neb/spin = style name of this fix command :l +Kspring = spring constant for parallel nudging force +(force/distance units or force units, see parallel keyword) :pre,ule + +[Examples:] + +fix 1 active neb/spin 1.0 + +[Description:] + +Add nudging forces to spins in the group for a multi-replica +simulation run via the "neb/spin"_neb_spin.html command to perform a +geodesic nudged elastic band (GNEB) calculation for finding the +transition state. +Hi-level explanations of GNEB are given with the +"neb/spin"_neb_spin.html command and on the +"Howto replica"_Howto_replica.html doc page. +The fix neb/spin command must be used with the "neb/spin" command and +defines how inter-replica nudging forces are computed. A GNEB +calculation is divided in two stages. In the first stage n replicas +are relaxed toward a MEP until convergence. In the second stage, the +climbing image scheme is enabled, so that the replica having the highest +energy relaxes toward the saddle point (i.e. the point of highest energy +along the MEP), and a second relaxation is performed. + +The nudging forces are calculated as explained in +"(BessarabB)"_#BessarabB). +See this reference for more explanation about their expression. + +[Restart, fix_modify, output, run start/stop, minimize info:] + +No information about this fix is written to "binary restart +files"_restart.html. None of the "fix_modify"_fix_modify.html options +are relevant to this fix. No global or per-atom quantities are stored +by this fix for access by various "output commands"_Howto_output.html. +No parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. + +The forces due to this fix are imposed during an energy minimization, +as invoked by the "minimize"_minimize.html command via the +"neb/spin"_neb_spin.html command. + +[Restrictions:] + +This command can only be used if LAMMPS was built with the SPIN +package. See the "Build package"_Build_package.html doc +page for more info. + +[Related commands:] + +"neb_spin"_neb_spin.html + +[Default:] + +none + +:line + +:link(BessarabB) +[(BessarabB)] Bessarab, Uzdin, Jonsson, Comp Phys Comm, 196, +335-347 (2015). diff --git a/doc/src/fix_nve_spin.txt b/doc/src/fix_nve_spin.txt index af435dc730..7b382bb6ad 100644 --- a/doc/src/fix_nve_spin.txt +++ b/doc/src/fix_nve_spin.txt @@ -73,4 +73,4 @@ instead of "array" is also valid. :link(Tranchida1) [(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson, -Journal of Computational Physics, (2018). +Journal of Computational Physics, 372, 406-425, (2018). diff --git a/doc/src/fix_precession_spin.txt b/doc/src/fix_precession_spin.txt index f16522c7b6..708b2bd7aa 100644 --- a/doc/src/fix_precession_spin.txt +++ b/doc/src/fix_precession_spin.txt @@ -14,24 +14,28 @@ fix ID group precession/spin style args :pre ID, group are documented in "fix"_fix.html command :ulb,l precession/spin = style name of this fix command :l -style = {zeeman} or {anisotropy} :l +style = {zeeman} or {anisotropy} or {cubic} :l {zeeman} args = H x y z H = intensity of the magnetic field (in Tesla) x y z = vector direction of the field {anisotropy} args = K x y z K = intensity of the magnetic anisotropy (in eV) x y z = vector direction of the anisotropy :pre + {cubic} args = K1 K2c n1x n1y n1x n2x n2y n2z n3x n3y n3z + K1 and K2c = intensity of the magnetic anisotropy (in eV) + n1x to n3z = three direction vectors of the cubic anisotropy :pre :ule [Examples:] fix 1 all precession/spin zeeman 0.1 0.0 0.0 1.0 -fix 1 all precession/spin anisotropy 0.001 0.0 0.0 1.0 +fix 1 3 precession/spin anisotropy 0.001 0.0 0.0 1.0 +fix 1 iron precession/spin cubic 0.001 0.0005 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1.0 fix 1 all precession/spin zeeman 0.1 0.0 0.0 1.0 anisotropy 0.001 0.0 0.0 1.0 :pre [Description:] -Impose a force torque to each magnetic spin in the group. +This fix applies a precession torque to each magnetic spin in the group. Style {zeeman} is used for the simulation of the interaction between the magnetic spins in the defined group and an external @@ -50,10 +54,29 @@ for the magnetic spins in the defined group: with n defining the direction of the anisotropy, and K (in eV) its intensity. If K>0, an easy axis is defined, and if K<0, an easy plane is defined. -In both cases, the choice of (x y z) imposes the vector direction for the force. -Only the direction of the vector is important; it's length is ignored. +Style {cubic} is used to simulate a cubic anisotropy, with three +possible easy axis for the magnetic spins in the defined group: -Both styles can be combined within one single command line. +:c,image(Eqs/fix_spin_cubic.jpg) + +with K1 and K2c (in eV) the intensity coefficients and +n1, n2 and n3 defining the three anisotropic directions +defined by the command (from n1x to n3z). +For n1 = (100), n2 = (010), and n3 = (001), K1 < 0 defines an +iron type anisotropy (easy axis along the (001)-type cube +edges), and K1 > 0 defines a nickel type anisotropy (easy axis +along the (111)-type cube diagonals). +K2^c > 0 also defines easy axis along the (111)-type cube +diagonals. +See chapter 2 of "(Skomski)"_#Skomski1 for more details on cubic +anisotropies. + +In all cases, the choice of (x y z) only imposes the vector +directions for the forces. Only the direction of the vector is +important; it's length is ignored (the entered vectors are +normalized). + +Those styles can be combined within one single command line. :line @@ -85,3 +108,9 @@ package"_Build_package.html doc page for more info. "atom_style spin"_atom_style.html [Default:] none + +:line + +:link(Skomski1) +[(Skomski)] Skomski, R. (2008). Simple models of magnetism. +Oxford University Press. diff --git a/doc/src/fix_print.txt b/doc/src/fix_print.txt index d23c1103d3..cafc180718 100644 --- a/doc/src/fix_print.txt +++ b/doc/src/fix_print.txt @@ -14,7 +14,7 @@ fix ID group-ID print N string keyword value ... :pre ID, group-ID are documented in "fix"_fix.html command :ulb,l print = style name of this fix command :l -N = print every N steps :l +N = print every N steps; N can be a variable (see below) :l string = text string to print with optional variable names :l zero or more keyword/value pairs may be appended :l keyword = {file} or {append} or {screen} or {title} :l @@ -40,6 +40,21 @@ If it contains variables it must be enclosed in double quotes to insure they are not evaluated when the input script line is read, but will instead be evaluated each time the string is printed. +Instead of a numeric value, N can be specified as an "equal-style +variable"_variable.html, which should be specified as v_name, where +name is the variable name. In this case, the variable is evaluated at +the beginning of a run to determine the [next] timestep at which the +string will be written out. On that timestep, the variable will be +evaluated again to determine the next timestep, etc. +Thus the variable should return timestep values. See the stagger() +and logfreq() and stride() math functions for "equal-style +variables"_variable.html, as examples of useful functions to use in +this context. For example, the following commands will print output at +timesteps 10,20,30,100,200,300,1000,2000,etc: + +variable s equal logfreq(10,3,10) +fix extra all print v_s "Coords of marker atom = $x $y $z" :pre + The specified group-ID is ignored by this fix. See the "variable"_variable.html command for a description of {equal} diff --git a/doc/src/fix_setforce.txt b/doc/src/fix_setforce.txt index 4b9abba52f..63713d87c2 100644 --- a/doc/src/fix_setforce.txt +++ b/doc/src/fix_setforce.txt @@ -8,6 +8,7 @@ fix setforce command :h3 fix setforce/kk command :h3 +fix setforce/spin command :h3 [Syntax:] @@ -27,6 +28,7 @@ keyword = {region} :l fix freeze indenter setforce 0.0 0.0 0.0 fix 2 edge setforce NULL 0.0 0.0 +fix 1 edge setforce/spin 0.0 0.0 0.0 fix 2 edge setforce NULL 0.0 v_oscillate :pre [Description:] @@ -65,6 +67,19 @@ to it. :line +Style {spin} suffix sets the components of the magnetic precession +vectors instead of the mechanical forces. This also erases all +previously computed magnetic precession vectors on the atom, though +additional magnetic fixes could add new forces. + +This command can be used to freeze the magnetic moment of certain +atoms in the simulation by zeroing their precession vector. + +All options defined above remain valid, they just apply to the magnetic +precession vectors instead of the forces. + +:line + Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -117,7 +132,10 @@ forces to any value besides zero when performing a minimization. Use the "fix addforce"_fix_addforce.html command if you want to apply a non-zero force to atoms during a minimization. -[Restrictions:] none +[Restrictions:] + +The fix {setforce/spin} only makes sense when LAMMPS was built with the +SPIN package. [Related commands:] diff --git a/doc/src/fix_wall_gran.txt b/doc/src/fix_wall_gran.txt index b517d48cca..4b3ff15cc9 100644 --- a/doc/src/fix_wall_gran.txt +++ b/doc/src/fix_wall_gran.txt @@ -17,13 +17,13 @@ wall/gran = style name of this fix command :l fstyle = style of force interactions between particles and wall :l possible choices: hooke, hooke/history, hertz/history, granular :pre fstyle_params = parameters associated with force interaction style :l - For {hooke}, {hooke/history}, and {hertz/history}, {fstyle_params} are: - Kn = elastic constant for normal particle repulsion (force/distance units or pressure units - see discussion below) - Kt = elastic constant for tangential contact (force/distance units or pressure units - see discussion below) - gamma_n = damping coefficient for collisions in normal direction (1/time units or 1/time-distance units - see discussion below) - gamma_t = damping coefficient for collisions in tangential direction (1/time units or 1/time-distance units - see discussion below) - xmu = static yield criterion (unitless value between 0.0 and 1.0e4) - dampflag = 0 or 1 if tangential damping force is excluded or included :pre + For {hooke}, {hooke/history}, and {hertz/history}, {fstyle_params} are: + Kn = elastic constant for normal particle repulsion (force/distance units or pressure units - see discussion below) + Kt = elastic constant for tangential contact (force/distance units or pressure units - see discussion below) + gamma_n = damping coefficient for collisions in normal direction (1/time units or 1/time-distance units - see discussion below) + gamma_t = damping coefficient for collisions in tangential direction (1/time units or 1/time-distance units - see discussion below) + xmu = static yield criterion (unitless value between 0.0 and 1.0e4) + dampflag = 0 or 1 if tangential damping force is excluded or included :pre For {granular}, {fstyle_params} are set using the same syntax as for the {pair_coeff} command of "pair_style granular"_pair_granular.html :pre wallstyle = {xplane} or {yplane} or {zplane} or {zcylinder} :l args = list of arguments for a particular style :l @@ -46,10 +46,10 @@ keyword = {wiggle} or {shear} :l fix 1 all wall/gran hooke 200000.0 NULL 50.0 NULL 0.5 0 xplane -10.0 10.0 fix 1 all wall/gran hooke/history 200000.0 NULL 50.0 NULL 0.5 0 zplane 0.0 NULL -fix 2 all wall/gran hooke 100000.0 20000.0 50.0 30.0 0.5 1 zcylinder 15.0 wiggle z 3.0 2.0 -fix 3 all wall/gran granular hooke 1000.0 50.0 tangential linear_nohistory 1.0 0.4 zplane 0.0 NULL -fix 4 all wall/gran granular jkr 1000.0 50.0 0.3 5.0 tangential mindlin 800.0 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall zcylinder 15.0 wiggle z 3.0 2.0 -fix 5 all wall/gran granular dmt 1000.0 50.0 0.3 10.0 tangential mindlin 800.0 0.5 0.1 roll sds 500.0 200.0 0.1 twisting marshall zplane 0.0 NULL :pre +fix 2 all wall/gran hooke 100000.0 20000.0 50.0 30.0 0.5 1 zcylinder 15.0 wiggle z 3.0 2.0 +fix 3 all wall/gran/region granular hooke 1000.0 50.0 tangential linear_nohistory 1.0 0.4 damping velocity region myBox +fix 4 all wall/gran/region granular jkr 1e5 1500.0 0.3 10.0 tangential mindlin NULL 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall region myCone +fix 5 all wall/gran/region granular dmt 1e5 0.2 0.3 10.0 tangential mindlin NULL 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall damping tsuji region myCone :pre [Description:] diff --git a/doc/src/fix_wall_gran_region.txt b/doc/src/fix_wall_gran_region.txt index 8a39d6b642..50dad364e0 100644 --- a/doc/src/fix_wall_gran_region.txt +++ b/doc/src/fix_wall_gran_region.txt @@ -17,23 +17,23 @@ wall/region = style name of this fix command :l fstyle = style of force interactions between particles and wall :l possible choices: hooke, hooke/history, hertz/history, granular :pre fstyle_params = parameters associated with force interaction style :l - For {hooke}, {hooke/history}, and {hertz/history}, {fstyle_params} are: - Kn = elastic constant for normal particle repulsion (force/distance units or pressure units - see discussion below) - Kt = elastic constant for tangential contact (force/distance units or pressure units - see discussion below) - gamma_n = damping coefficient for collisions in normal direction (1/time units or 1/time-distance units - see discussion below) - gamma_t = damping coefficient for collisions in tangential direction (1/time units or 1/time-distance units - see discussion below) - xmu = static yield criterion (unitless value between 0.0 and 1.0e4) - dampflag = 0 or 1 if tangential damping force is excluded or included :pre + For {hooke}, {hooke/history}, and {hertz/history}, {fstyle_params} are: + Kn = elastic constant for normal particle repulsion (force/distance units or pressure units - see discussion below) + Kt = elastic constant for tangential contact (force/distance units or pressure units - see discussion below) + gamma_n = damping coefficient for collisions in normal direction (1/time units or 1/time-distance units - see discussion below) + gamma_t = damping coefficient for collisions in tangential direction (1/time units or 1/time-distance units - see discussion below) + xmu = static yield criterion (unitless value between 0.0 and 1.0e4) + dampflag = 0 or 1 if tangential damping force is excluded or included :pre For {granular}, {fstyle_params} are set using the same syntax as for the {pair_coeff} command of "pair_style granular"_pair_granular.html :pre wallstyle = region (see "fix wall/gran"_fix_wall_gran.html for options for other kinds of walls) :l region-ID = region whose boundary will act as wall :l,ule [Examples:] -fix wall all wall/gran/region hooke/history 1000.0 200.0 200.0 100.0 0.5 1 region myCone -fix 3 all wall/gran/region granular hooke 1000.0 50.0 tangential linear_nohistory 1.0 0.4 region myBox -fix 4 all wall/gran/region granular jkr 1000.0 50.0 tangential linear_history 800.0 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall region myCone -fix 5 all wall/gran/region granular dmt 1000.0 50.0 0.3 10.0 tangential linear_history 800.0 0.5 0.1 roll sds 500.0 200.0 0.1 twisting marshall region myCone :pre +fix wall all wall/gran/region hooke/history 1000.0 200.0 200.0 100.0 0.5 1 region myCone +fix 3 all wall/gran/region granular hooke 1000.0 50.0 tangential linear_nohistory 1.0 0.4 damping velocity region myBox +fix 4 all wall/gran/region granular jkr 1e5 1500.0 0.3 10.0 tangential mindlin NULL 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall region myCone +fix 5 all wall/gran/region granular dmt 1e5 0.2 0.3 10.0 tangential mindlin NULL 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall damping tsuji region myCone :pre [Description:] diff --git a/doc/src/fixes.txt b/doc/src/fixes.txt index d77acf946d..d966b9a225 100644 --- a/doc/src/fixes.txt +++ b/doc/src/fixes.txt @@ -84,6 +84,7 @@ Fixes :h1 fix_msst fix_mvv_dpd fix_neb + fix_neb_spin fix_nh fix_nh_eff fix_nh_uef diff --git a/doc/src/lammps.book b/doc/src/lammps.book index e97ef4b994..2738c9b051 100644 --- a/doc/src/lammps.book +++ b/doc/src/lammps.book @@ -179,6 +179,7 @@ min_spin.html minimize.html molecule.html neb.html +neb_spin.html neigh_modify.html neighbor.html newton.html @@ -309,6 +310,7 @@ fix_mscg.html fix_msst.html fix_mvv_dpd.html fix_neb.html +fix_neb_spin.html fix_nh.html fix_nh_eff.html fix_nph_asphere.html @@ -572,6 +574,8 @@ pair_dipole.html pair_dpd.html pair_dpd_fdt.html pair_dsmc.html +pair_e3b.html +pair_drip.html pair_eam.html pair_edip.html pair_eff.html diff --git a/doc/src/lattice.txt b/doc/src/lattice.txt index 6f16dc5432..3b50dc044b 100644 --- a/doc/src/lattice.txt +++ b/doc/src/lattice.txt @@ -124,7 +124,7 @@ so that they describe a tilted parallelepiped. Via the {basis} keyword you add atoms, one at a time, to the unit cell. Its arguments are fractional coordinates (0.0 <= x,y,z < 1.0). The position vector x of a basis atom within the unit cell is thus a linear combination of -the the unit cell's 3 edge vectors, i.e. x = bx a1 + by a2 + bz a3, +the unit cell's 3 edge vectors, i.e. x = bx a1 + by a2 + bz a3, where bx,by,bz are the 3 values specified for the {basis} keyword. :line diff --git a/doc/src/molecule.txt b/doc/src/molecule.txt index 4c066b5e2e..e8b6bd8a7e 100644 --- a/doc/src/molecule.txt +++ b/doc/src/molecule.txt @@ -396,7 +396,7 @@ If flag = 0, no a,b,c,d values are listed on the line, just the If flag = 1, a,b,c are listed, where a = ID of central atom in the angle, and b,c the other two atoms in the angle. -If flag = 2, a,b are listed, where a = ID of atom in bond with the the +If flag = 2, a,b are listed, where a = ID of atom in bond with the lowest ID, and b = ID of atom in bond with the highest ID. If flag = 3, a,b,c are listed, where a = ID of central atom, diff --git a/doc/src/neb_spin.txt b/doc/src/neb_spin.txt new file mode 100644 index 0000000000..7dbd924cd2 --- /dev/null +++ b/doc/src/neb_spin.txt @@ -0,0 +1,375 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +neb/spin command :h3 + +[Syntax:] + +neb/spin etol ttol N1 N2 Nevery file-style arg keyword :pre + +etol = stopping tolerance for energy (energy units) :ulb,l +ttol = stopping tolerance for torque ( units) :l +N1 = max # of iterations (timesteps) to run initial NEB :l +N2 = max # of iterations (timesteps) to run barrier-climbing NEB :l +Nevery = print replica energies and reaction coordinates every this many timesteps :l +file-style = {final} or {each} or {none} :l + {final} arg = filename + filename = file with initial coords for final replica + coords for intermediate replicas are linearly interpolated + between first and last replica + {each} arg = filename + filename = unique filename for each replica (except first) + with its initial coords + {none} arg = no argument all replicas assumed to already have + their initial coords :pre +keyword = {verbose} +:ule + +[Examples:] + +neb/spin 0.1 0.0 1000 500 50 final coords.final +neb/spin 0.0 0.001 1000 500 50 each coords.initial.$i +neb/spin 0.0 0.001 1000 500 50 none verbose :pre + +[Description:] + +Perform a geodesic nudged elastic band (GNEB) calculation using multiple +replicas of a system. Two or more replicas must be used; the first +and last are the end points of the transition path. + +GNEB is a method for finding both the spin configurations and height +of the energy barrier associated with a transition state, e.g. +spins to perform a collective rotation from one energy basin to +another. +The implementation in LAMMPS follows the discussion in the +following paper: "(BessarabA)"_#BessarabA. + +Each replica runs on a partition of one or more processors. Processor +partitions are defined at run-time using the "-partition command-line +switch"_Run_options.html. Note that if you have MPI installed, you +can run a multi-replica simulation with more replicas (partitions) +than you have physical processors, e.g you can run a 10-replica +simulation on just one or two processors. You will simply not get the +performance speed-up you would see with one or more physical +processors per replica. See the "Howto replica"_Howto_replica.html +doc page for further discussion. + +NOTE: As explained below, a GNEB calculation performs a damped dynamics +minimization across all the replicas. The "spin"_min_spin.html +style minimizer has to be defined in your input script. + +When a GNEB calculation is performed, it is assumed that each replica +is running the same system, though LAMMPS does not check for this. +I.e. the simulation domain, the number of magnetic atoms, the +interaction potentials, and the starting configuration when the neb +command is issued should be the same for every replica. + +In a GNEB calculation each replica is connected to other replicas by +inter-replica nudging forces. These forces are imposed by the "fix +neb/spin"_fix_neb_spin.html command, which must be used in conjunction +with the neb command. +The group used to define the fix neb/spin command defines the +GNEB magnetic atoms which are the only ones that inter-replica springs +are applied to. +If the group does not include all magnetic atoms, then non-GNEB +magnetic atoms have no inter-replica springs and the torques they feel +and their precession motion is computed in the usual way due only +to other magnetic atoms within their replica. +Conceptually, the non-GNEB atoms provide a background force field for +the GNEB atoms. +Their magnetic spins can be allowed to evolve during the GNEB +minimization procedure. + +The initial spin configuration for each of the replicas can be +specified in different manners via the {file-style} setting, as +discussed below. Only atomic spins whose initial coordinates should +differ from the current configuration need to be specified. + +Conceptually, the initial and final configurations for the first +replica should be states on either side of an energy barrier. + +As explained below, the initial configurations of intermediate +replicas can be spin coordinates interpolated in a linear fashion +between the first and last replicas. This is often adequate for +simple transitions. For more complex transitions, it may lead to slow +convergence or even bad results if the minimum energy path (MEP, see +below) of states over the barrier cannot be correctly converged to +from such an initial path. In this case, you will want to generate +initial states for the intermediate replicas that are geometrically +closer to the MEP and read them in. + +:line + +For a {file-style} setting of {final}, a filename is specified which +contains atomic and spin coordinates for zero or more atoms, in the +format described below. +For each atom that appears in the file, the new coordinates are +assigned to that atom in the final replica. Each intermediate replica +also assigns a new spin to that atom in an interpolated manner. +This is done by using the current direction of the spin at the starting +point and the read-in direction as the final point. +The "angular distance" between them is calculated, and the new direction +is assigned to be a fraction of the angular distance. + +NOTE: The "angular distance" between the starting and final point is +evaluated in the geodesic sense, as described in +"(BessarabA)"_#BessarabA. + +NOTE: The angular interpolation between the starting and final point +is achieved using Rodrigues formula: + +:c,image(Eqs/neb_spin_rodrigues_formula.jpg) + +where m_i^I is the initial spin configuration for the spin i, +omega_i^nu is a rotation angle defined as: + +:c,image(Eqs/neb_spin_angle.jpg) + +with nu the image number, Q the total number of images, and +omega_i the total rotation between the initial and final spins. +k_i defines a rotation axis such as: + +:c,image(Eqs/neb_spin_k.jpg) + +if the initial and final spins are not aligned. +If the initial and final spins are aligned, then their cross +product is null, and the expression above does not apply. +If they point toward the same direction, the intermediate images +conserve the same orientation. +If the initial and final spins are aligned, but point toward +opposite directions, an arbitrary rotation vector belonging to +the plane perpendicular to initial and final spins is chosen. +In this case, a warning message is displayed. + +For a {file-style} setting of {each}, a filename is specified which is +assumed to be unique to each replica. +See the "neb"_neb.html documentation page for more information about this +option. + +For a {file-style} setting of {none}, no filename is specified. Each +replica is assumed to already be in its initial configuration at the +time the neb command is issued. This allows each replica to define +its own configuration by reading a replica-specific data or restart or +dump file, via the "read_data"_read_data.html, +"read_restart"_read_restart.html, or "read_dump"_read_dump.html +commands. The replica-specific names of these files can be specified +as in the discussion above for the {each} file-style. Also see the +section below for how a NEB calculation can produce restart files, so +that a long calculation can be restarted if needed. + +NOTE: None of the {file-style} settings change the initial +configuration of any atom in the first replica. The first replica +must thus be in the correct initial configuration at the time the neb +command is issued. + +:line + +A NEB calculation proceeds in two stages, each of which is a +minimization procedure, performed via damped dynamics. To enable +this, you must first define a damped spin dynamics +"min_style"_min_style.html, using the {spin} style (see +"min_spin"_min_spin.html for more information). +The other styles cannot be used, since they relax the lattice +degrees of freedom instead of the spins. + +The minimizer tolerances for energy and force are set by {etol} and +{ttol}, the same as for the "minimize"_minimize.html command. + +A non-zero {etol} means that the GNEB calculation will terminate if the +energy criterion is met by every replica. The energies being compared +to {etol} do not include any contribution from the inter-replica +nudging forces, since these are non-conservative. A non-zero {ttol} +means that the GNEB calculation will terminate if the torque criterion +is met by every replica. The torques being compared to {ttol} include +the inter-replica nudging forces. + +The maximum number of iterations in each stage is set by {N1} and +{N2}. These are effectively timestep counts since each iteration of +damped dynamics is like a single timestep in a dynamics +"run"_run.html. During both stages, the potential energy of each +replica and its normalized distance along the reaction path (reaction +coordinate RD) will be printed to the screen and log file every +{Nevery} timesteps. The RD is 0 and 1 for the first and last replica. +For intermediate replicas, it is the cumulative angular distance +(normalized by the total cumulative angular distance) between adjacent +replicas, where "distance" is defined as the length of the 3N-vector of +the geodesic distances in spin coordinates, with N the number of +GNEB spins involved (see equation (13) in "(BessarabA)"_#BessarabA). +These outputs allow you to monitor NEB's progress in +finding a good energy barrier. {N1} and {N2} must both be multiples +of {Nevery}. + +In the first stage of GNEB, the set of replicas should converge toward +a minimum energy path (MEP) of conformational states that transition +over a barrier. The MEP for a transition is defined as a sequence of +3N-dimensional spin states, each of which has a potential energy +gradient parallel to the MEP itself. +The configuration of highest energy along a MEP corresponds to a saddle +point. The replica states will also be roughly equally spaced along +the MEP due to the inter-replica nudging force added by the +"fix neb"_fix_neb.html command. + +In the second stage of GNEB, the replica with the highest energy is +selected and the inter-replica forces on it are converted to a force +that drives its spin coordinates to the top or saddle point of the +barrier, via the barrier-climbing calculation described in +"(BessarabA)"_#BessarabA. As before, the other replicas rearrange +themselves along the MEP so as to be roughly equally spaced. + +When both stages are complete, if the GNEB calculation was successful, +the configurations of the replicas should be along (close to) the MEP +and the replica with the highest energy should be a spin +configuration at (close to) the saddle point of the transition. The +potential energies for the set of replicas represents the energy +profile of the transition along the MEP. + +:line + +An atom map must be defined which it is not by default for "atom_style +atomic"_atom_style.html problems. The "atom_modify +map"_atom_modify.html command can be used to do this. + +An initial value can be defined for the timestep. Although, the {spin} +minimization algorithm is an adaptive timestep methodology, so that +this timestep is likely to evolve during the calculation. + +The minimizers in LAMMPS operate on all spins in your system, even +non-GNEB atoms, as defined above. + +:line + +Each file read by the neb/spin command containing spin coordinates used +to initialize one or more replicas must be formatted as follows. + +The file can be ASCII text or a gzipped text file (detected by a .gz +suffix). The file can contain initial blank lines or comment lines +starting with "#" which are ignored. The first non-blank, non-comment +line should list N = the number of lines to follow. The N successive +lines contain the following information: + +ID1 g1 x1 y1 z1 sx1 sy1 sz1 +ID2 g2 x2 y2 z2 sx2 sy2 sz2 +... +IDN gN yN zN sxN syN szN :pre + +The fields are the atom ID, the norm of the associated magnetic spin, +followed by the {x,y,z} coordinates and the {sx,sy,sz} spin coordinates. +The lines can be listed in any order. Additional trailing information on +the line is OK, such as a comment. + +Note that for a typical GNEB calculation you do not need to specify +initial spin coordinates for very many atoms to produce differing starting +and final replicas whose intermediate replicas will converge to the +energy barrier. Typically only new spin coordinates for atoms +geometrically near the barrier need be specified. + +Also note there is no requirement that the atoms in the file +correspond to the GNEB atoms in the group defined by the "fix +neb"_fix_neb.html command. Not every GNEB atom need be in the file, +and non-GNEB atoms can be listed in the file. + +:line + +Four kinds of output can be generated during a GNEB calculation: energy +barrier statistics, thermodynamic output by each replica, dump files, +and restart files. + +When running with multiple partitions (each of which is a replica in +this case), the print-out to the screen and master log.lammps file +contains a line of output, printed once every {Nevery} timesteps. It +contains the timestep, the maximum torque per replica, the maximum +torque per atom (in any replica), potential gradients in the initial, +final, and climbing replicas, the forward and backward energy +barriers, the total reaction coordinate (RDT), and the normalized +reaction coordinate and potential energy of each replica. + +The "maximum torque per replica" is the two-norm of the +3N-length vector given by the cross product of a spin by its +precession vector omega, in each replica, maximized across replicas, +which is what the {ttol} setting is checking against. In this case, N is +all the atoms in each replica. The "maximum torque per atom" is the +maximum torque component of any atom in any replica. The potential +gradients are the two-norm of the 3N-length magnetic precession vector +solely due to the interaction potential i.e. without adding in +inter-replica forces, and projected along the path tangent (as detailed +in Appendix D of "(BessarabA)"_#BessarabA). + +The "reaction coordinate" (RD) for each replica is the two-norm of the +3N-length vector of geodesic distances between its spins and the preceding +replica's spins (see equation (13) of "(BessarabA)"_#BessarabA), added to +the RD of the preceding replica. The RD of the first replica RD1 = 0.0; +the RD of the final replica RDN = RDT, the total reaction coordinate. +The normalized RDs are divided by RDT, so that they form a monotonically +increasing sequence from zero to one. When computing RD, N only includes +the spins being operated on by the fix neb/spin command. + +The forward (reverse) energy barrier is the potential energy of the +highest replica minus the energy of the first (last) replica. + +Supplementary information for all replicas can be printed out to the +screen and master log.lammps file by adding the verbose keyword. This +information include the following. +The "GradVidottan" are the projections of the potential gradient for +the replica i on its tangent vector (as detailed in Appendix D of +"(BessarabA)"_#BessarabA). +The "DNi" are the non normalized geodesic distances (see equation (13) +of "(BessarabA)"_#BessarabA), between a replica i and the next replica +i+1. For the last replica, this distance is not defined and a "NAN" +value is the corresponding output. + +When a NEB calculation does not converge properly, the supplementary +information can help understanding what is going wrong. + +When running on multiple partitions, LAMMPS produces additional log +files for each partition, e.g. log.lammps.0, log.lammps.1, etc. For a +GNEB calculation, these contain the thermodynamic output for each +replica. + +If "dump"_dump.html commands in the input script define a filename +that includes a {universe} or {uloop} style "variable"_variable.html, +then one dump file (per dump command) will be created for each +replica. At the end of the GNEB calculation, the final snapshot in +each file will contain the sequence of snapshots that transition the +system over the energy barrier. Earlier snapshots will show the +convergence of the replicas to the MEP. + +Likewise, "restart"_restart.html filenames can be specified with a +{universe} or {uloop} style "variable"_variable.html, to generate +restart files for each replica. These may be useful if the GNEB +calculation fails to converge properly to the MEP, and you wish to +restart the calculation from an intermediate point with altered +parameters. + +A c file script in provided in the tool/spin/interpolate_gneb +directory, that interpolates the MEP given the information provided +by the verbose output option (as detailed in Appendix D of +"(BessarabA)"_#BessarabA). + +:line + +[Restrictions:] + +This command can only be used if LAMMPS was built with the SPIN +package. See the "Build package"_Build_package.html doc +page for more info. + +:line + +[Related commands:] + +"min/spin"_min_spin.html, "fix neb/spin"_fix_neb_spin.html + +[Default:] + +none + +:line + +:link(BessarabA) +[(BessarabA)] Bessarab, Uzdin, Jonsson, Comp Phys Comm, 196, +335-347 (2015). diff --git a/doc/src/neigh_modify.txt b/doc/src/neigh_modify.txt index 6c4218cff5..c97cb53e43 100644 --- a/doc/src/neigh_modify.txt +++ b/doc/src/neigh_modify.txt @@ -187,9 +187,9 @@ used in neighbor list construction to sort and find neighboring atoms. By default, for "neighbor style bin"_neighbor.html, LAMMPS uses bins that are 1/2 the size of the maximum pair cutoff. For "neighbor style multi"_neighbor.html, the bins are 1/2 the size of the minimum pair -cutoff. Typically these are good values values for minimizing the -time for neighbor list construction. This setting overrides the -default. If you make it too big, there is little overhead due to +cutoff. Typically these are good values for minimizing the time for +neighbor list construction. This setting overrides the default. +If you make it too big, there is little overhead due to looping over bins, but more atoms are checked. If you make it too small, the optimal number of atoms is checked, but bin overhead goes up. If you set the binsize to 0.0, LAMMPS will use the default diff --git a/doc/src/neighbor.txt b/doc/src/neighbor.txt index 3e590eaff1..4a60f957d4 100644 --- a/doc/src/neighbor.txt +++ b/doc/src/neighbor.txt @@ -56,7 +56,7 @@ bin size is set to 1/2 of the shortest cutoff distance and multiple sets of bins are defined to search over for different atom types. This imposes some extra setup overhead, but the searches themselves may be much faster for the short-cutoff cases. See the "comm_modify -mode multi"_comm_modify.html command for a communication option option +mode multi"_comm_modify.html command for a communication option that may also be beneficial for simulations of this kind. The "neigh_modify"_neigh_modify.html command has additional options diff --git a/doc/src/package.txt b/doc/src/package.txt index 2f17b2c7f3..dfdecab0a5 100644 --- a/doc/src/package.txt +++ b/doc/src/package.txt @@ -638,7 +638,7 @@ except "omp" and "mode", are ignored if LAMMPS was not built with Xeon Phi co-processor support. These settings are made automatically if the "-sf intel" "command-line switch"_Run_options.html is used. If it is not used, you must invoke the package intel command in your input -script or or via the "-pk intel" "command-line +script or via the "-pk intel" "command-line switch"_Run_options.html. For the KOKKOS package, the option defaults for GPUs are neigh = full, diff --git a/doc/src/pair_airebo.txt b/doc/src/pair_airebo.txt index 3708fb287d..4956ba7575 100644 --- a/doc/src/pair_airebo.txt +++ b/doc/src/pair_airebo.txt @@ -36,7 +36,7 @@ pair_style airebo/morse 3.0 pair_coeff * * ../potentials/CH.airebo-m H C :pre pair_style rebo -pair_coeff * * ../potentials/CH.airebo H C :pre +pair_coeff * * ../potentials/CH.rebo H C :pre [Description:] @@ -57,7 +57,8 @@ The {rebo} pair style computes the Reactive Empirical Bond Order (REBO) Potential of "(Brenner)"_#Brenner. Note that this is the so-called 2nd generation REBO from 2002, not the original REBO from 1990. As discussed below, 2nd generation REBO is closely related to the -initial AIREBO; it is just a subset of the potential energy terms. +initial AIREBO; it is just a subset of the potential energy terms +with a few slightly different parameters The AIREBO potential consists of three terms: @@ -113,12 +114,12 @@ various dihedral angle preferences in hydrocarbon configurations. :line Only a single pair_coeff command is used with the {airebo}, {airebo} -or {rebo} style which specifies an AIREBO or AIREBO-M potential file -with parameters for C and H. Note that the {rebo} style in LAMMPS -uses the same AIREBO-formatted potential file. These are mapped to -LAMMPS atom types by specifying N additional arguments after the -filename in the pair_coeff command, where N is the number of LAMMPS -atom types: +or {rebo} style which specifies an AIREBO, REBO, or AIREBO-M potential +file with parameters for C and H. Note that as of LAMMPS version +15 May 2019 the {rebo} style in LAMMPS uses its own potential +file (CH.rebo). These are mapped to LAMMPS atom types by specifying +N additional arguments after the filename in the pair_coeff command, +where N is the number of LAMMPS atom types: filename N element names = mapping of AIREBO elements to atom types :ul diff --git a/doc/src/pair_drip.txt b/doc/src/pair_drip.txt new file mode 100644 index 0000000000..84c92b04e4 --- /dev/null +++ b/doc/src/pair_drip.txt @@ -0,0 +1,141 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +pair_style drip command :h3 + +[Syntax:] + +pair_style hybrid/overlay drip \[styles ...\] :pre + +styles = other styles to be overlayed with drip (optional) :ul + +[Examples:] + +pair_style hybrid/overlay drip +pair_coeff * * none +pair_coeff * * drip C.drip C :pre + +pair_style hybrid/overlay drip rebo +pair_coeff * * drip C.drip C +pair_coeff * * rebo CH.airebo C :pre + +pair_style hybrid/overlay drip rebo +pair_coeff * * drip C.drip C NULL +pair_coeff * * rebo CH.airebo C H :pre + + +[Description:] + +Style {drip} computes the interlayer interactions of layered materials using +the dihedral-angle-corrected registry-dependent (DRIP) potential as described +in "(Wen)"_#Wen2018, which is based on the "(Kolmogorov)"_#Kolmogorov2005 +potential and provides an improved prediction for forces. +The total potential energy of a system is + +:c,image(Eqs/pair_drip.jpg) + +where the {r^-6} term models the attractive London dispersion, +the exponential term is designed to capture the registry effect due to +overlapping {pi} bonds, and {fc} is a cutoff function. + + +This potential (DRIP) only provides the interlayer interactions between +graphene layers. So, to perform a realistic simulation, it should be used in +combination with an intralayer potential such as "REBO"_pair_airebo.html and +"Tersoff"_pair_tersoff.html. +To keep the intralayer interactions unaffected, we should avoid applying DRIP +to contribute energy to intralayer interactions. This can be achieved by +assigning different molecular IDs to atoms in different layers, and DRIP is +implemented such that only atoms with different molecular ID can interact with +each other. For this purpose, "atom style"_atom_style.html "molecular" or +"full" has to be used. + +On the other way around, "REBO"_pair_airebo.html ("Tersoff"_pair_tersoff.html +or any other potential used to provide the intralayer interactions) should not +interfere with the interlayer interactions described by DRIP. This is typically +automatically achieved using the commands provided in the {Examples} section +above, since the cutoff distance for carbon-carbon interaction in the intralayer +potentials (e.g. 2 Angstrom for "REBO"_pair_airebo.html) is much smaller than +the equilibrium layer distance of graphene layers (about 3.4 Angstrom). +If you want, you can enforce this by assigning different atom types to atoms in +different layers, and apply an intralayer potential to one atom type. +See "pair_hybrid"_pair_hybrid.html for details. + +:line + +The "pair_coeff"_pair_coeff.html command for DRIP takes {4+N} arguments, where +{N} is the number of LAMMPS atom types. The fist three arguments must be fixed +to be {* * drip}, the fourth argument is the path to the DRIP parameter file, +and the remaining N arguments specifying the mapping between element in the +parameter file and atom types. For example, if your LAMMPS simulation has 3 atom +types and you want all of them to be C, you would use the following pair_coeff +command: + +pair_coeff * * drip C.drip C C C :pre + +If a mapping value is specified as NULL, the mapping is not performed. This +could be useful when DRIP is used to model part of the system where other +element exists. Suppose you have a hydrocarbon system, with C of atom type 1 +and H of atom type 2, you can use the following command to inform DRIP not to +model H atoms: + +pair_style hybrid/overlay drip rebo +pair_coeff * * drip C.drip C NULL +pair_coeff * * rebo CH.airebo C H :pre + +NOTE: The potential parameters developed in "(Wen)"_#Wen2018 are provided with +LAMMPS (see the "potentials" directory). Besides those in "Wen"_#Wen2018, an +additional parameter "normal_cutoff", specific to the LAMMPS implementation, is +used to find the three nearest neighbors of an atom to construct the normal. + + +:line + +[Mixing, shift, table, tail correction, and restart info]: + +This pair style does not support the pair_modify mix, shift, table, +and tail options. + +This pair style does not write their information to binary restart files, since +it is stored in potential files. Thus, you need to re-specify the pair_style and +pair_coeff commands in an input script that reads a restart file. + +[Restrictions:] + +This pair style is part of the USER-MISC package. It is only enabled if LAMMPS +was built with that package. See the "Build package"_Build_package.html doc +page for more info. + +This pair potential requires the "newton"_newton.html setting to be "on" for +pair interactions. + + +The {C.drip} parameter file provided with LAMMPS (see the "potentials" +directory) is parameterized for metal "units"_units.html. You can use the DRIP +potential with any LAMMPS units, but you would need to create your own custom +parameter file with coefficients listed in the appropriate units, if your +simulation doesn't use "metal" units. + + +[Related commands:] + +"pair_style lebedeva_z"_pair_lebedeva_z.html, +"pair_style kolmogorov/crespi/z"_pair_kolmogorov_crespi_z.html, +"pair_style kolmogorov/crespi/full"_pair_kolmogorov_crespi_full.html, +"pair_style ilp/graphene/hbn"_pair_ilp_graphene_hbn.html. + + +:line + +:link(Wen2018) +[(Wen)] M. Wen, S. Carr, S. Fang, E. Kaxiras, and E. B. Tadmor, Phys. Rev. B, +98, 235404 (2018) + +:link(Kolmogorov2005) +[(Kolmogorov)] A. N. Kolmogorov, V. H. Crespi, Phys. Rev. B 71, 235415 (2005) + diff --git a/doc/src/pair_e3b.txt b/doc/src/pair_e3b.txt new file mode 100644 index 0000000000..fe4349a57d --- /dev/null +++ b/doc/src/pair_e3b.txt @@ -0,0 +1,140 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +pair_style e3b command :h3 + +[Syntax:] + +pair_style e3b Otype :pre +Otype = atom type for oxygen :l + +pair_coeff * * keyword :pre +one or more keyword/value pairs must be appended. :l +keyword = {preset} or {Ea} or {Eb} or {Ec} or {E2} or {K3} or {K2} or {Rs} or {Rc3} or {Rc2} or {bondL} or {neigh} :l +If the {preset} keyword is given, no others are needed. +Otherwise, all are mandatory except for {neigh}. +The {neigh} keyword is always optional. :l + {preset} arg = {2011} or {2015} = which set of predefined parameters to use + 2011 = use the potential parameters from "(Tainter 2011)"_#Tainter2011 + 2015 = use the potential parameters from "(Tainter 2015)"_#Tainter2015 + {Ea} arg = three-body energy for type A hydrogen bonding interactions (energy units) + {Eb} arg = three-body energy for type B hydrogen bonding interactions (energy units) + {Ec} arg = three-body energy for type C hydrogen bonding interactions (energy units) + {E2} arg = two-body energy correction (energy units) + {K3} arg = three-body exponential constant (inverse distance units) + {K2} arg = two-body exponential constant (inverse distance units) + {Rc3} arg = three-body cutoff (distance units) + {Rc2} arg = two-body cutoff (distance units) + {Rs} arg = three-body switching function cutoff (distance units) + {bondL} arg = intramolecular OH bond length (distance units) + {neigh} arg = approximate integer number of molecules within Rc3 of an oxygen atom :pre + +[Examples:] + +pair_style e3b 1 +pair_coeff * * Ea 35.85 Eb -240.2 Ec 449.3 E2 108269.9 K3 1.907 K2 4.872 Rc3 5.2 Rc2 5.2 Rs 5.0 bondL 0.9572 :pre + +pair_style hybrid/overlay e3b 1 lj/cut/tip4p/long 1 2 1 1 0.15 8.5 +pair_coeff * * e3b preset 2011 :pre + +[Description:] + +The {e3b} style computes an \"explicit three-body\" (E3B) potential for water "(Kumar 2008)"_#Kumar. + +:c,image(Eqs/e3b.jpg) + +This potential was developed as a water model that includes the three-body cooperativity of hydrogen bonding explicitly. +To use it in this way, it must be applied in conjunction with a conventional two-body water model, through {pair_style hybrid/overlay}. +The three body interactions are split into three types: A, B, and C. +Type A corresponds to anti-cooperative double hydrogen bond donor interactions. +Type B corresponds to the cooperative interaction of molecules that both donate and accept a hydrogen bond. +Type C corresponds to anti-cooperative double hydrogen bond acceptor interactions. +The three-body interactions are smoothly cutoff by the switching function s(r) between Rs and Rc3. +The two-body interactions are designed to correct for the effective many-body interactions implicitly included in the conventional two-body potential. +The two-body interactions are cut off sharply at Rc2, because K3 is typically significantly smaller than K2. +See "(Kumar 2008)"_#Kumar for more details. + +Only a single {pair_coeff} command is used with the {e3b} style. +The 1st two arguments must be * *. +The oxygen atom type for the pair style is passed as the only argument to the {pair_style} command, not in the {pair_coeff} command. +The hydrogen atom type is inferred by the ordering of the atoms. + +NOTE: Every atom of type Otype must be part of a water molecule. +Each water molecule must have consecutive IDs with the oxygen first. +This pair style does not test that this criteria is met. + +The {pair_coeff} command must have at least one keyword/value pair, as described above. +The {preset} keyword sets the potential parameters to the values used in "(Tainter 2011)"_#Tainter2011 or "(Tainter 2015)"_#Tainter2015. +To use the water models defined in those references, the {e3b} style should always be used in conjunction with an {lj/cut/tip4p/long} style through {pair_style hybrid/overlay}, as demonstrated in the second example above. +The {preset 2011} option should be used with the "TIP4P water model"_Howto_tip4p.html. +The {preset 2015} option should be used with the "TIP4P/2005 water model"_Howto_tip4p.html. +If the {preset} keyword is used, no other keyword is needed. +Changes to the preset parameters can be made by specifying the {preset} keyword followed by the specific parameter to change, like {Ea}. +Note that the other keywords must come after {preset} in the pair_style command. +The {e3b} style can also be used to implement any three-body potential of the same form by specifying all the keywords except {neigh}: {Ea}, {Eb}, {Ec}, {E2}, {K3}, {K2}, {Rc3}, {Rc2}, {Rs}, and {bondL}. +The keyword {bondL} specifies the intramolecular OH bond length of the water model being used. +This is needed to include H atoms that are within the cutoff even when the attached oxygen atom is not. + +This pair style allocates arrays sized according to the number of pairwise interactions within Rc3. +To do this it needs an estimate for the number of water molecules within Rc3 of an oxygen atom. +This estimate defaults to 10 and can be changed using the {neigh} keyword, which takes an integer as an argument. +If the neigh setting is too small, the simulation will fail with the error "neigh is too small". +If the neigh setting is too large, the pair style will use more memory than necessary. + +This pair style tallies a breakdown of the total E3B potential energy into sub-categories, which can be accessed via the "compute pair"_compute_pair.html command as a vector of values of length 4. +The 4 values correspond to the terms in the first equation above: the E2 term, the Ea term, the Eb term, and the Ec term. + +See the examples/USER/e3b directory for a complete example script. + +:line + +[Mixing, shift, table, tail correction, restart, rRESPA info]: + +This pair style does not support the "pair_modify"_pair_modify.html +shift, table, and tail options. + +This pair style does not write its information to "binary restart +files"_restart.html, since it is stored in potential files. Thus, you +need to re-specify the pair_style and pair_coeff commands in an input +script that reads a restart file. + +This pair style is incompatible with "respa"_run_style.html. + +:line + +[Restrictions:] + +This pair style is part of the USER-MISC package. It is only enabled +if LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. + +This pair style requires the "newton"_newton.html setting to be "on" +for pair interactions. + +This pair style requires a fixed number of atoms in the simulation, so it is incompatible with fixes like "fix deposit"_fix_deposit.html. +If the number of atoms changes between runs, this pair style must be re-initialized by calling the {pair_style} and {pair_coeffs} commands. +This is not a fundamental limitation of the pair style, but the code currently does not support a variable number of atoms. + +The {preset} keyword currently only works with real, metal, si, and cgs "units"_units.html. + +[Related commands:] + +"pair_coeff"_pair_coeff.html, "compute pair"_compute_pair.html + +[Default:] + +The option default for the {neigh} keyword is 10. + +:line + +:link(Kumar) +[(Kumar)] Kumar and Skinner, J. Phys. Chem. B, 112, 8311 (2008) +:link(Tainter2011) +[(Tainter 2011)] Tainter, Pieniazek, Lin, and Skinner, J. Chem. Phys., 134, 184501 (2011) +:link(Tainter2015) +[(Tainter 2015)] Tainter, Shi, and Skinner, 11, 2268 (2015) diff --git a/doc/src/pair_fep_soft.txt b/doc/src/pair_fep_soft.txt index d5e848cd1e..0cf2519c73 100644 --- a/doc/src/pair_fep_soft.txt +++ b/doc/src/pair_fep_soft.txt @@ -201,7 +201,7 @@ model. The usage of the TIP4P pair style is documented in the "pair_lj"_pair_lj.html styles. In the soft version the parameters n, alpha_LJ and alpha_C are set in the "pair_style"_pair_style.html command, after the specific parameters of the TIP4P water model and before the cutoffs. The -activation parameter lambda is supplied as an argument of the the +activation parameter lambda is supplied as an argument of the "pair_coeff"_pair_coeff.html command, after epsilon and sigma and before the optional cutoffs. @@ -210,7 +210,7 @@ Style {lj/charmm/coul/long/soft} implements a soft-core version of the modified "pair_lj_charmm"_pair_charmm.html style. In the soft version the parameters n, alpha_LJ and alpha_C are set in the "pair_style"_pair_style.html command, before the global cutoffs. The activation parameter lambda is introduced as an argument -of the the "pair_coeff"_pair_coeff.html command, after epsilon and sigma and +of the "pair_coeff"_pair_coeff.html command, after epsilon and sigma and before the optional eps14 and sigma14. Style {lj/class2/soft} implements a soft-core version of the 9-6 potential in diff --git a/doc/src/pair_granular.txt b/doc/src/pair_granular.txt index d287123246..f16cd9fe0b 100644 --- a/doc/src/pair_granular.txt +++ b/doc/src/pair_granular.txt @@ -24,22 +24,24 @@ cutoff = global cutoff (optional). See discussion below. :ul [Examples:] pair_style granular -pair_coeff * * hooke 1000.0 50.0 tangential linear_nohistory 1.0 0.4 :pre +pair_coeff * * hooke 1000.0 50.0 tangential linear_nohistory 1.0 0.4 damping mass_velocity :pre pair_style granular -pair_coeff * * hertz 1000.0 50.0 tangential mindlin NULL 1.0 0.4 :pre +pair_coeff * * hooke 1000.0 50.0 tangential linear_history 500.0 1.0 0.4 damping mass_velocity :pre pair_style granular -pair_coeff * * hertz/material 1e8 0.3 tangential mindlin_rescale NULL 1.0 0.4 damping tsuji :pre +pair_coeff * * hertz 1000.0 50.0 tangential mindlin 1000.0 1.0 0.4 :pre pair_style granular -pair_coeff 1 1 jkr 1000.0 50.0 tangential mindlin 800.0 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall -pair_coeff 2 2 hertz 200.0 20.0 tangential linear_history 300.0 1.0 0.1 rolling sds 200.0 100.0 0.1 twisting marshall :pre +pair_coeff * * hertz/material 1e8 0.3 0.3 tangential mindlin_rescale NULL 1.0 0.4 damping tsuji :pre pair_style granular -pair_coeff 1 1 hertz 1000.0 50.0 tangential mindlin 800.0 0.5 0.5 rolling sds 500.0 200.0 0.5 twisting marshall -pair_coeff 2 2 dmt 1000.0 50.0 0.3 10.0 tangential mindlin 800.0 0.5 0.1 roll sds 500.0 200.0 0.1 twisting marshall -pair_coeff 1 2 dmt 1000.0 50.0 0.3 10.0 tangential mindlin 800.0 0.5 0.1 roll sds 500.0 200.0 0.1 twisting marshall :pre +pair_coeff 1 * jkr 1000.0 500.0 0.3 10 tangential mindlin 800.0 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall +pair_coeff 2 2 hertz 200.0 100.0 tangential linear_history 300.0 1.0 0.1 rolling sds 200.0 100.0 0.1 twisting marshall :pre + +pair_style granular +pair_coeff 1 1 dmt 1000.0 50.0 0.3 0.0 tangential mindlin NULL 0.5 0.5 rolling sds 500.0 200.0 0.5 twisting marshall +pair_coeff 2 2 dmt 1000.0 50.0 0.3 10.0 tangential mindlin NULL 0.5 0.1 rolling sds 500.0 200.0 0.1 twisting marshall :pre [Description:] @@ -57,18 +59,18 @@ global, but can be set to different values for different combinations of particle types, as determined by the "pair_coeff"_pair_coeff.html command. If the contact model choice is the same for two particle types, the mixing for the cross-coefficients can be carried out -automatically. This is shown in the second example, where model +automatically. This is shown in the last example, where model choices are the same for type 1 - type 1 as for type 2 - type2 interactions, but coefficients are different. In this case, the -coefficients for type 2 - type interactions can be determined from +mixed coefficients for type 1 - type 2 interactions can be determined from mixing rules discussed below. For additional flexibility, coefficients as well as model forms can vary between particle types, -as shown in the third example: type 1- type 1 interactions are based -on a Hertzian normal contact model and 2-2 interactions are based on a -DMT cohesive model (see below). In that example, 1-1 and 2-2 -interactions have different model forms, in which case mixing of +as shown in the fourth example: type 1 - type 1 interactions are based +on a Johnson-Kendall-Roberts normal contact model and 2-2 interactions +are based on a DMT cohesive model (see below). In that example, 1-1 +and 2-2 interactions have different model forms, in which case mixing of coefficients cannot be determined, so 1-2 interactions must be -explicitly defined via the {pair_coeff 1 2} command, otherwise an +explicitly defined via the {pair_coeff 1 *} command, otherwise an error would result. :line @@ -189,6 +191,7 @@ other settings, potentially also the twisting damping). The options for the damping model currently supported are: {velocity} +{mass_velocity} {viscoelastic} {tsuji} :ol @@ -199,11 +202,23 @@ For {damping velocity}, the normal damping is simply equal to the user-specified damping coefficient in the {normal} model: \begin\{equation\} -\eta_n = \eta_\{n0\}\ +\eta_n = \eta_\{n0\} \end\{equation\} -Here, \(\gamma_n\) is the damping coefficient specified for the normal -contact model, in units of {mass}/{time}, +Here, \(\eta_\{n0\}\) is the damping coefficient specified for the normal +contact model, in units of {mass}/{time}. + +For {damping mass_velocity}, the normal damping is given by: + +\begin\{equation\} +\eta_n = \eta_\{n0\} m_\{eff\} +\end\{equation\} + +Here, \(\eta_\{n0\}\) is the damping coefficient specified for the normal +contact model, in units of {mass}/{time} and +\(m_\{eff\} = m_i m_j/(m_i + m_j)\) is the effective mass. +Use {damping mass_velocity} to reproduce the damping behavior of +{pair gran/hooke/*}. The {damping viscoelastic} model is based on the viscoelastic treatment of "(Brilliantov et al)"_#Brill1996, where the normal @@ -213,11 +228,10 @@ damping is given by: \eta_n = \eta_\{n0\}\ a m_\{eff\} \end\{equation\} -Here, \(m_\{eff\} = m_i m_j/(m_i + m_j)\) is the effective mass, {a} -is the contact radius, given by \(a =\sqrt\{R\delta\}\) for all models -except {jkr}, for which it is given implicitly according to \(delta = -a^2/R - 2\sqrt\{\pi \gamma a/E\}\). In this case, \eta_\{n0\}\ is in -units of 1/({time}*{distance}). +Here, {a} is the contact radius, given by \(a =\sqrt\{R\delta\}\) +for all models except {jkr}, for which it is given implicitly according +to \(\delta = a^2/R - 2\sqrt\{\pi \gamma a/E\}\). For {damping viscoelastic}, +\(\eta_\{n0\}\) is in units of 1/({time}*{distance}). The {tsuji} model is based on the work of "(Tsuji et al)"_#Tsuji1992. Here, the damping coefficient specified as part of @@ -564,6 +578,20 @@ Finally, the twisting torque on each particle is given by: :line +The {granular} pair style can reproduce the behavior of the +{pair gran/*} styles with the appropriate settings (some very +minor differences can be expected due to corrections in +displacement history frame-of-reference, and the application +of the torque at the center of the contact rather than +at each particle). The first example above +is equivalent to {pair gran/hooke 1000.0 NULL 50.0 50.0 0.4 1}. +The second example is equivalent to +{pair gran/hooke/history 1000.0 500.0 50.0 50.0 0.4 1}. +The third example is equivalent to +{pair gran/hertz/history 1000.0 500.0 50.0 50.0 0.4 1}. + +:line + LAMMPS automatically sets pairwise cutoff values for {pair_style granular} based on particle radii (and in the case of {jkr} pull-off distances). In the vast majority of situations, this is adequate. @@ -619,7 +647,7 @@ interactions is set to \(\mu_1\), and friction coefficient for type 2-type 2 interactions is set to \(\mu_2\), the friction coefficient for type1-type2 interactions is computed as \(\sqrt\{\mu_1\mu_2\}\) (unless explicitly specified to a different value by a {pair_coeff 1 2 -...} command. The exception to this is elastic modulus, only +...} command). The exception to this is elastic modulus, only applicable to {hertz/material}, {dmt} and {jkr} normal contact models. In that case, the effective elastic modulus is computed as: @@ -706,7 +734,7 @@ For the {pair_coeff} settings: {damping viscoelastic}, {rolling none}, J. M., & Poschel, T. (1996). Model for collisions in granular gases. Physical review E, 53(5), 5382. -:link(Tsuji1992) +:link(Tsuji1992) [(Tsuji et al, 1992)] Tsuji, Y., Tanaka, T., & Ishida, T. (1992). Lagrangian numerical simulation of plug flow of cohesionless particles in a horizontal pipe. Powder technology, 71(3), diff --git a/doc/src/pair_ilp_graphene_hbn.txt b/doc/src/pair_ilp_graphene_hbn.txt index 3a5d4accd5..4dd244c17f 100644 --- a/doc/src/pair_ilp_graphene_hbn.txt +++ b/doc/src/pair_ilp_graphene_hbn.txt @@ -21,7 +21,7 @@ pair_style hybrid/overlay ilp/graphene/hbn 16.0 1 pair_coeff * * ilp/graphene/hbn BNCH.ILP B N C :pre pair_style hybrid/overlay rebo tersoff ilp/graphene/hbn 16.0 coul/shield 16.0 -pair_coeff * * rebo CH.airebo NULL NULL C +pair_coeff * * rebo CH.rebo NULL NULL C pair_coeff * * tersoff BNC.tersoff B N NULL pair_coeff * * ilp/graphene/hbn BNCH.ILP B N C pair_coeff 1 1 coul/shield 0.70 @@ -50,11 +50,11 @@ calculating the normals. NOTE: This potential (ILP) is intended for interlayer interactions between two different layers of graphene, hexagonal boron nitride (h-BN) and their hetero-junction. To perform a realistic simulation, this potential must be used in combination with -intra-layer potential, such as "AIREBO"_pair_airebo.html or "Tersoff"_pair_tersoff.html potential. -To keep the intra-layer properties unaffected, the interlayer interaction +intralayer potential, such as "AIREBO"_pair_airebo.html or "Tersoff"_pair_tersoff.html potential. +To keep the intralayer properties unaffected, the interlayer interaction within the same layers should be avoided. Hence, each atom has to have a layer identifier such that atoms residing on the same layer interact via the -appropriate intra-layer potential and atoms residing on different layers +appropriate intralayer potential and atoms residing on different layers interact via the ILP. Here, the molecule id is chosen as the layer identifier, thus a data file with the "full" atom style is required to use this potential. @@ -117,6 +117,7 @@ units, if your simulation does not use {metal} units. "pair_coeff"_pair_coeff.html, "pair_none"_pair_none.html, "pair_style hybrid/overlay"_pair_hybrid.html, +"pair_style drip"_pair_drip.html, "pair_style pair_kolmogorov_crespi_z"_pair_kolmogorov_crespi_z.html, "pair_style pair_kolmogorov_crespi_full"_pair_kolmogorov_crespi_full.html, "pair_style pair_lebedeva_z"_pair_lebedeva_z.html, diff --git a/doc/src/pair_kolmogorov_crespi_full.txt b/doc/src/pair_kolmogorov_crespi_full.txt index 05effc5620..9ad5bfea84 100644 --- a/doc/src/pair_kolmogorov_crespi_full.txt +++ b/doc/src/pair_kolmogorov_crespi_full.txt @@ -22,7 +22,7 @@ pair_coeff * * none pair_coeff * * kolmogorov/crespi/full CH.KC C C :pre pair_style hybrid/overlay rebo kolmogorov/crespi/full 16.0 1 -pair_coeff * * rebo CH.airebo C H +pair_coeff * * rebo CH.rebo C H pair_coeff * * kolmogorov/crespi/full CH_taper.KC C H :pre [Description:] @@ -44,12 +44,12 @@ can be found in pair style "ilp/graphene/hbn"_pair_ilp_graphene_hbn.html. NOTE: This potential (ILP) is intended for interlayer interactions between two different layers of graphene. To perform a realistic simulation, this potential -must be used in combination with intra-layer potential, such as +must be used in combination with intralayer potential, such as "AIREBO"_pair_airebo.html or "Tersoff"_pair_tersoff.html potential. -To keep the intra-layer properties unaffected, the interlayer interaction +To keep the intralayer properties unaffected, the interlayer interaction within the same layers should be avoided. Hence, each atom has to have a layer identifier such that atoms residing on the same layer interact via the -appropriate intra-layer potential and atoms residing on different layers +appropriate intralayer potential and atoms residing on different layers interact via the ILP. Here, the molecule id is chosen as the layer identifier, thus a data file with the "full" atom style is required to use this potential. @@ -106,6 +106,7 @@ units. "pair_coeff"_pair_coeff.html, "pair_none"_pair_none.html, "pair_style hybrid/overlay"_pair_hybrid.html, +"pair_style drip"_pair_drip.html, "pair_style pair_lebedeva_z"_pair_lebedeva_z.html, "pair_style kolmogorov/crespi/z"_pair_kolmogorov_crespi_z.html, "pair_style ilp/graphene/hbn"_pair_ilp_graphene_hbn.html. diff --git a/doc/src/pair_kolmogorov_crespi_z.txt b/doc/src/pair_kolmogorov_crespi_z.txt index aabb3460e7..d45b5bd2e9 100644 --- a/doc/src/pair_kolmogorov_crespi_z.txt +++ b/doc/src/pair_kolmogorov_crespi_z.txt @@ -19,7 +19,7 @@ pair_coeff * * none pair_coeff 1 2 kolmogorov/crespi/z CC.KC C C :pre pair_style hybrid/overlay rebo kolmogorov/crespi/z 14.0 -pair_coeff * * rebo CH.airebo C C +pair_coeff * * rebo CH.rebo C C pair_coeff 1 2 kolmogorov/crespi/z CC.KC C C :pre [Description:] @@ -59,6 +59,7 @@ package"_Build_package.html doc page for more info. "pair_coeff"_pair_coeff.html, "pair_none"_pair_none.html, "pair_style hybrid/overlay"_pair_hybrid.html, +"pair_style drip"_pair_drip.html, "pair_style ilp/graphene/hbn"_pair_ilp_graphene_hbn.html. "pair_style kolmogorov/crespi/full"_pair_kolmogorov_crespi_full.html, "pair_style lebedeva/z"_pair_lebedeva_z.html diff --git a/doc/src/pair_lebedeva_z.txt b/doc/src/pair_lebedeva_z.txt index 9eab56d0d9..ad6c4c12f4 100644 --- a/doc/src/pair_lebedeva_z.txt +++ b/doc/src/pair_lebedeva_z.txt @@ -19,8 +19,8 @@ pair_coeff * * none pair_coeff 1 2 lebedeva/z CC.Lebedeva C C :pre pair_style hybrid/overlay rebo lebedeva/z 14.0 -pair_coeff * * rebo CH.airebo C C -pair_coeff 1 2 lebedeva/z CC.Lebedeva C C :pre +pair_coeff * * rebo CH.rebo C C +pair_coeff 1 2 lebedeva/z CC.Lebedeva C C :pre [Description:] @@ -53,6 +53,7 @@ package"_Build_package.html doc page for more info. "pair_coeff"_pair_coeff.html, "pair_style none"_pair_none.html, "pair_style hybrid/overlay"_pair_hybrid.html, +"pair_style drip"_pair_drip.html, "pair_style ilp/graphene/hbd"_pair_ilp_graphene_hbn.html, "pair_style kolmogorov/crespi/z"_pair_kolmogorov_crespi_z.html, "pair_style kolmogorov/crespi/full"_pair_kolmogorov_crespi_full.html. diff --git a/doc/src/pair_lj_long.txt b/doc/src/pair_lj_long.txt index 4e8410d062..e371030a76 100644 --- a/doc/src/pair_lj_long.txt +++ b/doc/src/pair_lj_long.txt @@ -91,7 +91,7 @@ is to enable LAMMPS to "find" the 2 H atoms associated with each O atom. For example, if the atom ID of an O atom in a TIP4P water molecule is 500, then its 2 H atoms must have IDs 501 and 502. -See the the "Howto tip4p"_Howto_tip4p.html doc page for more +See the "Howto tip4p"_Howto_tip4p.html doc page for more information on how to use the TIP4P pair style. Note that the neighbor list cutoff for Coulomb interactions is effectively extended by a distance 2*qdist when using the TIP4P pair style, to account for diff --git a/doc/src/pair_mdf.txt b/doc/src/pair_mdf.txt index 8a1551dded..44c9e7f67d 100644 --- a/doc/src/pair_mdf.txt +++ b/doc/src/pair_mdf.txt @@ -30,16 +30,16 @@ args = list of arguments for a particular style :l [Examples:] pair_style lj/mdf 2.5 3.0 -pair_coeff * * 1 1 -pair_coeff 1 1 1 1.1 2.8 3.0 3.2 :pre +pair_coeff * * 1.0 1.0 +pair_coeff 1 1 1.1 2.8 3.0 3.2 :pre pair_style buck 2.5 3.0 pair_coeff * * 100.0 1.5 200.0 pair_coeff * * 100.0 1.5 200.0 3.0 3.5 :pre pair_style lennard/mdf 2.5 3.0 -pair_coeff * * 1 1 -pair_coeff 1 1 1 1.1 2.8 3.0 3.2 :pre +pair_coeff * * 1.0 1.0 +pair_coeff 1 1 1021760.3664 2120.317338 3.0 3.2 :pre [Description:] @@ -69,11 +69,12 @@ standard 12-6 Lennard-Jones written in the epsilon/sigma form: :c,image(Eqs/pair_mdf-4.jpg) -The following coefficients must be defined for each pair of atoms -types via the pair_coeff command as in the examples above, or in the -data file or restart files read by the "read_data"_read_data.html or -"read_restart commands"_read_restart.html, or by mixing as described -below: +Either the first two or all of the following coefficients must be +defined for each pair of atoms types via the pair_coeff command as +in the examples above, or in the data file read by the +"read_data"_read_data.html. The two cutoffs default to the global +values and epsilon and sigma can also be determined by mixing as +described below: epsilon (energy units) sigma (distance units) @@ -83,7 +84,9 @@ r_{cut} (distance units) :ul :line For the {buck/mdf} pair_style, the potential energy, {E(r)}, is the -standard Buckingham potential: +standard Buckingham potential with three required coefficients. +The two cutoffs can be omitted and default to the corresponding +global values: :c,image(Eqs/pair_mdf-5.jpg) @@ -91,19 +94,20 @@ A (energy units) \rho (distance units) C (energy-distance^6 units) r_m (distance units) -r_{cut}$ (distance units) :ul +r_{cut} (distance units) :ul :line For the {lennard/mdf} pair_style, the potential energy, {E(r)}, is the -standard 12-6 Lennard-Jones written in the $A/B$ form: +standard 12-6 Lennard-Jones written in the A/B form: :c,image(Eqs/pair_mdf-6.jpg) The following coefficients must be defined for each pair of atoms types via the pair_coeff command as in the examples above, or in the -data file or restart files read by the read_data or read_restart -commands, or by mixing as described below: +data file read by the read_data commands, or by mixing as described below. +The two cutoffs default to their global values and must be either both +given or both left out: A (energy-distance^12 units) B (energy-distance^6 units) @@ -115,33 +119,23 @@ r_{cut} (distance units) :ul [Mixing, shift, table, tail correction, restart, rRESPA info]: For atom type pairs I,J and I != J, the epsilon and sigma coefficients -and cutoff distance for all of the lj/cut pair styles can be mixed. +and cutoff distances for the lj/mdf pair style can be mixed. The default mix value is {geometric}. See the "pair_modify" command -for details. +for details. The other two pair styles buck/mdf and lennard/mdf do not +support mixing, so all I,J pairs of coefficients must be specified +explicitly. -All of the {lj/cut} pair styles support the -"pair_modify"_pair_modify.html shift option for the energy of the -Lennard-Jones portion of the pair interaction. +None of the lj/mdf, buck/mdf, or lennard/mdf pair styles supports +the "pair_modify"_pair_modify.html shift option or long-range +tail corrections to pressure and energy. -The {lj/cut/coul/long} and {lj/cut/tip4p/long} pair styles support the -"pair_modify"_pair_modify.html table option since they can tabulate -the short-range portion of the long-range Coulombic interaction. +These styles write their information to "binary restart +files"_restart.html, so pair_style and pair_coeff commands do not need +to be specified in an input script that reads a restart file. -All of the {lj/cut} pair styles support the -"pair_modify"_pair_modify.html tail option for adding a long-range -tail correction to the energy and pressure for the Lennard-Jones -portion of the pair interaction. - -All of the {lj/cut} pair styles write their information to "binary -restart files"_restart.html, so pair_style and pair_coeff commands do -not need to be specified in an input script that reads a restart file. - -The {lj/cut} and {lj/cut/coul/long} pair styles support the use of the -{inner}, {middle}, and {outer} keywords of the "run_style -respa"_run_style.html command, meaning the pairwise forces can be -partitioned by distance at different levels of the rRESPA hierarchy. -The other styles only support the {pair} keyword of run_style respa. -See the "run_style"_run_style.html command for details. +These styles can only be used via the {pair} keyword of the "run_style +respa"_run_style.html command. They do not support the {inner}, +{middle}, {outer} keywords. :line diff --git a/doc/src/pair_spin_dmi.txt b/doc/src/pair_spin_dmi.txt index bc67e43ecd..9ddff8a8dc 100644 --- a/doc/src/pair_spin_dmi.txt +++ b/doc/src/pair_spin_dmi.txt @@ -88,4 +88,4 @@ package"_Build_package.html doc page for more info. Physical Review B, 88(18), 184422. (2013). :link(Tranchida5) [(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson, -Journal of Computational Physics, (2018). +Journal of Computational Physics, 372, 406-425, (2018). diff --git a/doc/src/pair_spin_exchange.txt b/doc/src/pair_spin_exchange.txt index 10d65a55a1..76a6d508d2 100644 --- a/doc/src/pair_spin_exchange.txt +++ b/doc/src/pair_spin_exchange.txt @@ -95,4 +95,4 @@ package"_Build_package.html doc page for more info. :link(Tranchida3) [(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson, -Journal of Computational Physics, (2018). +Journal of Computational Physics, 372, 406-425, (2018). diff --git a/doc/src/pair_spin_magelec.txt b/doc/src/pair_spin_magelec.txt index 151ecdec3d..206da4bb51 100644 --- a/doc/src/pair_spin_magelec.txt +++ b/doc/src/pair_spin_magelec.txt @@ -70,4 +70,4 @@ package"_Build_package.html doc page for more info. :link(Tranchida4) [(Tranchida)] Tranchida, Plimpton, Thibaudeau, and Thompson, -Journal of Computational Physics, (2018). +Journal of Computational Physics, 372, 406-425, (2018). diff --git a/doc/src/pair_spin_neel.txt b/doc/src/pair_spin_neel.txt index 8e2242f013..009ef7947d 100644 --- a/doc/src/pair_spin_neel.txt +++ b/doc/src/pair_spin_neel.txt @@ -80,4 +80,4 @@ package"_Build_package.html doc page for more info. :link(Tranchida6) [(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson, -Journal of Computational Physics, (2018). +Journal of Computational Physics, 372, 406-425, (2018). diff --git a/doc/src/pair_style.txt b/doc/src/pair_style.txt index f6fcd110d8..e305bc705d 100644 --- a/doc/src/pair_style.txt +++ b/doc/src/pair_style.txt @@ -147,6 +147,8 @@ accelerated styles exist. "dpd/fdt/energy"_pair_dpd_fdt.html - DPD for constant energy and enthalpy "dpd/tstat"_pair_dpd.html - pair-wise DPD thermostatting "dsmc"_pair_dsmc.html - Direct Simulation Monte Carlo (DSMC) +"e3b"_pair_e3b.html - Explicit-three body (E3B) water model +"drip"_pair_drip.html - Dihedral-angle-corrected registry-dependent interlayer potential (DRIP) "eam"_pair_eam.html - embedded atom method (EAM) "eam/alloy"_pair_eam.html - alloy EAM "eam/cd"_pair_eam.html - concentration-dependent EAM @@ -174,7 +176,7 @@ accelerated styles exist. "kolmogorov/crespi/full"_pair_kolmogorov_crespi_full.html - Kolmogorov-Crespi (KC) potential with no simplifications "kolmogorov/crespi/z"_pair_kolmogorov_crespi_z.html - Kolmogorov-Crespi (KC) potential with normals along z-axis "lcbop"_pair_lcbop.html - long-range bond-order potential (LCBOP) -"lebedeva/z"_pair_lebedeva_z.html - Lebedeva inter-layer potential for graphene with normals along z-axis +"lebedeva/z"_pair_lebedeva_z.html - Lebedeva interlayer potential for graphene with normals along z-axis "lennard/mdf"_pair_mdf.html - LJ potential in A/B form with a taper function "line/lj"_pair_line_lj.html - LJ potential between line segments "list"_pair_list.html - potential between pairs of atoms explicitly listed in an input file diff --git a/doc/src/pair_vashishta.txt b/doc/src/pair_vashishta.txt index 01d089b4de..7ffb16cc83 100644 --- a/doc/src/pair_vashishta.txt +++ b/doc/src/pair_vashishta.txt @@ -63,7 +63,7 @@ equally spaced in R^2 space from cutinner^2 to cutoff^2. For the two-body term in the above equation, a linear interpolation for each pairwise distance between adjacent points in the table. In practice the tabulated version can run 3-5x faster than the analytic version -with with moderate to little loss of accuracy for Ntable values +with moderate to little loss of accuracy for Ntable values between 10000 and 1000000. It is not recommended to use less than 5000 tabulation points. diff --git a/doc/src/pairs.txt b/doc/src/pairs.txt index 30dcc8fd4b..babdd2d1cc 100644 --- a/doc/src/pairs.txt +++ b/doc/src/pairs.txt @@ -31,7 +31,9 @@ Pair Styles :h1 pair_dipole pair_dpd pair_dpd_fdt + pair_drip pair_dsmc + pair_e3b pair_eam pair_edip pair_eff diff --git a/doc/src/python.txt b/doc/src/python.txt index 54d18d2f60..851183ddf4 100644 --- a/doc/src/python.txt +++ b/doc/src/python.txt @@ -480,7 +480,7 @@ information on those settings. If you use Python code which calls back to LAMMPS, via the SELF input argument explained above, there is an extra step required when building LAMMPS. LAMMPS must also be built as a shared library and -your Python function must be able to to load the Python module in +your Python function must be able to load the Python module in python/lammps.py that wraps the LAMMPS library interface. These are the same steps required to use Python by itself to wrap LAMMPS. Details on these steps are explained on the "Python"_Python_head.html diff --git a/doc/src/read_data.txt b/doc/src/read_data.txt index 30ee1201d9..62112ea886 100644 --- a/doc/src/read_data.txt +++ b/doc/src/read_data.txt @@ -701,7 +701,7 @@ of 0 means the atom is still inside the box when unwrapped. A value of 2 means add 2 box lengths to get the unwrapped coordinate. A value of -1 means subtract 1 box length to get the unwrapped coordinate. LAMMPS updates these flags as atoms cross periodic boundaries during -the simulation. The "dump"_dump.html command can output atom atom +the simulation. The "dump"_dump.html command can output atom coordinates in wrapped or unwrapped form, as well as the 3 image flags. diff --git a/doc/src/server_md.txt b/doc/src/server_md.txt index 03f3db7e19..495c890c59 100644 --- a/doc/src/server_md.txt +++ b/doc/src/server_md.txt @@ -65,7 +65,7 @@ in this pseudo code is a pointer to an instance of the CSlib. See the src/MESSAGE/server_md.cpp and src/MESSAGE/fix_client_md.cpp files for details on how LAMMPS uses these messages. See the examples/COUPLE/lammps_vasp/vasp_wrapper.py file for an example of how -a quantum code (VASP) can use use these messages. +a quantum code (VASP) can use these messages. The following pseudo-code uses these values, defined as enums. diff --git a/doc/src/tad.txt b/doc/src/tad.txt index effb998f94..62407532d6 100644 --- a/doc/src/tad.txt +++ b/doc/src/tad.txt @@ -62,7 +62,7 @@ results at a specified lower temperature. A good overview of accelerated dynamics methods for such systems is given in "this review paper"_#Voter2002 from the same group. In general, these methods assume that the long-time dynamics is dominated by infrequent events i.e. the -system is is confined to low energy basins for long periods, +system is confined to low energy basins for long periods, punctuated by brief, randomly-occurring transitions to adjacent basins. TAD is suitable for infrequent-event systems, where in addition, the transition kinetics are well-approximated by harmonic diff --git a/doc/src/variable.txt b/doc/src/variable.txt index 77c1f6eeb0..e90e9bd04b 100644 --- a/doc/src/variable.txt +++ b/doc/src/variable.txt @@ -293,7 +293,7 @@ list of runs (e.g. 1000) without having to list N strings in the input script. For the {string} style, a single string is assigned to the variable. -Two differences between this this and using the {index} style exist: +Two differences between this style and using the {index} style exist: a variable with {string} style can be redefined, e.g. by another command later in the input script, or if the script is read again in a loop. The other difference is that {string} performs variable substitution even if the @@ -359,7 +359,7 @@ per-atom values is read, a non-blank line is searched for in the file. A comment character "#" can be used anywhere on a line; text starting with the comment character is stripped. Blank lines are skipped. The first "word" of a non-blank line, delimited by white-space, is read as -the count N of per-atom lines to immediately follow. N can be be the +the count N of per-atom lines to immediately follow. N can be the total number of atoms in the system, or only a subset. The next N lines have the following format @@ -931,7 +931,7 @@ with ID = 243. Or they can take a variable name, specified as v_name, where name is the name of the variable, like x\[v_myIndex\]. The variable can be of any style except {vector} or {atom} or {atomfile} variables. The variable is evaluated and the result is expected to be -numeric and is cast to an integer (i.e. 3.4 becomes 3), to use an an +numeric and is cast to an integer (i.e. 3.4 becomes 3), to use an index, which must be a value from 1 to N. Note that a "formula" cannot be used as the argument between the brackets, e.g. x\[243+10\] or x\[v_myIndex+1\] are not allowed. To do this a single variable can diff --git a/doc/src/velocity.txt b/doc/src/velocity.txt index decdf2a923..4bbbc5ad45 100644 --- a/doc/src/velocity.txt +++ b/doc/src/velocity.txt @@ -157,7 +157,7 @@ is issued. The {bias} keyword with a {yes} setting is used by {create} and {scale}, but only if the {temp} keyword is also used to specify a "compute"_compute.html that calculates temperature in a desired way. -If the temperature compute also calculates a velocity bias, the the +If the temperature compute also calculates a velocity bias, the bias is subtracted from atom velocities before the {create} and {scale} operations are performed. After the operations, the bias is added back to the atom velocities. See the "Howto diff --git a/doc/src/write_coeff.txt b/doc/src/write_coeff.txt index 5dc4b331de..74d19b5c3d 100644 --- a/doc/src/write_coeff.txt +++ b/doc/src/write_coeff.txt @@ -26,11 +26,9 @@ coefficients in a way, that it can be read by LAMMPS with the option of "write_data"_write_data.html this can be used to move the Coeffs sections from a data file into a separate file. -NOTE: The write_coeff command is not yet fully implemented in two -respects. First, some pair styles do not yet write their coefficient -information into the coeff file. This means you will need to specify -that information in your input script that reads the data file, via -the "pair_coeff"_pair_coeff.html command. +NOTE: The write_coeff command is not yet fully implemented as +some pair styles do not output their coefficient information. +This means you will need to add/copy this information manually. :line diff --git a/doc/src/write_data.txt b/doc/src/write_data.txt index a8168b70a0..79e855dff3 100644 --- a/doc/src/write_data.txt +++ b/doc/src/write_data.txt @@ -106,7 +106,7 @@ written for all I,J pairs where I <= J. These coefficients will include any specific settings made in the input script up to that point. The presence of these I != J coefficients in the data file will effectively turn off the default mixing rule for the pair style. -Again, the coefficient values in the data file can can be overridden +Again, the coefficient values in the data file can be overridden in the input script after reading the data file, by specifying additional "pair_coeff"_pair_coeff.html commands for any desired I,J pairs. diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index a845673715..2d0575ca70 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -57,8 +57,10 @@ alchemical AlCu Alderton Alejandre +Aleksei alessandro Alessandro +ali aliceblue Allinger allocaters @@ -87,6 +89,7 @@ anharmonic anharmonicity aniso anisotropic +anisotropies anisotropy ansi antiquewhite @@ -200,6 +203,7 @@ Berkowitz berlin Berne Bertotti +Bessarab Beutler bgq Bh @@ -405,6 +409,7 @@ configfile configurational conformational Contrib +cooperativity coord Coord CoordN @@ -592,6 +597,7 @@ Dmax dmg dmi dnf +DNi Dobson Dodds dodgerblue @@ -650,6 +656,7 @@ Eacn eam eangle eatom +Eb Eba ebond ebook @@ -963,6 +970,8 @@ gmail gmake gmask Gmask +gneb +GNEB googlemail Gordan GPa @@ -1130,6 +1139,7 @@ incrementing indenter indenters indianred +indices inertiax inertiay inertiaz @@ -1156,6 +1166,7 @@ Interparticle interstitials Intr intra +intralayer intramolecular ints inv @@ -1188,6 +1199,7 @@ Itsets itype itypeN iva +Ivanov Ivector Iw ixcm @@ -1244,6 +1256,7 @@ jpg JPG jpl Jth +jtranch jtype jtypeN Juelich @@ -1272,6 +1285,7 @@ Katsnelson Katsura Kaufmann Kawata +Kaxiras Kayser kb kB @@ -2002,6 +2016,7 @@ ortho orthonormal orthorhombic ot +Otype Ouldridge outfile outmost @@ -2098,6 +2113,7 @@ picograms picosecond picoseconds pid +Pieniazek Pieter pimd Pisarev @@ -2368,6 +2384,7 @@ rNEMD ro Rochus Rockett +Rodrigues Rohart Ronchetti Rosati @@ -2466,6 +2483,7 @@ Shardlow shawn Shen Shenderova +Shi Shiga Shinoda shockvel @@ -2492,6 +2510,7 @@ sizex sj sjplimp sjtu +Skomski skyblue Skylake slateblue @@ -2629,6 +2648,7 @@ Tadmor Tafipolsky tagID tagint +Tainter Tait taitwater Tajkhorshid @@ -2772,6 +2792,7 @@ tt Tt TThis ttm +ttol tu Tuckerman tue @@ -2844,6 +2865,7 @@ utsa Uttormark uvm uwo +Uzdin vacf valent Valeriu @@ -2943,7 +2965,7 @@ wB Wbody webpage Weckner -WeinenE +WeinanE Wennberg Westview wget diff --git a/examples/SPIN/gneb/README b/examples/SPIN/gneb/README new file mode 100644 index 0000000000..9d43c775b6 --- /dev/null +++ b/examples/SPIN/gneb/README @@ -0,0 +1,13 @@ +Perform geodesic NEB calculations for spin configurations. +The two examples are: +- the magnetic switching of an iron nanoisland +- the collapse of a magnetic skyrmion + +Run those examples as: + +mpirun -np 3 lmp_mpi -in in.gneb.iron -partition 3x1 + +You should be able to use any number of replicas >= 3. + +In the interpolate/ directory, a c routine is provided to +interpolate the MEP. diff --git 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interactions for bcc iron +# (mass not necessary for fixed lattice calculation) + +read_data initial.iron_spin +mass 1 55.845 + +pair_style spin/exchange 3.5 +pair_coeff * * exchange 3.4 0.02726 0.2171 1.841 + +neighbor 0.1 bin +neigh_modify every 10 check yes delay 20 + +fix 1 all precession/spin zeeman 0.1 0.0 0.0 1.0 anisotropy 0.0001 1.0 0.0 0.0 +fix_modify 1 energy yes +fix 3 all neb/spin 1.0 + +timestep 0.0001 +thermo 100 + +compute out_mag all spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +variable magx equal c_out_mag[1] +variable magy equal c_out_mag[2] +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] + +thermo 100 +thermo_style custom step time v_magx v_magz v_magnorm etotal +thermo_modify format float %20.15g + +compute outsp all property/atom spx spy spz sp fmx fmy fmz +variable u universe 1 2 3 4 +dump 1 all custom 200 dump.$u type x y z c_outsp[1] c_outsp[2] c_outsp[3] + +min_style spin +min_modify alpha_damp 1.0 discrete_factor 10.0 +neb/spin 1.0e-12 1.0e-12 200000 100000 1000 final final.iron_spin verbose diff --git a/examples/SPIN/gneb/iron/initial.iron_spin b/examples/SPIN/gneb/iron/initial.iron_spin new file mode 100644 index 0000000000..1d28afe400 --- /dev/null +++ b/examples/SPIN/gneb/iron/initial.iron_spin @@ -0,0 +1,82 @@ +LAMMPS data file via write_data, version 4 Jan 2019, timestep = 0 + +32 atoms +1 atom types + +0.0000000000000000e+00 1.1465999999999999e+01 xlo xhi +0.0000000000000000e+00 1.1465999999999999e+01 ylo yhi +0.0000000000000000e+00 2.8664999999999998e+00 zlo zhi + +Masses + +1 55.845 + +Atoms # spin + +1 1 2.2000000000000002e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0 0 0 +2 1 2.2000000000000002e+00 1.4332499999999999e+00 1.4332499999999999e+00 1.4332499999999999e+00 1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0 0 0 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and interactions for bcc iron +# (mass not necessary for fixed lattice calculation) + +read_data initial.skyrmion +mass 1 55.845 + +pair_style hybrid/overlay spin/exchange 3.1 spin/dmi 3.1 +pair_coeff * * spin/exchange exchange 3.1 0.01593 0.06626915552 1.211 +pair_coeff * * spin/dmi dmi 3.1 0.12e-03 0.0 0.0 1.0 + +neighbor 0.1 bin +neigh_modify every 10 check yes delay 20 + +fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 anisotropy 5e-05 0.0 0.0 1.0 +fix_modify 1 energy yes +fix 2 all langevin/spin 0.0 0.0 21 +fix 3 all neb/spin 1.0 + +timestep 0.0001 + +compute out_mag all spin +variable magx equal c_out_mag[1] +variable magy equal c_out_mag[2] +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] + +thermo 100 +thermo_style custom step time v_magx v_magz v_magnorm etotal +thermo_modify format float %20.15g + +compute outsp all property/atom spx spy spz sp fmx fmy fmz +variable u universe 1 2 3 4 +dump 1 all custom 1 dump.$u type x y z c_outsp[1] c_outsp[2] c_outsp[3] + +min_style spin +min_modify alpha_damp 1.0 discrete_factor 10.0 +neb/spin 1.0e-9 1.0e-9 10000 10000 10 final final.skyrmion diff --git a/examples/SPIN/gneb/skyrmion/initial.skyrmion b/examples/SPIN/gneb/skyrmion/initial.skyrmion new file mode 100644 index 0000000000..f940aee182 --- /dev/null +++ b/examples/SPIN/gneb/skyrmion/initial.skyrmion @@ -0,0 +1,818 @@ +LAMMPS data file via write_data, version 28 Feb 2019, timestep = 6 + +400 atoms +1 atom types + +0.0000000000000000e+00 6.0000000000000000e+01 xlo xhi +0.0000000000000000e+00 6.0000000000000000e+01 ylo yhi +0.0000000000000000e+00 3.0000000000000000e+00 zlo zhi + +Masses + +1 55.845 + +Atoms # spin + +1 1 2.5000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 -3.9693242391277868e-03 -3.9693242391277929e-03 9.9998424434096433e-01 0 0 0 +21 1 2.5000000000000000e+00 3.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 -1.1868011343002482e-02 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0.0000000000000000e+00 +400 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 diff --git a/examples/SPIN/iron/in.spin.iron_cubic b/examples/SPIN/iron/in.spin.iron_cubic new file mode 100644 index 0000000000..d4703a2959 --- /dev/null +++ b/examples/SPIN/iron/in.spin.iron_cubic @@ -0,0 +1,60 @@ +# bcc iron in a 3d periodic box + +clear +units metal +atom_style spin + +dimension 3 +boundary p p p + +# necessary for the serial algorithm (sametag) +atom_modify map array + +lattice bcc 2.8665 +region box block 0.0 5.0 0.0 5.0 0.0 5.0 +create_box 1 box +create_atoms 1 box + +# setting mass, mag. moments, and interactions for bcc iron + +mass 1 55.845 +set group all spin 2.2 -1.0 0.0 0.0 +velocity all create 100 4928459 rot yes dist gaussian + +pair_style hybrid/overlay eam/alloy spin/exchange 3.5 +pair_coeff * * eam/alloy Fe_Mishin2006.eam.alloy Fe +pair_coeff * * spin/exchange exchange 3.4 0.02726 0.2171 1.841 +neighbor 0.1 bin +neigh_modify every 10 check yes delay 20 + +fix 1 all precession/spin cubic 0.001 0.0005 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1.0 +fix_modify 1 energy yes +fix 2 all langevin/spin 0.0 0.0 21 + +fix 3 all nve/spin lattice yes +timestep 0.0001 + +# compute and output options + +compute out_mag all spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +variable magx equal c_out_mag[1] +variable magy equal c_out_mag[2] +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo_style custom step time v_magx v_magy v_magz v_magnorm v_tmag v_emag pe etotal +thermo 50 + +compute outsp all property/atom spx spy spz sp fmx fmy fmz +dump 100 all custom 1 dump_iron.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] + +run 2000 +# min_style spin +# min_modify alpha_damp 1.0 discrete_factor 10 +# minimize 1.0e-16 1.0e-16 10000 10000 diff --git a/examples/SPIN/iron/log.11May18.spin.iron.g++.1 b/examples/SPIN/iron/log.11May18.spin.iron.g++.1 deleted file mode 100644 index 1b27478002..0000000000 --- a/examples/SPIN/iron/log.11May18.spin.iron.g++.1 +++ /dev/null @@ -1,1115 +0,0 @@ -LAMMPS (11 May 2018) -# bcc iron in a 3d periodic box - -clear -units metal -atom_style spin - -dimension 3 -boundary p p p - -# necessary for the serial algorithm (sametag) -atom_modify map array - -lattice bcc 2.8665 -Lattice spacing in x,y,z = 2.8665 2.8665 2.8665 -region box block 0.0 5.0 0.0 5.0 0.0 5.0 -create_box 1 box -Created orthogonal box = (0 0 0) to (14.3325 14.3325 14.3325) - 1 by 1 by 1 MPI processor grid -create_atoms 1 box -Created 250 atoms - Time spent = 0.000727415 secs - -# setting mass, mag. moments, and interactions for bcc iron - -mass 1 55.845 - -set group all spin/random 31 2.2 - 250 settings made for spin/random -velocity all create 100 4928459 rot yes dist gaussian - -pair_style hybrid/overlay eam/alloy spin/exchange 3.5 -pair_coeff * * eam/alloy Fe_Mishin2006.eam.alloy Fe -pair_coeff * * spin/exchange exchange 3.4 0.02726 0.2171 1.841 - -neighbor 0.1 bin -neigh_modify every 10 check yes delay 20 - -fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 -fix 2 all langevin/spin 0.0 0.0 21 - -fix 3 all nve/spin lattice yes -timestep 0.0001 - -# compute and output options - -compute out_mag all compute/spin -compute out_pe all pe -compute out_ke all ke -compute out_temp all temp - -variable magz equal c_out_mag[3] -variable magnorm equal c_out_mag[4] -variable emag equal c_out_mag[5] -variable tmag equal c_out_mag[6] - -thermo_style custom step time v_magnorm v_tmag temp v_emag ke pe etotal -thermo 50 - -compute outsp all property/atom spx spy spz sp fmx fmy fmz -dump 100 all custom 1 dump_iron.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] - -run 50000 -Neighbor list info ... - update every 10 steps, delay 20 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 5.77337 - ghost atom cutoff = 5.77337 - binsize = 2.88668, bins = 5 5 5 - 2 neighbor lists, perpetual/occasional/extra = 2 0 0 - (1) pair eam/alloy, perpetual, half/full from (2) - attributes: half, newton on - pair build: halffull/newton - stencil: none - bin: none - (2) pair spin/exchange, perpetual - attributes: full, newton on - pair build: full/bin/atomonly - stencil: full/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 7.319 | 7.319 | 7.319 Mbytes -Step Time v_magnorm v_tmag Temp v_emag KinEng PotEng TotEng - 0 0 0.076456975 9109.0924 100.00358 -0.85791269 3.2186929 -1070.8579 -1067.6392 - 50 0.005 0.076456974 9316.7659 96.663685 -0.86504718 3.1111957 -1070.7504 -1067.6392 - 100 0.01 0.076456983 9488.3743 86.965803 -0.88035771 2.7990619 -1070.4383 -1067.6392 - 150 0.015 0.076456973 9589.0566 72.421197 -0.8996913 2.3309324 -1069.9702 -1067.6392 - 200 0.02 0.076456944 9415.3095 55.633188 -0.921682 1.7905973 -1069.4298 -1067.6392 - 250 0.025 0.076456953 8878.9394 39.802206 -0.94649004 1.2810649 -1068.9203 -1067.6392 - 300 0.03 0.076457027 8203.3388 27.882295 -0.97253854 0.8974133 -1068.5366 -1067.6392 - 350 0.035 0.076457103 7720.309 21.776538 -0.99708692 0.70089477 -1068.3401 -1067.6392 - 400 0.04 0.076457117 7531.0683 21.857102 -1.0190244 0.70348778 -1068.3427 -1067.6392 - 450 0.045 0.076457072 7479.8073 26.959407 -1.0389343 0.86770942 -1068.5069 -1067.6392 - 500 0.05 0.076457001 7461.6683 34.92521 -1.0582008 1.124095 -1068.7633 -1067.6392 - 550 0.055 0.076456962 7396.1112 43.405912 -1.0785156 1.397053 -1069.0363 -1067.6392 - 600 0.06 0.076456997 7121.894 50.544844 -1.102048 1.626825 -1069.2661 -1067.6392 - 650 0.065 0.076457079 6683.4805 55.261218 -1.1296588 1.7786252 -1069.4179 -1067.6392 - 700 0.07 0.076457136 6313.6896 57.25083 -1.1595102 1.8426624 -1069.4819 -1067.6392 - 750 0.075 0.076457132 6199.0363 56.934336 -1.1893875 1.8324758 -1069.4717 -1067.6392 - 800 0.08 0.076457116 6265.997 55.266343 -1.2181223 1.7787901 -1069.418 -1067.6392 - 850 0.085 0.076457116 6326.5886 53.376453 -1.2443326 1.7179626 -1069.3572 -1067.6392 - 900 0.09 0.076457121 6336.1261 52.279557 -1.2676425 1.6826581 -1069.3219 -1067.6392 - 950 0.095 0.076457122 6288.4204 52.667743 -1.2902335 1.6951522 -1069.3344 -1067.6392 - 1000 0.1 0.076457135 6122.1622 54.684094 -1.314147 1.76005 -1069.3993 -1067.6392 - 1050 0.105 0.076457155 5830.2219 57.880399 -1.3392396 1.8629256 -1069.5022 -1067.6392 - 1100 0.11 0.076457162 5477.4214 61.505616 -1.3662331 1.979606 -1069.6188 -1067.6392 - 1150 0.115 0.076457195 5194.1423 64.810972 -1.3984474 2.0859914 -1069.7252 -1067.6392 - 1200 0.12 0.076457219 5096.2484 67.147472 -1.438326 2.1611935 -1069.8004 -1067.6392 - 1250 0.125 0.076457214 5180.7444 67.957533 -1.4822383 2.1872659 -1069.8265 -1067.6392 - 1300 0.13 0.076457208 5332.4483 66.96652 -1.5226303 2.1553694 -1069.7946 -1067.6392 - 1350 0.135 0.076457225 5441.1287 64.471602 -1.5553539 2.0750686 -1069.7143 -1067.6392 - 1400 0.14 0.076457244 5466.8622 61.292592 -1.5804721 1.9727496 -1069.612 -1067.6392 - 1450 0.145 0.07645724 5403.309 58.518161 -1.6006864 1.8834524 -1069.5227 -1067.6392 - 1500 0.15 0.076457224 5275.2171 57.1713 -1.6196756 1.8401027 -1069.4793 -1067.6392 - 1550 0.155 0.076457217 5122.7481 57.878063 -1.6407322 1.8628504 -1069.5021 -1067.6392 - 1600 0.16 0.076457217 4968.5049 60.639452 -1.6657935 1.9517278 -1069.591 -1067.6392 - 1650 0.165 0.076457208 4850.1861 64.668839 -1.690847 2.0814168 -1069.7206 -1067.6392 - 1700 0.17 0.076457217 4809.0194 68.693586 -1.7087416 2.2109564 -1069.8502 -1067.6392 - 1750 0.175 0.076457274 4835.8611 71.611033 -1.7188587 2.3048567 -1069.9441 -1067.6392 - 1800 0.18 0.076457318 4929.7428 72.815077 -1.7280248 2.3436098 -1069.9828 -1067.6392 - 1850 0.185 0.076457279 5036.6365 72.102335 -1.7426092 2.3206696 -1069.9599 -1067.6392 - 1900 0.19 0.076457222 5116.2436 69.579977 -1.7638235 2.2394856 -1069.8787 -1067.6392 - 1950 0.195 0.076457228 5207.2334 65.715745 -1.7895824 2.1151122 -1069.7543 -1067.6392 - 2000 0.2 0.076457288 5216.0413 61.340972 -1.8174915 1.9743068 -1069.6135 -1067.6392 - 2050 0.205 0.076457267 5023.1601 57.468628 -1.8456914 1.8496724 -1069.4889 -1067.6392 - 2100 0.21 0.076457198 4748.7818 55.033266 -1.8742291 1.7712884 -1069.4105 -1067.6392 - 2150 0.215 0.076457199 4558.1302 54.573806 -1.9035225 1.7565003 -1069.3957 -1067.6392 - 2200 0.22 0.076457185 4483.1644 56.074241 -1.9322669 1.804793 -1069.444 -1067.6392 - 2250 0.225 0.076457114 4430.1583 59.0552 -1.9577399 1.9007374 -1069.54 -1067.6392 - 2300 0.23 0.076457092 4353.7973 62.874849 -1.9801275 2.0236758 -1069.6629 -1067.6392 - 2350 0.235 0.076457145 4303.5275 66.892738 -2.0022129 2.1529947 -1069.7922 -1067.6392 - 2400 0.24 0.076457171 4258.6889 70.426826 -2.0233072 2.2667421 -1069.906 -1067.6392 - 2450 0.245 0.076457169 4178.5775 72.910422 -2.0405304 2.3466785 -1069.9859 -1067.6392 - 2500 0.25 0.07645717 4114.786 74.106367 -2.0531755 2.3851709 -1070.0244 -1067.6392 - 2550 0.255 0.076457136 4067.5017 74.169349 -2.0634674 2.3871981 -1070.0264 -1067.6392 - 2600 0.26 0.076457099 4045.3324 73.586199 -2.0755814 2.3684289 -1070.0077 -1067.6392 - 2650 0.265 0.076457099 4137.898 72.914235 -2.0913646 2.3468012 -1069.986 -1067.6392 - 2700 0.27 0.076457106 4332.063 72.583192 -2.1091075 2.3361464 -1069.9754 -1067.6392 - 2750 0.275 0.07645709 4465.1953 72.814559 -2.125099 2.3435931 -1069.9828 -1067.6392 - 2800 0.28 0.076457051 4516.5192 73.652154 -2.1371914 2.3705517 -1070.0098 -1067.6392 - 2850 0.285 0.076457019 4555.5962 75.060211 -2.1489378 2.4158711 -1070.0551 -1067.6392 - 2900 0.29 0.076457069 4544.2734 76.844795 -2.1667679 2.4733094 -1070.1125 -1067.6392 - 2950 0.295 0.076457172 4460.2109 78.48171 -2.1924421 2.5259948 -1070.1652 -1067.6392 - 3000 0.3 0.076457219 4323.2746 79.20682 -2.2209955 2.549333 -1070.1886 -1067.6392 - 3050 0.305 0.076457213 4155.688 78.543529 -2.2505299 2.5279844 -1070.1672 -1067.6392 - 3100 0.31 0.076457203 3969.6188 76.554785 -2.2858382 2.4639752 -1070.1032 -1067.6392 - 3150 0.315 0.076457187 3761.432 73.396149 -2.3245055 2.362312 -1070.0015 -1067.6392 - 3200 0.32 0.076457142 3602.8035 69.313196 -2.3577056 2.230899 -1069.8701 -1067.6392 - 3250 0.325 0.076457116 3505.707 65.032482 -2.3836874 2.0931209 -1069.7324 -1067.6392 - 3300 0.33 0.07645716 3424.8795 61.551539 -2.4057167 1.9810841 -1069.6203 -1067.6392 - 3350 0.335 0.076457236 3335.9672 59.709703 -2.4251844 1.9218031 -1069.561 -1067.6392 - 3400 0.34 0.076457298 3238.0186 60.026953 -2.4425501 1.9320141 -1069.5712 -1067.6392 - 3450 0.345 0.076457297 3185.0674 62.613739 -2.4593531 2.0152718 -1069.6545 -1067.6392 - 3500 0.35 0.07645723 3197.4087 67.011871 -2.4756907 2.1568291 -1069.7961 -1067.6392 - 3550 0.355 0.076457177 3216.1428 72.316209 -2.4911379 2.3275533 -1069.9668 -1067.6392 - 3600 0.36 0.076457165 3241.0326 77.550071 -2.5083858 2.4960092 -1070.1352 -1067.6392 - 3650 0.365 0.076457168 3309.6874 81.877688 -2.5306273 2.6352969 -1070.2745 -1067.6392 - 3700 0.37 0.07645718 3350.748 84.764646 -2.5595247 2.7282159 -1070.3674 -1067.6392 - 3750 0.375 0.07645721 3368.085 86.031781 -2.5938559 2.7689996 -1070.4082 -1067.6392 - 3800 0.38 0.076457208 3425.3173 85.733048 -2.6266899 2.7593847 -1070.3986 -1067.6392 - 3850 0.385 0.076457165 3420.4429 84.240647 -2.6514805 2.7113506 -1070.3506 -1067.6392 - 3900 0.39 0.076457146 3323.0403 82.320886 -2.6700966 2.6495616 -1070.2888 -1067.6392 - 3950 0.395 0.076457179 3273.2625 80.780607 -2.6892405 2.5999865 -1070.2392 -1067.6392 - 4000 0.4 0.076457229 3313.2671 79.92769 -2.709641 2.5725347 -1070.2118 -1067.6392 - 4050 0.405 0.076457272 3381.1117 79.663389 -2.7291493 2.564028 -1070.2033 -1067.6392 - 4100 0.41 0.07645731 3373.3005 79.895158 -2.7514856 2.5714877 -1070.2107 -1067.6392 - 4150 0.415 0.076457296 3279.6989 80.402828 -2.7788004 2.5878274 -1070.2271 -1067.6392 - 4200 0.42 0.076457251 3197.0478 80.770336 -2.8064773 2.599656 -1070.2389 -1067.6392 - 4250 0.425 0.076457243 3160.9065 80.756747 -2.8307967 2.5992186 -1070.2385 -1067.6392 - 4300 0.43 0.076457282 3173.9599 80.446488 -2.852192 2.5892326 -1070.2285 -1067.6392 - 4350 0.435 0.076457289 3185.8003 80.110494 -2.8726607 2.5784184 -1070.2177 -1067.6392 - 4400 0.44 0.076457262 3166.3054 80.045036 -2.8936787 2.5763116 -1070.2155 -1067.6392 - 4450 0.445 0.076457226 3177.4332 80.500194 -2.9171408 2.5909612 -1070.2302 -1067.6392 - 4500 0.45 0.076457174 3238.8362 81.573722 -2.9447352 2.6255135 -1070.2647 -1067.6392 - 4550 0.455 0.07645714 3277.7104 83.104228 -2.975052 2.6747741 -1070.314 -1067.6392 - 4600 0.46 0.076457157 3224.8571 84.845473 -3.0065552 2.7308174 -1070.37 -1067.6392 - 4650 0.465 0.076457215 3112.9952 86.608217 -3.03972 2.7875527 -1070.4268 -1067.6392 - 4700 0.47 0.076457254 3001.141 88.18732 -3.074928 2.8383773 -1070.4776 -1067.6392 - 4750 0.475 0.076457235 2904.0735 89.204263 -3.1082127 2.8711084 -1070.5103 -1067.6392 - 4800 0.48 0.076457195 2832.0276 89.24571 -3.134302 2.8724424 -1070.5117 -1067.6392 - 4850 0.485 0.076457172 2833.7453 88.206351 -3.1541802 2.8389899 -1070.4782 -1067.6392 - 4900 0.49 0.076457184 2941.993 86.310712 -3.1725372 2.7779773 -1070.4172 -1067.6392 - 4950 0.495 0.076457228 3082.4825 84.029047 -3.1931038 2.7045401 -1070.3438 -1067.6392 - 5000 0.5 0.07645727 3155.7095 81.99875 -3.2175967 2.6391934 -1070.2784 -1067.6392 - 5050 0.505 0.076457297 3162.1875 80.72053 -3.2420203 2.5980529 -1070.2373 -1067.6392 - 5100 0.51 0.076457279 3133.3889 80.483768 -3.2606472 2.5904325 -1070.2297 -1067.6392 - 5150 0.515 0.076457223 3144.6361 81.566513 -3.2759117 2.6252815 -1070.2645 -1067.6392 - 5200 0.52 0.076457166 3156.8183 84.062018 -3.2944729 2.7056013 -1070.3448 -1067.6392 - 5250 0.525 0.076457128 3059.9886 87.694328 -3.3209415 2.82251 -1070.4617 -1067.6392 - 5300 0.53 0.076457126 2891.6506 91.782947 -3.3547324 2.9541054 -1070.5933 -1067.6392 - 5350 0.535 0.076457151 2751.9451 95.417928 -3.3914125 3.0711001 -1070.7103 -1067.6392 - 5400 0.54 0.07645725 2681.0265 97.845096 -3.4276651 3.1492204 -1070.7885 -1067.6392 - 5450 0.545 0.076457325 2657.0871 98.736021 -3.4632111 3.1778955 -1070.8171 -1067.6392 - 5500 0.55 0.076457263 2653.1919 98.075727 -3.4957627 3.1566434 -1070.7959 -1067.6392 - 5550 0.555 0.076457185 2644.2053 96.114963 -3.5208827 3.0935347 -1070.7328 -1067.6392 - 5600 0.56 0.076457195 2622.4174 93.525807 -3.5389264 3.0102007 -1070.6494 -1067.6392 - 5650 0.565 0.07645725 2616.3851 91.264369 -3.5558733 2.9374145 -1070.5766 -1067.6392 - 5700 0.57 0.076457256 2608.2454 90.135397 -3.5771374 2.9010777 -1070.5403 -1067.6392 - 5750 0.575 0.076457193 2573.217 90.456889 -3.6030061 2.9114252 -1070.5507 -1067.6392 - 5800 0.58 0.076457145 2565.3325 92.099499 -3.6318265 2.9642939 -1070.6035 -1067.6392 - 5850 0.585 0.076457161 2566.2763 94.62532 -3.6627041 3.0455894 -1070.6848 -1067.6392 - 5900 0.59 0.076457186 2564.6814 97.321391 -3.6927592 3.1323645 -1070.7716 -1067.6392 - 5950 0.595 0.076457195 2570.6317 99.384979 -3.7170023 3.1987827 -1070.838 -1067.6392 - 6000 0.6 0.076457206 2556.8466 100.3814 -3.7363622 3.2308533 -1070.8701 -1067.6392 - 6050 0.605 0.076457195 2521.7989 100.35237 -3.7587516 3.2299188 -1070.8692 -1067.6392 - 6100 0.61 0.076457175 2476.1857 99.370382 -3.7869326 3.1983129 -1070.8375 -1067.6392 - 6150 0.615 0.076457178 2397.2805 97.465979 -3.8168635 3.1370182 -1070.7763 -1067.6392 - 6200 0.62 0.07645713 2286.8528 94.931714 -3.8450242 3.0554509 -1070.6947 -1067.6392 - 6250 0.625 0.076457116 2250.5238 92.438461 -3.8722441 2.9752036 -1070.6144 -1067.6392 - 6300 0.63 0.076457156 2338.521 90.714356 -3.9006124 2.9197119 -1070.5589 -1067.6392 - 6350 0.635 0.07645717 2433.0115 90.142291 -3.9291158 2.9012996 -1070.5405 -1067.6392 - 6400 0.64 0.076457159 2467.5348 90.771111 -3.9562691 2.9215387 -1070.5608 -1067.6392 - 6450 0.645 0.076457107 2475.8592 92.488016 -3.9828131 2.9767986 -1070.616 -1067.6392 - 6500 0.65 0.0764571 2489.7418 95.127451 -4.0122141 3.0617508 -1070.701 -1067.6392 - 6550 0.655 0.076457169 2500.4747 98.171693 -4.0419177 3.1597321 -1070.799 -1067.6392 - 6600 0.66 0.076457208 2530.7924 100.74938 -4.0631997 3.242697 -1070.8819 -1067.6392 - 6650 0.665 0.076457205 2539.1274 102.26227 -4.0743158 3.2913904 -1070.9306 -1067.6392 - 6700 0.67 0.076457193 2456.6296 102.74328 -4.083416 3.3068723 -1070.9461 -1067.6392 - 6750 0.675 0.076457138 2387.5795 102.56259 -4.0973623 3.3010567 -1070.9403 -1067.6392 - 6800 0.68 0.076457109 2401.1036 102.04306 -4.113996 3.284335 -1070.9236 -1067.6392 - 6850 0.685 0.076457149 2426.9334 101.49407 -4.1282015 3.2666654 -1070.9059 -1067.6392 - 6900 0.69 0.076457185 2389.4808 101.35428 -4.1401792 3.2621662 -1070.9014 -1067.6392 - 6950 0.695 0.076457175 2323.8732 101.97431 -4.1517617 3.2821222 -1070.9214 -1067.6392 - 7000 0.7 0.076457145 2273.8742 103.4638 -4.1630859 3.3300628 -1070.9693 -1067.6392 - 7050 0.705 0.076457126 2231.6619 105.80757 -4.1770066 3.4054989 -1071.0447 -1067.6392 - 7100 0.71 0.076457114 2185.0913 108.81901 -4.1989399 3.5024243 -1071.1417 -1067.6392 - 7150 0.715 0.076457137 2139.1488 111.85718 -4.2283649 3.60021 -1071.2394 -1067.6392 - 7200 0.72 0.076457149 2101.4843 113.84985 -4.2560033 3.6643459 -1071.3036 -1067.6392 - 7250 0.725 0.07645712 2118.2459 113.9441 -4.2761251 3.6673792 -1071.3066 -1067.6392 - 7300 0.73 0.076457121 2191.8612 111.95162 -4.2925363 3.6032496 -1071.2425 -1067.6392 - 7350 0.735 0.076457137 2227.2133 108.21226 -4.3103732 3.4828957 -1071.1221 -1067.6392 - 7400 0.74 0.076457111 2182.8818 103.43153 -4.3300151 3.329024 -1070.9683 -1067.6392 - 7450 0.745 0.076457109 2101.9195 98.839733 -4.354205 3.1812335 -1070.8205 -1067.6392 - 7500 0.75 0.076457149 2036.6331 95.828658 -4.3866968 3.0843197 -1070.7235 -1067.6392 - 7550 0.755 0.076457161 1994.7766 95.143411 -4.4221882 3.0622645 -1070.7015 -1067.6392 - 7600 0.76 0.076457127 1970.8688 96.749372 -4.4522754 3.1139536 -1070.7532 -1067.6392 - 7650 0.765 0.076457086 1994.0036 100.15642 -4.4763519 3.223612 -1070.8628 -1067.6392 - 7700 0.77 0.076457048 2073.628 104.50472 -4.498005 3.3635656 -1071.0028 -1067.6392 - 7750 0.775 0.076457027 2167.9613 108.65949 -4.5168957 3.49729 -1071.1365 -1067.6392 - 7800 0.78 0.07645702 2217.2571 111.71851 -4.5326316 3.5957471 -1071.235 -1067.6392 - 7850 0.785 0.076457018 2202.7741 113.32785 -4.548779 3.6475449 -1071.2868 -1067.6392 - 7900 0.79 0.076457015 2164.9013 113.50963 -4.5689927 3.6533954 -1071.2926 -1067.6392 - 7950 0.795 0.076457037 2130.7469 112.46016 -4.5932603 3.6196176 -1071.2589 -1067.6392 - 8000 0.8 0.076457043 2075.0145 110.59865 -4.6198672 3.5597035 -1071.1989 -1067.6392 - 8050 0.805 0.076457061 2007.4917 108.6927 -4.6506917 3.4983589 -1071.1376 -1067.6392 - 8100 0.81 0.076457077 1991.5702 107.59433 -4.6877068 3.4630069 -1071.1022 -1067.6392 - 8150 0.815 0.07645708 2031.0743 107.95739 -4.7305236 3.4746923 -1071.1139 -1067.6392 - 8200 0.82 0.076457089 2054.3404 109.99515 -4.7756305 3.5402792 -1071.1795 -1067.6392 - 8250 0.825 0.076457091 2082.2542 113.4122 -4.8195703 3.6502597 -1071.2895 -1067.6392 - 8300 0.83 0.076457089 2137.8944 117.42257 -4.8606167 3.7793367 -1071.4186 -1067.6392 - 8350 0.835 0.076457127 2145.0506 120.77123 -4.8931181 3.8871159 -1071.5263 -1067.6392 - 8400 0.84 0.076457184 2101.9996 122.34334 -4.9126837 3.9377155 -1071.5769 -1067.6392 - 8450 0.845 0.076457201 2057.1092 121.73484 -4.921619 3.9181301 -1071.5574 -1067.6392 - 8500 0.85 0.076457149 2005.1132 119.2385 -4.9251343 3.8377838 -1071.477 -1067.6392 - 8550 0.855 0.076457098 1942.6247 115.64537 -4.9291799 3.722136 -1071.3614 -1067.6392 - 8600 0.86 0.076457115 1910.1502 111.98317 -4.9396222 3.6042654 -1071.2435 -1067.6392 - 8650 0.865 0.076457185 1943.3663 109.19353 -4.9603011 3.5144784 -1071.1537 -1067.6392 - 8700 0.87 0.076457254 2019.4182 107.80177 -4.9898541 3.4696837 -1071.1089 -1067.6392 - 8750 0.875 0.076457249 2073.1225 107.76716 -5.0205034 3.4685697 -1071.1078 -1067.6392 - 8800 0.88 0.076457175 2088.6545 108.72646 -5.0437829 3.4994455 -1071.1387 -1067.6392 - 8850 0.885 0.076457093 2077.5406 110.36499 -5.0572565 3.5521827 -1071.1914 -1067.6392 - 8900 0.89 0.076457088 2039.5392 112.51291 -5.0650529 3.6213154 -1071.2605 -1067.6392 - 8950 0.895 0.076457167 2016.6853 114.99374 -5.0744542 3.7011627 -1071.3404 -1067.6392 - 9000 0.9 0.076457241 2000.3012 117.47475 -5.0917242 3.781016 -1071.4202 -1067.6392 - 9050 0.905 0.076457226 1957.0091 119.35854 -5.1139655 3.8416472 -1071.4809 -1067.6392 - 9100 0.91 0.076457166 1923.1545 120.23087 -5.1350957 3.869724 -1071.509 -1067.6392 - 9150 0.915 0.076457128 1933.618 120.11319 -5.1511544 3.8659364 -1071.5052 -1067.6392 - 9200 0.92 0.076457114 1961.4473 119.3017 -5.1596749 3.8398178 -1071.4791 -1067.6392 - 9250 0.925 0.076457136 1962.1 118.34889 -5.1642618 3.8091509 -1071.4484 -1067.6392 - 9300 0.93 0.076457156 1942.9357 117.84262 -5.1720815 3.7928561 -1071.4321 -1067.6392 - 9350 0.935 0.076457138 1911.4886 118.10075 -5.1877615 3.8011641 -1071.4404 -1067.6392 - 9400 0.94 0.076457123 1890.6033 118.99959 -5.2079977 3.830094 -1071.4693 -1067.6392 - 9450 0.945 0.076457145 1911.9879 120.23989 -5.2265042 3.8700141 -1071.5092 -1067.6392 - 9500 0.95 0.076457172 1944.8053 121.67513 -5.2423826 3.9162086 -1071.5554 -1067.6392 - 9550 0.955 0.076457175 1950.6137 123.16708 -5.2566963 3.9642282 -1071.6035 -1067.6392 - 9600 0.96 0.076457174 1953.467 124.46943 -5.2686278 4.0061451 -1071.6454 -1067.6392 - 9650 0.965 0.076457174 1991.321 125.52237 -5.2816008 4.0400348 -1071.6793 -1067.6392 - 9700 0.97 0.076457153 2064.4494 126.48746 -5.3037304 4.0710971 -1071.7103 -1067.6392 - 9750 0.975 0.076457119 2117.0576 127.38593 -5.3401962 4.100015 -1071.7392 -1067.6392 - 9800 0.98 0.076457147 2129.8396 127.90735 -5.38872 4.1167973 -1071.756 -1067.6392 - 9850 0.985 0.076457201 2114.5902 127.47883 -5.4369444 4.103005 -1071.7422 -1067.6392 - 9900 0.99 0.076457216 2054.2807 125.71916 -5.4695662 4.0463688 -1071.6856 -1067.6392 - 9950 0.995 0.076457168 1984.2158 123.01154 -5.4834672 3.9592219 -1071.5985 -1067.6392 - 10000 1 0.076457131 1962.6658 120.32305 -5.4872199 3.8726906 -1071.5119 -1067.6392 - 10050 1.005 0.076457159 1973.2973 118.61523 -5.4922129 3.8177233 -1071.457 -1067.6392 - 10100 1.01 0.076457216 1957.9424 118.36973 -5.5066432 3.8098215 -1071.4491 -1067.6392 - 10150 1.015 0.076457197 1942.1125 119.27525 -5.5290592 3.8389666 -1071.4782 -1067.6392 - 10200 1.02 0.076457142 1978.3009 120.6949 -5.5571675 3.8846591 -1071.5239 -1067.6392 - 10250 1.025 0.076457171 2058.9652 122.05983 -5.5914809 3.9285903 -1071.5678 -1067.6392 - 10300 1.03 0.07645722 2104.5325 122.92754 -5.6303584 3.9565181 -1071.5958 -1067.6392 - 10350 1.035 0.07645723 2072.9687 123.15237 -5.6697758 3.9637547 -1071.603 -1067.6392 - 10400 1.04 0.076457234 2012.912 123.02584 -5.7067292 3.9596822 -1071.5989 -1067.6392 - 10450 1.045 0.076457242 1971.6903 123.23438 -5.7426231 3.9663941 -1071.6056 -1067.6392 - 10500 1.05 0.0764573 1932.8929 124.43675 -5.7779702 4.0050935 -1071.6443 -1067.6392 - 10550 1.055 0.076457357 1892.1027 126.80016 -5.8082237 4.0811614 -1071.7204 -1067.6392 - 10600 1.06 0.076457317 1911.4422 130.09167 -5.8347562 4.1871012 -1071.8263 -1067.6392 - 10650 1.065 0.076457251 1994.4648 133.74505 -5.8634891 4.3046881 -1071.9439 -1067.6392 - 10700 1.07 0.076457242 2058.3043 136.94864 -5.8957766 4.4077983 -1072.047 -1067.6392 - 10750 1.075 0.076457284 2065.4421 138.83647 -5.9266133 4.4685595 -1072.1078 -1067.6392 - 10800 1.08 0.076457341 2054.3284 138.84647 -5.9519915 4.4688815 -1072.1081 -1067.6392 - 10850 1.085 0.076457339 2019.0718 136.8565 -5.9690783 4.4048328 -1072.0441 -1067.6392 - 10900 1.09 0.076457316 1950.5439 133.30535 -5.9772058 4.290536 -1071.9298 -1067.6392 - 10950 1.095 0.076457386 1880.7681 129.31046 -5.9839906 4.1619576 -1071.8012 -1067.6392 - 11000 1.1 0.076457422 1858.5762 126.17301 -5.9991286 4.0609761 -1071.7002 -1067.6392 - 11050 1.105 0.076457344 1895.8864 124.66179 -6.0225804 4.0123366 -1071.6516 -1067.6392 - 11100 1.11 0.076457251 1940.5442 124.88033 -6.0460181 4.0193704 -1071.6586 -1067.6392 - 11150 1.115 0.076457202 1961.4346 126.74742 -6.0683173 4.0794642 -1071.7187 -1067.6392 - 11200 1.12 0.076457268 1940.4836 129.91024 -6.0923522 4.1812618 -1071.8205 -1067.6392 - 11250 1.125 0.07645736 1893.8666 133.48134 -6.1129806 4.2962004 -1071.9354 -1067.6392 - 11300 1.13 0.076457404 1883.0365 136.68921 -6.127246 4.3994482 -1072.0387 -1067.6392 - 11350 1.135 0.076457466 1882.1011 139.1981 -6.1379481 4.480199 -1072.1194 -1067.6392 - 11400 1.14 0.076457485 1867.5435 140.91567 -6.1513193 4.5354803 -1072.1747 -1067.6392 - 11450 1.145 0.076457418 1847.4052 141.74281 -6.1759478 4.5621023 -1072.2013 -1067.6392 - 11500 1.15 0.076457338 1813.6291 141.28184 -6.2119682 4.5472657 -1072.1865 -1067.6392 - 11550 1.155 0.076457333 1784.6892 139.23575 -6.2525061 4.4814106 -1072.1206 -1067.6392 - 11600 1.16 0.076457369 1755.4332 135.80671 -6.2888206 4.3710442 -1072.0103 -1067.6392 - 11650 1.165 0.076457401 1699.9293 131.63594 -6.3110048 4.236805 -1071.876 -1067.6392 - 11700 1.17 0.076457404 1653.9907 128.00726 -6.3221466 4.120013 -1071.7592 -1067.6392 - 11750 1.175 0.076457374 1643.4316 126.38341 -6.3360107 4.067748 -1071.707 -1067.6392 - 11800 1.18 0.07645738 1673.0949 127.37545 -6.3582141 4.0996777 -1071.7389 -1067.6392 - 11850 1.185 0.076457443 1718.7225 130.55123 -6.3857492 4.2018928 -1071.8411 -1067.6392 - 11900 1.19 0.076457444 1724.682 134.87067 -6.4146926 4.3409171 -1071.9801 -1067.6392 - 11950 1.195 0.076457414 1724.3414 139.24431 -6.4451679 4.4816863 -1072.1209 -1067.6392 - 12000 1.2 0.07645743 1749.066 142.81679 -6.4797792 4.5966692 -1072.2359 -1067.6392 - 12050 1.205 0.076457426 1742.2617 144.86234 -6.5158489 4.6625067 -1072.3017 -1067.6392 - 12100 1.21 0.076457401 1675.5507 144.96503 -6.548258 4.6658119 -1072.305 -1067.6392 - 12150 1.215 0.076457385 1610.7217 143.28189 -6.5749551 4.6116388 -1072.2509 -1067.6392 - 12200 1.22 0.07645736 1594.8876 140.48135 -6.5962025 4.5215012 -1072.1607 -1067.6392 - 12250 1.225 0.076457308 1625.0427 137.50616 -6.6145044 4.4257425 -1072.065 -1067.6392 - 12300 1.23 0.076457299 1685.9568 135.20765 -6.6302129 4.3517632 -1071.991 -1067.6392 - 12350 1.235 0.07645735 1733.821 134.30584 -6.6414385 4.3227378 -1071.962 -1067.6392 - 12400 1.24 0.076457353 1729.246 135.30039 -6.6446018 4.3547479 -1071.994 -1067.6392 - 12450 1.245 0.076457334 1680.067 138.31057 -6.6400277 4.4516331 -1072.0909 -1067.6392 - 12500 1.25 0.076457325 1617.8899 143.09184 -6.6404768 4.6055219 -1072.2448 -1067.6392 - 12550 1.255 0.07645726 1599.1888 148.81179 -6.6580865 4.7896229 -1072.4289 -1067.6392 - 12600 1.26 0.076457209 1658.9431 154.06138 -6.6888278 4.9585849 -1072.5978 -1067.6392 - 12650 1.265 0.07645722 1736.4699 157.49898 -6.7220069 5.0692269 -1072.7085 -1067.6392 - 12700 1.27 0.076457274 1779.2323 158.32957 -6.7551291 5.09596 -1072.7352 -1067.6392 - 12750 1.275 0.076457311 1789.9676 156.14983 -6.7885643 5.0258035 -1072.665 -1067.6392 - 12800 1.28 0.076457268 1802.2393 151.08471 -6.8186653 4.8627787 -1072.502 -1067.6392 - 12850 1.285 0.076457196 1818.1637 144.48302 -6.8490939 4.650298 -1072.2895 -1067.6392 - 12900 1.29 0.076457211 1817.2314 138.47831 -6.8873527 4.4570318 -1072.0963 -1067.6392 - 12950 1.295 0.076457276 1820.0753 134.61334 -6.9279428 4.3326347 -1071.9719 -1067.6392 - 13000 1.3 0.076457312 1845.4907 133.46496 -6.9596793 4.2956734 -1071.9349 -1067.6392 - 13050 1.305 0.076457338 1874.3042 135.13413 -6.9813982 4.3493968 -1071.9886 -1067.6392 - 13100 1.31 0.076457326 1866.7738 139.17204 -6.9940579 4.4793602 -1072.1186 -1067.6392 - 13150 1.315 0.076457289 1832.5745 144.49783 -6.9974757 4.6507749 -1072.29 -1067.6392 - 13200 1.32 0.076457244 1807.0747 149.77919 -6.9983839 4.8207594 -1072.46 -1067.6392 - 13250 1.325 0.076457187 1796.8435 153.72265 -7.0061211 4.9476829 -1072.5869 -1067.6392 - 13300 1.33 0.076457166 1784.1488 155.25389 -7.0202393 4.9969671 -1072.6362 -1067.6392 - 13350 1.335 0.076457229 1753.2853 154.01439 -7.0330486 4.9570726 -1072.5963 -1067.6392 - 13400 1.34 0.0764573 1735.0082 150.84246 -7.0447346 4.8549818 -1072.4942 -1067.6392 - 13450 1.345 0.076457318 1726.8186 147.29221 -7.0628093 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-1078.61 -1067.6392 - 48700 4.87 0.07645693 968.07155 348.89288 -18.372402 11.229388 -1078.8686 -1067.6392 - 48750 4.875 0.076456873 954.48433 354.07093 -18.412323 11.396048 -1079.0353 -1067.6392 - 48800 4.88 0.076456838 951.82821 354.8518 -18.445418 11.421181 -1079.0604 -1067.6392 - 48850 4.885 0.076456946 955.18291 351.65785 -18.473652 11.318381 -1078.9576 -1067.6392 - 48900 4.89 0.076457014 961.21122 345.9779 -18.498732 11.135567 -1078.7748 -1067.6392 - 48950 4.895 0.076456863 971.60448 338.99359 -18.517002 10.910772 -1078.55 -1067.6392 - 49000 4.9 0.076456715 983.55102 331.29604 -18.525123 10.66302 -1078.3022 -1067.6392 - 49050 4.905 0.076456793 965.60848 324.24302 -18.535514 10.436013 -1078.0752 -1067.6392 - 49100 4.91 0.076456864 944.53951 319.79955 -18.557009 10.292997 -1077.9322 -1067.6392 - 49150 4.915 0.076456768 947.20225 319.09103 -18.582911 10.270192 -1077.9094 -1067.6392 - 49200 4.92 0.076456734 944.86084 321.47471 -18.607567 10.346913 -1077.9861 -1067.6392 - 49250 4.925 0.076456851 940.6342 324.66116 -18.626242 10.449471 -1078.0887 -1067.6392 - 49300 4.93 0.076456872 950.6162 326.9518 -18.64032 10.523198 -1078.1624 -1067.6392 - 49350 4.935 0.076456643 952.42705 328.08816 -18.649274 10.559772 -1078.199 -1067.6392 - 49400 4.94 0.076456451 940.33548 329.05106 -18.66058 10.590764 -1078.23 -1067.6392 - 49450 4.945 0.076456558 946.93554 331.05799 -18.683544 10.655358 -1078.2946 -1067.6392 - 49500 4.95 0.076456719 968.13429 334.1178 -18.710726 10.753841 -1078.3931 -1067.6392 - 49550 4.955 0.076456712 989.14725 337.02333 -18.733226 10.847357 -1078.4866 -1067.6392 - 49600 4.96 0.076456681 986.97561 338.47429 -18.752155 10.894058 -1078.5333 -1067.6392 - 49650 4.965 0.076456692 980.18259 338.36307 -18.779369 10.890478 -1078.5297 -1067.6392 - 49700 4.97 0.076456776 962.29895 337.41689 -18.815353 10.860024 -1078.4993 -1067.6392 - 49750 4.975 0.076456852 943.47442 335.97999 -18.836611 10.813777 -1078.453 -1067.6392 - 49800 4.98 0.076456829 951.10385 334.29845 -18.839995 10.759655 -1078.3989 -1067.6392 - 49850 4.985 0.076456797 968.57767 333.00568 -18.84792 10.718046 -1078.3573 -1067.6392 - 49900 4.99 0.076456886 973.40031 332.98155 -18.860429 10.71727 -1078.3565 -1067.6392 - 49950 4.995 0.076456914 964.32242 335.13156 -18.853933 10.786469 -1078.4257 -1067.6392 - 50000 5 0.076456921 972.52311 340.63067 -18.841947 10.963463 -1078.6027 -1067.6392 -Loop time of 90.4316 on 1 procs for 50000 steps with 250 atoms - -Performance: 4.777 ns/day, 5.024 hours/ns, 552.904 timesteps/s -99.3% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 37.302 | 37.302 | 37.302 | 0.0 | 41.25 -Neigh | 0.386 | 0.386 | 0.386 | 0.0 | 0.43 -Comm | 0.7718 | 0.7718 | 0.7718 | 0.0 | 0.85 -Output | 15.35 | 15.35 | 15.35 | 0.0 | 16.97 -Modify | 36.465 | 36.465 | 36.465 | 0.0 | 40.32 -Other | | 0.1579 | | | 0.17 - -Nlocal: 250 ave 250 max 250 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 1327 ave 1327 max 1327 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 7747 ave 7747 max 7747 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 15494 ave 15494 max 15494 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 15494 -Ave neighs/atom = 61.976 -Neighbor list builds = 614 -Dangerous builds = 0 - -Please see the log.cite file for references relevant to this simulation - -Total wall time: 0:01:30 diff --git a/examples/SPIN/iron/log.11May18.spin.iron.g++.4 b/examples/SPIN/iron/log.11May18.spin.iron.g++.4 deleted file mode 100644 index 1467f8e2c5..0000000000 --- a/examples/SPIN/iron/log.11May18.spin.iron.g++.4 +++ /dev/null @@ -1,1115 +0,0 @@ -LAMMPS (11 May 2018) -# bcc iron in a 3d periodic box - -clear -units metal -atom_style spin - -dimension 3 -boundary p p p - -# necessary for the serial algorithm (sametag) -atom_modify map array - -lattice bcc 2.8665 -Lattice spacing in x,y,z = 2.8665 2.8665 2.8665 -region box block 0.0 5.0 0.0 5.0 0.0 5.0 -create_box 1 box -Created orthogonal box = (0 0 0) to (14.3325 14.3325 14.3325) - 1 by 2 by 2 MPI processor grid -create_atoms 1 box -Created 250 atoms - Time spent = 0.00023818 secs - -# setting mass, mag. moments, and interactions for bcc iron - -mass 1 55.845 - -set group all spin/random 31 2.2 - 250 settings made for spin/random -velocity all create 100 4928459 rot yes dist gaussian - -pair_style hybrid/overlay eam/alloy spin/exchange 3.5 -pair_coeff * * eam/alloy Fe_Mishin2006.eam.alloy Fe -pair_coeff * * spin/exchange exchange 3.4 0.02726 0.2171 1.841 - -neighbor 0.1 bin -neigh_modify every 10 check yes delay 20 - -fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 -fix 2 all langevin/spin 0.0 0.0 21 - -fix 3 all nve/spin lattice yes -timestep 0.0001 - -# compute and output options - -compute out_mag all compute/spin -compute out_pe all pe -compute out_ke all ke -compute out_temp all temp - -variable magz equal c_out_mag[3] -variable magnorm equal c_out_mag[4] -variable emag equal c_out_mag[5] -variable tmag equal c_out_mag[6] - -thermo_style custom step time v_magnorm v_tmag temp v_emag ke pe etotal -thermo 50 - -compute outsp all property/atom spx spy spz sp fmx fmy fmz -dump 100 all custom 1 dump_iron.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] - -run 50000 -Neighbor list info ... - update every 10 steps, delay 20 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 5.77337 - ghost atom cutoff = 5.77337 - binsize = 2.88668, bins = 5 5 5 - 2 neighbor lists, perpetual/occasional/extra = 2 0 0 - (1) pair eam/alloy, perpetual, half/full from (2) - attributes: half, newton on - pair build: halffull/newton - stencil: none - bin: none - (2) pair spin/exchange, perpetual - attributes: full, newton on - pair build: full/bin/atomonly - stencil: full/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 7.265 | 7.265 | 7.265 Mbytes -Step Time v_magnorm v_tmag Temp v_emag KinEng PotEng TotEng - 0 0 0.076456975 9109.0924 100.00358 -0.85791269 3.2186929 -1070.8579 -1067.6392 - 50 0.005 0.076456995 9402.4007 96.298333 -0.85659448 3.0994366 -1070.7387 -1067.6392 - 100 0.01 0.076457028 9589.1846 86.330828 -0.87003341 2.7786247 -1070.4179 -1067.6392 - 150 0.015 0.076457074 9673.9268 71.603402 -0.89006992 2.3046111 -1069.9438 -1067.6392 - 200 0.02 0.076457106 9509.1148 54.648817 -0.91124541 1.7589146 -1069.3981 -1067.6392 - 250 0.025 0.076457128 9004.27 38.599515 -0.93187522 1.2423553 -1068.8816 -1067.6392 - 300 0.03 0.076457157 8353.4371 26.383018 -0.95082226 0.8491579 -1068.4884 -1067.6392 - 350 0.035 0.076457207 7911.1316 20.01039 -0.96826468 0.64404992 -1068.2833 -1067.6392 - 400 0.04 0.076457243 7775.9492 20.097682 -0.98706373 0.64685949 -1068.2861 -1067.6392 - 450 0.045 0.076457231 7737.1225 25.687511 -1.0095684 0.82677249 -1068.466 -1067.6392 - 500 0.05 0.076457204 7676.9809 34.604697 -1.0349855 1.113779 -1068.753 -1067.6392 - 550 0.055 0.076457196 7550.2809 44.251809 -1.0609123 1.4242788 -1069.0635 -1067.6392 - 600 0.06 0.076457188 7209.7657 52.475202 -1.0880854 1.6889551 -1069.3282 -1067.6392 - 650 0.065 0.07645718 6691.1787 57.926479 -1.1179657 1.8644087 -1069.5036 -1067.6392 - 700 0.07 0.076457185 6276.4003 60.030548 -1.1469999 1.9321298 -1069.5714 -1067.6392 - 750 0.075 0.07645719 6149.9253 59.122504 -1.1721939 1.9029037 -1069.5421 -1067.6392 - 800 0.08 0.076457195 6207.0587 56.349146 -1.1949365 1.813641 -1069.4529 -1067.6392 - 850 0.085 0.076457199 6328.4635 53.154464 -1.2164642 1.7108177 -1069.35 -1067.6392 - 900 0.09 0.076457199 6456.2716 50.837416 -1.2366018 1.6362417 -1069.2755 -1067.6392 - 950 0.095 0.076457222 6495.1064 50.234549 -1.2539657 1.6168379 -1069.2561 -1067.6392 - 1000 0.1 0.076457266 6416.775 51.592727 -1.2671834 1.6605519 -1069.2998 -1067.6392 - 1050 0.105 0.076457256 6305.9015 54.719414 -1.2794824 1.7611868 -1069.4004 -1067.6392 - 1100 0.11 0.076457222 6165.987 59.01343 -1.2960617 1.8993931 -1069.5386 -1067.6392 - 1150 0.115 0.076457194 5941.7807 63.475298 -1.317859 2.0430017 -1069.6822 -1067.6392 - 1200 0.12 0.076457182 5692.0982 67.036713 -1.3432854 2.1576286 -1069.7969 -1067.6392 - 1250 0.125 0.076457217 5543.1736 68.917405 -1.3719994 2.2181602 -1069.8574 -1067.6392 - 1300 0.13 0.076457263 5507.9968 68.753418 -1.4042339 2.2128821 -1069.8521 -1067.6392 - 1350 0.135 0.076457286 5500.7848 66.608286 -1.4385667 2.1438394 -1069.7831 -1067.6392 - 1400 0.14 0.076457254 5523.456 62.967429 -1.4712143 2.0266556 -1069.6659 -1067.6392 - 1450 0.145 0.076457188 5501.5777 58.75732 -1.4990458 1.89115 -1069.5304 -1067.6392 - 1500 0.15 0.076457175 5324.4931 55.246308 -1.5236774 1.7781453 -1069.4174 -1067.6392 - 1550 0.155 0.076457234 5025.5908 53.607297 -1.5492947 1.7253925 -1069.3646 -1067.6392 - 1600 0.16 0.076457297 4742.9546 54.443418 -1.5785798 1.7523036 -1069.3915 -1067.6392 - 1650 0.165 0.076457321 4558.083 57.572305 -1.6113848 1.8530093 -1069.4922 -1067.6392 - 1700 0.17 0.076457304 4479.4352 62.073307 -1.6443595 1.9978776 -1069.6371 -1067.6392 - 1750 0.175 0.076457272 4520.5577 66.677964 -1.6742729 2.146082 -1069.7853 -1067.6392 - 1800 0.18 0.076457253 4659.9114 70.277293 -1.7021557 2.2619292 -1069.9012 -1067.6392 - 1850 0.185 0.076457257 4734.1597 72.135028 -1.7307798 2.3217219 -1069.961 -1067.6392 - 1900 0.19 0.076457279 4632.2637 71.873382 -1.7598165 2.3133006 -1069.9525 -1067.6392 - 1950 0.195 0.076457276 4496.6621 69.52131 -1.7866398 2.2375973 -1069.8768 -1067.6392 - 2000 0.2 0.076457276 4507.4594 65.61098 -1.8106776 2.1117403 -1069.751 -1067.6392 - 2050 0.205 0.076457288 4652.9279 61.016261 -1.8317479 1.9638557 -1069.6031 -1067.6392 - 2100 0.21 0.076457307 4738.4188 56.745795 -1.8489776 1.8264074 -1069.4656 -1067.6392 - 2150 0.215 0.076457279 4643.423 53.837376 -1.8647516 1.7327977 -1069.372 -1067.6392 - 2200 0.22 0.076457215 4517.9871 53.044053 -1.8828305 1.707264 -1069.3465 -1067.6392 - 2250 0.225 0.07645717 4436.4399 54.521839 -1.9038753 1.7548277 -1069.3941 -1067.6392 - 2300 0.23 0.076457132 4318.8261 57.895634 -1.9276454 1.8634159 -1069.5026 -1067.6392 - 2350 0.235 0.076457114 4148.8616 62.484473 -1.9559372 2.0111113 -1069.6503 -1067.6392 - 2400 0.24 0.076457144 4014.8498 67.404243 -1.9902034 2.1694579 -1069.8087 -1067.6392 - 2450 0.245 0.076457189 4004.017 71.654167 -2.0278558 2.306245 -1069.9455 -1067.6392 - 2500 0.25 0.076457202 4109.5497 74.379393 -2.0629968 2.3939585 -1070.0332 -1067.6392 - 2550 0.255 0.076457205 4251.6933 75.255112 -2.0918484 2.4221442 -1070.0614 -1067.6392 - 2600 0.26 0.076457208 4320.6876 74.700611 -2.1169691 2.4042972 -1070.0435 -1067.6392 - 2650 0.265 0.076457197 4297.5527 73.627823 -2.143 2.3697686 -1070.009 -1067.6392 - 2700 0.27 0.076457213 4198.4852 72.957211 -2.1702374 2.3481845 -1069.9874 -1067.6392 - 2750 0.275 0.076457256 4019.2384 73.353574 -2.1967187 2.3609417 -1070.0002 -1067.6392 - 2800 0.28 0.076457288 3867.2492 75.083781 -2.2227117 2.4166298 -1070.0559 -1067.6392 - 2850 0.285 0.076457302 3879.8471 77.82546 -2.2488766 2.5048728 -1070.1441 -1067.6392 - 2900 0.29 0.076457321 4003.8986 80.741745 -2.2742584 2.5987357 -1070.238 -1067.6392 - 2950 0.295 0.076457347 4026.6754 82.934399 -2.3001834 2.669308 -1070.3085 -1067.6392 - 3000 0.3 0.076457334 3857.2183 83.701738 -2.3291113 2.6940054 -1070.3332 -1067.6392 - 3050 0.305 0.076457295 3640.7581 82.615991 -2.3614721 2.6590598 -1070.2983 -1067.6392 - 3100 0.31 0.07645725 3489.102 79.573679 -2.3943974 2.5611406 -1070.2004 -1067.6392 - 3150 0.315 0.076457232 3396.4301 74.896125 -2.4236621 2.4105899 -1070.0498 -1067.6392 - 3200 0.32 0.076457259 3378.11 69.450128 -2.4483292 2.2353063 -1069.8745 -1067.6392 - 3250 0.325 0.076457289 3463.7734 64.542714 -2.4729224 2.0773573 -1069.7166 -1067.6392 - 3300 0.33 0.076457318 3637.4971 61.346221 -2.500303 1.9744757 -1069.6137 -1067.6392 - 3350 0.335 0.076457361 3833.5389 60.346704 -2.5252732 1.9423055 -1069.5815 -1067.6392 - 3400 0.34 0.076457387 3965.2081 61.464125 -2.5426842 1.9782706 -1069.6175 -1067.6392 - 3450 0.345 0.076457375 3976.7956 64.41797 -2.5565409 2.0733424 -1069.7126 -1067.6392 - 3500 0.35 0.076457371 3862.8334 68.714547 -2.5743062 2.211631 -1069.8509 -1067.6392 - 3550 0.355 0.076457375 3697.284 73.534942 -2.5974674 2.3667792 -1070.006 -1067.6392 - 3600 0.36 0.076457362 3575.9012 77.902682 -2.6209385 2.5073583 -1070.1466 -1067.6392 - 3650 0.365 0.076457345 3550.0667 81.043684 -2.6394846 2.6084539 -1070.2477 -1067.6392 - 3700 0.37 0.076457309 3535.0981 82.730976 -2.65464 2.6627607 -1070.302 -1067.6392 - 3750 0.375 0.076457309 3444.1795 83.322515 -2.6736085 2.6817998 -1070.321 -1067.6392 - 3800 0.38 0.076457348 3323.7191 83.436143 -2.7008525 2.685457 -1070.3247 -1067.6392 - 3850 0.385 0.076457368 3252.5404 83.62535 -2.7353937 2.6915468 -1070.3308 -1067.6392 - 3900 0.39 0.076457344 3219.5349 84.088597 -2.7722909 2.7064568 -1070.3457 -1067.6392 - 3950 0.395 0.076457316 3210.4164 84.636475 -2.8060651 2.7240906 -1070.3633 -1067.6392 - 4000 0.4 0.076457319 3223.9708 85.042888 -2.8352998 2.7371713 -1070.3764 -1067.6392 - 4050 0.405 0.076457335 3232.7108 85.266853 -2.8607963 2.7443798 -1070.3836 -1067.6392 - 4100 0.41 0.076457314 3206.1428 85.444074 -2.8837721 2.7500838 -1070.3893 -1067.6392 - 4150 0.415 0.076457325 3146.4589 85.771643 -2.9074131 2.7606269 -1070.3999 -1067.6392 - 4200 0.42 0.076457395 3092.6283 86.24875 -2.9341331 2.775983 -1070.4152 -1067.6392 - 4250 0.425 0.07645742 3103.0319 86.563557 -2.9622203 2.7861153 -1070.4253 -1067.6392 - 4300 0.43 0.076457425 3116.9053 86.320099 -2.9880208 2.7782794 -1070.4175 -1067.6392 - 4350 0.435 0.076457427 3061.2259 85.306966 -3.0085539 2.7456709 -1070.3849 -1067.6392 - 4400 0.44 0.076457432 3033.5229 83.703441 -3.0243431 2.6940602 -1070.3333 -1067.6392 - 4450 0.445 0.076457411 3042.5167 82.058057 -3.0397518 2.6411023 -1070.2803 -1067.6392 - 4500 0.45 0.076457387 2994.5161 81.002427 -3.0597817 2.607126 -1070.2464 -1067.6392 - 4550 0.455 0.076457413 2868.381 80.936403 -3.086593 2.605001 -1070.2442 -1067.6392 - 4600 0.46 0.076457454 2716.5128 81.904984 -3.1192161 2.6361755 -1070.2754 -1067.6392 - 4650 0.465 0.076457402 2628.691 83.537981 -3.1529675 2.6887347 -1070.328 -1067.6392 - 4700 0.47 0.076457327 2609.7253 85.196185 -3.1819342 2.7421053 -1070.3813 -1067.6392 - 4750 0.475 0.076457328 2604.4797 86.479192 -3.2088497 2.7833999 -1070.4226 -1067.6392 - 4800 0.48 0.076457385 2610.7583 87.294321 -3.242028 2.8096355 -1070.4489 -1067.6392 - 4850 0.485 0.076457398 2649.7853 87.477655 -3.2810534 2.8155362 -1070.4548 -1067.6392 - 4900 0.49 0.076457371 2678.8351 86.820207 -3.3154833 2.7943757 -1070.4336 -1067.6392 - 4950 0.495 0.076457344 2687.9239 85.543066 -3.3381845 2.75327 -1070.3925 -1067.6392 - 5000 0.5 0.076457351 2720.6587 84.363474 -3.3508261 2.7153039 -1070.3545 -1067.6392 - 5050 0.505 0.076457408 2755.8291 84.030245 -3.3582878 2.7045787 -1070.3438 -1067.6392 - 5100 0.51 0.076457454 2753.2313 84.932962 -3.3648805 2.7336333 -1070.3729 -1067.6392 - 5150 0.515 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0.076457584 2457.9835 97.287991 -3.8600042 3.1312895 -1070.7705 -1067.6392 - 6350 0.635 0.076457603 2571.5799 96.270875 -3.9092353 3.0985528 -1070.7378 -1067.6392 - 6400 0.64 0.076457558 2610.0081 95.435983 -3.9541076 3.0716812 -1070.7109 -1067.6392 - 6450 0.645 0.076457543 2587.7565 94.898723 -3.9898259 3.054389 -1070.6936 -1067.6392 - 6500 0.65 0.076457571 2592.6987 94.73176 -4.0156724 3.0490152 -1070.6882 -1067.6392 - 6550 0.655 0.076457601 2601.6462 95.026393 -4.0381259 3.0584982 -1070.6977 -1067.6392 - 6600 0.66 0.076457634 2566.7039 95.637128 -4.0616088 3.0781552 -1070.7174 -1067.6392 - 6650 0.665 0.076457648 2514.9262 96.272229 -4.0866885 3.0985964 -1070.7378 -1067.6392 - 6700 0.67 0.076457667 2469.8505 96.811573 -4.1148394 3.1159556 -1070.7552 -1067.6392 - 6750 0.675 0.076457679 2455.7259 97.232643 -4.1435989 3.1295081 -1070.7687 -1067.6392 - 6800 0.68 0.076457673 2468.7089 97.598131 -4.1658056 3.1412716 -1070.7805 -1067.6392 - 6850 0.685 0.076457641 2449.9304 98.364281 -4.1815157 3.1659307 -1070.8052 -1067.6392 - 6900 0.69 0.076457591 2353.8798 100.13599 -4.1974942 3.2229545 -1070.8622 -1067.6392 - 6950 0.695 0.076457574 2209.8271 103.01376 -4.2144962 3.3155778 -1070.9548 -1067.6392 - 7000 0.7 0.07645757 2076.4986 106.68059 -4.2313568 3.4335975 -1071.0728 -1067.6392 - 7050 0.705 0.076457532 2018.5403 110.71749 -4.2520079 3.5635282 -1071.2028 -1067.6392 - 7100 0.71 0.076457492 2065.9887 114.55487 -4.281219 3.6870374 -1071.3263 -1067.6392 - 7150 0.715 0.07645748 2155.5459 117.3116 -4.3158586 3.7757647 -1071.415 -1067.6392 - 7200 0.72 0.076457494 2209.3453 118.11442 -4.3476298 3.8016043 -1071.4408 -1067.6392 - 7250 0.725 0.076457549 2217.3813 116.73458 -4.3751538 3.757193 -1071.3964 -1067.6392 - 7300 0.73 0.076457599 2194.6993 113.55369 -4.4007611 3.6548138 -1071.294 -1067.6392 - 7350 0.735 0.07645757 2162.8509 109.25439 -4.4239789 3.5164373 -1071.1557 -1067.6392 - 7400 0.74 0.076457504 2179.0418 104.7754 -4.4453985 3.3722777 -1071.0115 -1067.6392 - 7450 0.745 0.076457518 2259.2856 101.07787 -4.4663409 3.2532696 -1070.8925 -1067.6392 - 7500 0.75 0.076457572 2343.5535 98.882501 -4.4873841 3.1826101 -1070.8218 -1067.6392 - 7550 0.755 0.076457589 2398.2908 98.45877 -4.5060042 3.1689719 -1070.8082 -1067.6392 - 7600 0.76 0.076457555 2420.4319 99.704417 -4.5200225 3.209064 -1070.8483 -1067.6392 - 7650 0.765 0.076457552 2411.7072 102.42806 -4.5350873 3.2967265 -1070.936 -1067.6392 - 7700 0.77 0.076457571 2387.7867 106.24775 -4.5597359 3.4196662 -1071.0589 -1067.6392 - 7750 0.775 0.076457574 2378.614 110.33425 -4.5954327 3.5511934 -1071.1904 -1067.6392 - 7800 0.78 0.076457546 2386.339 113.47426 -4.6333762 3.6522573 -1071.2915 -1067.6392 - 7850 0.785 0.076457584 2373.6185 114.65304 -4.6634531 3.6901971 -1071.3294 -1067.6392 - 7900 0.79 0.076457607 2346.7767 113.53184 -4.6813286 3.6541104 -1071.2933 -1067.6392 - 7950 0.795 0.076457576 2325.1204 110.53074 -4.6884073 3.5575175 -1071.1968 -1067.6392 - 8000 0.8 0.076457577 2299.9447 106.81524 -4.6940716 3.4379313 -1071.0772 -1067.6392 - 8050 0.805 0.076457592 2281.6434 103.78514 -4.7080773 3.3404052 -1070.9796 -1067.6392 - 8100 0.81 0.076457595 2279.2037 102.50084 -4.7334489 3.2990691 -1070.9383 -1067.6392 - 8150 0.815 0.076457635 2249.7793 103.47522 -4.7690042 3.3304303 -1070.9697 -1067.6392 - 8200 0.82 0.076457642 2189.9745 106.45522 -4.8073957 3.426344 -1071.0656 -1067.6392 - 8250 0.825 0.076457606 2149.0282 110.6545 -4.8397042 3.5615011 -1071.2007 -1067.6392 - 8300 0.83 0.076457542 2135.0181 115.25463 -4.8644908 3.7095598 -1071.3488 -1067.6392 - 8350 0.835 0.076457496 2133.8536 119.41482 -4.8843171 3.8434585 -1071.4827 -1067.6392 - 8400 0.84 0.076457518 2133.1467 122.18695 -4.8996144 3.932682 -1071.5719 -1067.6392 - 8450 0.845 0.076457578 2134.2861 123.01595 -4.9155444 3.9593637 -1071.5986 -1067.6392 - 8500 0.85 0.076457574 2141.613 121.9466 -4.9391276 3.9249459 -1071.5642 -1067.6392 - 8550 0.855 0.076457587 2138.9082 119.39807 -4.9693983 3.8429195 -1071.4822 -1067.6392 - 8600 0.86 0.076457616 2068.0673 116.09276 -5.000552 3.7365357 -1071.3758 -1067.6392 - 8650 0.865 0.076457587 1952.0961 112.98671 -5.0303107 3.6365649 -1071.2758 -1067.6392 - 8700 0.87 0.076457563 1866.7421 110.99219 -5.0605853 3.5723697 -1071.2116 -1067.6392 - 8750 0.875 0.07645759 1830.3031 110.63824 -5.0918767 3.5609778 -1071.2002 -1067.6392 - 8800 0.88 0.076457593 1839.3749 111.91657 -5.1197801 3.6021218 -1071.2414 -1067.6392 - 8850 0.885 0.07645757 1836.93 114.56856 -5.1423719 3.687478 -1071.3267 -1067.6392 - 8900 0.89 0.076457579 1795.2859 118.25516 -5.1643112 3.8061342 -1071.4454 -1067.6392 - 8950 0.895 0.076457614 1766.8498 122.31379 -5.1895303 3.9367641 -1071.576 -1067.6392 - 9000 0.9 0.076457668 1777.4862 125.80875 -5.2189311 4.0492522 -1071.6885 -1067.6392 - 9050 0.905 0.076457701 1778.9988 127.84202 -5.250791 4.1146947 -1071.7539 -1067.6392 - 9100 0.91 0.076457703 1756.3985 127.83199 -5.2809641 4.1143719 -1071.7536 -1067.6392 - 9150 0.915 0.076457636 1750.7698 125.64781 -5.3037451 4.0440723 -1071.6833 -1067.6392 - 9200 0.92 0.076457553 1795.5785 121.64446 -5.3145968 3.9152214 -1071.5545 -1067.6392 - 9250 0.925 0.076457546 1884.6389 116.77819 -5.317446 3.7585968 -1071.3978 -1067.6392 - 9300 0.93 0.076457575 1961.0059 112.44866 -5.3248028 3.6192473 -1071.2585 -1067.6392 - 9350 0.935 0.076457586 1988.8357 109.85485 -5.3452949 3.5357635 -1071.175 -1067.6392 - 9400 0.94 0.076457583 1972.3793 109.57616 -5.3783713 3.5267939 -1071.166 -1067.6392 - 9450 0.945 0.076457572 1948.7911 111.48324 -5.4161951 3.5881745 -1071.2274 -1067.6392 - 9500 0.95 0.076457563 1922.5709 114.9318 -5.4492314 3.6991693 -1071.3384 -1067.6392 - 9550 0.955 0.076457545 1887.2071 119.14996 -5.473804 3.8349339 -1071.4742 -1067.6392 - 9600 0.96 0.076457569 1854.7259 123.36854 -5.4904613 3.9707121 -1071.6099 -1067.6392 - 9650 0.965 0.076457622 1827.4781 126.8424 -5.4992845 4.0825212 -1071.7218 -1067.6392 - 9700 0.97 0.076457643 1811.2431 129.09763 -5.503264 4.1551074 -1071.7943 -1067.6392 - 9750 0.975 0.076457625 1802.4995 130.06103 -5.5091498 4.1861153 -1071.8253 -1067.6392 - 9800 0.98 0.076457569 1802.206 129.93881 -5.5226464 4.1821816 -1071.8214 -1067.6392 - 9850 0.985 0.076457512 1815.5438 128.98667 -5.542848 4.1515359 -1071.7908 -1067.6392 - 9900 0.99 0.076457501 1820.5473 127.45475 -5.5621249 4.1022301 -1071.7415 -1067.6392 - 9950 0.995 0.076457538 1816.8204 125.90549 -5.5773991 4.0523658 -1071.6916 -1067.6392 - 10000 1 0.076457537 1784.5276 125.28779 -5.5974427 4.0324847 -1071.6717 -1067.6392 - 10050 1.005 0.076457529 1720.376 126.28509 -5.6322599 4.0645836 -1071.7038 -1067.6392 - 10100 1.01 0.076457551 1689.9106 128.66253 -5.6814138 4.1411033 -1071.7803 -1067.6392 - 10150 1.015 0.076457539 1713.0249 131.40846 -5.7369528 4.2294833 -1071.8687 -1067.6392 - 10200 1.02 0.076457489 1743.8221 133.3229 -5.789472 4.2911009 -1071.9303 -1067.6392 - 10250 1.025 0.076457427 1770.5405 133.47365 -5.8284105 4.2959531 -1071.9352 -1067.6392 - 10300 1.03 0.076457402 1784.3689 131.77123 -5.852419 4.2411593 -1071.8804 -1067.6392 - 10350 1.035 0.076457432 1759.9766 128.82223 -5.8669372 4.1462436 -1071.7855 -1067.6392 - 10400 1.04 0.076457457 1756.0701 125.3228 -5.8723914 4.0336114 -1071.6728 -1067.6392 - 10450 1.045 0.076457431 1796.2676 122.12283 -5.8711897 3.930618 -1071.5698 -1067.6392 - 10500 1.05 0.076457363 1832.5849 120.24945 -5.8728862 3.870322 -1071.5096 -1067.6392 - 10550 1.055 0.076457315 1825.9591 120.26647 -5.8808515 3.8708698 -1071.5101 -1067.6392 - 10600 1.06 0.076457322 1783.5912 121.98369 -5.8879416 3.9261399 -1071.5654 -1067.6392 - 10650 1.065 0.07645737 1765.4445 124.88567 -5.8906657 4.0195423 -1071.6588 -1067.6392 - 10700 1.07 0.076457449 1789.2376 128.29349 -5.8943984 4.1292256 -1071.7685 -1067.6392 - 10750 1.075 0.076457481 1818.6141 131.12076 -5.9023895 4.2202233 -1071.8595 -1067.6392 - 10800 1.08 0.076457417 1821.6989 132.13157 -5.9106221 4.2527572 -1071.892 -1067.6392 - 10850 1.085 0.076457331 1835.7675 130.83646 -5.9174483 4.2110729 -1071.8503 -1067.6392 - 10900 1.09 0.076457313 1863.9325 127.86582 -5.9253528 4.1154608 -1071.7547 -1067.6392 - 10950 1.095 0.076457328 1879.7524 124.69175 -5.9376375 4.0133007 -1071.6525 -1067.6392 - 11000 1.1 0.07645735 1877.2445 122.96147 -5.9563654 3.9576103 -1071.5968 -1067.6392 - 11050 1.105 0.076457334 1853.502 123.73028 -5.9816201 3.9823552 -1071.6216 -1067.6392 - 11100 1.11 0.076457299 1840.4 127.02072 -6.0118687 4.0882605 -1071.7275 -1067.6392 - 11150 1.115 0.076457349 1868.0417 131.88474 -6.0432323 4.2448126 -1071.884 -1067.6392 - 11200 1.12 0.076457425 1906.0826 137.04774 -6.0742843 4.4109879 -1072.0502 -1067.6392 - 11250 1.125 0.076457409 1916.8851 141.44887 -6.1055084 4.5526417 -1072.1919 -1067.6392 - 11300 1.13 0.076457315 1929.063 144.55599 -6.1379843 4.6526467 -1072.2919 -1067.6392 - 11350 1.135 0.07645728 1963.9888 146.27645 -6.1715945 4.7080209 -1072.3473 -1067.6392 - 11400 1.14 0.076457317 2003.9719 146.52242 -6.201081 4.7159377 -1072.3552 -1067.6392 - 11450 1.145 0.076457337 2032.7751 145.14866 -6.2190123 4.6717222 -1072.311 -1067.6392 - 11500 1.15 0.076457346 2007.3165 142.48643 -6.228223 4.5860364 -1072.2253 -1067.6392 - 11550 1.155 0.076457364 1930.307 139.42166 -6.2424032 4.4873945 -1072.1266 -1067.6392 - 11600 1.16 0.076457384 1815.1751 136.55133 -6.2668555 4.3950107 -1072.0342 -1067.6392 - 11650 1.165 0.076457374 1692.3408 134.02582 -6.2982889 4.3137251 -1071.953 -1067.6392 - 11700 1.17 0.076457362 1632.1328 131.95661 -6.333283 4.2471259 -1071.8864 -1067.6392 - 11750 1.175 0.07645735 1668.5268 130.40398 -6.3655085 4.1971534 -1071.8364 -1067.6392 - 11800 1.18 0.076457303 1739.9788 129.31098 -6.3892439 4.1619742 -1071.8012 -1067.6392 - 11850 1.185 0.076457253 1807.7337 128.65584 -6.4083517 4.1408881 -1071.7801 -1067.6392 - 11900 1.19 0.0764573 1826.428 128.39557 -6.4305339 4.1325111 -1071.7717 -1067.6392 - 11950 1.195 0.076457354 1740.376 128.35778 -6.456201 4.1312949 -1071.7705 -1067.6392 - 12000 1.2 0.076457321 1628.3377 128.64127 -6.4864265 4.1404191 -1071.7797 -1067.6392 - 12050 1.205 0.076457228 1610.9113 129.62765 -6.5236327 4.1721667 -1071.8114 -1067.6392 - 12100 1.21 0.07645719 1647.6711 131.56179 -6.5624185 4.2344183 -1071.8736 -1067.6392 - 12150 1.215 0.076457244 1667.2405 134.45387 -6.593096 4.327502 -1071.9667 -1067.6392 - 12200 1.22 0.076457281 1650.0369 138.29884 -6.6148053 4.4512554 -1072.0905 -1067.6392 - 12250 1.225 0.076457269 1610.0214 142.96914 -6.6359085 4.6015728 -1072.2408 -1067.6392 - 12300 1.23 0.076457261 1594.6496 147.74828 -6.6580315 4.755393 -1072.3946 -1067.6392 - 12350 1.235 0.076457238 1609.8485 151.54432 -6.6730075 4.8775714 -1072.5168 -1067.6392 - 12400 1.24 0.076457201 1649.4384 153.78009 -6.6795567 4.9495317 -1072.5888 -1067.6392 - 12450 1.245 0.076457189 1676.2248 154.4468 -6.6837801 4.9709901 -1072.6102 -1067.6392 - 12500 1.25 0.076457239 1670.814 153.58107 -6.6881901 4.9431258 -1072.5824 -1067.6392 - 12550 1.255 0.076457285 1649.8854 151.2045 -6.6908201 4.8666342 -1072.5059 -1067.6392 - 12600 1.26 0.076457284 1650.7306 147.66332 -6.6919133 4.7526585 -1072.3919 -1067.6392 - 12650 1.265 0.076457189 1716.8308 143.58784 -6.6915867 4.6214861 -1072.2607 -1067.6392 - 12700 1.27 0.076457085 1831.8331 139.80608 -6.6912135 4.4997672 -1072.139 -1067.6392 - 12750 1.275 0.076457143 1914.1068 137.09279 -6.6943577 4.4124378 -1072.0517 -1067.6392 - 12800 1.28 0.076457209 1952.4216 135.78967 -6.7027456 4.370496 -1072.0097 -1067.6392 - 12850 1.285 0.076457218 1975.0105 135.8441 -6.71489 4.3722479 -1072.0115 -1067.6392 - 12900 1.29 0.076457295 1973.6709 137.16928 -6.7284709 4.4148997 -1072.0541 -1067.6392 - 12950 1.295 0.076457414 1949.6975 139.70897 -6.7419581 4.4966417 -1072.1359 -1067.6392 - 13000 1.3 0.076457467 1910.5263 143.0515 -6.7515077 4.6042234 -1072.2435 -1067.6392 - 13050 1.305 0.076457461 1863.8288 146.61488 -6.7594325 4.7189138 -1072.3581 -1067.6392 - 13100 1.31 0.07645739 1808.6316 149.91966 -6.7746805 4.8252807 -1072.4645 -1067.6392 - 13150 1.315 0.07645729 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-1077.8284 -1067.6392 - 45000 4.5 0.07645794 879.79667 318.12269 -17.875334 10.239026 -1077.8783 -1067.6392 - 45050 4.505 0.076457864 861.6753 323.54624 -17.930753 10.413587 -1078.0528 -1067.6392 - 45100 4.51 0.076457773 868.31935 329.69269 -17.990903 10.611415 -1078.2506 -1067.6392 - 45150 4.515 0.076457818 892.5502 332.57348 -18.015322 10.704136 -1078.3434 -1067.6392 - 45200 4.52 0.076457979 934.55633 331.51408 -18.006044 10.670038 -1078.3093 -1067.6392 - 45250 4.525 0.076457934 969.26205 329.02929 -17.994029 10.590063 -1078.2293 -1067.6392 - 45300 4.53 0.076457821 986.82839 326.98424 -17.994973 10.524241 -1078.1635 -1067.6392 - 45350 4.535 0.076457878 969.0246 325.50185 -18.001111 10.47653 -1078.1158 -1067.6392 - 45400 4.54 0.076458012 949.66785 324.76289 -18.004536 10.452746 -1078.092 -1067.6392 - 45450 4.545 0.076457931 934.25079 325.87047 -18.014727 10.488394 -1078.1276 -1067.6392 - 45500 4.55 0.076457855 926.68239 328.82491 -18.026773 10.583485 -1078.2227 -1067.6392 - 45550 4.555 0.076457796 929.74295 331.7329 -18.027681 10.677081 -1078.3163 -1067.6392 - 45600 4.56 0.076457858 934.2471 332.34645 -18.020161 10.696829 -1078.3361 -1067.6392 - 45650 4.565 0.076457947 919.70747 330.09857 -18.007458 10.624479 -1078.2637 -1067.6392 - 45700 4.57 0.076457972 912.95486 326.17283 -17.995078 10.498126 -1078.1374 -1067.6392 - 45750 4.575 0.076457896 941.11127 321.60716 -17.994665 10.351176 -1077.9904 -1067.6392 - 45800 4.58 0.076457862 966.79612 317.78513 -18.009696 10.228161 -1077.8674 -1067.6392 - 45850 4.585 0.076457935 944.28578 315.85752 -18.027571 10.16612 -1077.8053 -1067.6392 - 45900 4.59 0.076458044 901.04422 316.68004 -18.043848 10.192593 -1077.8318 -1067.6392 - 45950 4.595 0.076458007 879.51756 320.93625 -18.067698 10.329582 -1077.9688 -1067.6392 - 46000 4.6 0.076457964 872.83739 327.90148 -18.094801 10.553764 -1078.193 -1067.6392 - 46050 4.605 0.076457967 876.29409 335.50363 -18.112035 10.798445 -1078.4377 -1067.6392 - 46100 4.61 0.076457881 897.82101 341.25719 -18.123994 10.983628 -1078.6229 -1067.6392 - 46150 4.615 0.076457848 917.72011 342.09311 -18.135768 11.010532 -1078.6498 -1067.6392 - 46200 4.62 0.076457904 935.79066 336.81461 -18.142721 10.84064 -1078.4799 -1067.6392 - 46250 4.625 0.07645791 958.856 329.24209 -18.153564 10.596912 -1078.2361 -1067.6392 - 46300 4.63 0.076457941 976.84674 323.74284 -18.177828 10.419914 -1078.0591 -1067.6392 - 46350 4.635 0.076457974 986.64452 321.53234 -18.208728 10.348768 -1077.988 -1067.6392 - 46400 4.64 0.076457862 996.7259 323.14828 -18.22492 10.400778 -1078.04 -1067.6392 - 46450 4.645 0.076457805 1006.0233 328.59085 -18.21408 10.575952 -1078.2152 -1067.6392 - 46500 4.65 0.076457941 1004.0925 335.85497 -18.186199 10.809753 -1078.449 -1067.6392 - 46550 4.655 0.076457976 986.50596 341.77518 -18.164044 11.0003 -1078.6395 -1067.6392 - 46600 4.66 0.076457959 977.94506 343.98758 -18.166618 11.071507 -1078.7107 -1067.6392 - 46650 4.665 0.07645792 979.65854 341.91053 -18.193889 11.004656 -1078.6439 -1067.6392 - 46700 4.67 0.07645783 995.8469 337.32643 -18.237006 10.857113 -1078.4963 -1067.6392 - 46750 4.675 0.076457742 996.88168 332.71719 -18.282271 10.708761 -1078.348 -1067.6392 - 46800 4.68 0.076457785 982.69373 328.43469 -18.306019 10.570925 -1078.2102 -1067.6392 - 46850 4.685 0.076457823 978.36015 323.5801 -18.306181 10.414677 -1078.0539 -1067.6392 - 46900 4.69 0.076457791 962.75325 318.03098 -18.3112 10.236074 -1077.8753 -1067.6392 - 46950 4.695 0.076457771 943.72644 312.62711 -18.333493 10.062146 -1077.7014 -1067.6392 - 47000 4.7 0.076457655 933.06364 309.79024 -18.359925 9.9708393 -1077.6101 -1067.6392 - 47050 4.705 0.076457527 923.63321 312.99794 -18.385002 10.074082 -1077.7133 -1067.6392 - 47100 4.71 0.076457491 918.61147 323.5351 -18.420653 10.413228 -1078.0525 -1067.6392 - 47150 4.715 0.076457637 920.24413 338.17027 -18.464512 10.884273 -1078.5235 -1067.6392 - 47200 4.72 0.076457729 914.26076 351.25395 -18.491106 11.305381 -1078.9446 -1067.6392 - 47250 4.725 0.07645769 894.45791 358.77754 -18.490423 11.547534 -1079.1868 -1067.6392 - 47300 4.73 0.076457673 866.24513 359.47999 -18.476062 11.570142 -1079.2094 -1067.6392 - 47350 4.735 0.076457644 850.87063 353.65236 -18.459228 11.382576 -1079.0218 -1067.6392 - 47400 4.74 0.07645765 861.60254 342.84162 -18.444647 11.034624 -1078.6739 -1067.6392 - 47450 4.745 0.076457629 868.52502 329.8691 -18.432312 10.617093 -1078.2563 -1067.6392 - 47500 4.75 0.076457475 874.96863 318.16288 -18.423034 10.240319 -1077.8795 -1067.6392 - 47550 4.755 0.076457461 893.70831 310.61468 -18.425459 9.9973745 -1077.6366 -1067.6392 - 47600 4.76 0.076457507 898.58686 308.29041 -18.437291 9.9225663 -1077.5618 -1067.6392 - 47650 4.765 0.076457495 906.98902 310.84197 -18.447354 10.00469 -1077.6439 -1067.6392 - 47700 4.77 0.076457476 917.08363 317.51731 -18.453233 10.219541 -1077.8588 -1067.6392 - 47750 4.775 0.07645741 913.18684 326.63525 -18.458615 10.513009 -1078.1522 -1067.6392 - 47800 4.78 0.076457341 914.30453 335.22798 -18.466228 10.789573 -1078.4288 -1067.6392 - 47850 4.785 0.076457324 930.54553 340.64884 -18.477564 10.964047 -1078.6033 -1067.6392 - 47900 4.79 0.076457362 944.82928 342.0923 -18.497904 11.010506 -1078.6497 -1067.6392 - 47950 4.795 0.076457403 948.97835 339.9758 -18.525445 10.942385 -1078.5816 -1067.6392 - 48000 4.8 0.076457478 949.55048 335.14347 -18.544304 10.786853 -1078.4261 -1067.6392 - 48050 4.805 0.076457492 934.49484 329.4616 -18.547259 10.603977 -1078.2432 -1067.6392 - 48100 4.81 0.076457483 906.2488 325.50663 -18.537762 10.476683 -1078.1159 -1067.6392 - 48150 4.815 0.076457537 907.61196 324.83016 -18.527959 10.454911 -1078.0941 -1067.6392 - 48200 4.82 0.076457521 928.41301 327.05163 -18.532299 10.526411 -1078.1656 -1067.6392 - 48250 4.825 0.076457453 941.11541 331.5379 -18.558254 10.670805 -1078.31 -1067.6392 - 48300 4.83 0.07645744 943.62955 337.63093 -18.594136 10.866914 -1078.5061 -1067.6392 - 48350 4.835 0.076457431 950.73848 343.5387 -18.62029 11.05706 -1078.6963 -1067.6392 - 48400 4.84 0.076457508 977.05827 347.46226 -18.634634 11.183342 -1078.8226 -1067.6392 - 48450 4.845 0.076457572 985.51176 349.38288 -18.652405 11.245159 -1078.8844 -1067.6392 - 48500 4.85 0.0764575 966.51991 350.00883 -18.680976 11.265306 -1078.9045 -1067.6392 - 48550 4.855 0.076457449 952.81522 348.84984 -18.705088 11.228003 -1078.8672 -1067.6392 - 48600 4.86 0.07645757 956.4504 345.07299 -18.706134 11.106442 -1078.7457 -1067.6392 - 48650 4.865 0.076457648 962.27213 339.6091 -18.687227 10.930583 -1078.5698 -1067.6392 - 48700 4.87 0.076457531 951.28586 335.48047 -18.675207 10.797699 -1078.4369 -1067.6392 - 48750 4.875 0.076457622 939.27346 335.37698 -18.691822 10.794368 -1078.4336 -1067.6392 - 48800 4.88 0.07645763 929.93644 338.62392 -18.723472 10.898874 -1078.5381 -1067.6392 - 48850 4.885 0.07645746 927.0018 341.61788 -18.739309 10.995236 -1078.6345 -1067.6392 - 48900 4.89 0.076457454 933.2133 341.45716 -18.734537 10.990064 -1078.6293 -1067.6392 - 48950 4.895 0.076457525 927.17347 338.03446 -18.732333 10.879901 -1078.5191 -1067.6392 - 49000 4.9 0.076457565 934.00454 333.29208 -18.749493 10.727264 -1078.3665 -1067.6392 - 49050 4.905 0.076457546 946.42674 329.88244 -18.783172 10.617522 -1078.2568 -1067.6392 - 49100 4.91 0.076457456 953.85036 329.62056 -18.816988 10.609094 -1078.2483 -1067.6392 - 49150 4.915 0.076457497 981.62511 332.41677 -18.829947 10.699092 -1078.3383 -1067.6392 - 49200 4.92 0.076457502 1010.935 336.90702 -18.819016 10.843614 -1078.4828 -1067.6392 - 49250 4.925 0.076457418 1025.5157 341.57069 -18.807495 10.993718 -1078.6329 -1067.6392 - 49300 4.93 0.076457502 1027.8193 344.89678 -18.811783 11.100771 -1078.74 -1067.6392 - 49350 4.935 0.076457543 1020.505 345.48293 -18.816811 11.119636 -1078.7589 -1067.6392 - 49400 4.94 0.076457478 1016.2039 342.92093 -18.803277 11.037176 -1078.6764 -1067.6392 - 49450 4.945 0.07645749 1018.2955 337.76884 -18.778837 10.871352 -1078.5106 -1067.6392 - 49500 4.95 0.07645759 1012.1553 330.63853 -18.761954 10.641858 -1078.2811 -1067.6392 - 49550 4.955 0.076457651 985.5222 322.69351 -18.765732 10.386141 -1078.0254 -1067.6392 - 49600 4.96 0.076457607 966.22788 316.25074 -18.798665 10.178775 -1077.818 -1067.6392 - 49650 4.965 0.076457494 961.04675 313.18195 -18.839015 10.080004 -1077.7192 -1067.6392 - 49700 4.97 0.076457431 960.65868 314.4735 -18.863274 10.121574 -1077.7608 -1067.6392 - 49750 4.975 0.076457515 966.54445 320.68235 -18.880959 10.32141 -1077.9606 -1067.6392 - 49800 4.98 0.076457498 965.47876 331.30789 -18.90627 10.663401 -1078.3026 -1067.6392 - 49850 4.985 0.076457382 964.05595 343.93887 -18.938996 11.069939 -1078.7092 -1067.6392 - 49900 4.99 0.076457357 944.93024 354.89734 -18.970612 11.422646 -1079.0619 -1067.6392 - 49950 4.995 0.076457532 918.77322 361.48317 -18.987516 11.634616 -1079.2739 -1067.6392 - 50000 5 0.07645762 900.51128 363.08297 -18.994661 11.686107 -1079.3253 -1067.6392 -Loop time of 52.5523 on 4 procs for 50000 steps with 250 atoms - -Performance: 8.220 ns/day, 2.920 hours/ns, 951.434 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 | 10.242 | 10.478 | 10.799 | 6.3 | 19.94 -Neigh | 0.10368 | 0.10776 | 0.11329 | 1.1 | 0.21 -Comm | 2.4492 | 2.7097 | 2.8852 | 11.0 | 5.16 -Output | 5.5737 | 5.9107 | 6.2742 | 11.8 | 11.25 -Modify | 32.833 | 33.256 | 33.661 | 5.2 | 63.28 -Other | | 0.09063 | | | 0.17 - -Nlocal: 62.5 ave 66 max 57 min -Histogram: 1 0 0 0 0 1 0 0 1 1 -Nghost: 772 ave 785 max 755 min -Histogram: 1 0 0 0 0 0 2 0 0 1 -Neighs: 1931 ave 2025 max 1751 min -Histogram: 1 0 0 0 0 0 1 0 0 2 -FullNghs: 3862 ave 4082 max 3518 min -Histogram: 1 0 0 0 0 1 0 0 1 1 - -Total # of neighbors = 15448 -Ave neighs/atom = 61.792 -Neighbor list builds = 614 -Dangerous builds = 0 - -Please see the log.cite file for references relevant to this simulation - -Total wall time: 0:00:52 diff --git a/examples/SPIN/iron/log.30Apr19.spin.iron.g++.1 b/examples/SPIN/iron/log.30Apr19.spin.iron.g++.1 new file mode 100644 index 0000000000..f02c43e28c --- /dev/null +++ b/examples/SPIN/iron/log.30Apr19.spin.iron.g++.1 @@ -0,0 +1,1117 @@ +LAMMPS (30 Apr 2019) + using 1 OpenMP thread(s) per MPI task +# bcc iron in a 3d periodic box + +clear + using 1 OpenMP thread(s) per MPI task +units metal +atom_style spin + +dimension 3 +boundary p p p + +# necessary for the serial algorithm (sametag) +atom_modify map array + +lattice bcc 2.8665 +Lattice spacing in x,y,z = 2.8665 2.8665 2.8665 +region box block 0.0 5.0 0.0 5.0 0.0 5.0 +create_box 1 box +Created orthogonal box = (0 0 0) to (14.3325 14.3325 14.3325) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 250 atoms + create_atoms CPU = 0.00074935 secs + +# setting mass, mag. moments, and interactions for bcc iron + +mass 1 55.845 + +set group all spin/random 31 2.2 + 250 settings made for spin/random +velocity all create 100 4928459 rot yes dist gaussian + +pair_style hybrid/overlay eam/alloy spin/exchange 3.5 +pair_coeff * * eam/alloy Fe_Mishin2006.eam.alloy Fe +pair_coeff * * spin/exchange exchange 3.4 0.02726 0.2171 1.841 + +neighbor 0.1 bin +neigh_modify every 10 check yes delay 20 + +fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 +fix 2 all langevin/spin 0.0 0.0 21 + +fix 3 all nve/spin lattice yes +timestep 0.0001 + +# compute and output options + +compute out_mag all spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo_style custom step time v_magnorm v_tmag temp v_emag ke pe etotal +thermo 50 + +compute outsp all property/atom spx spy spz sp fmx fmy fmz +dump 100 all custom 1 dump_iron.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] + +run 50000 +Neighbor list info ... + update every 10 steps, delay 20 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 5.77337 + ghost atom cutoff = 5.77337 + binsize = 2.88668, bins = 5 5 5 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair eam/alloy, perpetual, half/full from (2) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none + (2) pair spin/exchange, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 7.319 | 7.319 | 7.319 Mbytes +Step Time v_magnorm v_tmag Temp v_emag KinEng PotEng TotEng + 0 0 0.076456975 9109.0924 100.00358 -0.85791269 3.2186929 -1070.8579 -1067.6392 + 50 0.005 0.076456974 9316.7659 96.663685 -0.86504718 3.1111957 -1070.7504 -1067.6392 + 100 0.01 0.076456983 9488.3743 86.965803 -0.88035771 2.7990619 -1070.4383 -1067.6392 + 150 0.015 0.076456973 9589.0566 72.421197 -0.8996913 2.3309324 -1069.9702 -1067.6392 + 200 0.02 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0.076457114 2185.0532 108.81826 -4.1989101 3.5024002 -1071.1416 -1067.6392 + 7150 0.715 0.076457137 2139.1143 111.85634 -4.2283255 3.6001832 -1071.2394 -1067.6392 + 7200 0.72 0.076457149 2101.4939 113.84909 -4.2559584 3.6643212 -1071.3036 -1067.6392 + 7250 0.725 0.07645712 2118.2862 113.94356 -4.2760809 3.6673619 -1071.3066 -1067.6392 + 7300 0.73 0.076457121 2191.9037 111.95148 -4.2925005 3.6032452 -1071.2425 -1067.6392 + 7350 0.735 0.076457137 2227.2391 108.2126 -4.3103519 3.4829066 -1071.1221 -1067.6392 + 7400 0.74 0.076457111 2182.826 103.4321 -4.3300063 3.3290426 -1070.9683 -1067.6392 + 7450 0.745 0.076457109 2101.7168 98.840049 -4.3541992 3.1812437 -1070.8205 -1067.6392 + 7500 0.75 0.076457149 2036.3108 95.828239 -4.386682 3.0843062 -1070.7235 -1067.6392 + 7550 0.755 0.076457161 1994.4837 95.142177 -4.4221587 3.0622248 -1070.7015 -1067.6392 + 7600 0.76 0.076457127 1970.6785 96.747859 -4.4522387 3.1139049 -1070.7531 -1067.6392 + 7650 0.765 0.076457086 1993.9417 100.15534 -4.4763203 3.2235774 -1070.8628 -1067.6392 + 7700 0.77 0.076457048 2073.7836 104.50424 -4.4979798 3.3635502 -1071.0028 -1067.6392 + 7750 0.775 0.076457026 2168.4033 108.65953 -4.5168753 3.4972912 -1071.1365 -1067.6392 + 7800 0.78 0.07645702 2217.6427 111.71942 -4.5326251 3.5957762 -1071.235 -1067.6392 + 7850 0.785 0.076457017 2202.5357 113.33023 -4.5487958 3.6476215 -1071.2869 -1067.6392 + 7900 0.79 0.076457015 2164.601 113.51362 -4.5690254 3.653524 -1071.2928 -1067.6392 + 7950 0.795 0.076457037 2131.6906 112.46493 -4.5932729 3.6197711 -1071.259 -1067.6392 + 8000 0.8 0.076457042 2076.7626 110.60384 -4.6198371 3.5598705 -1071.1991 -1067.6392 + 8050 0.805 0.07645706 2008.3681 108.69863 -4.6506123 3.4985496 -1071.1378 -1067.6392 + 8100 0.81 0.076457078 1991.1056 107.59889 -4.6874954 3.4631539 -1071.1024 -1067.6392 + 8150 0.815 0.076457081 2030.108 107.96066 -4.7301631 3.4747976 -1071.114 -1067.6392 + 8200 0.82 0.07645709 2053.0781 110.00158 -4.7752612 3.5404861 -1071.1797 -1067.6392 + 8250 0.825 0.076457092 2080.7633 113.42163 -4.8192627 3.650563 -1071.2898 -1067.6392 + 8300 0.83 0.076457092 2136.3278 117.426 -4.8602394 3.7794468 -1071.4187 -1067.6392 + 8350 0.835 0.076457128 2143.1741 120.76905 -4.8928022 3.8870456 -1071.5263 -1067.6392 + 8400 0.84 0.076457182 2096.2614 122.36127 -4.9132303 3.9382923 -1071.5775 -1067.6392 + 8450 0.845 0.076457199 2045.0508 121.81432 -4.9242986 3.9206885 -1071.5599 -1067.6392 + 8500 0.85 0.076457148 1988.55 119.39197 -4.9305717 3.8427231 -1071.482 -1067.6392 + 8550 0.855 0.076457089 1927.6698 115.82938 -4.9366606 3.7280586 -1071.3673 -1067.6392 + 8600 0.86 0.0764571 1904.9377 112.15467 -4.9485473 3.6097852 -1071.249 -1067.6392 + 8650 0.865 0.076457183 1942.1657 109.35829 -4.9712735 3.5197814 -1071.159 -1067.6392 + 8700 0.87 0.076457275 1995.7079 107.97044 -5.0032067 3.4751123 -1071.1143 -1067.6392 + 8750 0.875 0.076457274 2021.2979 107.91844 -5.0351272 3.4734386 -1071.1127 -1067.6392 + 8800 0.88 0.076457159 2019.7716 108.89001 -5.0595657 3.5047095 -1071.1439 -1067.6392 + 8850 0.885 0.076457056 1997.5026 110.65412 -5.0764543 3.5614886 -1071.2007 -1067.6392 + 8900 0.89 0.076457086 1958.2352 113.01816 -5.0898539 3.6375771 -1071.2768 -1067.6392 + 8950 0.895 0.076457184 1948.1688 115.69887 -5.1049282 3.723858 -1071.3631 -1067.6392 + 9000 0.9 0.076457251 1946.4034 118.2422 -5.125187 3.8057169 -1071.4449 -1067.6392 + 9050 0.905 0.076457271 1929.5103 120.07623 -5.1485984 3.8647467 -1071.504 -1067.6392 + 9100 0.91 0.076457223 1920.5823 120.83551 -5.1696144 3.8891848 -1071.5284 -1067.6392 + 9150 0.915 0.07645719 1947.9739 120.53164 -5.1820234 3.8794043 -1071.5186 -1067.6392 + 9200 0.92 0.076457191 2021.9322 119.4904 -5.1820769 3.8458913 -1071.4851 -1067.6392 + 9250 0.925 0.076457189 2120.5676 118.28073 -5.1733083 3.8069571 -1071.4462 -1067.6392 + 9300 0.93 0.076457202 2218.9759 117.51293 -5.1649043 3.7822448 -1071.4215 -1067.6392 + 9350 0.935 0.07645722 2256.6996 117.52636 -5.163384 3.7826772 -1071.4219 -1067.6392 + 9400 0.94 0.076457192 2219.8074 118.22843 -5.1666597 3.8052737 -1071.4445 -1067.6392 + 9450 0.945 0.076457133 2130.6686 119.30164 -5.1680994 3.8398158 -1071.479 -1067.6392 + 9500 0.95 0.076457125 2013.4271 120.65247 -5.1678977 3.8832933 -1071.5225 -1067.6392 + 9550 0.955 0.076457169 1923.3398 122.44923 -5.1747845 3.9411236 -1071.5804 -1067.6392 + 9600 0.96 0.076457205 1913.1904 124.48108 -5.1900088 4.0065202 -1071.6458 -1067.6392 + 9650 0.965 0.076457203 1960.3017 126.09586 -5.2054982 4.0584932 -1071.6977 -1067.6392 + 9700 0.97 0.0764572 1993.4886 126.91655 -5.2204458 4.0849076 -1071.7241 -1067.6392 + 9750 0.975 0.076457237 2016.3395 126.88895 -5.2391789 4.0840193 -1071.7233 -1067.6392 + 9800 0.98 0.076457278 2059.2841 125.9798 -5.2613642 4.0547577 -1071.694 -1067.6392 + 9850 0.985 0.076457268 2076.0892 124.30551 -5.2849423 4.0008692 -1071.6401 -1067.6392 + 9900 0.99 0.076457232 2054.9566 122.26397 -5.3097299 3.9351607 -1071.5744 -1067.6392 + 9950 0.995 0.076457211 2050.2277 120.49535 -5.3384666 3.8782362 -1071.5175 -1067.6392 + 10000 1 0.076457247 2069.6559 119.63397 -5.374562 3.8505122 -1071.4897 -1067.6392 + 10050 1.005 0.076457306 2079.8366 119.92165 -5.4169176 3.8597712 -1071.499 -1067.6392 + 10100 1.01 0.076457317 2051.4213 121.0737 -5.4602428 3.896851 -1071.5361 -1067.6392 + 10150 1.015 0.076457329 2026.2947 122.36851 -5.4975255 3.9385254 -1071.5778 -1067.6392 + 10200 1.02 0.076457353 2042.1162 122.97997 -5.5239278 3.9582059 -1071.5974 -1067.6392 + 10250 1.025 0.076457364 2059.2177 122.42397 -5.5402625 3.9403105 -1071.5795 -1067.6392 + 10300 1.03 0.076457332 2037.1418 120.82131 -5.5531843 3.8887277 -1071.528 -1067.6392 + 10350 1.035 0.076457305 1953.9125 118.75093 -5.5690263 3.8220908 -1071.4613 -1067.6392 + 10400 1.04 0.076457265 1845.8999 116.97821 -5.5872522 3.7650343 -1071.4043 -1067.6392 + 10450 1.045 0.076457218 1789.9704 116.44416 -5.6054265 3.7478455 -1071.3871 -1067.6392 + 10500 1.05 0.076457227 1790.1722 117.85441 -5.6201726 3.7932355 -1071.4325 -1067.6392 + 10550 1.055 0.076457265 1792.8951 121.26237 -5.6302348 3.9029234 -1071.5422 -1067.6392 + 10600 1.06 0.076457285 1801.2253 126.08926 -5.6408443 4.0582808 -1071.6975 -1067.6392 + 10650 1.065 0.076457276 1848.312 131.30844 -5.6585268 4.2262642 -1071.8655 -1067.6392 + 10700 1.07 0.076457228 1899.189 135.63605 -5.6833 4.3655515 -1072.0048 -1067.6392 + 10750 1.075 0.076457196 1933.4466 137.94816 -5.7116789 4.4399687 -1072.0792 -1067.6392 + 10800 1.08 0.076457209 1952.1407 137.53149 -5.7380474 4.4265577 -1072.0658 -1067.6392 + 10850 1.085 0.076457232 1956.2467 134.36784 -5.7597709 4.3247333 -1071.964 -1067.6392 + 10900 1.09 0.076457254 1935.3183 129.23046 -5.7778262 4.1593827 -1071.7986 -1067.6392 + 10950 1.095 0.07645725 1894.1382 123.56602 -5.7940915 3.9770683 -1071.6163 -1067.6392 + 11000 1.1 0.076457202 1869.9315 119.13104 -5.8115801 3.8343249 -1071.4736 -1067.6392 + 11050 1.105 0.076457157 1872.2105 117.1706 -5.8302554 3.7712266 -1071.4105 -1067.6392 + 11100 1.11 0.076457121 1910.0087 117.93509 -5.8479403 3.7958325 -1071.4351 -1067.6392 + 11150 1.115 0.076457111 1974.5822 120.8604 -5.8628947 3.8899857 -1071.5292 -1067.6392 + 11200 1.12 0.076457152 2017.5386 125.16424 -5.8764671 4.0285084 -1071.6677 -1067.6392 + 11250 1.125 0.076457215 2006.1464 130.14791 -5.8926588 4.1889116 -1071.8281 -1067.6392 + 11300 1.13 0.076457208 1981.6806 134.97307 -5.9111129 4.344213 -1071.9834 -1067.6392 + 11350 1.135 0.076457154 1955.8911 138.78712 -5.9293384 4.4669713 -1072.1062 -1067.6392 + 11400 1.14 0.076457103 1903.025 141.01634 -5.9477992 4.5387205 -1072.178 -1067.6392 + 11450 1.145 0.076457082 1861.8231 141.41934 -5.9709229 4.5516912 -1072.1909 -1067.6392 + 11500 1.15 0.076457105 1864.1 139.85754 -5.999873 4.5014233 -1072.1407 -1067.6392 + 11550 1.155 0.076457135 1864.553 136.29668 -6.0269465 4.3868144 -1072.026 -1067.6392 + 11600 1.16 0.076457167 1838.5238 131.42789 -6.0482365 4.2301086 -1071.8693 -1067.6392 + 11650 1.165 0.076457207 1805.0176 126.80497 -6.0718009 4.0813163 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11.069889 -1078.7091 -1067.6392 + 49200 4.92 0.076456985 960.59968 346.43043 -18.994109 11.150132 -1078.7894 -1067.6392 + 49250 4.925 0.076456928 945.53084 343.0733 -18.986613 11.042081 -1078.6813 -1067.6392 + 49300 4.93 0.076456888 920.51419 333.13647 -18.959986 10.722256 -1078.3615 -1067.6392 + 49350 4.935 0.076456851 907.35436 320.38291 -18.938752 10.311773 -1077.951 -1067.6392 + 49400 4.94 0.07645685 893.81547 310.99739 -18.938412 10.009692 -1077.6489 -1067.6392 + 49450 4.945 0.076456896 870.23823 309.67527 -18.95594 9.9671388 -1077.6064 -1067.6392 + 49500 4.95 0.076456955 872.77052 317.13999 -18.978605 10.207397 -1077.8466 -1067.6392 + 49550 4.955 0.076456967 894.83445 330.73629 -18.98876 10.645004 -1078.2842 -1067.6392 + 49600 4.96 0.076456979 912.1661 346.73247 -18.984428 11.159854 -1078.7991 -1067.6392 + 49650 4.965 0.076456993 915.70238 361.26297 -18.978545 11.627529 -1079.2668 -1067.6392 + 49700 4.97 0.076456983 924.58803 370.71298 -18.984487 11.931685 -1079.5709 -1067.6392 + 49750 4.975 0.076456922 944.17323 372.65166 -18.998747 11.994083 -1079.6333 -1067.6392 + 49800 4.98 0.076456923 948.92864 367.69228 -19.0113 11.834461 -1079.4737 -1067.6392 + 49850 4.985 0.076456921 953.93531 359.51215 -19.018592 11.571177 -1079.2104 -1067.6392 + 49900 4.99 0.076456974 963.60708 351.14054 -19.013112 11.301731 -1078.941 -1067.6392 + 49950 4.995 0.076456997 970.081 343.67798 -19.003119 11.061543 -1078.7008 -1067.6392 + 50000 5 0.076457012 1001.2522 337.57276 -19.005327 10.865041 -1078.5043 -1067.6392 +Loop time of 149.65 on 1 procs for 50000 steps with 250 atoms + +Performance: 2.887 ns/day, 8.314 hours/ns, 334.113 timesteps/s +98.8% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 56.939 | 56.939 | 56.939 | 0.0 | 38.05 +Neigh | 0.65017 | 0.65017 | 0.65017 | 0.0 | 0.43 +Comm | 1.4958 | 1.4958 | 1.4958 | 0.0 | 1.00 +Output | 37.503 | 37.503 | 37.503 | 0.0 | 25.06 +Modify | 52.788 | 52.788 | 52.788 | 0.0 | 35.27 +Other | | 0.2742 | | | 0.18 + +Nlocal: 250 ave 250 max 250 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1335 ave 1335 max 1335 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 7746 ave 7746 max 7746 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 15492 ave 15492 max 15492 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 15492 +Ave neighs/atom = 61.968 +Neighbor list builds = 608 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:02:29 diff --git a/examples/SPIN/iron/log.30Apr19.spin.iron.g++.4 b/examples/SPIN/iron/log.30Apr19.spin.iron.g++.4 new file mode 100644 index 0000000000..6fc3e307f0 --- /dev/null +++ b/examples/SPIN/iron/log.30Apr19.spin.iron.g++.4 @@ -0,0 +1,1117 @@ +LAMMPS (30 Apr 2019) + using 1 OpenMP thread(s) per MPI task +# bcc iron in a 3d periodic box + +clear + using 1 OpenMP thread(s) per MPI task +units metal +atom_style spin + +dimension 3 +boundary p p p + +# necessary for the serial algorithm (sametag) +atom_modify map array + +lattice bcc 2.8665 +Lattice spacing in x,y,z = 2.8665 2.8665 2.8665 +region box block 0.0 5.0 0.0 5.0 0.0 5.0 +create_box 1 box +Created orthogonal box = (0 0 0) to (14.3325 14.3325 14.3325) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 250 atoms + create_atoms CPU = 0.00056982 secs + +# setting mass, mag. moments, and interactions for bcc iron + +mass 1 55.845 + +set group all spin/random 31 2.2 + 250 settings made for spin/random +velocity all create 100 4928459 rot yes dist gaussian + +pair_style hybrid/overlay eam/alloy spin/exchange 3.5 +pair_coeff * * eam/alloy Fe_Mishin2006.eam.alloy Fe +pair_coeff * * spin/exchange exchange 3.4 0.02726 0.2171 1.841 + +neighbor 0.1 bin +neigh_modify every 10 check yes delay 20 + +fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 +fix 2 all langevin/spin 0.0 0.0 21 + +fix 3 all nve/spin lattice yes +timestep 0.0001 + +# compute and output options + +compute out_mag all spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo_style custom step time v_magnorm v_tmag temp v_emag ke pe etotal +thermo 50 + +compute outsp all property/atom spx spy spz sp fmx fmy fmz +dump 100 all custom 1 dump_iron.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] + +run 50000 +Neighbor list info ... + update every 10 steps, delay 20 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 5.77337 + ghost atom cutoff = 5.77337 + binsize = 2.88668, bins = 5 5 5 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair eam/alloy, perpetual, half/full from (2) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none + (2) pair spin/exchange, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 7.265 | 7.265 | 7.265 Mbytes +Step Time v_magnorm v_tmag Temp v_emag KinEng PotEng TotEng + 0 0 0.076456975 9109.0924 100.00358 -0.85791269 3.2186929 -1070.8579 -1067.6392 + 50 0.005 0.076456995 9402.4007 96.298333 -0.85659448 3.0994366 -1070.7387 -1067.6392 + 100 0.01 0.076457028 9589.1846 86.330828 -0.87003341 2.7786247 -1070.4179 -1067.6392 + 150 0.015 0.076457074 9673.9268 71.603402 -0.89006992 2.3046111 -1069.9438 -1067.6392 + 200 0.02 0.076457106 9509.1148 54.648817 -0.91124541 1.7589146 -1069.3981 -1067.6392 + 250 0.025 0.076457128 9004.27 38.599515 -0.93187522 1.2423553 -1068.8816 -1067.6392 + 300 0.03 0.076457157 8353.4371 26.383018 -0.95082226 0.8491579 -1068.4884 -1067.6392 + 350 0.035 0.076457207 7911.1316 20.01039 -0.96826468 0.64404992 -1068.2833 -1067.6392 + 400 0.04 0.076457243 7775.9492 20.097682 -0.98706373 0.64685949 -1068.2861 -1067.6392 + 450 0.045 0.076457231 7737.1225 25.687511 -1.0095684 0.82677249 -1068.466 -1067.6392 + 500 0.05 0.076457204 7676.9809 34.604697 -1.0349855 1.113779 -1068.753 -1067.6392 + 550 0.055 0.076457196 7550.2809 44.251809 -1.0609123 1.4242788 -1069.0635 -1067.6392 + 600 0.06 0.076457188 7209.7657 52.475202 -1.0880854 1.6889551 -1069.3282 -1067.6392 + 650 0.065 0.07645718 6691.1787 57.926479 -1.1179657 1.8644087 -1069.5036 -1067.6392 + 700 0.07 0.076457185 6276.4003 60.030548 -1.1469999 1.9321298 -1069.5714 -1067.6392 + 750 0.075 0.07645719 6149.9253 59.122504 -1.1721939 1.9029037 -1069.5421 -1067.6392 + 800 0.08 0.076457195 6207.0587 56.349146 -1.1949365 1.813641 -1069.4529 -1067.6392 + 850 0.085 0.076457199 6328.4635 53.154464 -1.2164642 1.7108177 -1069.35 -1067.6392 + 900 0.09 0.076457199 6456.2716 50.837416 -1.2366018 1.6362417 -1069.2755 -1067.6392 + 950 0.095 0.076457222 6495.1064 50.234549 -1.2539657 1.6168379 -1069.2561 -1067.6392 + 1000 0.1 0.076457266 6416.775 51.592727 -1.2671834 1.6605519 -1069.2998 -1067.6392 + 1050 0.105 0.076457256 6305.9015 54.719414 -1.2794824 1.7611868 -1069.4004 -1067.6392 + 1100 0.11 0.076457222 6165.987 59.01343 -1.2960617 1.8993931 -1069.5386 -1067.6392 + 1150 0.115 0.076457194 5941.7807 63.475298 -1.317859 2.0430017 -1069.6822 -1067.6392 + 1200 0.12 0.076457182 5692.0982 67.036713 -1.3432854 2.1576286 -1069.7969 -1067.6392 + 1250 0.125 0.076457217 5543.1736 68.917405 -1.3719994 2.2181602 -1069.8574 -1067.6392 + 1300 0.13 0.076457263 5507.9968 68.753418 -1.4042339 2.2128821 -1069.8521 -1067.6392 + 1350 0.135 0.076457286 5500.7848 66.608286 -1.4385667 2.1438394 -1069.7831 -1067.6392 + 1400 0.14 0.076457254 5523.456 62.967429 -1.4712143 2.0266556 -1069.6659 -1067.6392 + 1450 0.145 0.076457188 5501.5777 58.75732 -1.4990458 1.89115 -1069.5304 -1067.6392 + 1500 0.15 0.076457175 5324.4931 55.246308 -1.5236774 1.7781453 -1069.4174 -1067.6392 + 1550 0.155 0.076457234 5025.5908 53.607297 -1.5492947 1.7253925 -1069.3646 -1067.6392 + 1600 0.16 0.076457297 4742.9546 54.443418 -1.5785798 1.7523036 -1069.3915 -1067.6392 + 1650 0.165 0.076457321 4558.083 57.572305 -1.6113848 1.8530093 -1069.4922 -1067.6392 + 1700 0.17 0.076457304 4479.4352 62.073307 -1.6443595 1.9978776 -1069.6371 -1067.6392 + 1750 0.175 0.076457272 4520.5577 66.677964 -1.6742729 2.146082 -1069.7853 -1067.6392 + 1800 0.18 0.076457253 4659.9114 70.277293 -1.7021557 2.2619292 -1069.9012 -1067.6392 + 1850 0.185 0.076457257 4734.1597 72.135028 -1.7307798 2.3217219 -1069.961 -1067.6392 + 1900 0.19 0.076457279 4632.2637 71.873382 -1.7598165 2.3133006 -1069.9525 -1067.6392 + 1950 0.195 0.076457276 4496.6621 69.52131 -1.7866398 2.2375973 -1069.8768 -1067.6392 + 2000 0.2 0.076457276 4507.4594 65.61098 -1.8106776 2.1117403 -1069.751 -1067.6392 + 2050 0.205 0.076457288 4652.9279 61.016261 -1.8317479 1.9638557 -1069.6031 -1067.6392 + 2100 0.21 0.076457307 4738.4188 56.745795 -1.8489776 1.8264074 -1069.4656 -1067.6392 + 2150 0.215 0.076457279 4643.423 53.837376 -1.8647516 1.7327977 -1069.372 -1067.6392 + 2200 0.22 0.076457215 4517.9871 53.044053 -1.8828305 1.707264 -1069.3465 -1067.6392 + 2250 0.225 0.07645717 4436.4399 54.521839 -1.9038753 1.7548277 -1069.3941 -1067.6392 + 2300 0.23 0.076457132 4318.8261 57.895634 -1.9276454 1.8634159 -1069.5026 -1067.6392 + 2350 0.235 0.076457114 4148.8616 62.484473 -1.9559372 2.0111113 -1069.6503 -1067.6392 + 2400 0.24 0.076457144 4014.8498 67.404243 -1.9902034 2.1694579 -1069.8087 -1067.6392 + 2450 0.245 0.076457189 4004.017 71.654167 -2.0278558 2.306245 -1069.9455 -1067.6392 + 2500 0.25 0.076457202 4109.5497 74.379393 -2.0629968 2.3939585 -1070.0332 -1067.6392 + 2550 0.255 0.076457205 4251.6933 75.255112 -2.0918484 2.4221442 -1070.0614 -1067.6392 + 2600 0.26 0.076457208 4320.6876 74.700611 -2.1169691 2.4042972 -1070.0435 -1067.6392 + 2650 0.265 0.076457197 4297.5527 73.627823 -2.143 2.3697686 -1070.009 -1067.6392 + 2700 0.27 0.076457213 4198.4852 72.957211 -2.1702374 2.3481845 -1069.9874 -1067.6392 + 2750 0.275 0.076457256 4019.2384 73.353574 -2.1967187 2.3609417 -1070.0002 -1067.6392 + 2800 0.28 0.076457288 3867.2492 75.083781 -2.2227117 2.4166298 -1070.0559 -1067.6392 + 2850 0.285 0.076457302 3879.8471 77.82546 -2.2488766 2.5048728 -1070.1441 -1067.6392 + 2900 0.29 0.076457321 4003.8986 80.741745 -2.2742584 2.5987357 -1070.238 -1067.6392 + 2950 0.295 0.076457347 4026.6754 82.934399 -2.3001834 2.669308 -1070.3085 -1067.6392 + 3000 0.3 0.076457334 3857.2183 83.701738 -2.3291113 2.6940054 -1070.3332 -1067.6392 + 3050 0.305 0.076457295 3640.7581 82.615991 -2.3614721 2.6590598 -1070.2983 -1067.6392 + 3100 0.31 0.07645725 3489.102 79.573679 -2.3943974 2.5611406 -1070.2004 -1067.6392 + 3150 0.315 0.076457232 3396.4301 74.896125 -2.4236621 2.4105899 -1070.0498 -1067.6392 + 3200 0.32 0.076457259 3378.11 69.450128 -2.4483292 2.2353063 -1069.8745 -1067.6392 + 3250 0.325 0.076457289 3463.7734 64.542714 -2.4729224 2.0773573 -1069.7166 -1067.6392 + 3300 0.33 0.076457318 3637.4971 61.346221 -2.500303 1.9744757 -1069.6137 -1067.6392 + 3350 0.335 0.076457361 3833.5389 60.346704 -2.5252732 1.9423055 -1069.5815 -1067.6392 + 3400 0.34 0.076457387 3965.2081 61.464125 -2.5426842 1.9782706 -1069.6175 -1067.6392 + 3450 0.345 0.076457375 3976.7956 64.41797 -2.5565409 2.0733424 -1069.7126 -1067.6392 + 3500 0.35 0.076457371 3862.8334 68.714547 -2.5743062 2.211631 -1069.8509 -1067.6392 + 3550 0.355 0.076457375 3697.284 73.534942 -2.5974674 2.3667792 -1070.006 -1067.6392 + 3600 0.36 0.076457362 3575.9012 77.902682 -2.6209385 2.5073583 -1070.1466 -1067.6392 + 3650 0.365 0.076457345 3550.0667 81.043684 -2.6394846 2.6084539 -1070.2477 -1067.6392 + 3700 0.37 0.076457309 3535.0981 82.730976 -2.65464 2.6627607 -1070.302 -1067.6392 + 3750 0.375 0.076457309 3444.1795 83.322515 -2.6736085 2.6817998 -1070.321 -1067.6392 + 3800 0.38 0.076457348 3323.7191 83.436143 -2.7008525 2.685457 -1070.3247 -1067.6392 + 3850 0.385 0.076457368 3252.5404 83.62535 -2.7353937 2.6915468 -1070.3308 -1067.6392 + 3900 0.39 0.076457344 3219.5349 84.088597 -2.7722909 2.7064568 -1070.3457 -1067.6392 + 3950 0.395 0.076457316 3210.4164 84.636475 -2.8060651 2.7240906 -1070.3633 -1067.6392 + 4000 0.4 0.076457319 3223.9708 85.042888 -2.8352998 2.7371713 -1070.3764 -1067.6392 + 4050 0.405 0.076457335 3232.7108 85.266853 -2.8607963 2.7443798 -1070.3836 -1067.6392 + 4100 0.41 0.076457314 3206.1428 85.444074 -2.8837721 2.7500838 -1070.3893 -1067.6392 + 4150 0.415 0.076457325 3146.4589 85.771643 -2.9074131 2.7606269 -1070.3999 -1067.6392 + 4200 0.42 0.076457395 3092.6283 86.24875 -2.9341331 2.775983 -1070.4152 -1067.6392 + 4250 0.425 0.07645742 3103.0319 86.563557 -2.9622203 2.7861153 -1070.4253 -1067.6392 + 4300 0.43 0.076457425 3116.9053 86.320099 -2.9880208 2.7782794 -1070.4175 -1067.6392 + 4350 0.435 0.076457427 3061.2259 85.306966 -3.0085539 2.7456709 -1070.3849 -1067.6392 + 4400 0.44 0.076457432 3033.5229 83.703441 -3.0243431 2.6940602 -1070.3333 -1067.6392 + 4450 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2.7153039 -1070.3545 -1067.6392 + 5050 0.505 0.076457408 2755.8292 84.030245 -3.3582878 2.7045787 -1070.3438 -1067.6392 + 5100 0.51 0.076457454 2753.2313 84.932962 -3.3648805 2.7336333 -1070.3729 -1067.6392 + 5150 0.515 0.076457453 2706.7195 86.928397 -3.3711152 2.7978579 -1070.4371 -1067.6392 + 5200 0.52 0.076457474 2678.177 89.583728 -3.3768576 2.8833218 -1070.5226 -1067.6392 + 5250 0.525 0.076457519 2699.6154 92.51484 -3.3860255 2.9776619 -1070.6169 -1067.6392 + 5300 0.53 0.076457531 2703.409 95.385751 -3.4040809 3.0700644 -1070.7093 -1067.6392 + 5350 0.535 0.076457501 2642.6927 97.779641 -3.4335521 3.1471136 -1070.7863 -1067.6392 + 5400 0.54 0.076457502 2536.3506 99.09318 -3.4686216 3.1893909 -1070.8286 -1067.6392 + 5450 0.545 0.076457526 2496.939 98.768917 -3.4975315 3.1789543 -1070.8182 -1067.6392 + 5500 0.55 0.07645752 2590.2956 96.816601 -3.5146308 3.1161175 -1070.7554 -1067.6392 + 5550 0.555 0.07645751 2736.468 93.934193 -3.5252273 3.0233449 -1070.6626 -1067.6392 + 5600 0.56 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1.02 0.076457733 1899.2476 128.11218 -5.6733688 4.12339 -1071.7626 -1067.6392 + 10250 1.025 0.076457747 1895.8986 127.94169 -5.6840919 4.1179026 -1071.7571 -1067.6392 + 10300 1.03 0.076457816 1877.4598 127.6041 -5.7004798 4.107037 -1071.7463 -1067.6392 + 10350 1.035 0.076457876 1829.2074 127.11751 -5.7241722 4.0913757 -1071.7306 -1067.6392 + 10400 1.04 0.076457884 1806.0757 126.48167 -5.756364 4.0709108 -1071.7101 -1067.6392 + 10450 1.045 0.076457869 1822.1953 125.5947 -5.7930905 4.042363 -1071.6816 -1067.6392 + 10500 1.05 0.076457879 1827.9173 124.33858 -5.8252681 4.0019336 -1071.6412 -1067.6392 + 10550 1.055 0.076457858 1812.1963 122.79649 -5.8435788 3.9523004 -1071.5915 -1067.6392 + 10600 1.06 0.076457791 1797.2949 121.53225 -5.8488847 3.9116096 -1071.5508 -1067.6392 + 10650 1.065 0.076457757 1775.25 121.32451 -5.8518555 3.9049236 -1071.5442 -1067.6392 + 10700 1.07 0.076457792 1740.3273 122.44046 -5.8607258 3.9408413 -1071.5801 -1067.6392 + 10750 1.075 0.076457855 1729.7945 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334.77591 -17.228637 10.775023 -1078.4143 -1067.6392 + 45450 4.545 0.076458455 1089.9234 332.91387 -17.252893 10.715091 -1078.3543 -1067.6392 + 45500 4.55 0.076458651 1088.2901 328.25855 -17.279739 10.565256 -1078.2045 -1067.6392 + 45550 4.555 0.076458679 1067.4543 322.55465 -17.319717 10.381672 -1078.0209 -1067.6392 + 45600 4.56 0.076458491 1051.2478 317.7723 -17.374362 10.227748 -1077.867 -1067.6392 + 45650 4.565 0.076458315 1034.4257 314.73532 -17.430482 10.130001 -1077.7692 -1067.6392 + 45700 4.57 0.076458379 1013.128 312.65325 -17.476583 10.062987 -1077.7022 -1067.6392 + 45750 4.575 0.076458582 1006.4499 309.50085 -17.496142 9.9615252 -1077.6008 -1067.6392 + 45800 4.58 0.07645865 1024.4651 304.73909 -17.49261 9.8082641 -1077.4475 -1067.6392 + 45850 4.585 0.076458631 1046.9622 300.08416 -17.492695 9.6584417 -1077.2977 -1067.6392 + 45900 4.59 0.076458586 1042.5796 296.72782 -17.49113 9.5504152 -1077.1896 -1067.6392 + 45950 4.595 0.076458607 1008.0854 295.42286 -17.47404 9.508414 -1077.1476 -1067.6392 + 46000 4.6 0.07645866 1008.1817 297.6509 -17.457674 9.5801252 -1077.2194 -1067.6392 + 46050 4.605 0.076458648 1055.0177 303.82712 -17.454258 9.7789116 -1077.4181 -1067.6392 + 46100 4.61 0.076458681 1067.8096 312.06106 -17.459314 10.043927 -1077.6832 -1067.6392 + 46150 4.615 0.076458697 1032.3327 319.35809 -17.472054 10.278788 -1077.918 -1067.6392 + 46200 4.62 0.076458669 1011.4049 323.68987 -17.497176 10.41821 -1078.0574 -1067.6392 + 46250 4.625 0.076458694 1013.1694 324.55935 -17.524643 10.446195 -1078.0854 -1067.6392 + 46300 4.63 0.076458699 1019.9594 322.92316 -17.537516 10.393533 -1078.0328 -1067.6392 + 46350 4.635 0.076458638 1019.574 321.37933 -17.53535 10.343843 -1077.9831 -1067.6392 + 46400 4.64 0.076458549 1012.1208 322.2852 -17.529784 10.372999 -1078.0122 -1067.6392 + 46450 4.645 0.076458548 1009.7285 324.98438 -17.51749 10.459874 -1078.0991 -1067.6392 + 46500 4.65 0.076458739 1028.6359 327.73895 -17.495382 10.548533 -1078.1878 -1067.6392 + 46550 4.655 0.076458848 1054.5382 329.99374 -17.486615 10.621105 -1078.2603 -1067.6392 + 46600 4.66 0.076458871 1059.0432 330.41234 -17.496838 10.634578 -1078.2738 -1067.6392 + 46650 4.665 0.076458903 1042.6963 327.41225 -17.503279 10.538018 -1078.1773 -1067.6392 + 46700 4.67 0.076458964 1022.4908 322.64011 -17.50695 10.384422 -1078.0237 -1067.6392 + 46750 4.675 0.076458954 994.76603 319.77739 -17.52877 10.292284 -1077.9315 -1067.6392 + 46800 4.68 0.076458851 984.77354 320.04823 -17.564766 10.301001 -1077.9402 -1067.6392 + 46850 4.685 0.076458817 982.80807 322.12061 -17.59199 10.367702 -1078.0069 -1067.6392 + 46900 4.69 0.076458814 979.08705 324.60632 -17.607769 10.447706 -1078.0869 -1067.6392 + 46950 4.695 0.076458855 991.35981 325.87675 -17.625638 10.488596 -1078.1278 -1067.6392 + 47000 4.7 0.076459013 990.03823 324.25249 -17.644352 10.436318 -1078.0756 -1067.6392 + 47050 4.705 0.076459109 971.57257 320.13246 -17.664176 10.303712 -1077.9429 -1067.6392 + 47100 4.71 0.076459008 942.51677 315.82868 -17.695488 10.165191 -1077.8044 -1067.6392 + 47150 4.715 0.076458834 914.38458 312.92259 -17.729828 10.071656 -1077.7109 -1067.6392 + 47200 4.72 0.076458733 915.09427 311.73756 -17.757168 10.033515 -1077.6727 -1067.6392 + 47250 4.725 0.076458745 929.51292 311.72739 -17.778102 10.033188 -1077.6724 -1067.6392 + 47300 4.73 0.076458807 924.69906 311.5334 -17.787073 10.026944 -1077.6662 -1067.6392 + 47350 4.735 0.076458753 911.78727 310.21898 -17.784392 9.9846387 -1077.6239 -1067.6392 + 47400 4.74 0.076458811 927.84413 308.28881 -17.783399 9.9225147 -1077.5617 -1067.6392 + 47450 4.745 0.076458948 980.47197 307.41202 -17.799967 9.8942944 -1077.5335 -1067.6392 + 47500 4.75 0.076458921 1017.4095 308.92974 -17.837931 9.9431434 -1077.5824 -1067.6392 + 47550 4.755 0.076458813 1013.2842 313.10487 -17.889197 10.077523 -1077.7168 -1067.6392 + 47600 4.76 0.076458768 999.59926 319.59121 -17.94301 10.286291 -1077.9255 -1067.6392 + 47650 4.765 0.07645894 987.28899 327.28821 -17.990152 10.534025 -1078.1733 -1067.6392 + 47700 4.77 0.076459039 970.5822 333.98868 -18.025704 10.749685 -1078.3889 -1067.6392 + 47750 4.775 0.076458976 960.77569 337.1295 -18.039516 10.850774 -1078.49 -1067.6392 + 47800 4.78 0.076458945 970.90315 335.79522 -18.031317 10.80783 -1078.4471 -1067.6392 + 47850 4.785 0.07645907 982.20263 331.08028 -18.021902 10.656076 -1078.2953 -1067.6392 + 47900 4.79 0.076459119 990.67784 324.66683 -18.027289 10.449654 -1078.0889 -1067.6392 + 47950 4.795 0.076459083 998.43821 318.73987 -18.04994 10.25889 -1077.8981 -1067.6392 + 48000 4.8 0.076459069 1008.9151 315.53792 -18.077243 10.155833 -1077.7951 -1067.6392 + 48050 4.805 0.076458972 1028.1309 316.51509 -18.096678 10.187284 -1077.8265 -1067.6392 + 48100 4.81 0.076458972 1046.4248 321.4715 -18.10541 10.34681 -1077.986 -1067.6392 + 48150 4.815 0.076458847 1072.5091 328.3071 -18.108273 10.566819 -1078.2061 -1067.6392 + 48200 4.82 0.076458729 1115.3266 334.27433 -18.108253 10.758879 -1078.3981 -1067.6392 + 48250 4.825 0.076458863 1132.7705 338.0335 -18.108395 10.879871 -1078.5191 -1067.6392 + 48300 4.83 0.076458983 1104.4857 340.31669 -18.122648 10.953357 -1078.5926 -1067.6392 + 48350 4.835 0.076458942 1068.6895 341.52058 -18.147861 10.992105 -1078.6313 -1067.6392 + 48400 4.84 0.076458895 1050.2826 340.59905 -18.165876 10.962445 -1078.6017 -1067.6392 + 48450 4.845 0.076458979 1048.172 336.60118 -18.175839 10.83377 -1078.473 -1067.6392 + 48500 4.85 0.076458957 1026.5586 330.00847 -18.186406 10.621579 -1078.2608 -1067.6392 + 48550 4.855 0.076458886 999.91162 322.83938 -18.201023 10.390836 -1078.0301 -1067.6392 + 48600 4.86 0.076458961 989.90718 317.46387 -18.226455 10.217821 -1077.8571 -1067.6392 + 48650 4.865 0.076459015 982.96635 315.18649 -18.260376 10.144522 -1077.7838 -1067.6392 + 48700 4.87 0.076458922 987.30339 316.51586 -18.291398 10.187309 -1077.8265 -1067.6392 + 48750 4.875 0.076458754 1001.7173 321.20925 -18.314994 10.338369 -1077.9776 -1067.6392 + 48800 4.88 0.07645878 1018.8788 327.87563 -18.327226 10.552932 -1078.1922 -1067.6392 + 48850 4.885 0.076458771 1034.4957 334.62729 -18.332453 10.770239 -1078.4095 -1067.6392 + 48900 4.89 0.076458899 1028.6393 339.07218 -18.341739 10.913301 -1078.5525 -1067.6392 + 48950 4.895 0.076459103 1007.6856 338.61189 -18.356096 10.898487 -1078.5377 -1067.6392 + 49000 4.9 0.076459192 999.24745 332.23323 -18.365334 10.693184 -1078.3324 -1067.6392 + 49050 4.905 0.076459086 996.76706 322.52584 -18.367263 10.380744 -1078.02 -1067.6392 + 49100 4.91 0.076459029 995.85019 315.08451 -18.370824 10.14124 -1077.7805 -1067.6392 + 49150 4.915 0.076459032 983.16555 314.29119 -18.382926 10.115706 -1077.7549 -1067.6392 + 49200 4.92 0.076459075 965.8709 319.65382 -18.396231 10.288306 -1077.9275 -1067.6392 + 49250 4.925 0.076459124 962.09918 328.07092 -18.405747 10.559217 -1078.1984 -1067.6392 + 49300 4.93 0.076459019 986.327 337.01122 -18.409264 10.846968 -1078.4862 -1067.6392 + 49350 4.935 0.076458927 1004.57 345.36436 -18.407413 11.11582 -1078.7551 -1067.6392 + 49400 4.94 0.076458977 993.98483 352.63606 -18.40944 11.349865 -1078.9891 -1067.6392 + 49450 4.945 0.076459082 991.26185 357.60801 -18.416364 11.509891 -1079.1491 -1067.6392 + 49500 4.95 0.076459093 1024.0819 359.05103 -18.425791 11.556336 -1079.1956 -1067.6392 + 49550 4.955 0.076458927 1033.8368 356.67554 -18.441932 11.479879 -1079.1191 -1067.6392 + 49600 4.96 0.076458838 1019.5756 350.49667 -18.455292 11.281007 -1078.9202 -1067.6392 + 49650 4.965 0.076458925 1015.2811 341.2581 -18.44834 10.983657 -1078.6229 -1067.6392 + 49700 4.97 0.076458904 1000.5326 331.64361 -18.423481 10.674207 -1078.3134 -1067.6392 + 49750 4.975 0.076458763 997.47426 325.30523 -18.400499 10.470201 -1078.1094 -1067.6392 + 49800 4.98 0.076458774 1001.6165 323.8013 -18.387438 10.421796 -1078.061 -1067.6392 + 49850 4.985 0.076458923 1003.6919 325.43465 -18.371483 10.474367 -1078.1136 -1067.6392 + 49900 4.99 0.076458997 1014.0371 327.90126 -18.352198 10.553757 -1078.193 -1067.6392 + 49950 4.995 0.076458983 1024.0345 329.92754 -18.340929 10.618974 -1078.2582 -1067.6392 + 50000 5 0.076458894 1024.5951 330.62163 -18.327421 10.641314 -1078.2805 -1067.6392 +Loop time of 104.807 on 4 procs for 50000 steps with 250 atoms + +Performance: 4.122 ns/day, 5.823 hours/ns, 477.068 timesteps/s +98.2% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 16.436 | 16.633 | 16.862 | 4.5 | 15.87 +Neigh | 0.16699 | 0.17008 | 0.17166 | 0.4 | 0.16 +Comm | 4.1416 | 4.3331 | 4.5047 | 7.9 | 4.13 +Output | 10.767 | 11.845 | 12.706 | 20.7 | 11.30 +Modify | 70.815 | 71.648 | 72.683 | 8.2 | 68.36 +Other | | 0.1775 | | | 0.17 + +Nlocal: 62.5 ave 65 max 60 min +Histogram: 1 0 0 0 1 0 1 0 0 1 +Nghost: 757.75 ave 776 max 743 min +Histogram: 1 0 0 1 1 0 0 0 0 1 +Neighs: 1932.75 ave 2015 max 1844 min +Histogram: 1 0 0 0 1 1 0 0 0 1 +FullNghs: 3865.5 ave 4024 max 3710 min +Histogram: 1 0 0 1 0 0 1 0 0 1 + +Total # of neighbors = 15462 +Ave neighs/atom = 61.848 +Neighbor list builds = 612 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:01:45 diff --git a/examples/SPIN/iron/log.30Apr19.spin.iron_cubic.g++.1 b/examples/SPIN/iron/log.30Apr19.spin.iron_cubic.g++.1 new file mode 100644 index 0000000000..ee1e71131e --- /dev/null +++ b/examples/SPIN/iron/log.30Apr19.spin.iron_cubic.g++.1 @@ -0,0 +1,161 @@ +LAMMPS (30 Apr 2019) + using 1 OpenMP thread(s) per MPI task +# bcc iron in a 3d periodic box + +clear + using 1 OpenMP thread(s) per MPI task +units metal +atom_style spin + +dimension 3 +boundary p p p + +# necessary for the serial algorithm (sametag) +atom_modify map array + +lattice bcc 2.8665 +Lattice spacing in x,y,z = 2.8665 2.8665 2.8665 +region box block 0.0 5.0 0.0 5.0 0.0 5.0 +create_box 1 box +Created orthogonal box = (0 0 0) to (14.3325 14.3325 14.3325) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 250 atoms + create_atoms CPU = 0.0527296 secs + +# setting mass, mag. moments, and interactions for bcc iron + +mass 1 55.845 +set group all spin 2.2 -1.0 0.0 0.0 + 250 settings made for spin +velocity all create 100 4928459 rot yes dist gaussian + +pair_style hybrid/overlay eam/alloy spin/exchange 3.5 +pair_coeff * * eam/alloy Fe_Mishin2006.eam.alloy Fe +pair_coeff * * spin/exchange exchange 3.4 0.02726 0.2171 1.841 +neighbor 0.1 bin +neigh_modify every 10 check yes delay 20 + +fix 1 all precession/spin cubic 0.001 0.0005 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1.0 +fix_modify 1 energy yes +fix 2 all langevin/spin 0.0 0.0 21 + +fix 3 all nve/spin lattice yes +timestep 0.0001 + +# compute and output options + +compute out_mag all spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +variable magx equal c_out_mag[1] +variable magy equal c_out_mag[2] +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo_style custom step time v_magx v_magy v_magz v_magnorm v_tmag v_emag pe etotal +thermo 50 + +compute outsp all property/atom spx spy spz sp fmx fmy fmz +dump 100 all custom 1 dump_iron.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] + +run 2000 +Neighbor list info ... + update every 10 steps, delay 20 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 5.77337 + ghost atom cutoff = 5.77337 + binsize = 2.88668, bins = 5 5 5 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair eam/alloy, perpetual, half/full from (2) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none + (2) pair spin/exchange, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 7.319 | 7.319 | 7.319 Mbytes +Step Time v_magx v_magy v_magz v_magnorm v_tmag v_emag PotEng TotEng + 0 0 -1 0 0 1 0 -55.58269 -1125.5827 -1122.364 + 50 0.005 -1 0 0 1 0 -55.581417 -1125.4672 -1122.364 + 100 0.01 -1 0 0 1 0 -55.577759 -1125.1389 -1122.364 + 150 0.015 -1 0 0 1 0 -55.57219 -1124.6538 -1122.364 + 200 0.02 -1 0 0 1 0 -55.565438 -1124.099 -1122.364 + 250 0.025 -1 0 0 1 0 -55.558379 -1123.5779 -1122.364 + 300 0.03 -1 0 0 1 0 -55.551886 -1123.1862 -1122.364 + 350 0.035 -1 0 0 1 0 -55.546675 -1122.9858 -1122.364 + 400 0.04 -1 0 0 1 0 -55.543187 -1122.9869 -1122.364 + 450 0.045 -1 0 0 1 0 -55.54154 -1123.1498 -1122.364 + 500 0.05 -1 0 0 1 0 -55.541574 -1123.4037 -1122.364 + 550 0.055 -1 0 0 1 0 -55.542941 -1123.672 -1122.364 + 600 0.06 -1 0 0 1 0 -55.545209 -1123.8931 -1122.364 + 650 0.065 -1 0 0 1 0 -55.547951 -1124.0315 -1122.364 + 700 0.07 -1 0 0 1 0 -55.550801 -1124.0798 -1122.364 + 750 0.075 -1 0 0 1 0 -55.553483 -1124.0546 -1122.364 + 800 0.08 -1 0 0 1 0 -55.555816 -1123.9877 -1122.364 + 850 0.085 -1 0 0 1 0 -55.557706 -1123.916 -1122.364 + 900 0.09 -1 0 0 1 0 -55.55913 -1123.8714 -1122.364 + 950 0.095 -1 0 0 1 0 -55.560111 -1123.8726 -1122.364 + 1000 0.1 -1 0 0 1 0 -55.560705 -1123.9215 -1122.364 + 1050 0.105 -1 0 0 1 0 -55.560979 -1124.0049 -1122.364 + 1100 0.11 -1 0 0 1 0 -55.561005 -1124.0998 -1122.364 + 1150 0.115 -1 0 0 1 0 -55.560847 -1124.1802 -1122.364 + 1200 0.12 -1 0 0 1 0 -55.560562 -1124.2247 -1122.364 + 1250 0.125 -1 0 0 1 0 -55.560199 -1124.2224 -1122.364 + 1300 0.13 -1 0 0 1 0 -55.559804 -1124.1752 -1122.364 + 1350 0.135 -1 0 0 1 0 -55.559416 -1124.0977 -1122.364 + 1400 0.14 -1 0 0 1 0 -55.559073 -1124.0124 -1122.364 + 1450 0.145 -1 0 0 1 0 -55.558803 -1123.9437 -1122.364 + 1500 0.15 -1 0 0 1 0 -55.558617 -1123.9107 -1122.364 + 1550 0.155 -1 0 0 1 0 -55.558503 -1123.9224 -1122.364 + 1600 0.16 -1 0 0 1 0 -55.558425 -1123.9749 -1122.364 + 1650 0.165 -1 0 0 1 0 -55.558323 -1124.0529 -1122.364 + 1700 0.17 -1 0 0 1 0 -55.558122 -1124.1331 -1122.364 + 1750 0.175 -1 0 0 1 0 -55.557751 -1124.1899 -1122.364 + 1800 0.18 -1 0 0 1 0 -55.557157 -1124.2023 -1122.364 + 1850 0.185 -1 0 0 1 0 -55.556326 -1124.1592 -1122.364 + 1900 0.19 -1 0 0 1 0 -55.555301 -1124.0633 -1122.364 + 1950 0.195 -1 0 0 1 0 -55.554178 -1123.9313 -1122.364 + 2000 0.2 -1 0 0 1 0 -55.553099 -1123.7904 -1122.364 +Loop time of 254.052 on 1 procs for 2000 steps with 250 atoms + +Performance: 0.068 ns/day, 352.850 hours/ns, 7.872 timesteps/s +99.5% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 60.584 | 60.584 | 60.584 | 0.0 | 23.85 +Neigh | 0.34793 | 0.34793 | 0.34793 | 0.0 | 0.14 +Comm | 1.9994 | 1.9994 | 1.9994 | 0.0 | 0.79 +Output | 126.24 | 126.24 | 126.24 | 0.0 | 49.69 +Modify | 64.475 | 64.475 | 64.475 | 0.0 | 25.38 +Other | | 0.4024 | | | 0.16 + +Nlocal: 250 ave 250 max 250 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1419 ave 1419 max 1419 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 7878 ave 7878 max 7878 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 15756 ave 15756 max 15756 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 15756 +Ave neighs/atom = 63.024 +Neighbor list builds = 12 +Dangerous builds = 0 +# min_style spin +# min_modify alpha_damp 1.0 discrete_factor 10 +# minimize 1.0e-16 1.0e-16 10000 10000 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:04:16 diff --git a/examples/SPIN/iron/log.30Apr19.spin.iron_cubic.g++.4 b/examples/SPIN/iron/log.30Apr19.spin.iron_cubic.g++.4 new file mode 100644 index 0000000000..677805d26a --- /dev/null +++ b/examples/SPIN/iron/log.30Apr19.spin.iron_cubic.g++.4 @@ -0,0 +1,161 @@ +LAMMPS (30 Apr 2019) + using 1 OpenMP thread(s) per MPI task +# bcc iron in a 3d periodic box + +clear + using 1 OpenMP thread(s) per MPI task +units metal +atom_style spin + +dimension 3 +boundary p p p + +# necessary for the serial algorithm (sametag) +atom_modify map array + +lattice bcc 2.8665 +Lattice spacing in x,y,z = 2.8665 2.8665 2.8665 +region box block 0.0 5.0 0.0 5.0 0.0 5.0 +create_box 1 box +Created orthogonal box = (0 0 0) to (14.3325 14.3325 14.3325) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 250 atoms + create_atoms CPU = 0.000627756 secs + +# setting mass, mag. moments, and interactions for bcc iron + +mass 1 55.845 +set group all spin 2.2 -1.0 0.0 0.0 + 250 settings made for spin +velocity all create 100 4928459 rot yes dist gaussian + +pair_style hybrid/overlay eam/alloy spin/exchange 3.5 +pair_coeff * * eam/alloy Fe_Mishin2006.eam.alloy Fe +pair_coeff * * spin/exchange exchange 3.4 0.02726 0.2171 1.841 +neighbor 0.1 bin +neigh_modify every 10 check yes delay 20 + +fix 1 all precession/spin cubic 0.001 0.0005 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1.0 +fix_modify 1 energy yes +fix 2 all langevin/spin 0.0 0.0 21 + +fix 3 all nve/spin lattice yes +timestep 0.0001 + +# compute and output options + +compute out_mag all spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +variable magx equal c_out_mag[1] +variable magy equal c_out_mag[2] +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo_style custom step time v_magx v_magy v_magz v_magnorm v_tmag v_emag pe etotal +thermo 50 + +compute outsp all property/atom spx spy spz sp fmx fmy fmz +dump 100 all custom 1 dump_iron.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] + +run 2000 +Neighbor list info ... + update every 10 steps, delay 20 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 5.77337 + ghost atom cutoff = 5.77337 + binsize = 2.88668, bins = 5 5 5 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair eam/alloy, perpetual, half/full from (2) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none + (2) pair spin/exchange, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 7.265 | 7.265 | 7.265 Mbytes +Step Time v_magx v_magy v_magz v_magnorm v_tmag v_emag PotEng TotEng + 0 0 -1 0 0 1 0 -55.58269 -1125.5827 -1122.364 + 50 0.005 -1 0 0 1 0 -55.581457 -1125.4635 -1122.364 + 100 0.01 -1 0 0 1 0 -55.577922 -1125.1262 -1122.364 + 150 0.015 -1 0 0 1 0 -55.572562 -1124.6305 -1122.364 + 200 0.02 -1 0 0 1 0 -55.566098 -1124.067 -1122.364 + 250 0.025 -1 0 0 1 0 -55.559384 -1123.5412 -1122.364 + 300 0.03 -1 0 0 1 0 -55.553261 -1123.1491 -1122.364 + 350 0.035 -1 0 0 1 0 -55.548413 -1122.9526 -1122.364 + 400 0.04 -1 0 0 1 0 -55.545248 -1122.9623 -1122.364 + 450 0.045 -1 0 0 1 0 -55.54387 -1123.1395 -1122.364 + 500 0.05 -1 0 0 1 0 -55.544101 -1123.4126 -1122.364 + 550 0.055 -1 0 0 1 0 -55.54558 -1123.7021 -1122.364 + 600 0.06 -1 0 0 1 0 -55.547857 -1123.9414 -1122.364 + 650 0.065 -1 0 0 1 0 -55.550495 -1124.0897 -1122.364 + 700 0.07 -1 0 0 1 0 -55.553127 -1124.136 -1122.364 + 750 0.075 -1 0 0 1 0 -55.555497 -1124.0961 -1122.364 + 800 0.08 -1 0 0 1 0 -55.557466 -1124.0053 -1122.364 + 850 0.085 -1 0 0 1 0 -55.559001 -1123.9069 -1122.364 + 900 0.09 -1 0 0 1 0 -55.560147 -1123.8404 -1122.364 + 950 0.095 -1 0 0 1 0 -55.560992 -1123.8312 -1122.364 + 1000 0.1 -1 0 0 1 0 -55.561635 -1123.8853 -1122.364 + 1050 0.105 -1 0 0 1 0 -55.562156 -1123.9898 -1122.364 + 1100 0.11 -1 0 0 1 0 -55.562594 -1124.1174 -1122.364 + 1150 0.115 -1 0 0 1 0 -55.562944 -1124.2349 -1122.364 + 1200 0.12 -1 0 0 1 0 -55.563163 -1124.3115 -1122.364 + 1250 0.125 -1 0 0 1 0 -55.563193 -1124.3273 -1122.364 + 1300 0.13 -1 0 0 1 0 -55.562982 -1124.2776 -1122.364 + 1350 0.135 -1 0 0 1 0 -55.562513 -1124.1744 -1122.364 + 1400 0.14 -1 0 0 1 0 -55.561812 -1124.0433 -1122.364 + 1450 0.145 -1 0 0 1 0 -55.560956 -1123.9169 -1122.364 + 1500 0.15 -1 0 0 1 0 -55.560057 -1123.8268 -1122.364 + 1550 0.155 -1 0 0 1 0 -55.559235 -1123.7951 -1122.364 + 1600 0.16 -1 0 0 1 0 -55.55859 -1123.8282 -1122.364 + 1650 0.165 -1 0 0 1 0 -55.558174 -1123.9155 -1122.364 + 1700 0.17 -1 0 0 1 0 -55.557974 -1124.0311 -1122.364 + 1750 0.175 -1 0 0 1 0 -55.557913 -1124.1409 -1122.364 + 1800 0.18 -1 0 0 1 0 -55.55788 -1124.212 -1122.364 + 1850 0.185 -1 0 0 1 0 -55.557753 -1124.2208 -1122.364 + 1900 0.19 -1 0 0 1 0 -55.557448 -1124.1596 -1122.364 + 1950 0.195 -1 0 0 1 0 -55.556942 -1124.0384 -1122.364 + 2000 0.2 -1 0 0 1 0 -55.556288 -1123.883 -1122.364 +Loop time of 4.39485 on 4 procs for 2000 steps with 250 atoms + +Performance: 3.932 ns/day, 6.104 hours/ns, 455.078 timesteps/s +98.3% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.64527 | 0.6695 | 0.71114 | 3.3 | 15.23 +Neigh | 0.0032711 | 0.0034365 | 0.0036387 | 0.3 | 0.08 +Comm | 0.14872 | 0.19108 | 0.21485 | 6.1 | 4.35 +Output | 0.40622 | 0.43119 | 0.45149 | 2.5 | 9.81 +Modify | 3.0688 | 3.0921 | 3.1179 | 1.0 | 70.36 +Other | | 0.007548 | | | 0.17 + +Nlocal: 62.5 ave 67 max 57 min +Histogram: 1 0 0 0 0 1 0 1 0 1 +Nghost: 850.5 ave 856 max 847 min +Histogram: 1 0 1 1 0 0 0 0 0 1 +Neighs: 1968.75 ave 2101 max 1792 min +Histogram: 1 0 0 0 0 1 0 1 0 1 +FullNghs: 3937.5 ave 4217 max 3583 min +Histogram: 1 0 0 0 0 1 0 1 0 1 + +Total # of neighbors = 15750 +Ave neighs/atom = 63 +Neighbor list builds = 12 +Dangerous builds = 0 +# min_style spin +# min_modify alpha_damp 1.0 discrete_factor 10 +# minimize 1.0e-16 1.0e-16 10000 10000 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:04 diff --git a/examples/SPIN/nickel/in.spin.nickel_cubic b/examples/SPIN/nickel/in.spin.nickel_cubic new file mode 100644 index 0000000000..3c97b284ae --- /dev/null +++ b/examples/SPIN/nickel/in.spin.nickel_cubic @@ -0,0 +1,60 @@ +# fcc nickel in a 3d periodic box + +clear +units metal +atom_style spin + +dimension 3 +boundary p p p + +# necessary for the serial algorithm (sametag) +atom_modify map array + +lattice fcc 3.524 +region box block 0.0 5.0 0.0 5.0 0.0 5.0 +create_box 1 box +create_atoms 1 box + +# setting mass, mag. moments, and interactions for cobalt + +mass 1 58.69 + +set group all spin/random 31 0.63 +#set group all spin 0.63 0.0 0.0 1.0 +velocity all create 100 4928459 rot yes dist gaussian + +pair_style hybrid/overlay eam/alloy spin/exchange 4.0 +pair_coeff * * eam/alloy Ni99.eam.alloy Ni +pair_coeff * * spin/exchange exchange 4.0 0.50 0.2280246862 1.229983475 + +neighbor 0.1 bin +neigh_modify every 10 check yes delay 20 + +fix 1 all precession/spin cubic -0.0001 0.0 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1.0 & + zeeman 0.0 0.0 0.0 1.0 +fix_modify 1 energy yes +fix 2 all langevin/spin 0.0 0.0 21 + +fix 3 all nve/spin lattice yes +timestep 0.0001 + +# compute and output options + +compute out_mag all spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo_style custom step time v_magnorm v_emag temp v_tmag etotal +thermo 50 + +compute outsp all property/atom spx spy spz sp fmx fmy fmz +dump 50 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7] + +run 2000 + diff --git a/examples/SPIN/nickel/log.11May18.spin.nickel.g++.1 b/examples/SPIN/nickel/log.30Apr19.spin.nickel.g++.1 similarity index 89% rename from examples/SPIN/nickel/log.11May18.spin.nickel.g++.1 rename to examples/SPIN/nickel/log.30Apr19.spin.nickel.g++.1 index 82f54f4e6b..8d7284f5e2 100644 --- a/examples/SPIN/nickel/log.11May18.spin.nickel.g++.1 +++ b/examples/SPIN/nickel/log.30Apr19.spin.nickel.g++.1 @@ -1,7 +1,9 @@ -LAMMPS (11 May 2018) +LAMMPS (30 Apr 2019) + using 1 OpenMP thread(s) per MPI task # fcc nickel in a 3d periodic box clear + using 1 OpenMP thread(s) per MPI task units metal atom_style spin @@ -19,7 +21,7 @@ Created orthogonal box = (0 0 0) to (17.62 17.62 17.62) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 500 atoms - Time spent = 0.000804186 secs + create_atoms CPU = 0.000835896 secs # setting mass, mag. moments, and interactions for cobalt @@ -45,7 +47,7 @@ timestep 0.0001 # compute and output options -compute out_mag all compute/spin +compute out_mag all spin compute out_pe all pe compute out_ke all ke compute out_temp all temp @@ -122,20 +124,20 @@ Step Time v_magnorm v_emag Temp v_tmag TotEng 1900 0.19 0.028733796 -28.785208 228.39889 316.9972 -2218.1018 1950 0.195 0.028733826 -28.9724 228.84666 309.8027 -2218.1018 2000 0.2 0.02873386 -29.175039 228.918 297.88519 -2218.1018 -Loop time of 10.033 on 1 procs for 2000 steps with 500 atoms +Loop time of 15.9256 on 1 procs for 2000 steps with 500 atoms -Performance: 1.722 ns/day, 13.935 hours/ns, 199.342 timesteps/s -99.4% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 1.085 ns/day, 22.119 hours/ns, 125.584 timesteps/s +99.2% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 3.909 | 3.909 | 3.909 | 0.0 | 38.96 -Neigh | 0.031031 | 0.031031 | 0.031031 | 0.0 | 0.31 -Comm | 0.046559 | 0.046559 | 0.046559 | 0.0 | 0.46 -Output | 2.4087 | 2.4087 | 2.4087 | 0.0 | 24.01 -Modify | 3.625 | 3.625 | 3.625 | 0.0 | 36.13 -Other | | 0.01268 | | | 0.13 +Pair | 5.8677 | 5.8677 | 5.8677 | 0.0 | 36.84 +Neigh | 0.051965 | 0.051965 | 0.051965 | 0.0 | 0.33 +Comm | 0.088829 | 0.088829 | 0.088829 | 0.0 | 0.56 +Output | 4.7019 | 4.7019 | 4.7019 | 0.0 | 29.52 +Modify | 5.199 | 5.199 | 5.199 | 0.0 | 32.65 +Other | | 0.01632 | | | 0.10 Nlocal: 500 ave 500 max 500 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -154,4 +156,4 @@ Dangerous builds = 0 Please see the log.cite file for references relevant to this simulation -Total wall time: 0:00:10 +Total wall time: 0:00:16 diff --git a/examples/SPIN/nickel/log.11May18.spin.nickel.g++.4 b/examples/SPIN/nickel/log.30Apr19.spin.nickel.g++.4 similarity index 89% rename from examples/SPIN/nickel/log.11May18.spin.nickel.g++.4 rename to examples/SPIN/nickel/log.30Apr19.spin.nickel.g++.4 index 373271459f..a186253db3 100644 --- a/examples/SPIN/nickel/log.11May18.spin.nickel.g++.4 +++ b/examples/SPIN/nickel/log.30Apr19.spin.nickel.g++.4 @@ -1,7 +1,9 @@ -LAMMPS (11 May 2018) +LAMMPS (30 Apr 2019) + using 1 OpenMP thread(s) per MPI task # fcc nickel in a 3d periodic box clear + using 1 OpenMP thread(s) per MPI task units metal atom_style spin @@ -19,7 +21,7 @@ Created orthogonal box = (0 0 0) to (17.62 17.62 17.62) 1 by 2 by 2 MPI processor grid create_atoms 1 box Created 500 atoms - Time spent = 0.000523567 secs + create_atoms CPU = 0.000492096 secs # setting mass, mag. moments, and interactions for cobalt @@ -45,7 +47,7 @@ timestep 0.0001 # compute and output options -compute out_mag all compute/spin +compute out_mag all spin compute out_pe all pe compute out_ke all ke compute out_temp all temp @@ -122,20 +124,20 @@ Step Time v_magnorm v_emag Temp v_tmag TotEng 1900 0.19 0.028733864 -27.967999 220.53947 322.9504 -2218.1018 1950 0.195 0.028733863 -28.173041 221.61407 318.63401 -2218.1018 2000 0.2 0.028733853 -28.362177 224.22281 310.55185 -2218.1018 -Loop time of 3.95094 on 4 procs for 2000 steps with 500 atoms +Loop time of 7.69012 on 4 procs for 2000 steps with 500 atoms -Performance: 4.374 ns/day, 5.487 hours/ns, 506.208 timesteps/s -98.1% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 2.247 ns/day, 10.681 hours/ns, 260.074 timesteps/s +98.6% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 1.0289 | 1.0467 | 1.0811 | 2.0 | 26.49 -Neigh | 0.0079527 | 0.0081946 | 0.0084369 | 0.2 | 0.21 -Comm | 0.094456 | 0.13311 | 0.15138 | 6.2 | 3.37 -Output | 0.69702 | 0.71998 | 0.74483 | 2.1 | 18.22 -Modify | 2.0107 | 2.0383 | 2.0598 | 1.3 | 51.59 -Other | | 0.004668 | | | 0.12 +Pair | 1.5623 | 1.5999 | 1.6541 | 2.7 | 20.80 +Neigh | 0.012559 | 0.013043 | 0.013682 | 0.4 | 0.17 +Comm | 0.1843 | 0.24254 | 0.27935 | 7.2 | 3.15 +Output | 1.4749 | 1.5228 | 1.5694 | 2.9 | 19.80 +Modify | 4.2492 | 4.3019 | 4.3507 | 1.8 | 55.94 +Other | | 0.009925 | | | 0.13 Nlocal: 125 ave 132 max 120 min Histogram: 2 0 0 0 0 1 0 0 0 1 @@ -154,4 +156,4 @@ Dangerous builds = 0 Please see the log.cite file for references relevant to this simulation -Total wall time: 0:00:04 +Total wall time: 0:00:07 diff --git a/examples/SPIN/nickel/log.30Apr19.spin.nickel_cubic.g++.1 b/examples/SPIN/nickel/log.30Apr19.spin.nickel_cubic.g++.1 new file mode 100644 index 0000000000..425572dedf --- /dev/null +++ b/examples/SPIN/nickel/log.30Apr19.spin.nickel_cubic.g++.1 @@ -0,0 +1,160 @@ +LAMMPS (30 Apr 2019) + using 1 OpenMP thread(s) per MPI task +# fcc nickel in a 3d periodic box + +clear + using 1 OpenMP thread(s) per MPI task +units metal +atom_style spin + +dimension 3 +boundary p p p + +# necessary for the serial algorithm (sametag) +atom_modify map array + +lattice fcc 3.524 +Lattice spacing in x,y,z = 3.524 3.524 3.524 +region box block 0.0 5.0 0.0 5.0 0.0 5.0 +create_box 1 box +Created orthogonal box = (0 0 0) to (17.62 17.62 17.62) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 500 atoms + create_atoms CPU = 0.00068903 secs + +# setting mass, mag. moments, and interactions for cobalt + +mass 1 58.69 + +set group all spin/random 31 0.63 + 500 settings made for spin/random +#set group all spin 0.63 0.0 0.0 1.0 +velocity all create 100 4928459 rot yes dist gaussian + +pair_style hybrid/overlay eam/alloy spin/exchange 4.0 +pair_coeff * * eam/alloy Ni99.eam.alloy Ni +pair_coeff * * spin/exchange exchange 4.0 0.50 0.2280246862 1.229983475 + +neighbor 0.1 bin +neigh_modify every 10 check yes delay 20 + +fix 1 all precession/spin cubic -0.0001 0.0 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1.0 zeeman 0.0 0.0 0.0 1.0 +fix_modify 1 energy yes +fix 2 all langevin/spin 0.0 0.0 21 + +fix 3 all nve/spin lattice yes +timestep 0.0001 + +# compute and output options + +compute out_mag all spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo_style custom step time v_magnorm v_emag temp v_tmag etotal +thermo 50 + +compute outsp all property/atom spx spy spz sp fmx fmy fmz +dump 50 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7] + +run 2000 +Neighbor list info ... + update every 10 steps, delay 20 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 5.90375 + ghost atom cutoff = 5.90375 + binsize = 2.95187, bins = 6 6 6 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair eam/alloy, perpetual, half/full from (2) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none + (2) pair spin/exchange, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 7.384 | 7.384 | 7.384 Mbytes +Step Time v_magnorm v_emag Temp v_tmag TotEng + 0 0 0.028733803 0.455085 100.03408 -8603.706 -2218.0905 + 50 0.005 0.028732021 0.11535308 101.47887 -34407.888 -2218.0904 + 100 0.01 0.0287304 -0.665283 101.73105 6238.4535 -2218.09 + 150 0.015 0.028729403 -1.8105707 99.629794 2452.7607 -2218.0896 + 200 0.02 0.028731067 -3.224763 94.849715 1501.8625 -2218.0895 + 250 0.025 0.028732765 -4.8207784 88.447019 1110.3291 -2218.0895 + 300 0.03 0.028728169 -6.5331538 82.697813 905.2202 -2218.0896 + 350 0.035 0.02871707 -8.3059526 80.122838 772.40218 -2218.0896 + 400 0.04 0.028706605 -10.077613 82.389555 672.72236 -2218.0895 + 450 0.045 0.028701727 -11.78634 89.823176 595.82956 -2218.0894 + 500 0.05 0.028706691 -13.380919 101.39804 536.65866 -2218.0894 + 550 0.055 0.028714065 -14.824128 115.07511 491.25787 -2218.0893 + 600 0.06 0.028713691 -16.093505 128.58093 459.82107 -2218.089 + 650 0.065 0.028713232 -17.181217 140.22137 441.15183 -2218.089 + 700 0.07 0.02871245 -18.113035 149.60156 426.80154 -2218.0889 + 750 0.075 0.028712431 -18.954952 157.56849 413.61924 -2218.0891 + 800 0.08 0.02872489 -19.762756 164.91833 408.49483 -2218.0892 + 850 0.085 0.028733709 -20.538757 171.69348 407.47868 -2218.0894 + 900 0.09 0.028737031 -21.256095 177.71981 400.24086 -2218.0894 + 950 0.095 0.028743446 -21.908156 183.31613 390.46773 -2218.089 + 1000 0.1 0.028751809 -22.516179 189.01672 383.80802 -2218.0888 + 1050 0.105 0.028761625 -23.084057 194.48882 376.54433 -2218.089 + 1100 0.11 0.028768138 -23.565036 198.12295 366.13309 -2218.0891 + 1150 0.115 0.028770301 -23.937136 198.95102 354.82763 -2218.089 + 1200 0.12 0.028771334 -24.273509 198.31348 347.20512 -2218.0891 + 1250 0.125 0.028769662 -24.672789 198.26173 344.02095 -2218.0889 + 1300 0.13 0.028774175 -25.13917 199.48259 337.81596 -2218.0889 + 1350 0.135 0.028795936 -25.594094 201.33509 329.891 -2218.0889 + 1400 0.14 0.028824328 -25.978285 203.4984 328.81092 -2218.0886 + 1450 0.145 0.028846467 -26.299501 206.52931 328.61151 -2218.0886 + 1500 0.15 0.028858261 -26.605847 211.09044 324.29045 -2218.0888 + 1550 0.155 0.028852825 -26.92321 216.70656 317.24339 -2218.0888 + 1600 0.16 0.02885238 -27.232535 221.73117 312.50182 -2218.0888 + 1650 0.165 0.028857985 -27.513725 224.82466 312.32346 -2218.0887 + 1700 0.17 0.028863985 -27.764471 225.85697 312.80779 -2218.0887 + 1750 0.175 0.028868714 -27.983273 225.71411 315.37238 -2218.0888 + 1800 0.18 0.028871144 -28.187572 225.78979 319.44034 -2218.0888 + 1850 0.185 0.028865191 -28.395615 226.7477 321.25107 -2218.0889 + 1900 0.19 0.028855316 -28.597095 227.90237 319.98739 -2218.0889 + 1950 0.195 0.028853072 -28.79277 228.54008 313.04557 -2218.0886 + 2000 0.2 0.028855814 -29.015073 228.8643 300.40018 -2218.0885 +Loop time of 16.5858 on 1 procs for 2000 steps with 500 atoms + +Performance: 1.042 ns/day, 23.036 hours/ns, 120.585 timesteps/s +99.1% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 5.8835 | 5.8835 | 5.8835 | 0.0 | 35.47 +Neigh | 0.05244 | 0.05244 | 0.05244 | 0.0 | 0.32 +Comm | 0.092997 | 0.092997 | 0.092997 | 0.0 | 0.56 +Output | 5.213 | 5.213 | 5.213 | 0.0 | 31.43 +Modify | 5.3275 | 5.3275 | 5.3275 | 0.0 | 32.12 +Other | | 0.01636 | | | 0.10 + +Nlocal: 500 ave 500 max 500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1956 ave 1956 max 1956 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 19507 ave 19507 max 19507 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 39014 ave 39014 max 39014 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 39014 +Ave neighs/atom = 78.028 +Neighbor list builds = 21 +Dangerous builds = 0 + + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:16 diff --git a/examples/SPIN/nickel/log.30Apr19.spin.nickel_cubic.g++.4 b/examples/SPIN/nickel/log.30Apr19.spin.nickel_cubic.g++.4 new file mode 100644 index 0000000000..fd9ce80533 --- /dev/null +++ b/examples/SPIN/nickel/log.30Apr19.spin.nickel_cubic.g++.4 @@ -0,0 +1,160 @@ +LAMMPS (30 Apr 2019) + using 1 OpenMP thread(s) per MPI task +# fcc nickel in a 3d periodic box + +clear + using 1 OpenMP thread(s) per MPI task +units metal +atom_style spin + +dimension 3 +boundary p p p + +# necessary for the serial algorithm (sametag) +atom_modify map array + +lattice fcc 3.524 +Lattice spacing in x,y,z = 3.524 3.524 3.524 +region box block 0.0 5.0 0.0 5.0 0.0 5.0 +create_box 1 box +Created orthogonal box = (0 0 0) to (17.62 17.62 17.62) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 500 atoms + create_atoms CPU = 0.000639439 secs + +# setting mass, mag. moments, and interactions for cobalt + +mass 1 58.69 + +set group all spin/random 31 0.63 + 500 settings made for spin/random +#set group all spin 0.63 0.0 0.0 1.0 +velocity all create 100 4928459 rot yes dist gaussian + +pair_style hybrid/overlay eam/alloy spin/exchange 4.0 +pair_coeff * * eam/alloy Ni99.eam.alloy Ni +pair_coeff * * spin/exchange exchange 4.0 0.50 0.2280246862 1.229983475 + +neighbor 0.1 bin +neigh_modify every 10 check yes delay 20 + +fix 1 all precession/spin cubic -0.0001 0.0 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1.0 zeeman 0.0 0.0 0.0 1.0 +fix_modify 1 energy yes +fix 2 all langevin/spin 0.0 0.0 21 + +fix 3 all nve/spin lattice yes +timestep 0.0001 + +# compute and output options + +compute out_mag all spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo_style custom step time v_magnorm v_emag temp v_tmag etotal +thermo 50 + +compute outsp all property/atom spx spy spz sp fmx fmy fmz +dump 50 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7] + +run 2000 +Neighbor list info ... + update every 10 steps, delay 20 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 5.90375 + ghost atom cutoff = 5.90375 + binsize = 2.95187, bins = 6 6 6 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair eam/alloy, perpetual, half/full from (2) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none + (2) pair spin/exchange, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 7.298 | 7.298 | 7.298 Mbytes +Step Time v_magnorm v_emag Temp v_tmag TotEng + 0 0 0.028733803 0.455085 100.03408 -8603.706 -2218.0905 + 50 0.005 0.028732088 0.2980989 98.74184 -13360.862 -2218.0904 + 100 0.01 0.02873076 -0.32911738 97.074246 12749.405 -2218.09 + 150 0.015 0.028730298 -1.3537059 94.073558 3353.8731 -2218.0897 + 200 0.02 0.028733079 -2.6807428 89.419616 1868.0661 -2218.0895 + 250 0.025 0.028735725 -4.2256641 84.074249 1317.4563 -2218.0893 + 300 0.03 0.028728939 -5.9209085 80.063263 1033.1632 -2218.0893 + 350 0.035 0.028716731 -7.6957087 79.36782 849.1925 -2218.0893 + 400 0.04 0.02871114 -9.4720832 83.055773 718.36408 -2218.0893 + 450 0.045 0.02870879 -11.19254 91.28713 624.04151 -2218.0891 + 500 0.05 0.028708873 -12.832707 103.50343 551.85983 -2218.0892 + 550 0.055 0.028710315 -14.370603 118.16778 497.19527 -2218.0893 + 600 0.06 0.028707016 -15.769641 132.83264 462.57721 -2218.089 + 650 0.065 0.028706727 -17.018362 145.39247 445.40608 -2218.0888 + 700 0.07 0.028710482 -18.137792 154.80131 439.71677 -2218.0889 + 750 0.075 0.028705169 -19.130471 160.53663 437.67621 -2218.0892 + 800 0.08 0.028695336 -19.988452 162.95918 430.42912 -2218.089 + 850 0.085 0.028688393 -20.758389 164.33238 420.42991 -2218.0889 + 900 0.09 0.028684101 -21.521505 167.76167 412.29955 -2218.089 + 950 0.095 0.028684705 -22.314351 174.918 403.31757 -2218.0891 + 1000 0.1 0.028691284 -23.080026 184.60192 391.677 -2218.0893 + 1050 0.105 0.028687846 -23.714845 193.76312 379.81345 -2218.0893 + 1100 0.11 0.028682371 -24.191738 200.43041 372.65414 -2218.0893 + 1150 0.115 0.028684765 -24.569816 204.39323 368.53291 -2218.0891 + 1200 0.12 0.028678139 -24.892093 205.879 364.46365 -2218.0892 + 1250 0.125 0.028669738 -25.160227 205.09197 361.98015 -2218.0893 + 1300 0.13 0.028666626 -25.367813 202.69136 360.10649 -2218.0891 + 1350 0.135 0.028665511 -25.520784 199.79027 359.68033 -2218.0892 + 1400 0.14 0.02866749 -25.655936 197.91217 361.218 -2218.0892 + 1450 0.145 0.028666916 -25.80086 198.1933 361.5167 -2218.0889 + 1500 0.15 0.028660248 -25.953194 200.8243 356.0167 -2218.089 + 1550 0.155 0.028641778 -26.137444 205.80307 349.94961 -2218.0887 + 1600 0.16 0.028626894 -26.393372 212.6879 347.30341 -2218.0888 + 1650 0.165 0.028619835 -26.707923 219.63834 340.80511 -2218.0885 + 1700 0.17 0.028615681 -27.023214 224.25635 329.60947 -2218.0882 + 1750 0.175 0.02861597 -27.301445 225.47908 321.35253 -2218.0884 + 1800 0.18 0.028614544 -27.53764 224.03527 320.92639 -2218.0884 + 1850 0.185 0.02860894 -27.741581 221.74286 323.07034 -2218.0884 + 1900 0.19 0.028604135 -27.943034 220.659 322.60989 -2218.0884 + 1950 0.195 0.028602672 -28.160901 221.85908 318.8957 -2218.0885 + 2000 0.2 0.028597155 -28.365986 224.55298 311.53587 -2218.0886 +Loop time of 7.21663 on 4 procs for 2000 steps with 500 atoms + +Performance: 2.394 ns/day, 10.023 hours/ns, 277.138 timesteps/s +98.1% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.6337 | 1.6726 | 1.7259 | 2.7 | 23.18 +Neigh | 0.013023 | 0.01361 | 0.014188 | 0.4 | 0.19 +Comm | 0.19005 | 0.24933 | 0.2905 | 7.5 | 3.45 +Output | 1.4595 | 1.5171 | 1.5725 | 3.4 | 21.02 +Modify | 3.6943 | 3.7537 | 3.8093 | 2.3 | 52.01 +Other | | 0.01025 | | | 0.14 + +Nlocal: 125 ave 132 max 121 min +Histogram: 2 0 0 0 1 0 0 0 0 1 +Nghost: 1099 ave 1103 max 1092 min +Histogram: 1 0 0 0 0 1 0 0 0 2 +Neighs: 4877 ave 5097 max 4747 min +Histogram: 2 0 0 0 1 0 0 0 0 1 +FullNghs: 9754 ave 10298 max 9440 min +Histogram: 2 0 0 0 1 0 0 0 0 1 + +Total # of neighbors = 39016 +Ave neighs/atom = 78.032 +Neighbor list builds = 21 +Dangerous builds = 0 + + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:07 diff --git a/examples/SPIN/read_restart/in.spin.read_data b/examples/SPIN/read_restart/in.spin.read_data index 17343994b5..a450421699 100644 --- a/examples/SPIN/read_restart/in.spin.read_data +++ b/examples/SPIN/read_restart/in.spin.read_data @@ -40,6 +40,6 @@ thermo_style custom step time v_magnorm v_emag v_tmag temp etotal thermo_modify format float %20.15g compute outsp all property/atom spx spy spz sp fmx fmy fmz -dump 10 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7] +dump 1 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7] run 100 diff --git a/examples/SPIN/setforce_spin/in.spinmin.setforce b/examples/SPIN/setforce_spin/in.spinmin.setforce new file mode 100644 index 0000000000..10d4df66ed --- /dev/null +++ b/examples/SPIN/setforce_spin/in.spinmin.setforce @@ -0,0 +1,59 @@ + +units metal +dimension 3 +boundary f f f +atom_style spin + +# necessary for the serial algorithm (sametag) +atom_modify map array + +lattice sc 3.0 +region box block 0.0 10.0 0.0 10.0 0.0 1.0 +create_box 2 box +region reg1 block 0.0 10.0 0.0 5.0 0.0 1.0 +region reg2 block 0.0 10.0 6.0 10.0 0.0 1.0 +create_atoms 1 region reg1 +create_atoms 2 region reg2 + +# setting mass, mag. moments, and interactions for bcc iron + +mass 1 55.845 +mass 2 55.845 +set region reg1 spin 2.2 0.0 0.0 1.0 +set region reg2 spin/random 31 2.2 + +group fixed_spin region reg1 + +pair_style hybrid/overlay spin/exchange 3.1 spin/dmi 3.1 +pair_coeff * * spin/exchange exchange 3.1 -0.01593 0.06626915552 1.211 +pair_coeff * * spin/dmi dmi 3.1 0.12e-03 0.0 0.0 1.0 + +neighbor 0.1 bin +neigh_modify every 10 check yes delay 20 + +fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 anisotropy 5e-05 0.0 0.0 1.0 +fix_modify 1 energy yes +fix 2 fixed_spin setforce/spin 0.0 0.0 0.0 +fix 3 all langevin/spin 0.0 0.1 21 +fix 4 all nve/spin lattice no + +timestep 0.0001 + +compute out_mag all spin +variable magx equal c_out_mag[1] +variable magy equal c_out_mag[2] +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo 1000 +thermo_style custom step time v_magx v_magz v_magnorm v_tmag etotal +thermo_modify format float %20.15g + +compute outsp all property/atom spx spy spz sp fmx fmy fmz +dump 1 all custom 1000 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[5] c_outsp[6] c_outsp[7] + +min_style spin +min_modify alpha_damp 1.0 discrete_factor 20.0 +minimize 1.0e-16 1.0e-16 50000 1000 diff --git a/examples/USER/e3b/README b/examples/USER/e3b/README new file mode 100644 index 0000000000..8ef1a54fa2 --- /dev/null +++ b/examples/USER/e3b/README @@ -0,0 +1,6 @@ +The input script in.lammps simulates bulk water using the 2015 E3B potential. + +This script also demonstrates the use of compute pair to calculate the +potential energy contribution of the e3b pair style. These potential energy +contributions can be found in the output file e3b.txt. See the LAMMPS +documentation for more details. diff --git a/examples/USER/e3b/e3b_box.data b/examples/USER/e3b/e3b_box.data new file mode 100644 index 0000000000..a8e586d101 --- /dev/null +++ b/examples/USER/e3b/e3b_box.data @@ -0,0 +1,1973 @@ +LAMMPS data file via write_data, version 29 Mar 2019, timestep = 39 + +648 atoms +2 atom types +432 bonds +1 bond types +216 angles +1 angle types + +-9.3223199999999995e+00 9.3223199999999995e+00 xlo xhi +-9.3223199999999995e+00 9.3223199999999995e+00 ylo yhi +-9.3223199999999995e+00 9.3223199999999995e+00 zlo zhi + +Masses + +1 15.9994 +2 1.008 + +Atoms # full + +4 2 1 -1.1128000000000000e+00 -6.2644497247646571e+00 -8.9277464158309368e+00 -9.2289638586118450e+00 0 0 0 +7 3 1 -1.1128000000000000e+00 -3.4579165298402557e+00 -9.3034804390504036e+00 9.3191750579333963e+00 0 0 -1 +22 8 1 -1.1128000000000000e+00 -6.5784482972256972e+00 -6.0892991832768422e+00 9.2636286576365379e+00 0 0 -1 +24 8 2 5.5640000000000001e-01 -6.2883569860033823e+00 -6.9950268404476086e+00 -9.2706312989165927e+00 0 0 0 +25 9 1 -1.1128000000000000e+00 -3.3071046162069297e+00 -5.9155959538749325e+00 -9.1188397160115429e+00 0 0 0 +27 9 2 5.5640000000000001e-01 -3.2823042762063119e+00 -6.8458680022542051e+00 -8.8946163939947560e+00 0 0 0 +42 14 2 5.5640000000000001e-01 -6.3256322964305269e+00 -3.1196227750426266e+00 -8.5528488303959271e+00 0 0 0 +110 37 2 5.5640000000000001e-01 -8.9998610428778356e+00 -8.6212661373931603e+00 -6.4645003783963153e+00 0 0 0 +112 38 1 -1.1128000000000000e+00 -6.5966491070165834e+00 9.3025413834938782e+00 -6.2217969584742789e+00 0 -1 0 +113 38 2 5.5640000000000001e-01 -5.9817429896518188e+00 -8.8746554430354880e+00 -6.7873958824780498e+00 0 0 0 +115 39 1 -1.1128000000000000e+00 -3.4933004864070534e+00 -9.2643750182275308e+00 -6.1619122531520487e+00 0 0 0 +128 43 2 5.5640000000000001e-01 -8.5037100225273328e+00 -6.0419047338974883e+00 -6.3265593527963118e+00 0 0 0 +130 44 1 -1.1128000000000000e+00 -6.5938400537352857e+00 -6.3296469738236736e+00 -6.3038747094843490e+00 0 0 0 +131 44 2 5.5640000000000001e-01 -6.1349220971745542e+00 -5.5744656099438208e+00 -6.6715707806794615e+00 0 0 0 +132 44 2 5.5640000000000001e-01 -5.9752727386530129e+00 -6.7043153198407488e+00 -5.6766388979201148e+00 0 0 0 +133 45 1 -1.1128000000000000e+00 -3.5131404208428663e+00 -6.1191443287179963e+00 -6.3008694521708692e+00 0 0 0 +135 45 2 5.5640000000000001e-01 -3.1346852339994076e+00 -6.7762160100519910e+00 -5.7167799434876931e+00 0 0 0 +150 50 2 5.5640000000000001e-01 -6.2431423113920745e+00 -3.6165700027211560e+00 -5.6579187614303921e+00 0 0 0 +151 51 1 -1.1128000000000000e+00 -3.1434110782616576e+00 -3.1256540201103058e+00 -5.9202452679304773e+00 0 0 0 +221 74 2 5.5640000000000001e-01 -6.7444881935803283e+00 -8.9030287031244733e+00 -3.5761535166551890e+00 0 0 0 +235 79 1 -1.1128000000000000e+00 -9.1866518096599830e+00 -6.5759222319011803e+00 -3.1754531292526251e+00 0 0 0 +237 79 2 5.5640000000000001e-01 -9.2379325291654446e+00 -5.7878171834688663e+00 -3.7161287850599662e+00 0 0 0 +238 80 1 -1.1128000000000000e+00 -6.3413599098490261e+00 -6.1316935797332519e+00 -3.4358136117783338e+00 0 0 0 +240 80 2 5.5640000000000001e-01 -5.3906055749810404e+00 -6.1350392952630486e+00 -3.3252638822853786e+00 0 0 0 +241 81 1 -1.1128000000000000e+00 -3.3180948977737104e+00 -6.1988382043626240e+00 -3.3963035643280772e+00 0 0 0 +11 4 2 5.5640000000000001e-01 -1.2599895896217728e-01 -8.7361463159924657e+00 -8.9400975936363309e+00 0 0 0 +28 10 1 -1.1128000000000000e+00 -2.2589008359315407e-01 -6.5032785885453253e+00 -9.2555357922080610e+00 0 0 0 +30 10 2 5.5640000000000001e-01 4.4753718954535809e-01 -6.1160439894689098e+00 -8.6960173658952229e+00 0 0 0 +31 11 1 -1.1128000000000000e+00 2.7839302629692626e+00 -6.1151028871259880e+00 -9.1826874981947704e+00 0 0 0 +48 16 2 5.5640000000000001e-01 4.2833119581027301e-01 -3.5309985930883907e+00 -8.7644335968963230e+00 0 0 0 +116 39 2 5.5640000000000001e-01 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543 +200 1 545 544 546 +201 1 614 613 615 +202 1 632 631 633 +203 1 635 634 636 +204 1 83 82 84 +205 1 515 514 516 +206 1 530 529 531 +207 1 551 550 552 +208 1 638 637 639 +209 1 641 640 642 +210 1 17 16 18 +211 1 89 88 90 +212 1 92 91 93 +213 1 521 520 522 +214 1 626 625 627 +215 1 644 643 645 +216 1 647 646 648 diff --git a/examples/USER/e3b/in.e3b-tip4p2005 b/examples/USER/e3b/in.e3b-tip4p2005 new file mode 100644 index 0000000000..ffb03969d2 --- /dev/null +++ b/examples/USER/e3b/in.e3b-tip4p2005 @@ -0,0 +1,95 @@ +#LAMMPS input file +#to simulate bulk E3B3 water model + +##################################################################### + +variable samp_rate equal 10 +variable thermo_rate equal 10 +variable Wlat equal 3.10744 #for water density 0.997g/mL +variable L equal 3 #(L*2)^3 = Nmolec, L=3 -> N=216 + +variable equil equal 100 +variable run equal 100 + +variable ts equal 2.0 +variable Tdamp equal 100*${ts} +variable Pdamp equal 1000*${ts} +variable myT equal 298.0 +variable myP equal 1.0 + +units real +atom_style full + +dimension 3 + +boundary p p p + +############################################################################# +#setup box +read_data e3b_box.data + +############################################################################# +#set up potential + +pair_style hybrid/overlay e3b 1 lj/cut/tip4p/long 1 2 1 1 0.1546 8.5 +pair_modify table 0 table/disp 0 shift yes + +bond_style harmonic +angle_style harmonic + +kspace_style pppm/tip4p 1.0e-6 + +pair_coeff * * lj/cut/tip4p/long 0.0 0.0 +pair_coeff 1 1 lj/cut/tip4p/long 0.1852 3.1589 +pair_coeff * * e3b preset 2015 + +#potential coeffs aren't too important since will be rigid anyways +bond_coeff 1 554.13 0.9572 +angle_coeff 1 45.769 104.52 + +############################################################################# +#setup for run +thermo ${thermo_rate} +thermo_style custom step vol temp epair pe etotal press density + +timestep ${ts} +run_style verlet + +neighbor 2.0 bin +neigh_modify every 1 delay 3 check yes + +############################################################################# + +#dump positions only in first batch run +#dump 7 all custom ${samp_rate} dump.lammpstrj id x y z +#dump_modify 7 sort id + +############################################################################# +#initialize velocity and rigid constraint + +fix rigid all shake 1.0e-8 100 0 b 1 a 1 t 1 2 +velocity all create ${myT} 15856 dist gaussian rot yes mom yes + +#scale velocity +run 0 +velocity all scale ${myT} + +compute e3b all pair e3b +fix e3b all ave/time 1 1 ${thermo_rate} c_e3b c_e3b[*] & + file e3b.txt title2 "step pe_e3b pe_e2 pe_ea pe_eb pe_ec" + +############################################################################# +#equilibrate bulk water at NVT + +fix 1 all nvt temp ${myT} ${myT} ${Tdamp} +run ${equil} + +############################################################################# +#run at NVT + +#dump 1 all custom ${samp_rate} dump.lammpstrj id x y z type +#dump_modify 1 sort id + +run ${run} + +# write_restart lammps.restart diff --git a/examples/USER/e3b/log.29Mar2019.e3b-tip4p2005.g++.1 b/examples/USER/e3b/log.29Mar2019.e3b-tip4p2005.g++.1 new file mode 100644 index 0000000000..71803f3581 --- /dev/null +++ b/examples/USER/e3b/log.29Mar2019.e3b-tip4p2005.g++.1 @@ -0,0 +1,332 @@ +LAMMPS (29 Mar 2019) +#LAMMPS input file +#to simulate bulk E3B3 water model + +##################################################################### + +variable samp_rate equal 10 +variable thermo_rate equal 10 +variable Wlat equal 3.10744 #for water density 0.997g/mL +variable L equal 3 #(L*2)^3 = Nmolec, L=3 -> N=216 + +variable equil equal 100 +variable run equal 100 + +variable ts equal 2.0 +variable Tdamp equal 100*${ts} +variable Tdamp equal 100*2 +variable Pdamp equal 1000*${ts} +variable Pdamp equal 1000*2 +variable myT equal 298.0 +variable myP equal 1.0 + +units real +atom_style full + +dimension 3 + +boundary p p p + +############################################################################# +#setup box +read_data e3b_box.data + orthogonal box = (-9.32232 -9.32232 -9.32232) to (9.32232 9.32232 9.32232) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 648 atoms + reading velocities ... + 648 velocities + scanning bonds ... + 2 = max bonds/atom + scanning angles ... + 1 = max angles/atom + reading bonds ... + 432 bonds + reading angles ... + 216 angles + 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 = 0.000257254 secs + read_data CPU = 0.00286555 secs + +############################################################################# +#set up potential + +pair_style hybrid/overlay e3b 1 lj/cut/tip4p/long 1 2 1 1 0.1546 8.5 +pair_modify table 0 table/disp 0 shift yes + +bond_style harmonic +angle_style harmonic + +kspace_style pppm/tip4p 1.0e-6 + +pair_coeff * * lj/cut/tip4p/long 0.0 0.0 +pair_coeff 1 1 lj/cut/tip4p/long 0.1852 3.1589 +pair_coeff * * e3b preset 2015 + +#potential coeffs aren't too important since will be rigid anyways +bond_coeff 1 554.13 0.9572 +angle_coeff 1 45.769 104.52 + +############################################################################# +#setup for run +thermo ${thermo_rate} +thermo 10 +thermo_style custom step vol temp epair pe etotal press density + +timestep ${ts} +timestep 2 +run_style verlet + +neighbor 2.0 bin +neigh_modify every 1 delay 3 check yes + +############################################################################# + +#dump positions only in first batch run +#dump 7 all custom ${samp_rate} dump.lammpstrj id x y z +#dump_modify 7 sort id + +############################################################################# +#initialize velocity and rigid constraint + +fix rigid all shake 1.0e-8 100 0 b 1 a 1 t 1 2 + 0 = # of size 2 clusters + 0 = # of size 3 clusters + 0 = # of size 4 clusters + 216 = # of frozen angles + find clusters CPU = 0.000185728 secs +velocity all create ${myT} 15856 dist gaussian rot yes mom yes +velocity all create 298 15856 dist gaussian rot yes mom yes + +#scale velocity +run 0 +PPPM initialization ... + extracting TIP4P info from pair style + using polynomial approximation for long-range coulomb (../kspace.cpp:319) + G vector (1/distance) = 0.409658 + grid = 36 36 36 + stencil order = 5 + estimated absolute RMS force accuracy = 0.000341883 + estimated relative force accuracy = 1.02957e-06 + using double precision FFTs + 3d grid and FFT values/proc = 91125 46656 +Neighbor list info ... + update every 1 steps, delay 3 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 10.8092 + ghost atom cutoff = 10.8092 + binsize = 5.4046, bins = 4 4 4 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair e3b, perpetual, skip from (2) + attributes: half, newton on + pair build: skip + stencil: none + bin: none + (2) pair lj/cut/tip4p/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 16.4 | 16.4 | 16.4 Mbytes +Step Volume Temp E_pair PotEng TotEng Press Density + 0 6481.2982 298 -512.62432 -512.62432 -129.77504 14088.322 0.99697602 +Loop time of 1.19209e-06 on 1 procs for 0 steps with 648 atoms + +251.7% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 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 | | 1.192e-06 | | |100.00 + +Nlocal: 648 ave 648 max 648 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 5943 ave 5943 max 5943 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 18984 ave 18984 max 18984 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 18984 +Ave neighs/atom = 29.2963 +Ave special neighs/atom = 2 +Neighbor list builds = 0 +Dangerous builds = 0 +velocity all scale ${myT} +velocity all scale 298 + +compute e3b all pe/e3b +fix e3b all ave/time 1 1 ${thermo_rate} c_e3b c_e3b[*] file e3b.txt title2 "step pe_e3b pe_ea pe_eb pe_ec pe_e2" +fix e3b all ave/time 1 1 10 c_e3b c_e3b[*] file e3b.txt title2 "step pe_e3b pe_ea pe_eb pe_ec pe_e2" + +############################################################################# +#equilibrate bulk water at NVT + +fix 1 all nvt temp ${myT} ${myT} ${Tdamp} +fix 1 all nvt temp 298 ${myT} ${Tdamp} +fix 1 all nvt temp 298 298 ${Tdamp} +fix 1 all nvt temp 298 298 200 +run ${equil} +run 100 +PPPM initialization ... + extracting TIP4P info from pair style + using polynomial approximation for long-range coulomb (../kspace.cpp:319) + G vector (1/distance) = 0.409658 + grid = 36 36 36 + stencil order = 5 + estimated absolute RMS force accuracy = 0.000341883 + estimated relative force accuracy = 1.02957e-06 + using double precision FFTs + 3d grid and FFT values/proc = 91125 46656 +Neighbor list info ... + update every 1 steps, delay 3 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 10.8092 + ghost atom cutoff = 10.8092 + binsize = 5.4046, bins = 4 4 4 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair e3b, perpetual, skip from (2) + attributes: half, newton on + pair build: skip + stencil: none + bin: none + (2) pair lj/cut/tip4p/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 16.88 | 16.88 | 16.88 Mbytes +Step Volume Temp E_pair PotEng TotEng Press Density + 0 6481.2982 298 -512.33264 -512.33264 -129.48336 14091.383 0.99697602 + 10 6481.2982 905.58028 -1442.0378 -1442.0378 -278.61245 -798.38952 0.99697602 + 20 6481.2982 816.39844 -1363.5999 -1363.5999 -314.74903 3023.9064 0.99697602 + 30 6481.2982 783.3897 -1370.6594 -1370.6594 -364.21587 7095.4765 0.99697602 + 40 6481.2982 793.12519 -1425.8404 -1425.8404 -406.88933 7030.242 0.99697602 + 50 6481.2982 810.90264 -1495.4822 -1495.4822 -453.69195 6944.2325 0.99697602 + 60 6481.2982 766.64937 -1491.2317 -1491.2317 -506.29493 9062.0151 0.99697602 + 70 6481.2982 761.77292 -1538.7368 -1538.7368 -560.06492 7693.2197 0.99697602 + 80 6481.2982 730.44938 -1554.1818 -1554.1818 -615.75215 7345.9601 0.99697602 + 90 6481.2982 695.46244 -1563.9869 -1563.9869 -670.50605 7809.0685 0.99697602 + 100 6481.2982 691.5674 -1613.2754 -1613.2754 -724.79866 7143.062 0.99697602 +Loop time of 1.94577 on 1 procs for 100 steps with 648 atoms + +Performance: 8.881 ns/day, 2.702 hours/ns, 51.393 timesteps/s +99.7% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.91572 | 0.91572 | 0.91572 | 0.0 | 47.06 +Bond | 6.7234e-05 | 6.7234e-05 | 6.7234e-05 | 0.0 | 0.00 +Kspace | 0.92654 | 0.92654 | 0.92654 | 0.0 | 47.62 +Neigh | 0.087331 | 0.087331 | 0.087331 | 0.0 | 4.49 +Comm | 0.0054724 | 0.0054724 | 0.0054724 | 0.0 | 0.28 +Output | 0.0003047 | 0.0003047 | 0.0003047 | 0.0 | 0.02 +Modify | 0.0093319 | 0.0093319 | 0.0093319 | 0.0 | 0.48 +Other | | 0.001007 | | | 0.05 + +Nlocal: 648 ave 648 max 648 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 5911 ave 5911 max 5911 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 19136 ave 19136 max 19136 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 19136 +Ave neighs/atom = 29.5309 +Ave special neighs/atom = 2 +Neighbor list builds = 15 +Dangerous builds = 0 + +############################################################################# +#run at NVT + +#dump 1 all custom ${samp_rate} dump.lammpstrj id x y z type +#dump_modify 1 sort id + +run ${run} +run 100 +PPPM initialization ... + extracting TIP4P info from pair style + using polynomial approximation for long-range coulomb (../kspace.cpp:319) + G vector (1/distance) = 0.409658 + grid = 36 36 36 + stencil order = 5 + estimated absolute RMS force accuracy = 0.000341883 + estimated relative force accuracy = 1.02957e-06 + using double precision FFTs + 3d grid and FFT values/proc = 91125 46656 +Neighbor list info ... + update every 1 steps, delay 3 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 10.8092 + ghost atom cutoff = 10.8092 + binsize = 5.4046, bins = 4 4 4 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair e3b, perpetual, skip from (2) + attributes: half, newton on + pair build: skip + stencil: none + bin: none + (2) pair lj/cut/tip4p/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 16.88 | 16.88 | 16.88 Mbytes +Step Volume Temp E_pair PotEng TotEng Press Density + 100 6481.2982 691.5674 -1613.2754 -1613.2754 -724.79866 7131.3961 0.99697602 + 110 6481.2982 668.27004 -1635.5867 -1635.5867 -777.04068 6965.8705 0.99697602 + 120 6481.2982 646.18686 -1659.5025 -1659.5025 -829.32738 6196.7432 0.99697602 + 130 6481.2982 650.7802 -1716.9557 -1716.9557 -880.87943 5626.5466 0.99697602 + 140 6481.2982 586.262 -1681.8052 -1681.8052 -928.61728 6103.747 0.99697602 + 150 6481.2982 615.88299 -1767.8614 -1767.8614 -976.61859 3897.648 0.99697602 + 160 6481.2982 585.23516 -1773.2038 -1773.2038 -1021.3352 4821.7742 0.99697602 + 170 6481.2982 558.77885 -1782.2817 -1782.2817 -1064.4022 5092.7248 0.99697602 + 180 6481.2982 564.01576 -1830.0301 -1830.0301 -1105.4226 4316.1636 0.99697602 + 190 6481.2982 526.53776 -1821.3122 -1821.3122 -1144.8538 4529.5062 0.99697602 + 200 6481.2982 537.81273 -1873.6662 -1873.6662 -1182.7226 4244.313 0.99697602 +Loop time of 1.9157 on 1 procs for 100 steps with 648 atoms + +Performance: 9.020 ns/day, 2.661 hours/ns, 52.200 timesteps/s +99.6% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.90464 | 0.90464 | 0.90464 | 0.0 | 47.22 +Bond | 6.9141e-05 | 6.9141e-05 | 6.9141e-05 | 0.0 | 0.00 +Kspace | 0.92769 | 0.92769 | 0.92769 | 0.0 | 48.43 +Neigh | 0.067551 | 0.067551 | 0.067551 | 0.0 | 3.53 +Comm | 0.0051386 | 0.0051386 | 0.0051386 | 0.0 | 0.27 +Output | 0.00029993 | 0.00029993 | 0.00029993 | 0.0 | 0.02 +Modify | 0.0092504 | 0.0092504 | 0.0092504 | 0.0 | 0.48 +Other | | 0.001062 | | | 0.06 + +Nlocal: 648 ave 648 max 648 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 5901 ave 5901 max 5901 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 18971 ave 18971 max 18971 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 18971 +Ave neighs/atom = 29.2762 +Ave special neighs/atom = 2 +Neighbor list builds = 12 +Dangerous builds = 0 + +# write_restart lammps.restart + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:03 diff --git a/examples/USER/e3b/log.29Mar2019.e3b-tip4p2005.g++.4 b/examples/USER/e3b/log.29Mar2019.e3b-tip4p2005.g++.4 new file mode 100644 index 0000000000..b61ffa5a8f --- /dev/null +++ b/examples/USER/e3b/log.29Mar2019.e3b-tip4p2005.g++.4 @@ -0,0 +1,332 @@ +LAMMPS (29 Mar 2019) +#LAMMPS input file +#to simulate bulk E3B3 water model + +##################################################################### + +variable samp_rate equal 10 +variable thermo_rate equal 10 +variable Wlat equal 3.10744 #for water density 0.997g/mL +variable L equal 3 #(L*2)^3 = Nmolec, L=3 -> N=216 + +variable equil equal 100 +variable run equal 100 + +variable ts equal 2.0 +variable Tdamp equal 100*${ts} +variable Tdamp equal 100*2 +variable Pdamp equal 1000*${ts} +variable Pdamp equal 1000*2 +variable myT equal 298.0 +variable myP equal 1.0 + +units real +atom_style full + +dimension 3 + +boundary p p p + +############################################################################# +#setup box +read_data e3b_box.data + orthogonal box = (-9.32232 -9.32232 -9.32232) to (9.32232 9.32232 9.32232) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 648 atoms + reading velocities ... + 648 velocities + scanning bonds ... + 2 = max bonds/atom + scanning angles ... + 1 = max angles/atom + reading bonds ... + 432 bonds + reading angles ... + 216 angles + 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 = 0.00029397 secs + read_data CPU = 0.00397325 secs + +############################################################################# +#set up potential + +pair_style hybrid/overlay e3b 1 lj/cut/tip4p/long 1 2 1 1 0.1546 8.5 +pair_modify table 0 table/disp 0 shift yes + +bond_style harmonic +angle_style harmonic + +kspace_style pppm/tip4p 1.0e-6 + +pair_coeff * * lj/cut/tip4p/long 0.0 0.0 +pair_coeff 1 1 lj/cut/tip4p/long 0.1852 3.1589 +pair_coeff * * e3b preset 2015 + +#potential coeffs aren't too important since will be rigid anyways +bond_coeff 1 554.13 0.9572 +angle_coeff 1 45.769 104.52 + +############################################################################# +#setup for run +thermo ${thermo_rate} +thermo 10 +thermo_style custom step vol temp epair pe etotal press density + +timestep ${ts} +timestep 2 +run_style verlet + +neighbor 2.0 bin +neigh_modify every 1 delay 3 check yes + +############################################################################# + +#dump positions only in first batch run +#dump 7 all custom ${samp_rate} dump.lammpstrj id x y z +#dump_modify 7 sort id + +############################################################################# +#initialize velocity and rigid constraint + +fix rigid all shake 1.0e-8 100 0 b 1 a 1 t 1 2 + 0 = # of size 2 clusters + 0 = # of size 3 clusters + 0 = # of size 4 clusters + 216 = # of frozen angles + find clusters CPU = 0.000289917 secs +velocity all create ${myT} 15856 dist gaussian rot yes mom yes +velocity all create 298 15856 dist gaussian rot yes mom yes + +#scale velocity +run 0 +PPPM initialization ... + extracting TIP4P info from pair style + using polynomial approximation for long-range coulomb (../kspace.cpp:319) + G vector (1/distance) = 0.409658 + grid = 36 36 36 + stencil order = 5 + estimated absolute RMS force accuracy = 0.000341883 + estimated relative force accuracy = 1.02957e-06 + using double precision FFTs + 3d grid and FFT values/proc = 32805 11664 +Neighbor list info ... + update every 1 steps, delay 3 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 10.8092 + ghost atom cutoff = 10.8092 + binsize = 5.4046, bins = 4 4 4 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair e3b, perpetual, skip from (2) + attributes: half, newton on + pair build: skip + stencil: none + bin: none + (2) pair lj/cut/tip4p/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 10.69 | 10.69 | 10.69 Mbytes +Step Volume Temp E_pair PotEng TotEng Press Density + 0 6481.2982 298 -512.62432 -512.62432 -129.77504 14088.322 0.99697602 +Loop time of 3.30806e-05 on 4 procs for 0 steps with 648 atoms + +77.1% 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 | 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 | | 3.308e-05 | | |100.00 + +Nlocal: 162 ave 168 max 157 min +Histogram: 2 0 0 0 0 0 0 1 0 1 +Nghost: 3738 ave 3743 max 3732 min +Histogram: 1 0 1 0 0 0 0 0 0 2 +Neighs: 4746 ave 5380 max 4318 min +Histogram: 1 1 0 0 1 0 0 0 0 1 + +Total # of neighbors = 18984 +Ave neighs/atom = 29.2963 +Ave special neighs/atom = 2 +Neighbor list builds = 0 +Dangerous builds = 0 +velocity all scale ${myT} +velocity all scale 298 + +compute e3b all pe/e3b +fix e3b all ave/time 1 1 ${thermo_rate} c_e3b c_e3b[*] file e3b.txt title2 "step pe_e3b pe_ea pe_eb pe_ec pe_e2" +fix e3b all ave/time 1 1 10 c_e3b c_e3b[*] file e3b.txt title2 "step pe_e3b pe_ea pe_eb pe_ec pe_e2" + +############################################################################# +#equilibrate bulk water at NVT + +fix 1 all nvt temp ${myT} ${myT} ${Tdamp} +fix 1 all nvt temp 298 ${myT} ${Tdamp} +fix 1 all nvt temp 298 298 ${Tdamp} +fix 1 all nvt temp 298 298 200 +run ${equil} +run 100 +PPPM initialization ... + extracting TIP4P info from pair style + using polynomial approximation for long-range coulomb (../kspace.cpp:319) + G vector (1/distance) = 0.409658 + grid = 36 36 36 + stencil order = 5 + estimated absolute RMS force accuracy = 0.000341883 + estimated relative force accuracy = 1.02957e-06 + using double precision FFTs + 3d grid and FFT values/proc = 32805 11664 +Neighbor list info ... + update every 1 steps, delay 3 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 10.8092 + ghost atom cutoff = 10.8092 + binsize = 5.4046, bins = 4 4 4 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair e3b, perpetual, skip from (2) + attributes: half, newton on + pair build: skip + stencil: none + bin: none + (2) pair lj/cut/tip4p/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 11.18 | 11.18 | 11.18 Mbytes +Step Volume Temp E_pair PotEng TotEng Press Density + 0 6481.2982 298 -512.33264 -512.33264 -129.48336 14091.383 0.99697602 + 10 6481.2982 905.58028 -1442.0378 -1442.0378 -278.61245 -798.38952 0.99697602 + 20 6481.2982 816.39844 -1363.5999 -1363.5999 -314.74903 3023.9064 0.99697602 + 30 6481.2982 783.3897 -1370.6594 -1370.6594 -364.21587 7095.4765 0.99697602 + 40 6481.2982 793.12519 -1425.8404 -1425.8404 -406.88933 7030.242 0.99697602 + 50 6481.2982 810.90264 -1495.4822 -1495.4822 -453.69195 6944.2325 0.99697602 + 60 6481.2982 766.64937 -1491.2317 -1491.2317 -506.29493 9062.0151 0.99697602 + 70 6481.2982 761.77292 -1538.7368 -1538.7368 -560.06492 7693.2197 0.99697602 + 80 6481.2982 730.44938 -1554.1818 -1554.1818 -615.75215 7345.9601 0.99697602 + 90 6481.2982 695.46244 -1563.9869 -1563.9869 -670.50605 7809.0685 0.99697602 + 100 6481.2982 691.5674 -1613.2754 -1613.2754 -724.79866 7143.062 0.99697602 +Loop time of 1.20724 on 4 procs for 100 steps with 648 atoms + +Performance: 14.314 ns/day, 1.677 hours/ns, 82.834 timesteps/s +97.6% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.37421 | 0.39416 | 0.42739 | 3.2 | 32.65 +Bond | 5.8651e-05 | 7.1406e-05 | 8.2016e-05 | 0.0 | 0.01 +Kspace | 0.67929 | 0.71762 | 0.74038 | 2.8 | 59.44 +Neigh | 0.042206 | 0.042236 | 0.042263 | 0.0 | 3.50 +Comm | 0.0248 | 0.031467 | 0.035969 | 2.7 | 2.61 +Output | 0.00064564 | 0.0008018 | 0.0012648 | 0.0 | 0.07 +Modify | 0.018263 | 0.01869 | 0.019076 | 0.2 | 1.55 +Other | | 0.002194 | | | 0.18 + +Nlocal: 162 ave 170 max 151 min +Histogram: 1 0 0 0 0 1 0 1 0 1 +Nghost: 3726.75 ave 3737 max 3720 min +Histogram: 1 0 1 1 0 0 0 0 0 1 +Neighs: 4784 ave 5474 max 4389 min +Histogram: 1 1 1 0 0 0 0 0 0 1 + +Total # of neighbors = 19136 +Ave neighs/atom = 29.5309 +Ave special neighs/atom = 2 +Neighbor list builds = 15 +Dangerous builds = 0 + +############################################################################# +#run at NVT + +#dump 1 all custom ${samp_rate} dump.lammpstrj id x y z type +#dump_modify 1 sort id + +run ${run} +run 100 +PPPM initialization ... + extracting TIP4P info from pair style + using polynomial approximation for long-range coulomb (../kspace.cpp:319) + G vector (1/distance) = 0.409658 + grid = 36 36 36 + stencil order = 5 + estimated absolute RMS force accuracy = 0.000341883 + estimated relative force accuracy = 1.02957e-06 + using double precision FFTs + 3d grid and FFT values/proc = 32805 11664 +Neighbor list info ... + update every 1 steps, delay 3 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 10.8092 + ghost atom cutoff = 10.8092 + binsize = 5.4046, bins = 4 4 4 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair e3b, perpetual, skip from (2) + attributes: half, newton on + pair build: skip + stencil: none + bin: none + (2) pair lj/cut/tip4p/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 11.18 | 11.18 | 11.18 Mbytes +Step Volume Temp E_pair PotEng TotEng Press Density + 100 6481.2982 691.5674 -1613.2754 -1613.2754 -724.79866 7131.3961 0.99697602 + 110 6481.2982 668.27004 -1635.5867 -1635.5867 -777.04068 6965.8705 0.99697602 + 120 6481.2982 646.18686 -1659.5025 -1659.5025 -829.32738 6196.7432 0.99697602 + 130 6481.2982 650.7802 -1716.9557 -1716.9557 -880.87943 5626.5466 0.99697602 + 140 6481.2982 586.262 -1681.8052 -1681.8052 -928.61728 6103.747 0.99697602 + 150 6481.2982 615.88299 -1767.8614 -1767.8614 -976.61859 3897.648 0.99697602 + 160 6481.2982 585.23516 -1773.2038 -1773.2038 -1021.3352 4821.7742 0.99697602 + 170 6481.2982 558.77885 -1782.2817 -1782.2817 -1064.4022 5092.7248 0.99697602 + 180 6481.2982 564.01576 -1830.0301 -1830.0301 -1105.4226 4316.1636 0.99697602 + 190 6481.2982 526.53776 -1821.3122 -1821.3122 -1144.8538 4529.5062 0.99697602 + 200 6481.2982 537.81273 -1873.6662 -1873.6662 -1182.7226 4244.313 0.99697602 +Loop time of 1.21286 on 4 procs for 100 steps with 648 atoms + +Performance: 14.247 ns/day, 1.685 hours/ns, 82.450 timesteps/s +97.6% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.37664 | 0.39663 | 0.4367 | 3.8 | 32.70 +Bond | 6.175e-05 | 6.7353e-05 | 7.4148e-05 | 0.0 | 0.01 +Kspace | 0.6969 | 0.73237 | 0.75103 | 2.5 | 60.38 +Neigh | 0.033138 | 0.03317 | 0.033202 | 0.0 | 2.73 +Comm | 0.022651 | 0.02763 | 0.034947 | 3.0 | 2.28 +Output | 0.00065303 | 0.00096697 | 0.0018971 | 0.0 | 0.08 +Modify | 0.017379 | 0.018252 | 0.018955 | 0.4 | 1.50 +Other | | 0.003775 | | | 0.31 + +Nlocal: 162 ave 175 max 156 min +Histogram: 1 2 0 0 0 0 0 0 0 1 +Nghost: 3689.5 ave 3721 max 3651 min +Histogram: 1 0 0 0 0 1 1 0 0 1 +Neighs: 4742.75 ave 5159 max 4485 min +Histogram: 2 0 0 0 1 0 0 0 0 1 + +Total # of neighbors = 18971 +Ave neighs/atom = 29.2762 +Ave special neighs/atom = 2 +Neighbor list builds = 12 +Dangerous builds = 0 + +# write_restart lammps.restart + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:02 diff --git a/examples/USER/misc/drip/C.drip b/examples/USER/misc/drip/C.drip new file mode 120000 index 0000000000..44959e2423 --- /dev/null +++ b/examples/USER/misc/drip/C.drip @@ -0,0 +1 @@ +../../../../potentials/C.drip \ No newline at end of file diff --git a/examples/USER/misc/drip/CH.rebo b/examples/USER/misc/drip/CH.rebo new file mode 120000 index 0000000000..c5a6a40100 --- /dev/null +++ b/examples/USER/misc/drip/CH.rebo @@ -0,0 +1 @@ +../../../../potentials/CH.rebo \ No newline at end of file diff --git a/examples/USER/misc/drip/README.txt b/examples/USER/misc/drip/README.txt new file mode 100644 index 0000000000..26a8e3dd00 --- /dev/null +++ b/examples/USER/misc/drip/README.txt @@ -0,0 +1,6 @@ +in.C_drip: + Use DRIP and REBO to relax a bilayer graphene. + +in.CH_drip: + Use DRIP and REBO to relax a bilayer graphene with additional hydrogen atoms + on top of it. diff --git a/examples/USER/misc/drip/data.C b/examples/USER/misc/drip/data.C new file mode 100644 index 0000000000..18ff6af645 --- /dev/null +++ b/examples/USER/misc/drip/data.C @@ -0,0 +1,416 @@ +LAMMPS data file + +400 atoms +1 atom types + +0.0 2.465000000000000e+01 xlo xhi +0.0 2.134752620328641e+01 ylo yhi +0.0 3.000000000000000e+01 zlo zhi +1.232500000000000e+01 0.000000000000000e+00 0.000000000000000e+00 xy xz yz + +Masses + +1 12.011 + +Atoms # molecular + +1 1 1 0.000000000000000e+00 0.000000000000000e+00 1.498097531971289e+01 +2 1 1 9.859999999999999e+00 1.707802096262913e+01 1.489139792549795e+01 +3 1 1 2.588250000000000e+01 6.404257860985923e+00 1.495586615731768e+01 +4 1 1 2.711500000000000e+01 7.115842067762138e+00 1.501795235919980e+01 +5 1 1 4.930000000000000e+00 8.539010481314564e+00 1.492827527515956e+01 +6 1 1 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+542 2 2 2.465000000000000e+01 9.962178894866991e+00 2.000000000000000e+01 +543 2 2 2.588250000000000e+01 9.250594688090777e+00 2.000000000000000e+01 +544 2 2 8.627500000000000e+00 9.250594688090777e+00 2.000000000000000e+01 +545 2 2 3.574249999999999e+01 2.063594199651019e+01 2.000000000000000e+01 diff --git a/examples/USER/misc/drip/in.CH_drip b/examples/USER/misc/drip/in.CH_drip new file mode 100644 index 0000000000..cf67fae639 --- /dev/null +++ b/examples/USER/misc/drip/in.CH_drip @@ -0,0 +1,30 @@ +# Define unit set and class of atomic model +units metal +atom_style molecular + +# BC +boundary p p s + +# read config +read_data data.CH + + +# potential +pair_style hybrid/overlay drip rebo +pair_coeff * * drip C.drip C NULL # only applies to species 1, i.e. C +pair_coeff * * rebo CH.rebo C H # species 1 is C and species 2 is H + + +compute peratom all pe/atom + +# set what thermodynamic information to print to log +thermo 10 # print every 1 timestep + +# set what information to write to dump file +dump id all custom 1 lammps.dump id type x y z fx fy fz c_peratom +dump_modify id every 10 format line "%d %d %13.5e %13.5e %13.5e %13.5e %13.5e %13.5e %13.5e" +dump_modify id sort id + +# minimize energy +minimize 1.0e-15 1.0e-15 100 100 + diff --git a/examples/USER/misc/drip/in.C_drip b/examples/USER/misc/drip/in.C_drip new file mode 100644 index 0000000000..0b66d0b9f7 --- /dev/null +++ b/examples/USER/misc/drip/in.C_drip @@ -0,0 +1,29 @@ +# Define unit set and class of atomic model +units metal +atom_style molecular + +# BC +boundary p p s + +# read config +read_data data.C + + +# potential +pair_style hybrid/overlay drip rebo +pair_coeff * * drip C.drip C +pair_coeff * * rebo CH.rebo C + +compute peratom all pe/atom + +# set what thermodynamic information to print to log +thermo 10 # print every 1 timestep + +# set what information to write to dump file +dump id all custom 1 lammps.dump id type x y z fx fy fz c_peratom +dump_modify id every 10 format line "%d %d %13.5e %13.5e %13.5e %13.5e %13.5e %13.5e %13.5e" +dump_modify id sort id + +# minimize energy +minimize 1.0e-15 1.0e-15 100 100 + diff --git a/examples/USER/misc/drip/log.30Apr19.CH_drip.g++.1 b/examples/USER/misc/drip/log.30Apr19.CH_drip.g++.1 new file mode 100644 index 0000000000..9aad2cd22f --- /dev/null +++ b/examples/USER/misc/drip/log.30Apr19.CH_drip.g++.1 @@ -0,0 +1,111 @@ +LAMMPS (30 Apr 2019) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88) + using 1 OpenMP thread(s) per MPI task +# Define unit set and class of atomic model +units metal +atom_style molecular + +# BC +boundary p p s + +# read config +read_data data.CH + triclinic box = (0 0 0) to (24.65 21.3475 30) with tilt (12.325 0 0) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 545 atoms + 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 = 0.000152826 secs + read_data CPU = 0.000973701 secs + + +# potential +pair_style hybrid/overlay drip rebo +pair_coeff * * drip C.drip C NULL # only applies to species 1, i.e. C +Reading potential file C.drip with DATE: 2019-04-19 +pair_coeff * * rebo CH.rebo C H # species 1 is C and species 2 is H +Reading potential file CH.rebo with DATE: 2018-7-3 + + +compute peratom all pe/atom + +# set what thermodynamic information to print to log +thermo 10 # print every 1 timestep + +# set what information to write to dump file +dump id all custom 1 lammps.dump id type x y z fx fy fz c_peratom +dump_modify id every 10 format line "%d %d %13.5e %13.5e %13.5e %13.5e %13.5e %13.5e %13.5e" +dump_modify id sort id + +# minimize energy +minimize 1.0e-15 1.0e-15 100 100 +WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 17.7 + ghost atom cutoff = 17.7 + binsize = 8.85, bins = 5 3 1 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair drip, perpetual, skip from (2) + attributes: full, newton on, ghost + pair build: skip/ghost + stencil: none + bin: none + (2) pair rebo, perpetual + attributes: full, newton on, ghost + pair build: full/bin/ghost + stencil: full/ghost/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 12.92 | 12.92 | 12.92 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 0 0 -2884.3731 0 -2884.3731 366196.9 2779.5956 + 10 0 -3240.4807 0 -3240.4807 -20237.368 2779.5956 + 20 0 -3281.0671 0 -3281.0671 -13303.696 2779.5956 + 30 0 -3282.2176 0 -3282.2176 -19187.215 2779.5956 + 40 0 -3282.4004 0 -3282.4004 -21740.059 2779.5956 + 50 0 -3282.4755 0 -3282.4755 -22659.554 2779.5956 + 57 0 -3282.5011 0 -3282.5011 -23313.198 2779.5956 +Loop time of 3.04218 on 1 procs for 57 steps with 545 atoms + +99.8% CPU use with 1 MPI tasks x 1 OpenMP threads + +Minimization stats: + Stopping criterion = max force evaluations + Energy initial, next-to-last, final = + -2884.37307546 -3282.49993222 -3282.5010627 + Force two-norm initial, final = 115.342 0.193154 + Force max component initial, final = 12.0934 0.03617 + Final line search alpha, max atom move = 1 0.03617 + Iterations, force evaluations = 57 100 + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 3.0291 | 3.0291 | 3.0291 | 0.0 | 99.57 +Bond | 1.8835e-05 | 1.8835e-05 | 1.8835e-05 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.0016081 | 0.0016081 | 0.0016081 | 0.0 | 0.05 +Output | 0.0079796 | 0.0079796 | 0.0079796 | 0.0 | 0.26 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 0.003517 | | | 0.12 + +Nlocal: 545 ave 545 max 545 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 3175 ave 3175 max 3175 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: 294122 ave 294122 max 294122 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 294122 +Ave neighs/atom = 539.673 +Ave special neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds = 0 + +Total wall time: 0:00:03 diff --git a/examples/USER/misc/drip/log.30Apr19.CH_drip.g++.4 b/examples/USER/misc/drip/log.30Apr19.CH_drip.g++.4 new file mode 100644 index 0000000000..9d439bca45 --- /dev/null +++ b/examples/USER/misc/drip/log.30Apr19.CH_drip.g++.4 @@ -0,0 +1,111 @@ +LAMMPS (30 Apr 2019) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88) + using 1 OpenMP thread(s) per MPI task +# Define unit set and class of atomic model +units metal +atom_style molecular + +# BC +boundary p p s + +# read config +read_data data.CH + triclinic box = (0 0 0) to (24.65 21.3475 30) with tilt (12.325 0 0) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 545 atoms + 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 = 0.000135422 secs + read_data CPU = 0.00368595 secs + + +# potential +pair_style hybrid/overlay drip rebo +pair_coeff * * drip C.drip C NULL # only applies to species 1, i.e. C +Reading potential file C.drip with DATE: 2019-04-19 +pair_coeff * * rebo CH.rebo C H # species 1 is C and species 2 is H +Reading potential file CH.rebo with DATE: 2018-7-3 + + +compute peratom all pe/atom + +# set what thermodynamic information to print to log +thermo 10 # print every 1 timestep + +# set what information to write to dump file +dump id all custom 1 lammps.dump id type x y z fx fy fz c_peratom +dump_modify id every 10 format line "%d %d %13.5e %13.5e %13.5e %13.5e %13.5e %13.5e %13.5e" +dump_modify id sort id + +# minimize energy +minimize 1.0e-15 1.0e-15 100 100 +WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 17.7 + ghost atom cutoff = 17.7 + binsize = 8.85, bins = 5 3 1 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair drip, perpetual, skip from (2) + attributes: full, newton on, ghost + pair build: skip/ghost + stencil: none + bin: none + (2) pair rebo, perpetual + attributes: full, newton on, ghost + pair build: full/bin/ghost + stencil: full/ghost/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 11.03 | 11.1 | 11.16 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 0 0 -2884.3731 0 -2884.3731 366196.9 2779.5956 + 10 0 -3240.4807 0 -3240.4807 -20237.368 2779.5956 + 20 0 -3281.0671 0 -3281.0671 -13303.696 2779.5956 + 30 0 -3282.2176 0 -3282.2176 -19187.216 2779.5956 + 40 0 -3282.4004 0 -3282.4004 -21740.027 2779.5956 + 50 0 -3282.4753 0 -3282.4753 -22682.604 2779.5956 + 57 0 -3282.5023 0 -3282.5023 -23355.081 2779.5956 +Loop time of 1.66218 on 4 procs for 57 steps with 545 atoms + +99.0% CPU use with 4 MPI tasks x 1 OpenMP threads + +Minimization stats: + Stopping criterion = max force evaluations + Energy initial, next-to-last, final = + -2884.37307546 -3282.50070864 -3282.50227121 + Force two-norm initial, final = 115.342 0.228488 + Force max component initial, final = 12.0934 0.03365 + Final line search alpha, max atom move = 1 0.03365 + Iterations, force evaluations = 57 100 + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.5571 | 1.5945 | 1.6314 | 2.3 | 95.93 +Bond | 2.265e-05 | 2.9087e-05 | 3.4571e-05 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.020248 | 0.05608 | 0.092328 | 11.8 | 3.37 +Output | 0.0053282 | 0.0054213 | 0.0056982 | 0.2 | 0.33 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 0.006172 | | | 0.37 + +Nlocal: 136.25 ave 177 max 100 min +Histogram: 2 0 0 0 0 0 0 0 1 1 +Nghost: 2874.75 ave 2912 max 2835 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 73530.5 ave 73544 max 73517 min +Histogram: 1 0 0 0 1 1 0 0 0 1 + +Total # of neighbors = 294122 +Ave neighs/atom = 539.673 +Ave special neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds = 0 + +Total wall time: 0:00:01 diff --git a/examples/USER/misc/drip/log.30Apr19.C_drip.g++.1 b/examples/USER/misc/drip/log.30Apr19.C_drip.g++.1 new file mode 100644 index 0000000000..6f19cee048 --- /dev/null +++ b/examples/USER/misc/drip/log.30Apr19.C_drip.g++.1 @@ -0,0 +1,110 @@ +LAMMPS (30 Apr 2019) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88) + using 1 OpenMP thread(s) per MPI task +# Define unit set and class of atomic model +units metal +atom_style molecular + +# BC +boundary p p s + +# read config +read_data data.C + triclinic box = (0 0 0) to (24.65 21.3475 30) with tilt (12.325 0 0) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 400 atoms + 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 = 0.000912905 secs + read_data CPU = 0.00252986 secs + + +# potential +pair_style hybrid/overlay drip rebo +pair_coeff * * drip C.drip C +Reading potential file C.drip with DATE: 2019-04-19 +pair_coeff * * rebo CH.rebo C +Reading potential file CH.rebo with DATE: 2018-7-3 + +compute peratom all pe/atom + +# set what thermodynamic information to print to log +thermo 10 # print every 1 timestep + +# set what information to write to dump file +dump id all custom 1 lammps.dump id type x y z fx fy fz c_peratom +dump_modify id every 10 format line "%d %d %13.5e %13.5e %13.5e %13.5e %13.5e %13.5e %13.5e" +dump_modify id sort id + +# minimize energy +minimize 1.0e-15 1.0e-15 100 100 +WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 17.7 + ghost atom cutoff = 17.7 + binsize = 8.85, bins = 5 3 1 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair drip, perpetual + attributes: full, newton on, ghost + pair build: full/bin/ghost + stencil: full/ghost/bin/3d + bin: standard + (2) pair rebo, perpetual, copy from (1) + attributes: full, newton on, ghost + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 12.21 | 12.21 | 12.21 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 0 0 -2941.0549 0 -2941.0549 -52204.715 2052.0534 + 10 0 -2966.9787 0 -2966.9787 -29717.01 2052.0534 + 20 0 -2967.0695 0 -2967.0695 -29614.636 2052.0534 + 30 0 -2967.0859 0 -2967.0859 -29867.385 2052.0534 + 40 0 -2967.0888 0 -2967.0888 -29997.486 2052.0534 + 50 0 -2967.0896 0 -2967.0896 -30072.387 2052.0534 + 51 0 -2967.0896 0 -2967.0896 -30076.548 2052.0534 +Loop time of 2.93337 on 1 procs for 51 steps with 400 atoms + +99.8% CPU use with 1 MPI tasks x 1 OpenMP threads + +Minimization stats: + Stopping criterion = max force evaluations + Energy initial, next-to-last, final = + -2941.05486197 -2967.08958376 -2967.08962073 + Force two-norm initial, final = 35.5666 0.0471918 + Force max component initial, final = 6.23617 0.0050012 + Final line search alpha, max atom move = 1 0.0050012 + Iterations, force evaluations = 51 101 + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 2.9239 | 2.9239 | 2.9239 | 0.0 | 99.68 +Bond | 1.2398e-05 | 1.2398e-05 | 1.2398e-05 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.0010808 | 0.0010808 | 0.0010808 | 0.0 | 0.04 +Output | 0.0059283 | 0.0059283 | 0.0059283 | 0.0 | 0.20 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 0.002466 | | | 0.08 + +Nlocal: 400 ave 400 max 400 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 2357 ave 2357 max 2357 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: 294122 ave 294122 max 294122 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 294122 +Ave neighs/atom = 735.305 +Ave special neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds = 0 + +Total wall time: 0:00:03 diff --git a/examples/USER/misc/drip/log.30Apr19.C_drip.g++.4 b/examples/USER/misc/drip/log.30Apr19.C_drip.g++.4 new file mode 100644 index 0000000000..54f9462b59 --- /dev/null +++ b/examples/USER/misc/drip/log.30Apr19.C_drip.g++.4 @@ -0,0 +1,111 @@ +LAMMPS (30 Apr 2019) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88) + using 1 OpenMP thread(s) per MPI task +# Define unit set and class of atomic model +units metal +atom_style molecular + +# BC +boundary p p s + +# read config +read_data data.C + triclinic box = (0 0 0) to (24.65 21.3475 30) with tilt (12.325 0 0) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 400 atoms + 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 = 0.0003407 secs + read_data CPU = 0.00411105 secs + + +# potential +pair_style hybrid/overlay drip rebo +pair_coeff * * drip C.drip C +Reading potential file C.drip with DATE: 2019-04-19 +pair_coeff * * rebo CH.rebo C +Reading potential file CH.rebo with DATE: 2018-7-3 + +compute peratom all pe/atom + +# set what thermodynamic information to print to log +thermo 10 # print every 1 timestep + +# set what information to write to dump file +dump id all custom 1 lammps.dump id type x y z fx fy fz c_peratom +dump_modify id every 10 format line "%d %d %13.5e %13.5e %13.5e %13.5e %13.5e %13.5e %13.5e" +dump_modify id sort id + +# minimize energy +minimize 1.0e-15 1.0e-15 100 100 +WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 17.7 + ghost atom cutoff = 17.7 + binsize = 8.85, bins = 5 3 1 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair drip, perpetual + attributes: full, newton on, ghost + pair build: full/bin/ghost + stencil: full/ghost/bin/3d + bin: standard + (2) pair rebo, perpetual, copy from (1) + attributes: full, newton on, ghost + pair build: copy + stencil: none + bin: none +WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/domain.cpp:934) +Per MPI rank memory allocation (min/avg/max) = 10.7 | 10.77 | 10.83 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 0 0 -2941.0549 0 -2941.0549 -52204.715 2052.0534 + 10 0 -2966.9787 0 -2966.9787 -29717.01 2052.0534 + 20 0 -2967.0695 0 -2967.0695 -29614.636 2052.0534 + 30 0 -2967.0859 0 -2967.0859 -29867.385 2052.0534 + 40 0 -2967.0888 0 -2967.0888 -29997.486 2052.0534 + 50 0 -2967.0896 0 -2967.0896 -30072.387 2052.0534 + 51 0 -2967.0896 0 -2967.0896 -30076.548 2052.0534 +Loop time of 1.47901 on 4 procs for 51 steps with 400 atoms + +99.1% CPU use with 4 MPI tasks x 1 OpenMP threads + +Minimization stats: + Stopping criterion = max force evaluations + Energy initial, next-to-last, final = + -2941.05486197 -2967.08958376 -2967.08962073 + Force two-norm initial, final = 35.5666 0.0471918 + Force max component initial, final = 6.23617 0.0050012 + Final line search alpha, max atom move = 1 0.0050012 + Iterations, force evaluations = 51 101 + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.4314 | 1.4405 | 1.4548 | 0.8 | 97.40 +Bond | 1.955e-05 | 2.265e-05 | 2.4796e-05 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.014506 | 0.029363 | 0.038964 | 5.5 | 1.99 +Output | 0.00424 | 0.0043345 | 0.0046172 | 0.2 | 0.29 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 0.004772 | | | 0.32 + +Nlocal: 100 ave 100 max 100 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 2132 ave 2132 max 2132 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: 73530.5 ave 73544 max 73517 min +Histogram: 1 0 0 0 1 1 0 0 0 1 + +Total # of neighbors = 294122 +Ave neighs/atom = 735.305 +Ave special neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds = 0 + +Total wall time: 0:00:01 diff --git a/examples/USER/misc/kolmogorov_crespi_z/CH.airebo b/examples/USER/misc/kolmogorov_crespi_z/CH.airebo deleted file mode 120000 index e43e44c133..0000000000 --- a/examples/USER/misc/kolmogorov_crespi_z/CH.airebo +++ /dev/null @@ -1 +0,0 @@ -../../../../potentials/CH.airebo \ No newline at end of file diff --git a/examples/USER/misc/kolmogorov_crespi_z/CH.rebo b/examples/USER/misc/kolmogorov_crespi_z/CH.rebo new file mode 120000 index 0000000000..c5a6a40100 --- /dev/null +++ b/examples/USER/misc/kolmogorov_crespi_z/CH.rebo @@ -0,0 +1 @@ +../../../../potentials/CH.rebo \ No newline at end of file diff --git a/examples/USER/misc/kolmogorov_crespi_z/in.bilayer-graphene b/examples/USER/misc/kolmogorov_crespi_z/in.bilayer-graphene index 3d63fc09ed..b019b3e5bb 100644 --- a/examples/USER/misc/kolmogorov_crespi_z/in.bilayer-graphene +++ b/examples/USER/misc/kolmogorov_crespi_z/in.bilayer-graphene @@ -22,7 +22,7 @@ group adsorbant type 2 ######################## Potential defition ######################## pair_style hybrid/overlay rebo kolmogorov/crespi/z 14.0 #################################################################### -pair_coeff * * rebo CH.airebo C C # chemical +pair_coeff * * rebo CH.rebo C C # chemical pair_coeff 1 2 kolmogorov/crespi/z CC.KC C C # long-range #################################################################### diff --git a/examples/USER/misc/kolmogorov_crespi_z/log.16Mar18.bilayer-graphene.g++.1 b/examples/USER/misc/kolmogorov_crespi_z/log.16Mar18.bilayer-graphene.g++.1 deleted file mode 100644 index 3ba8bfd5df..0000000000 --- a/examples/USER/misc/kolmogorov_crespi_z/log.16Mar18.bilayer-graphene.g++.1 +++ /dev/null @@ -1,208 +0,0 @@ -LAMMPS (8 Mar 2018) - using 1 OpenMP thread(s) per MPI task -# Initialization -units metal -boundary p p p -atom_style atomic -processors * * 1 # domain decomposition over x and y - -# System and atom definition -# we use 2 atom types so that inter- and intra-layer -# interactions can be specified separately -read_data data.bilayer-graphene # read lammps data file - orthogonal box = (0 0 -20) to (17.04 19.6761 40) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 256 atoms -mass 1 12.0107 # carbon mass (g/mole) | membrane -mass 2 12.0107 # carbon mass (g/mole) | adsorbate -# Neighbor update settings -neighbor 2.0 bin -neigh_modify every 1 -neigh_modify delay 0 -neigh_modify check yes -# Separate atom groups -group membrane type 1 -128 atoms in group membrane -group adsorbant type 2 -128 atoms in group adsorbant - -######################## Potential defition ######################## -pair_style hybrid/overlay rebo kolmogorov/crespi/z 14.0 -#################################################################### -pair_coeff * * rebo CH.airebo C C # chemical -Reading potential file CH.airebo with DATE: 2011-10-25 -pair_coeff 1 2 kolmogorov/crespi/z CC.KC C C # long-range -#################################################################### - -#### Simulation settings #### -timestep 0.0001 -velocity all create 300.0 12345 -fix thermostat all nve -compute COM1 membrane com -compute COM2 adsorbant com -############################ - -# Output -#dump 1 all xyz 100 trajec.xyz -#dump_modify 1 format line "%s %12.6f %12.6f %12.6f" element "C" "C" -thermo 10 -thermo_style custom step time etotal pe temp c_COM1[3] c_COM2[3] # spcpu -thermo_modify line one format float %14.8f - -###### Run molecular dynamics ###### -run 1000 -Neighbor list info ... - 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 - binsize = 8, bins = 3 3 8 - 3 neighbor lists, perpetual/occasional/extra = 3 0 0 - (1) pair rebo, perpetual - attributes: full, newton on, ghost - pair build: full/bin/ghost - stencil: full/ghost/bin/3d - bin: standard - (2) pair kolmogorov/crespi/z, perpetual, skip from (3) - attributes: half, newton on - pair build: skip - stencil: none - bin: none - (3) neighbor class addition, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 4.998 | 4.998 | 4.998 Mbytes -Step Time TotEng PotEng Temp c_COM1[3] c_COM2[3] - 0 0.00000000 -1888.67041214 -1898.55881323 300.00000000 0.00000000 3.30000000 - 10 0.00100000 -1888.67037221 -1898.21029897 289.42778520 -0.00020126 3.30020126 - 20 0.00200000 -1888.67021541 -1897.22943612 259.67456089 -0.00041357 3.30041357 - 30 0.00300000 -1888.66999308 -1895.86681311 218.34126559 -0.00063673 3.30063673 - 40 0.00400000 -1888.66978354 -1894.47163830 176.02000692 -0.00087055 3.30087055 - 50 0.00500000 -1888.66966068 -1893.37123377 142.63902862 -0.00111486 3.30111486 - 60 0.00600000 -1888.66966132 -1892.75822749 124.04127205 -0.00136952 3.30136952 - 70 0.00700000 -1888.66976974 -1892.63445751 120.28297808 -0.00163441 3.30163441 - 80 0.00800000 -1888.66992867 -1892.83467462 126.35245792 -0.00190946 3.30190946 - 90 0.00900000 -1888.67006868 -1893.11387069 134.81862145 -0.00219458 3.30219458 - 100 0.01000000 -1888.67013621 -1893.25481851 139.09272853 -0.00248973 3.30248973 - 110 0.01100000 -1888.67011201 -1893.15155790 135.96068294 -0.00279489 3.30279489 - 120 0.01200000 -1888.67001496 -1892.84002960 126.51230266 -0.00311004 3.30311004 - 130 0.01300000 -1888.66988997 -1892.47004238 115.29120968 -0.00343519 3.30343519 - 140 0.01400000 -1888.66979230 -1892.23503116 108.16426723 -0.00377038 3.30377038 - 150 0.01500000 -1888.66976478 -1892.28630583 109.72070257 -0.00411562 3.30411562 - 160 0.01600000 -1888.66982054 -1892.66640611 121.25071190 -0.00447099 3.30447099 - 170 0.01700000 -1888.66993790 -1893.28862637 140.12442721 -0.00483654 3.30483654 - 180 0.01800000 -1888.67007017 -1893.97029258 160.80119589 -0.00521235 3.30521235 - 190 0.01900000 -1888.67016712 -1894.50458787 177.00801243 -0.00559851 3.30559851 - 200 0.02000000 -1888.67019459 -1894.73890106 184.11590729 -0.00599512 3.30599512 - 210 0.02100000 -1888.67014420 -1894.62906014 180.78501932 -0.00640230 3.30640230 - 220 0.02200000 -1888.67003680 -1894.25249103 169.36370738 -0.00682016 3.30682016 - 230 0.02300000 -1888.66991386 -1893.77601613 154.91186767 -0.00724883 3.30724883 - 240 0.02400000 -1888.66982525 -1893.38995084 143.20188490 -0.00768845 3.30768845 - 250 0.02500000 -1888.66980630 -1893.23138936 138.39193056 -0.00813913 3.30813913 - 260 0.02600000 -1888.66986130 -1893.32993923 141.38012476 -0.00860097 3.30860097 - 270 0.02700000 -1888.66996305 -1893.60070606 149.59171763 -0.00907408 3.30907408 - 280 0.02800000 -1888.67006686 -1893.88587226 158.24010433 -0.00955849 3.30955849 - 290 0.02900000 -1888.67012981 -1894.02402669 162.42960292 -0.01005424 3.31005424 - 300 0.03000000 -1888.67012722 -1893.91715234 159.18726627 -0.01056129 3.31056129 - 310 0.03100000 -1888.67005731 -1893.57037242 148.66857852 -0.01107957 3.31107957 - 320 0.03200000 -1888.66994573 -1893.09358619 134.20694883 -0.01160898 3.31160898 - 330 0.03300000 -1888.66983589 -1892.66132663 121.09614207 -0.01214935 3.31214935 - 340 0.03400000 -1888.66977410 -1892.44446345 114.51869676 -0.01270046 3.31270046 - 350 0.03500000 -1888.66978826 -1892.53901235 117.38674604 -0.01326207 3.31326207 - 360 0.03600000 -1888.66987439 -1892.92337288 129.04508371 -0.01383390 3.31383390 - 370 0.03700000 -1888.66999800 -1893.46445570 145.45701555 -0.01441561 3.31441561 - 380 0.03800000 -1888.67010960 -1893.97065516 160.81100020 -0.01500688 3.31500688 - 390 0.03900000 -1888.67016540 -1894.26835818 169.84119247 -0.01560734 3.31560734 - 400 0.04000000 -1888.67014667 -1894.26967975 169.88185546 -0.01621664 3.31621664 - 410 0.04100000 -1888.67006166 -1894.00321069 161.80014280 -0.01683442 3.31683442 - 420 0.04200000 -1888.66994367 -1893.60086324 149.59707418 -0.01746033 3.31746033 - 430 0.04300000 -1888.66984058 -1893.24559841 138.82197275 -0.01809405 3.31809405 - 440 0.04400000 -1888.66979399 -1893.09727874 134.32357877 -0.01873527 3.31873527 - 450 0.04500000 -1888.66982139 -1893.22837442 138.30000378 -0.01938373 3.31938373 - 460 0.04600000 -1888.66990972 -1893.59670383 149.47191354 -0.02003918 3.32003918 - 470 0.04700000 -1888.67002173 -1894.06542598 163.68887743 -0.02070143 3.32070143 - 480 0.04800000 -1888.67011389 -1894.46010842 175.66018439 -0.02137030 3.32137030 - 490 0.04900000 -1888.67015175 -1894.63688098 181.02206322 -0.02204565 3.32204565 - 500 0.05000000 -1888.67012158 -1894.53632221 177.97216882 -0.02272740 3.32272740 - 510 0.05100000 -1888.67003762 -1894.20444731 167.90610436 -0.02341547 3.32341547 - 520 0.05200000 -1888.66993151 -1893.77231066 154.79891353 -0.02410981 3.32410981 - 530 0.05300000 -1888.66984505 -1893.40525927 143.66572038 -0.02481040 3.32481040 - 540 0.05400000 -1888.66981408 -1893.23762083 138.58074854 -0.02551724 3.32551724 - 550 0.05500000 -1888.66985005 -1893.31793594 141.01630317 -0.02623032 3.32623032 - 560 0.05600000 -1888.66993737 -1893.59069013 149.28862751 -0.02694963 3.32694963 - 570 0.05700000 -1888.67003852 -1893.92089571 159.30352588 -0.02767517 3.32767517 - 580 0.05800000 -1888.67011322 -1894.15124753 166.28980524 -0.02840691 3.32840691 - 590 0.05900000 -1888.67013192 -1894.16548041 166.72104345 -0.02914478 3.32914478 - 600 0.06000000 -1888.67008713 -1893.93443318 159.71275856 -0.02988871 3.32988871 - 610 0.06100000 -1888.66999438 -1893.52841656 147.39760646 -0.03063856 3.33063856 - 620 0.06200000 -1888.66988809 -1893.09235021 134.17119963 -0.03139416 3.33139416 - 630 0.06300000 -1888.66980996 -1892.79172016 125.05288240 -0.03215531 3.33215531 - 640 0.06400000 -1888.66979261 -1892.74755390 123.71346730 -0.03292176 3.33292176 - 650 0.06500000 -1888.66984332 -1892.98665459 130.96590324 -0.03369323 3.33369323 - 660 0.06600000 -1888.66994245 -1893.42999868 144.41332389 -0.03446937 3.33446937 - 670 0.06700000 -1888.67005233 -1893.92310681 159.37018806 -0.03524986 3.33524986 - 680 0.06800000 -1888.67013309 -1894.29451581 170.63575808 -0.03603430 3.33603430 - 690 0.06900000 -1888.67015452 -1894.41878117 174.40514192 -0.03682229 3.33682229 - 700 0.07000000 -1888.67010897 -1894.26288036 169.67671530 -0.03761343 3.33761343 - 710 0.07100000 -1888.67001367 -1893.89812904 158.61357114 -0.03840729 3.33840729 - 720 0.07200000 -1888.66990378 -1893.47348746 145.73388454 -0.03920344 3.33920344 - 730 0.07300000 -1888.66982212 -1893.15984839 136.22099960 -0.04000148 3.34000148 - 740 0.07400000 -1888.66980109 -1893.08373746 133.91254029 -0.04080098 3.34080098 - 750 0.07500000 -1888.66984794 -1893.27755511 139.79127024 -0.04160156 3.34160156 - 760 0.07600000 -1888.66994215 -1893.66837365 151.64528967 -0.04240282 3.34240282 - 770 0.07700000 -1888.67004554 -1894.10941206 165.02263027 -0.04320441 3.34320441 - 780 0.07800000 -1888.67011702 -1894.43947545 175.03411436 -0.04400599 3.34400599 - 790 0.07900000 -1888.67013297 -1894.54590471 178.26254255 -0.04480726 3.34480726 - 800 0.08000000 -1888.67008751 -1894.40384142 173.95392406 -0.04560792 3.34560792 - 810 0.08100000 -1888.66999923 -1894.08389003 164.24973321 -0.04640773 3.34640773 - 820 0.08200000 -1888.66990447 -1893.72313979 153.30795965 -0.04720647 3.34720647 - 830 0.08300000 -1888.66984367 -1893.46839190 145.58111626 -0.04800393 3.34800393 - 840 0.08400000 -1888.66984156 -1893.41412536 143.93481093 -0.04879995 3.34879995 - 850 0.08500000 -1888.66989670 -1893.56426154 148.48805553 -0.04959439 3.34959439 - 860 0.08600000 -1888.66998222 -1893.83463719 156.68827294 -0.05038713 3.35038713 - 870 0.08700000 -1888.67006171 -1894.09325045 164.53181920 -0.05117805 3.35117805 - 880 0.08800000 -1888.67010273 -1894.21712661 168.28880100 -0.05196706 3.35196706 - 890 0.08900000 -1888.67008993 -1894.14263950 166.02935656 -0.05275408 3.35275408 - 900 0.09000000 -1888.67002891 -1893.89014571 158.37090587 -0.05353904 3.35353904 - 910 0.09100000 -1888.66994326 -1893.55535709 148.21649469 -0.05432186 3.35432186 - 920 0.09200000 -1888.66986526 -1893.27257949 139.63979178 -0.05510247 3.35510247 - 930 0.09300000 -1888.66982730 -1893.16330891 136.32582949 -0.05588078 3.35588078 - 940 0.09400000 -1888.66984631 -1893.28643285 140.06065785 -0.05665670 3.35665670 - 950 0.09500000 -1888.66991503 -1893.61245342 149.94957268 -0.05743015 3.35743015 - 960 0.09600000 -1888.67000691 -1894.03423922 162.74316516 -0.05820101 3.35820101 - 970 0.09700000 -1888.67008649 -1894.40848025 174.09469037 -0.05896915 3.35896915 - 980 0.09800000 -1888.67012436 -1894.61056767 180.22458605 -0.05973444 3.35973444 - 990 0.09900000 -1888.67010608 -1894.58107659 179.33042338 -0.06049672 3.36049672 - 1000 0.10000000 -1888.67003981 -1894.34773305 172.25312330 -0.06125581 3.36125581 -Loop time of 3.90147 on 1 procs for 1000 steps with 256 atoms - -Performance: 2.215 ns/day, 10.837 hours/ns, 256.314 timesteps/s -99.4% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 3.8786 | 3.8786 | 3.8786 | 0.0 | 99.41 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.010816 | 0.010816 | 0.010816 | 0.0 | 0.28 -Output | 0.002461 | 0.002461 | 0.002461 | 0.0 | 0.06 -Modify | 0.0051703 | 0.0051703 | 0.0051703 | 0.0 | 0.13 -Other | | 0.004447 | | | 0.11 - -Nlocal: 256 ave 256 max 256 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 1721 ave 1721 max 1721 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 37312 ave 37312 max 37312 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 94592 ave 94592 max 94592 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 94592 -Ave neighs/atom = 369.5 -Neighbor list builds = 0 -Dangerous builds = 0 -Total wall time: 0:00:03 diff --git a/examples/USER/misc/kolmogorov_crespi_z/log.16Mar18.bilayer-graphene.g++.4 b/examples/USER/misc/kolmogorov_crespi_z/log.16Mar18.bilayer-graphene.g++.4 deleted file mode 100644 index b2dd551654..0000000000 --- a/examples/USER/misc/kolmogorov_crespi_z/log.16Mar18.bilayer-graphene.g++.4 +++ /dev/null @@ -1,208 +0,0 @@ -LAMMPS (8 Mar 2018) - using 1 OpenMP thread(s) per MPI task -# Initialization -units metal -boundary p p p -atom_style atomic -processors * * 1 # domain decomposition over x and y - -# System and atom definition -# we use 2 atom types so that inter- and intra-layer -# interactions can be specified separately -read_data data.bilayer-graphene # read lammps data file - orthogonal box = (0 0 -20) to (17.04 19.6761 40) - 2 by 2 by 1 MPI processor grid - reading atoms ... - 256 atoms -mass 1 12.0107 # carbon mass (g/mole) | membrane -mass 2 12.0107 # carbon mass (g/mole) | adsorbate -# Neighbor update settings -neighbor 2.0 bin -neigh_modify every 1 -neigh_modify delay 0 -neigh_modify check yes -# Separate atom groups -group membrane type 1 -128 atoms in group membrane -group adsorbant type 2 -128 atoms in group adsorbant - -######################## Potential defition ######################## -pair_style hybrid/overlay rebo kolmogorov/crespi/z 14.0 -#################################################################### -pair_coeff * * rebo CH.airebo C C # chemical -Reading potential file CH.airebo with DATE: 2011-10-25 -pair_coeff 1 2 kolmogorov/crespi/z CC.KC C C # long-range -#################################################################### - -#### Simulation settings #### -timestep 0.0001 -velocity all create 300.0 12345 -fix thermostat all nve -compute COM1 membrane com -compute COM2 adsorbant com -############################ - -# Output -#dump 1 all xyz 100 trajec.xyz -#dump_modify 1 format line "%s %12.6f %12.6f %12.6f" element "C" "C" -thermo 10 -thermo_style custom step time etotal pe temp c_COM1[3] c_COM2[3] # spcpu -thermo_modify line one format float %14.8f - -###### Run molecular dynamics ###### -run 1000 -Neighbor list info ... - 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 - binsize = 8, bins = 3 3 8 - 3 neighbor lists, perpetual/occasional/extra = 3 0 0 - (1) pair rebo, perpetual - attributes: full, newton on, ghost - pair build: full/bin/ghost - stencil: full/ghost/bin/3d - bin: standard - (2) pair kolmogorov/crespi/z, perpetual, skip from (3) - attributes: half, newton on - pair build: skip - stencil: none - bin: none - (3) neighbor class addition, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 4.572 | 4.572 | 4.572 Mbytes -Step Time TotEng PotEng Temp c_COM1[3] c_COM2[3] - 0 0.00000000 -1888.67041214 -1898.55881323 300.00000000 0.00000000 3.30000000 - 10 0.00100000 -1888.67037221 -1898.21029897 289.42778520 -0.00020126 3.30020126 - 20 0.00200000 -1888.67021541 -1897.22943612 259.67456089 -0.00041357 3.30041357 - 30 0.00300000 -1888.66999308 -1895.86681311 218.34126559 -0.00063673 3.30063673 - 40 0.00400000 -1888.66978354 -1894.47163830 176.02000692 -0.00087055 3.30087055 - 50 0.00500000 -1888.66966068 -1893.37123377 142.63902862 -0.00111486 3.30111486 - 60 0.00600000 -1888.66966132 -1892.75822749 124.04127205 -0.00136952 3.30136952 - 70 0.00700000 -1888.66976974 -1892.63445751 120.28297808 -0.00163441 3.30163441 - 80 0.00800000 -1888.66992867 -1892.83467462 126.35245792 -0.00190946 3.30190946 - 90 0.00900000 -1888.67006868 -1893.11387069 134.81862145 -0.00219458 3.30219458 - 100 0.01000000 -1888.67013621 -1893.25481851 139.09272853 -0.00248973 3.30248973 - 110 0.01100000 -1888.67011201 -1893.15155790 135.96068294 -0.00279489 3.30279489 - 120 0.01200000 -1888.67001496 -1892.84002960 126.51230266 -0.00311004 3.30311004 - 130 0.01300000 -1888.66988997 -1892.47004238 115.29120968 -0.00343519 3.30343519 - 140 0.01400000 -1888.66979230 -1892.23503116 108.16426723 -0.00377038 3.30377038 - 150 0.01500000 -1888.66976478 -1892.28630583 109.72070257 -0.00411562 3.30411562 - 160 0.01600000 -1888.66982054 -1892.66640611 121.25071190 -0.00447099 3.30447099 - 170 0.01700000 -1888.66993790 -1893.28862637 140.12442721 -0.00483654 3.30483654 - 180 0.01800000 -1888.67007017 -1893.97029258 160.80119589 -0.00521235 3.30521235 - 190 0.01900000 -1888.67016712 -1894.50458787 177.00801243 -0.00559851 3.30559851 - 200 0.02000000 -1888.67019459 -1894.73890106 184.11590729 -0.00599512 3.30599512 - 210 0.02100000 -1888.67014420 -1894.62906014 180.78501932 -0.00640230 3.30640230 - 220 0.02200000 -1888.67003680 -1894.25249103 169.36370738 -0.00682016 3.30682016 - 230 0.02300000 -1888.66991386 -1893.77601613 154.91186767 -0.00724883 3.30724883 - 240 0.02400000 -1888.66982525 -1893.38995084 143.20188490 -0.00768845 3.30768845 - 250 0.02500000 -1888.66980630 -1893.23138936 138.39193056 -0.00813913 3.30813913 - 260 0.02600000 -1888.66986130 -1893.32993923 141.38012476 -0.00860097 3.30860097 - 270 0.02700000 -1888.66996305 -1893.60070606 149.59171763 -0.00907408 3.30907408 - 280 0.02800000 -1888.67006686 -1893.88587226 158.24010433 -0.00955849 3.30955849 - 290 0.02900000 -1888.67012981 -1894.02402669 162.42960292 -0.01005424 3.31005424 - 300 0.03000000 -1888.67012722 -1893.91715234 159.18726627 -0.01056129 3.31056129 - 310 0.03100000 -1888.67005731 -1893.57037242 148.66857852 -0.01107957 3.31107957 - 320 0.03200000 -1888.66994573 -1893.09358619 134.20694883 -0.01160898 3.31160898 - 330 0.03300000 -1888.66983589 -1892.66132663 121.09614207 -0.01214935 3.31214935 - 340 0.03400000 -1888.66977410 -1892.44446345 114.51869676 -0.01270046 3.31270046 - 350 0.03500000 -1888.66978826 -1892.53901235 117.38674604 -0.01326207 3.31326207 - 360 0.03600000 -1888.66987439 -1892.92337288 129.04508371 -0.01383390 3.31383390 - 370 0.03700000 -1888.66999800 -1893.46445570 145.45701555 -0.01441561 3.31441561 - 380 0.03800000 -1888.67010960 -1893.97065516 160.81100020 -0.01500688 3.31500688 - 390 0.03900000 -1888.67016540 -1894.26835818 169.84119247 -0.01560734 3.31560734 - 400 0.04000000 -1888.67014667 -1894.26967975 169.88185546 -0.01621664 3.31621664 - 410 0.04100000 -1888.67006166 -1894.00321069 161.80014280 -0.01683442 3.31683442 - 420 0.04200000 -1888.66994367 -1893.60086324 149.59707418 -0.01746033 3.31746033 - 430 0.04300000 -1888.66984058 -1893.24559841 138.82197275 -0.01809405 3.31809405 - 440 0.04400000 -1888.66979399 -1893.09727874 134.32357877 -0.01873527 3.31873527 - 450 0.04500000 -1888.66982139 -1893.22837442 138.30000378 -0.01938373 3.31938373 - 460 0.04600000 -1888.66990972 -1893.59670383 149.47191354 -0.02003918 3.32003918 - 470 0.04700000 -1888.67002173 -1894.06542598 163.68887743 -0.02070143 3.32070143 - 480 0.04800000 -1888.67011389 -1894.46010842 175.66018439 -0.02137030 3.32137030 - 490 0.04900000 -1888.67015175 -1894.63688098 181.02206322 -0.02204565 3.32204565 - 500 0.05000000 -1888.67012158 -1894.53632221 177.97216882 -0.02272740 3.32272740 - 510 0.05100000 -1888.67003762 -1894.20444731 167.90610436 -0.02341547 3.32341547 - 520 0.05200000 -1888.66993151 -1893.77231066 154.79891353 -0.02410981 3.32410981 - 530 0.05300000 -1888.66984505 -1893.40525927 143.66572038 -0.02481040 3.32481040 - 540 0.05400000 -1888.66981408 -1893.23762083 138.58074854 -0.02551724 3.32551724 - 550 0.05500000 -1888.66985005 -1893.31793594 141.01630317 -0.02623032 3.32623032 - 560 0.05600000 -1888.66993737 -1893.59069013 149.28862751 -0.02694963 3.32694963 - 570 0.05700000 -1888.67003852 -1893.92089571 159.30352588 -0.02767517 3.32767517 - 580 0.05800000 -1888.67011322 -1894.15124753 166.28980524 -0.02840691 3.32840691 - 590 0.05900000 -1888.67013192 -1894.16548041 166.72104345 -0.02914478 3.32914478 - 600 0.06000000 -1888.67008713 -1893.93443318 159.71275856 -0.02988871 3.32988871 - 610 0.06100000 -1888.66999438 -1893.52841656 147.39760646 -0.03063856 3.33063856 - 620 0.06200000 -1888.66988809 -1893.09235021 134.17119963 -0.03139416 3.33139416 - 630 0.06300000 -1888.66980996 -1892.79172016 125.05288240 -0.03215531 3.33215531 - 640 0.06400000 -1888.66979261 -1892.74755390 123.71346730 -0.03292176 3.33292176 - 650 0.06500000 -1888.66984332 -1892.98665459 130.96590324 -0.03369323 3.33369323 - 660 0.06600000 -1888.66994245 -1893.42999868 144.41332389 -0.03446937 3.33446937 - 670 0.06700000 -1888.67005233 -1893.92310681 159.37018806 -0.03524986 3.33524986 - 680 0.06800000 -1888.67013309 -1894.29451581 170.63575808 -0.03603430 3.33603430 - 690 0.06900000 -1888.67015452 -1894.41878117 174.40514192 -0.03682229 3.33682229 - 700 0.07000000 -1888.67010897 -1894.26288036 169.67671530 -0.03761343 3.33761343 - 710 0.07100000 -1888.67001367 -1893.89812904 158.61357114 -0.03840729 3.33840729 - 720 0.07200000 -1888.66990378 -1893.47348746 145.73388454 -0.03920344 3.33920344 - 730 0.07300000 -1888.66982212 -1893.15984839 136.22099960 -0.04000148 3.34000148 - 740 0.07400000 -1888.66980109 -1893.08373746 133.91254029 -0.04080098 3.34080098 - 750 0.07500000 -1888.66984794 -1893.27755511 139.79127024 -0.04160156 3.34160156 - 760 0.07600000 -1888.66994215 -1893.66837365 151.64528967 -0.04240282 3.34240282 - 770 0.07700000 -1888.67004554 -1894.10941206 165.02263027 -0.04320441 3.34320441 - 780 0.07800000 -1888.67011702 -1894.43947545 175.03411436 -0.04400599 3.34400599 - 790 0.07900000 -1888.67013297 -1894.54590471 178.26254255 -0.04480726 3.34480726 - 800 0.08000000 -1888.67008751 -1894.40384142 173.95392406 -0.04560792 3.34560792 - 810 0.08100000 -1888.66999923 -1894.08389003 164.24973321 -0.04640773 3.34640773 - 820 0.08200000 -1888.66990447 -1893.72313979 153.30795965 -0.04720647 3.34720647 - 830 0.08300000 -1888.66984367 -1893.46839190 145.58111626 -0.04800393 3.34800393 - 840 0.08400000 -1888.66984156 -1893.41412536 143.93481093 -0.04879995 3.34879995 - 850 0.08500000 -1888.66989670 -1893.56426154 148.48805553 -0.04959439 3.34959439 - 860 0.08600000 -1888.66998222 -1893.83463719 156.68827294 -0.05038713 3.35038713 - 870 0.08700000 -1888.67006171 -1894.09325045 164.53181920 -0.05117805 3.35117805 - 880 0.08800000 -1888.67010273 -1894.21712661 168.28880100 -0.05196706 3.35196706 - 890 0.08900000 -1888.67008993 -1894.14263950 166.02935656 -0.05275408 3.35275408 - 900 0.09000000 -1888.67002891 -1893.89014571 158.37090587 -0.05353904 3.35353904 - 910 0.09100000 -1888.66994326 -1893.55535709 148.21649469 -0.05432186 3.35432186 - 920 0.09200000 -1888.66986526 -1893.27257949 139.63979178 -0.05510247 3.35510247 - 930 0.09300000 -1888.66982730 -1893.16330891 136.32582949 -0.05588078 3.35588078 - 940 0.09400000 -1888.66984631 -1893.28643285 140.06065785 -0.05665670 3.35665670 - 950 0.09500000 -1888.66991503 -1893.61245342 149.94957268 -0.05743015 3.35743015 - 960 0.09600000 -1888.67000691 -1894.03423922 162.74316516 -0.05820101 3.35820101 - 970 0.09700000 -1888.67008649 -1894.40848025 174.09469037 -0.05896915 3.35896915 - 980 0.09800000 -1888.67012436 -1894.61056767 180.22458605 -0.05973444 3.35973444 - 990 0.09900000 -1888.67010608 -1894.58107659 179.33042338 -0.06049672 3.36049672 - 1000 0.10000000 -1888.67003981 -1894.34773305 172.25312330 -0.06125581 3.36125581 -Loop time of 1.32192 on 4 procs for 1000 steps with 256 atoms - -Performance: 6.536 ns/day, 3.672 hours/ns, 756.476 timesteps/s -98.6% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 1.1157 | 1.172 | 1.2369 | 4.0 | 88.66 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.071678 | 0.13667 | 0.19304 | 11.8 | 10.34 -Output | 0.0029244 | 0.0031272 | 0.0035112 | 0.4 | 0.24 -Modify | 0.0016961 | 0.0017477 | 0.0017846 | 0.1 | 0.13 -Other | | 0.008334 | | | 0.63 - -Nlocal: 64 ave 64 max 64 min -Histogram: 4 0 0 0 0 0 0 0 0 0 -Nghost: 1265 ave 1265 max 1265 min -Histogram: 4 0 0 0 0 0 0 0 0 0 -Neighs: 9328 ave 9328 max 9328 min -Histogram: 4 0 0 0 0 0 0 0 0 0 -FullNghs: 23648 ave 23648 max 23648 min -Histogram: 4 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 94592 -Ave neighs/atom = 369.5 -Neighbor list builds = 0 -Dangerous builds = 0 -Total wall time: 0:00:01 diff --git a/examples/USER/misc/kolmogorov_crespi_z/log.30Apr19.bilayer-graphene.g++.1 b/examples/USER/misc/kolmogorov_crespi_z/log.30Apr19.bilayer-graphene.g++.1 new file mode 100644 index 0000000000..5c8616749e --- /dev/null +++ b/examples/USER/misc/kolmogorov_crespi_z/log.30Apr19.bilayer-graphene.g++.1 @@ -0,0 +1,210 @@ +LAMMPS (30 Apr 2019) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88) + using 1 OpenMP thread(s) per MPI task +# Initialization +units metal +boundary p p p +atom_style atomic +processors * * 1 # domain decomposition over x and y + +# System and atom definition +# we use 2 atom types so that inter- and intra-layer +# interactions can be specified separately +read_data data.bilayer-graphene # read lammps data file + orthogonal box = (0 0 -20) to (17.04 19.6761 40) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 256 atoms + read_data CPU = 0.000291348 secs +mass 1 12.0107 # carbon mass (g/mole) | membrane +mass 2 12.0107 # carbon mass (g/mole) | adsorbate +# Neighbor update settings +neighbor 2.0 bin +neigh_modify every 1 +neigh_modify delay 0 +neigh_modify check yes +# Separate atom groups +group membrane type 1 +128 atoms in group membrane +group adsorbant type 2 +128 atoms in group adsorbant + +######################## Potential defition ######################## +pair_style hybrid/overlay rebo kolmogorov/crespi/z 14.0 +#################################################################### +pair_coeff * * rebo CH.rebo C C # chemical +Reading potential file CH.rebo with DATE: 2018-7-3 +pair_coeff 1 2 kolmogorov/crespi/z CC.KC C C # long-range +#################################################################### + +#### Simulation settings #### +timestep 0.0001 +velocity all create 300.0 12345 +fix thermostat all nve +compute COM1 membrane com +compute COM2 adsorbant com +############################ + +# Output +#dump 1 all xyz 100 trajec.xyz +#dump_modify 1 format line "%s %12.6f %12.6f %12.6f" element "C" "C" +thermo 10 +thermo_style custom step time etotal pe temp c_COM1[3] c_COM2[3] # spcpu +thermo_modify line one format float %14.8f + +###### Run molecular dynamics ###### +run 1000 +Neighbor list info ... + 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 + binsize = 8, bins = 3 3 8 + 3 neighbor lists, perpetual/occasional/extra = 3 0 0 + (1) pair rebo, perpetual + attributes: full, newton on, ghost + pair build: full/bin/ghost + stencil: full/ghost/bin/3d + bin: standard + (2) pair kolmogorov/crespi/z, perpetual, skip from (3) + attributes: half, newton on + pair build: skip + stencil: none + bin: none + (3) neighbor class addition, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.998 | 4.998 | 4.998 Mbytes +Step Time TotEng PotEng Temp c_COM1[3] c_COM2[3] + 0 0.00000000 -1888.67041233 -1898.55881343 300.00000000 0.00000000 3.30000000 + 10 0.00100000 -1888.67037240 -1898.21029916 289.42778520 -0.00020126 3.30020126 + 20 0.00200000 -1888.67021561 -1897.22943631 259.67456089 -0.00041357 3.30041357 + 30 0.00300000 -1888.66999327 -1895.86681330 218.34126559 -0.00063673 3.30063673 + 40 0.00400000 -1888.66978373 -1894.47163849 176.02000692 -0.00087055 3.30087055 + 50 0.00500000 -1888.66966087 -1893.37123396 142.63902861 -0.00111486 3.30111486 + 60 0.00600000 -1888.66966151 -1892.75822768 124.04127204 -0.00136952 3.30136952 + 70 0.00700000 -1888.66976993 -1892.63445770 120.28297806 -0.00163441 3.30163441 + 80 0.00800000 -1888.66992887 -1892.83467481 126.35245790 -0.00190946 3.30190946 + 90 0.00900000 -1888.67006887 -1893.11387088 134.81862143 -0.00219458 3.30219458 + 100 0.01000000 -1888.67013641 -1893.25481870 139.09272852 -0.00248973 3.30248973 + 110 0.01100000 -1888.67011221 -1893.15155809 135.96068294 -0.00279489 3.30279489 + 120 0.01200000 -1888.67001516 -1892.84002980 126.51230266 -0.00311004 3.30311004 + 130 0.01300000 -1888.66989017 -1892.47004258 115.29120969 -0.00343519 3.30343519 + 140 0.01400000 -1888.66979250 -1892.23503136 108.16426724 -0.00377038 3.30377038 + 150 0.01500000 -1888.66976498 -1892.28630603 109.72070258 -0.00411562 3.30411562 + 160 0.01600000 -1888.66982073 -1892.66640631 121.25071190 -0.00447099 3.30447099 + 170 0.01700000 -1888.66993810 -1893.28862656 140.12442720 -0.00483654 3.30483654 + 180 0.01800000 -1888.67007037 -1893.97029277 160.80119589 -0.00521235 3.30521235 + 190 0.01900000 -1888.67016732 -1894.50458806 177.00801243 -0.00559851 3.30559851 + 200 0.02000000 -1888.67019479 -1894.73890125 184.11590729 -0.00599512 3.30599512 + 210 0.02100000 -1888.67014440 -1894.62906034 180.78501933 -0.00640230 3.30640230 + 220 0.02200000 -1888.67003699 -1894.25249122 169.36370739 -0.00682016 3.30682016 + 230 0.02300000 -1888.66991405 -1893.77601632 154.91186768 -0.00724883 3.30724883 + 240 0.02400000 -1888.66982545 -1893.38995103 143.20188490 -0.00768845 3.30768845 + 250 0.02500000 -1888.66980650 -1893.23138955 138.39193054 -0.00813913 3.30813913 + 260 0.02600000 -1888.66986149 -1893.32993943 141.38012473 -0.00860097 3.30860097 + 270 0.02700000 -1888.66996324 -1893.60070625 149.59171759 -0.00907408 3.30907408 + 280 0.02800000 -1888.67006705 -1893.88587245 158.24010430 -0.00955849 3.30955849 + 290 0.02900000 -1888.67013001 -1894.02402688 162.42960290 -0.01005424 3.31005424 + 300 0.03000000 -1888.67012741 -1893.91715254 159.18726627 -0.01056129 3.31056129 + 310 0.03100000 -1888.67005750 -1893.57037262 148.66857854 -0.01107957 3.31107957 + 320 0.03200000 -1888.66994592 -1893.09358639 134.20694885 -0.01160898 3.31160898 + 330 0.03300000 -1888.66983608 -1892.66132683 121.09614209 -0.01214935 3.31214935 + 340 0.03400000 -1888.66977429 -1892.44446364 114.51869677 -0.01270046 3.31270046 + 350 0.03500000 -1888.66978845 -1892.53901254 117.38674604 -0.01326207 3.31326207 + 360 0.03600000 -1888.66987459 -1892.92337308 129.04508370 -0.01383390 3.31383390 + 370 0.03700000 -1888.66999819 -1893.46445589 145.45701553 -0.01441561 3.31441561 + 380 0.03800000 -1888.67010979 -1893.97065536 160.81100019 -0.01500688 3.31500688 + 390 0.03900000 -1888.67016559 -1894.26835837 169.84119248 -0.01560734 3.31560734 + 400 0.04000000 -1888.67014686 -1894.26967995 169.88185548 -0.01621664 3.31621664 + 410 0.04100000 -1888.67006186 -1894.00321089 161.80014284 -0.01683442 3.31683442 + 420 0.04200000 -1888.66994386 -1893.60086344 149.59707422 -0.01746033 3.31746033 + 430 0.04300000 -1888.66984078 -1893.24559860 138.82197278 -0.01809405 3.31809405 + 440 0.04400000 -1888.66979419 -1893.09727893 134.32357877 -0.01873527 3.31873527 + 450 0.04500000 -1888.66982159 -1893.22837461 138.30000376 -0.01938373 3.31938373 + 460 0.04600000 -1888.66990991 -1893.59670402 149.47191350 -0.02003918 3.32003918 + 470 0.04700000 -1888.67002193 -1894.06542618 163.68887740 -0.02070143 3.32070143 + 480 0.04800000 -1888.67011408 -1894.46010861 175.66018436 -0.02137030 3.32137030 + 490 0.04900000 -1888.67015195 -1894.63688117 181.02206322 -0.02204565 3.32204565 + 500 0.05000000 -1888.67012178 -1894.53632241 177.97216884 -0.02272740 3.32272740 + 510 0.05100000 -1888.67003782 -1894.20444750 167.90610440 -0.02341547 3.32341547 + 520 0.05200000 -1888.66993171 -1893.77231086 154.79891357 -0.02410981 3.32410981 + 530 0.05300000 -1888.66984524 -1893.40525947 143.66572040 -0.02481040 3.32481040 + 540 0.05400000 -1888.66981428 -1893.23762103 138.58074854 -0.02551724 3.32551724 + 550 0.05500000 -1888.66985024 -1893.31793613 141.01630314 -0.02623032 3.32623032 + 560 0.05600000 -1888.66993756 -1893.59069032 149.28862746 -0.02694963 3.32694963 + 570 0.05700000 -1888.67003871 -1893.92089591 159.30352583 -0.02767517 3.32767517 + 580 0.05800000 -1888.67011342 -1894.15124772 166.28980520 -0.02840691 3.32840691 + 590 0.05900000 -1888.67013211 -1894.16548061 166.72104344 -0.02914478 3.32914478 + 600 0.06000000 -1888.67008732 -1893.93443338 159.71275857 -0.02988871 3.32988871 + 610 0.06100000 -1888.66999458 -1893.52841675 147.39760649 -0.03063856 3.33063856 + 620 0.06200000 -1888.66988829 -1893.09235041 134.17119966 -0.03139416 3.33139416 + 630 0.06300000 -1888.66981016 -1892.79172036 125.05288241 -0.03215531 3.33215531 + 640 0.06400000 -1888.66979281 -1892.74755409 123.71346729 -0.03292176 3.33292176 + 650 0.06500000 -1888.66984352 -1892.98665478 130.96590321 -0.03369323 3.33369323 + 660 0.06600000 -1888.66994264 -1893.42999887 144.41332385 -0.03446937 3.33446937 + 670 0.06700000 -1888.67005253 -1893.92310700 159.37018803 -0.03524986 3.33524986 + 680 0.06800000 -1888.67013328 -1894.29451600 170.63575807 -0.03603430 3.33603430 + 690 0.06900000 -1888.67015472 -1894.41878137 174.40514195 -0.03682229 3.33682229 + 700 0.07000000 -1888.67010916 -1894.26288055 169.67671536 -0.03761343 3.33761343 + 710 0.07100000 -1888.67001386 -1893.89812923 158.61357122 -0.03840729 3.33840729 + 720 0.07200000 -1888.66990397 -1893.47348765 145.73388461 -0.03920344 3.33920344 + 730 0.07300000 -1888.66982231 -1893.15984859 136.22099965 -0.04000148 3.34000148 + 740 0.07400000 -1888.66980129 -1893.08373765 133.91254030 -0.04080098 3.34080098 + 750 0.07500000 -1888.66984814 -1893.27755530 139.79127022 -0.04160156 3.34160156 + 760 0.07600000 -1888.66994235 -1893.66837384 151.64528962 -0.04240282 3.34240282 + 770 0.07700000 -1888.67004573 -1894.10941225 165.02263022 -0.04320441 3.34320441 + 780 0.07800000 -1888.67011722 -1894.43947564 175.03411433 -0.04400599 3.34400599 + 790 0.07900000 -1888.67013317 -1894.54590490 178.26254255 -0.04480726 3.34480726 + 800 0.08000000 -1888.67008771 -1894.40384162 173.95392409 -0.04560792 3.34560792 + 810 0.08100000 -1888.66999942 -1894.08389023 164.24973325 -0.04640773 3.34640773 + 820 0.08200000 -1888.66990467 -1893.72313999 153.30795968 -0.04720647 3.34720647 + 830 0.08300000 -1888.66984387 -1893.46839210 145.58111627 -0.04800393 3.34800393 + 840 0.08400000 -1888.66984175 -1893.41412556 143.93481091 -0.04879995 3.34879995 + 850 0.08500000 -1888.66989690 -1893.56426173 148.48805548 -0.04959439 3.34959439 + 860 0.08600000 -1888.66998242 -1893.83463738 156.68827289 -0.05038713 3.35038713 + 870 0.08700000 -1888.67006191 -1894.09325064 164.53181916 -0.05117805 3.35117805 + 880 0.08800000 -1888.67010292 -1894.21712680 168.28880099 -0.05196706 3.35196706 + 890 0.08900000 -1888.67009013 -1894.14263970 166.02935659 -0.05275408 3.35275408 + 900 0.09000000 -1888.67002911 -1893.89014590 158.37090593 -0.05353904 3.35353904 + 910 0.09100000 -1888.66994346 -1893.55535729 148.21649476 -0.05432186 3.35432186 + 920 0.09200000 -1888.66986545 -1893.27257968 139.63979183 -0.05510247 3.35510247 + 930 0.09300000 -1888.66982750 -1893.16330910 136.32582951 -0.05588078 3.35588078 + 940 0.09400000 -1888.66984650 -1893.28643304 140.06065783 -0.05665670 3.35665670 + 950 0.09500000 -1888.66991522 -1893.61245361 149.94957262 -0.05743015 3.35743015 + 960 0.09600000 -1888.67000710 -1894.03423941 162.74316510 -0.05820101 3.35820101 + 970 0.09700000 -1888.67008668 -1894.40848044 174.09469033 -0.05896915 3.35896915 + 980 0.09800000 -1888.67012456 -1894.61056787 180.22458605 -0.05973444 3.35973444 + 990 0.09900000 -1888.67010627 -1894.58107679 179.33042341 -0.06049672 3.36049672 + 1000 0.10000000 -1888.67004000 -1894.34773324 172.25312335 -0.06125581 3.36125581 +Loop time of 2.60456 on 1 procs for 1000 steps with 256 atoms + +Performance: 3.317 ns/day, 7.235 hours/ns, 383.942 timesteps/s +99.7% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 2.5864 | 2.5864 | 2.5864 | 0.0 | 99.30 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.0079134 | 0.0079134 | 0.0079134 | 0.0 | 0.30 +Output | 0.0027175 | 0.0027175 | 0.0027175 | 0.0 | 0.10 +Modify | 0.00419 | 0.00419 | 0.00419 | 0.0 | 0.16 +Other | | 0.00331 | | | 0.13 + +Nlocal: 256 ave 256 max 256 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1721 ave 1721 max 1721 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 37312 ave 37312 max 37312 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 94592 ave 94592 max 94592 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 94592 +Ave neighs/atom = 369.5 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:02 diff --git a/examples/USER/misc/kolmogorov_crespi_z/log.30Apr19.bilayer-graphene.g++.4 b/examples/USER/misc/kolmogorov_crespi_z/log.30Apr19.bilayer-graphene.g++.4 new file mode 100644 index 0000000000..13d402b512 --- /dev/null +++ b/examples/USER/misc/kolmogorov_crespi_z/log.30Apr19.bilayer-graphene.g++.4 @@ -0,0 +1,210 @@ +LAMMPS (30 Apr 2019) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88) + using 1 OpenMP thread(s) per MPI task +# Initialization +units metal +boundary p p p +atom_style atomic +processors * * 1 # domain decomposition over x and y + +# System and atom definition +# we use 2 atom types so that inter- and intra-layer +# interactions can be specified separately +read_data data.bilayer-graphene # read lammps data file + orthogonal box = (0 0 -20) to (17.04 19.6761 40) + 2 by 2 by 1 MPI processor grid + reading atoms ... + 256 atoms + read_data CPU = 0.0488505 secs +mass 1 12.0107 # carbon mass (g/mole) | membrane +mass 2 12.0107 # carbon mass (g/mole) | adsorbate +# Neighbor update settings +neighbor 2.0 bin +neigh_modify every 1 +neigh_modify delay 0 +neigh_modify check yes +# Separate atom groups +group membrane type 1 +128 atoms in group membrane +group adsorbant type 2 +128 atoms in group adsorbant + +######################## Potential defition ######################## +pair_style hybrid/overlay rebo kolmogorov/crespi/z 14.0 +#################################################################### +pair_coeff * * rebo CH.rebo C C # chemical +Reading potential file CH.rebo with DATE: 2018-7-3 +pair_coeff 1 2 kolmogorov/crespi/z CC.KC C C # long-range +#################################################################### + +#### Simulation settings #### +timestep 0.0001 +velocity all create 300.0 12345 +fix thermostat all nve +compute COM1 membrane com +compute COM2 adsorbant com +############################ + +# Output +#dump 1 all xyz 100 trajec.xyz +#dump_modify 1 format line "%s %12.6f %12.6f %12.6f" element "C" "C" +thermo 10 +thermo_style custom step time etotal pe temp c_COM1[3] c_COM2[3] # spcpu +thermo_modify line one format float %14.8f + +###### Run molecular dynamics ###### +run 1000 +Neighbor list info ... + 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 + binsize = 8, bins = 3 3 8 + 3 neighbor lists, perpetual/occasional/extra = 3 0 0 + (1) pair rebo, perpetual + attributes: full, newton on, ghost + pair build: full/bin/ghost + stencil: full/ghost/bin/3d + bin: standard + (2) pair kolmogorov/crespi/z, perpetual, skip from (3) + attributes: half, newton on + pair build: skip + stencil: none + bin: none + (3) neighbor class addition, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.572 | 4.572 | 4.572 Mbytes +Step Time TotEng PotEng Temp c_COM1[3] c_COM2[3] + 0 0.00000000 -1888.67041233 -1898.55881343 300.00000000 0.00000000 3.30000000 + 10 0.00100000 -1888.67037240 -1898.21029916 289.42778520 -0.00020126 3.30020126 + 20 0.00200000 -1888.67021561 -1897.22943631 259.67456089 -0.00041357 3.30041357 + 30 0.00300000 -1888.66999327 -1895.86681330 218.34126559 -0.00063673 3.30063673 + 40 0.00400000 -1888.66978373 -1894.47163849 176.02000692 -0.00087055 3.30087055 + 50 0.00500000 -1888.66966087 -1893.37123396 142.63902861 -0.00111486 3.30111486 + 60 0.00600000 -1888.66966151 -1892.75822768 124.04127204 -0.00136952 3.30136952 + 70 0.00700000 -1888.66976993 -1892.63445770 120.28297806 -0.00163441 3.30163441 + 80 0.00800000 -1888.66992887 -1892.83467481 126.35245790 -0.00190946 3.30190946 + 90 0.00900000 -1888.67006887 -1893.11387088 134.81862143 -0.00219458 3.30219458 + 100 0.01000000 -1888.67013641 -1893.25481870 139.09272852 -0.00248973 3.30248973 + 110 0.01100000 -1888.67011221 -1893.15155809 135.96068294 -0.00279489 3.30279489 + 120 0.01200000 -1888.67001516 -1892.84002980 126.51230266 -0.00311004 3.30311004 + 130 0.01300000 -1888.66989017 -1892.47004258 115.29120969 -0.00343519 3.30343519 + 140 0.01400000 -1888.66979250 -1892.23503136 108.16426724 -0.00377038 3.30377038 + 150 0.01500000 -1888.66976498 -1892.28630603 109.72070258 -0.00411562 3.30411562 + 160 0.01600000 -1888.66982073 -1892.66640631 121.25071190 -0.00447099 3.30447099 + 170 0.01700000 -1888.66993810 -1893.28862656 140.12442720 -0.00483654 3.30483654 + 180 0.01800000 -1888.67007037 -1893.97029277 160.80119589 -0.00521235 3.30521235 + 190 0.01900000 -1888.67016732 -1894.50458806 177.00801243 -0.00559851 3.30559851 + 200 0.02000000 -1888.67019479 -1894.73890125 184.11590729 -0.00599512 3.30599512 + 210 0.02100000 -1888.67014440 -1894.62906034 180.78501933 -0.00640230 3.30640230 + 220 0.02200000 -1888.67003699 -1894.25249122 169.36370739 -0.00682016 3.30682016 + 230 0.02300000 -1888.66991405 -1893.77601632 154.91186768 -0.00724883 3.30724883 + 240 0.02400000 -1888.66982545 -1893.38995103 143.20188490 -0.00768845 3.30768845 + 250 0.02500000 -1888.66980650 -1893.23138955 138.39193054 -0.00813913 3.30813913 + 260 0.02600000 -1888.66986149 -1893.32993943 141.38012473 -0.00860097 3.30860097 + 270 0.02700000 -1888.66996324 -1893.60070625 149.59171759 -0.00907408 3.30907408 + 280 0.02800000 -1888.67006705 -1893.88587245 158.24010430 -0.00955849 3.30955849 + 290 0.02900000 -1888.67013001 -1894.02402688 162.42960290 -0.01005424 3.31005424 + 300 0.03000000 -1888.67012741 -1893.91715254 159.18726627 -0.01056129 3.31056129 + 310 0.03100000 -1888.67005750 -1893.57037262 148.66857854 -0.01107957 3.31107957 + 320 0.03200000 -1888.66994592 -1893.09358639 134.20694885 -0.01160898 3.31160898 + 330 0.03300000 -1888.66983608 -1892.66132683 121.09614209 -0.01214935 3.31214935 + 340 0.03400000 -1888.66977429 -1892.44446364 114.51869677 -0.01270046 3.31270046 + 350 0.03500000 -1888.66978845 -1892.53901254 117.38674604 -0.01326207 3.31326207 + 360 0.03600000 -1888.66987459 -1892.92337308 129.04508370 -0.01383390 3.31383390 + 370 0.03700000 -1888.66999819 -1893.46445589 145.45701553 -0.01441561 3.31441561 + 380 0.03800000 -1888.67010979 -1893.97065536 160.81100019 -0.01500688 3.31500688 + 390 0.03900000 -1888.67016559 -1894.26835837 169.84119248 -0.01560734 3.31560734 + 400 0.04000000 -1888.67014686 -1894.26967995 169.88185548 -0.01621664 3.31621664 + 410 0.04100000 -1888.67006186 -1894.00321089 161.80014284 -0.01683442 3.31683442 + 420 0.04200000 -1888.66994386 -1893.60086344 149.59707422 -0.01746033 3.31746033 + 430 0.04300000 -1888.66984078 -1893.24559860 138.82197278 -0.01809405 3.31809405 + 440 0.04400000 -1888.66979419 -1893.09727893 134.32357877 -0.01873527 3.31873527 + 450 0.04500000 -1888.66982159 -1893.22837461 138.30000376 -0.01938373 3.31938373 + 460 0.04600000 -1888.66990991 -1893.59670402 149.47191350 -0.02003918 3.32003918 + 470 0.04700000 -1888.67002193 -1894.06542618 163.68887740 -0.02070143 3.32070143 + 480 0.04800000 -1888.67011408 -1894.46010861 175.66018436 -0.02137030 3.32137030 + 490 0.04900000 -1888.67015195 -1894.63688117 181.02206322 -0.02204565 3.32204565 + 500 0.05000000 -1888.67012178 -1894.53632241 177.97216884 -0.02272740 3.32272740 + 510 0.05100000 -1888.67003782 -1894.20444750 167.90610440 -0.02341547 3.32341547 + 520 0.05200000 -1888.66993171 -1893.77231086 154.79891357 -0.02410981 3.32410981 + 530 0.05300000 -1888.66984524 -1893.40525947 143.66572040 -0.02481040 3.32481040 + 540 0.05400000 -1888.66981428 -1893.23762103 138.58074854 -0.02551724 3.32551724 + 550 0.05500000 -1888.66985024 -1893.31793613 141.01630314 -0.02623032 3.32623032 + 560 0.05600000 -1888.66993756 -1893.59069032 149.28862746 -0.02694963 3.32694963 + 570 0.05700000 -1888.67003871 -1893.92089591 159.30352583 -0.02767517 3.32767517 + 580 0.05800000 -1888.67011342 -1894.15124772 166.28980520 -0.02840691 3.32840691 + 590 0.05900000 -1888.67013211 -1894.16548061 166.72104344 -0.02914478 3.32914478 + 600 0.06000000 -1888.67008732 -1893.93443338 159.71275857 -0.02988871 3.32988871 + 610 0.06100000 -1888.66999458 -1893.52841675 147.39760649 -0.03063856 3.33063856 + 620 0.06200000 -1888.66988829 -1893.09235041 134.17119966 -0.03139416 3.33139416 + 630 0.06300000 -1888.66981016 -1892.79172036 125.05288241 -0.03215531 3.33215531 + 640 0.06400000 -1888.66979281 -1892.74755409 123.71346729 -0.03292176 3.33292176 + 650 0.06500000 -1888.66984352 -1892.98665478 130.96590321 -0.03369323 3.33369323 + 660 0.06600000 -1888.66994264 -1893.42999887 144.41332385 -0.03446937 3.33446937 + 670 0.06700000 -1888.67005253 -1893.92310700 159.37018803 -0.03524986 3.33524986 + 680 0.06800000 -1888.67013328 -1894.29451600 170.63575807 -0.03603430 3.33603430 + 690 0.06900000 -1888.67015472 -1894.41878137 174.40514195 -0.03682229 3.33682229 + 700 0.07000000 -1888.67010916 -1894.26288055 169.67671536 -0.03761343 3.33761343 + 710 0.07100000 -1888.67001386 -1893.89812923 158.61357122 -0.03840729 3.33840729 + 720 0.07200000 -1888.66990397 -1893.47348765 145.73388461 -0.03920344 3.33920344 + 730 0.07300000 -1888.66982231 -1893.15984859 136.22099965 -0.04000148 3.34000148 + 740 0.07400000 -1888.66980129 -1893.08373765 133.91254030 -0.04080098 3.34080098 + 750 0.07500000 -1888.66984814 -1893.27755530 139.79127022 -0.04160156 3.34160156 + 760 0.07600000 -1888.66994235 -1893.66837384 151.64528962 -0.04240282 3.34240282 + 770 0.07700000 -1888.67004573 -1894.10941225 165.02263022 -0.04320441 3.34320441 + 780 0.07800000 -1888.67011722 -1894.43947564 175.03411433 -0.04400599 3.34400599 + 790 0.07900000 -1888.67013317 -1894.54590490 178.26254255 -0.04480726 3.34480726 + 800 0.08000000 -1888.67008771 -1894.40384162 173.95392409 -0.04560792 3.34560792 + 810 0.08100000 -1888.66999942 -1894.08389023 164.24973325 -0.04640773 3.34640773 + 820 0.08200000 -1888.66990467 -1893.72313999 153.30795968 -0.04720647 3.34720647 + 830 0.08300000 -1888.66984387 -1893.46839210 145.58111627 -0.04800393 3.34800393 + 840 0.08400000 -1888.66984175 -1893.41412556 143.93481091 -0.04879995 3.34879995 + 850 0.08500000 -1888.66989690 -1893.56426173 148.48805548 -0.04959439 3.34959439 + 860 0.08600000 -1888.66998242 -1893.83463738 156.68827289 -0.05038713 3.35038713 + 870 0.08700000 -1888.67006191 -1894.09325064 164.53181916 -0.05117805 3.35117805 + 880 0.08800000 -1888.67010292 -1894.21712680 168.28880099 -0.05196706 3.35196706 + 890 0.08900000 -1888.67009013 -1894.14263970 166.02935659 -0.05275408 3.35275408 + 900 0.09000000 -1888.67002911 -1893.89014590 158.37090593 -0.05353904 3.35353904 + 910 0.09100000 -1888.66994346 -1893.55535729 148.21649476 -0.05432186 3.35432186 + 920 0.09200000 -1888.66986545 -1893.27257968 139.63979183 -0.05510247 3.35510247 + 930 0.09300000 -1888.66982750 -1893.16330910 136.32582951 -0.05588078 3.35588078 + 940 0.09400000 -1888.66984650 -1893.28643304 140.06065783 -0.05665670 3.35665670 + 950 0.09500000 -1888.66991522 -1893.61245361 149.94957262 -0.05743015 3.35743015 + 960 0.09600000 -1888.67000710 -1894.03423941 162.74316510 -0.05820101 3.35820101 + 970 0.09700000 -1888.67008668 -1894.40848044 174.09469033 -0.05896915 3.35896915 + 980 0.09800000 -1888.67012456 -1894.61056787 180.22458605 -0.05973444 3.35973444 + 990 0.09900000 -1888.67010627 -1894.58107679 179.33042341 -0.06049672 3.36049672 + 1000 0.10000000 -1888.67004000 -1894.34773324 172.25312335 -0.06125581 3.36125581 +Loop time of 1.55992 on 4 procs for 1000 steps with 256 atoms + +Performance: 5.539 ns/day, 4.333 hours/ns, 641.059 timesteps/s +96.5% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.3161 | 1.3724 | 1.4128 | 3.0 | 87.98 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.11734 | 0.16017 | 0.21617 | 8.9 | 10.27 +Output | 0.0032182 | 0.0051764 | 0.010916 | 4.6 | 0.33 +Modify | 0.0020187 | 0.0022321 | 0.0026002 | 0.5 | 0.14 +Other | | 0.0199 | | | 1.28 + +Nlocal: 64 ave 64 max 64 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 1265 ave 1265 max 1265 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 9328 ave 9328 max 9328 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 23648 ave 23648 max 23648 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 94592 +Ave neighs/atom = 369.5 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:01 diff --git a/examples/airebo/CH.rebo b/examples/airebo/CH.rebo new file mode 120000 index 0000000000..9272e57972 --- /dev/null +++ b/examples/airebo/CH.rebo @@ -0,0 +1 @@ +../../potentials/CH.rebo \ No newline at end of file diff --git a/examples/airebo/in.airebo-0-0 b/examples/airebo/in.airebo-0-0 new file mode 100644 index 0000000000..077da68912 --- /dev/null +++ b/examples/airebo/in.airebo-0-0 @@ -0,0 +1,22 @@ +# AIREBO polyethelene benchmark + +units metal +atom_style atomic + +read_data data.airebo + +replicate 17 16 2 + +neighbor 0.5 bin +neigh_modify delay 5 every 1 + +pair_style airebo 3.0 0 0 +pair_coeff * * CH.airebo C H + +velocity all create 300.0 761341 + +fix 1 all nve +timestep 0.0005 + +thermo 10 +run 100 diff --git a/examples/airebo/in.rebo2 b/examples/airebo/in.rebo2 new file mode 100644 index 0000000000..e06cf462ca --- /dev/null +++ b/examples/airebo/in.rebo2 @@ -0,0 +1,22 @@ +# REBO polyethelene benchmark + +units metal +atom_style atomic + +read_data data.airebo + +replicate 17 16 2 + +neighbor 0.5 bin +neigh_modify delay 5 every 1 + +pair_style rebo +pair_coeff * * CH.rebo C H + +velocity all create 300.0 761341 + +fix 1 all nve +timestep 0.0005 + +thermo 10 +run 100 diff --git a/examples/airebo/log.30Apr2019.airebo-0-0.g++.1 b/examples/airebo/log.30Apr2019.airebo-0-0.g++.1 new file mode 100644 index 0000000000..47f5f04a83 --- /dev/null +++ b/examples/airebo/log.30Apr2019.airebo-0-0.g++.1 @@ -0,0 +1,89 @@ +LAMMPS (30 Apr 2019) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88) + using 1 OpenMP thread(s) per MPI task +# AIREBO polyethelene benchmark + +units metal +atom_style atomic + +read_data data.airebo + orthogonal box = (-2.1 -2.1 0) to (2.1 2.1 25.579) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 60 atoms + read_data CPU = 0.000232458 secs + +replicate 17 16 2 + orthogonal box = (-2.1 -2.1 0) to (69.3 65.1 51.158) + 1 by 1 by 1 MPI processor grid + 32640 atoms + replicate CPU = 0.00206327 secs + +neighbor 0.5 bin +neigh_modify delay 5 every 1 + +pair_style airebo 3.0 0 0 +pair_coeff * * CH.airebo C H +Reading potential file CH.airebo with DATE: 2011-10-25 + +velocity all create 300.0 761341 + +fix 1 all nve +timestep 0.0005 + +thermo 10 +run 100 +Neighbor list info ... + update every 1 steps, delay 5 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6.5 + ghost atom cutoff = 6.5 + binsize = 3.25, bins = 22 21 16 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair airebo, perpetual + attributes: full, newton on, ghost + pair build: full/bin/ghost + stencil: full/ghost/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 34.21 | 34.21 | 34.21 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 300 -138442.83 0 -137177.16 2463.0755 + 10 179.38448 -137931.29 0 -137174.48 15656.69 + 20 206.89283 -138047.06 0 -137174.19 -24047.407 + 30 150.81289 -137807.48 0 -137171.21 -16524.191 + 40 173.24289 -137902.32 0 -137171.42 -5721.7187 + 50 151.80722 -137812.37 0 -137171.91 3489.8954 + 60 199.06038 -138013.7 0 -137173.88 17887.025 + 70 217.84848 -138093.82 0 -137174.73 -12266.16 + 80 202.34667 -138029.28 0 -137175.59 -7623.6634 + 90 194.92367 -137997.12 0 -137174.75 -32277.173 + 100 185.2078 -137954.64 0 -137173.26 -6888.5104 +Loop time of 9.70367 on 1 procs for 100 steps with 32640 atoms + +Performance: 0.445 ns/day, 53.909 hours/ns, 10.305 timesteps/s +99.5% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 7.2508 | 7.2508 | 7.2508 | 0.0 | 74.72 +Neigh | 2.3573 | 2.3573 | 2.3573 | 0.0 | 24.29 +Comm | 0.03116 | 0.03116 | 0.03116 | 0.0 | 0.32 +Output | 0.0014739 | 0.0014739 | 0.0014739 | 0.0 | 0.02 +Modify | 0.0447 | 0.0447 | 0.0447 | 0.0 | 0.46 +Other | | 0.01819 | | | 0.19 + +Nlocal: 32640 ave 32640 max 32640 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 26460 ave 26460 max 26460 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: 4.90213e+06 ave 4.90213e+06 max 4.90213e+06 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 4902134 +Ave neighs/atom = 150.188 +Neighbor list builds = 9 +Dangerous builds = 0 +Total wall time: 0:00:10 diff --git a/examples/airebo/log.30Apr2019.airebo-0-0.g++.4 b/examples/airebo/log.30Apr2019.airebo-0-0.g++.4 new file mode 100644 index 0000000000..a777e17885 --- /dev/null +++ b/examples/airebo/log.30Apr2019.airebo-0-0.g++.4 @@ -0,0 +1,89 @@ +LAMMPS (30 Apr 2019) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88) + using 1 OpenMP thread(s) per MPI task +# AIREBO polyethelene benchmark + +units metal +atom_style atomic + +read_data data.airebo + orthogonal box = (-2.1 -2.1 0) to (2.1 2.1 25.579) + 1 by 1 by 4 MPI processor grid + reading atoms ... + 60 atoms + read_data CPU = 0.000363827 secs + +replicate 17 16 2 + orthogonal box = (-2.1 -2.1 0) to (69.3 65.1 51.158) + 2 by 2 by 1 MPI processor grid + 32640 atoms + replicate CPU = 0.00244427 secs + +neighbor 0.5 bin +neigh_modify delay 5 every 1 + +pair_style airebo 3.0 0 0 +pair_coeff * * CH.airebo C H +Reading potential file CH.airebo with DATE: 2011-10-25 + +velocity all create 300.0 761341 + +fix 1 all nve +timestep 0.0005 + +thermo 10 +run 100 +Neighbor list info ... + update every 1 steps, delay 5 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6.5 + ghost atom cutoff = 6.5 + binsize = 3.25, bins = 22 21 16 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair airebo, perpetual + attributes: full, newton on, ghost + pair build: full/bin/ghost + stencil: full/ghost/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 11.75 | 11.94 | 12.13 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 300 -138442.83 0 -137177.16 2463.0755 + 10 179.38448 -137931.29 0 -137174.48 15656.69 + 20 206.89283 -138047.06 0 -137174.19 -24047.407 + 30 150.81289 -137807.48 0 -137171.21 -16524.191 + 40 173.24289 -137902.32 0 -137171.42 -5721.7187 + 50 151.80722 -137812.37 0 -137171.91 3489.8954 + 60 199.06038 -138013.7 0 -137173.88 17887.025 + 70 217.84848 -138093.82 0 -137174.73 -12266.16 + 80 202.34667 -138029.28 0 -137175.59 -7623.6634 + 90 194.92367 -137997.12 0 -137174.75 -32277.173 + 100 185.2078 -137954.64 0 -137173.26 -6888.5104 +Loop time of 6.71962 on 4 procs for 100 steps with 32640 atoms + +Performance: 0.643 ns/day, 37.331 hours/ns, 14.882 timesteps/s +96.6% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 4.4598 | 4.6375 | 4.7708 | 5.5 | 69.01 +Neigh | 1.5903 | 1.6452 | 1.7207 | 3.8 | 24.48 +Comm | 0.16708 | 0.37041 | 0.56709 | 25.1 | 5.51 +Output | 0.001061 | 0.0059808 | 0.0090635 | 4.3 | 0.09 +Modify | 0.030086 | 0.03154 | 0.032522 | 0.5 | 0.47 +Other | | 0.02897 | | | 0.43 + +Nlocal: 8160 ave 8163 max 8157 min +Histogram: 1 1 0 0 0 0 0 0 1 1 +Nghost: 11605.8 ave 11615 max 11593 min +Histogram: 1 0 0 0 0 0 2 0 0 1 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 1.22553e+06 ave 1.22734e+06 max 1.22455e+06 min +Histogram: 2 0 0 1 0 0 0 0 0 1 + +Total # of neighbors = 4902134 +Ave neighs/atom = 150.188 +Neighbor list builds = 9 +Dangerous builds = 0 +Total wall time: 0:00:07 diff --git a/examples/airebo/log.27Nov18.airebo-m.g++.1 b/examples/airebo/log.30Apr2019.airebo-m.g++.1 similarity index 65% rename from examples/airebo/log.27Nov18.airebo-m.g++.1 rename to examples/airebo/log.30Apr2019.airebo-m.g++.1 index 44d8b9d59c..0115756737 100644 --- a/examples/airebo/log.27Nov18.airebo-m.g++.1 +++ b/examples/airebo/log.30Apr2019.airebo-m.g++.1 @@ -1,36 +1,38 @@ -LAMMPS (27 Nov 2018) +LAMMPS (30 Apr 2019) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88) using 1 OpenMP thread(s) per MPI task # AIREBO polyethelene benchmark -units metal -atom_style atomic +units metal +atom_style atomic -read_data data.airebo +read_data data.airebo orthogonal box = (-2.1 -2.1 0) to (2.1 2.1 25.579) 1 by 1 by 1 MPI processor grid reading atoms ... 60 atoms + read_data CPU = 0.000225067 secs -replicate 17 16 2 +replicate 17 16 2 orthogonal box = (-2.1 -2.1 0) to (69.3 65.1 51.158) 1 by 1 by 1 MPI processor grid 32640 atoms - Time spent = 0.00141144 secs + replicate CPU = 0.00226521 secs -neighbor 0.5 bin -neigh_modify delay 5 every 1 +neighbor 0.5 bin +neigh_modify delay 5 every 1 -pair_style airebo/morse 3.0 1 1 -pair_coeff * * ../../potentials/CH.airebo-m C H -Reading potential file ../../potentials/CH.airebo-m with DATE: 2016-03-15 +pair_style airebo/morse 3.0 1 1 +pair_coeff * * CH.airebo-m C H +Reading potential file CH.airebo-m with DATE: 2016-03-15 -velocity all create 300.0 761341 +velocity all create 300.0 761341 -fix 1 all nve -timestep 0.0005 +fix 1 all nve +timestep 0.0005 -thermo 10 -run 100 +thermo 10 +run 100 Neighbor list info ... update every 1 steps, delay 5 steps, check yes max neighbors/atom: 2000, page size: 100000 @@ -45,7 +47,7 @@ Neighbor list info ... bin: standard Per MPI rank memory allocation (min/avg/max) = 106.4 | 106.4 | 106.4 Mbytes Step Temp E_pair E_mol TotEng Press - 0 300 -139283.82 0 -138018.14 152.25271 + 0 300 -139283.82 0 -138018.14 152.25266 10 166.76148 -138718.75 0 -138015.19 17412.343 20 207.7293 -138891.79 0 -138015.4 -19395.339 30 138.54469 -138596.42 0 -138011.92 -11909.248 @@ -55,21 +57,21 @@ Step Temp E_pair E_mol TotEng Press 70 185.72779 -138799.18 0 -138015.61 -10803.744 80 164.28396 -138709.5 0 -138016.4 -1524.7353 90 180.26403 -138776.42 0 -138015.9 -27143.467 - 100 164.05694 -138706.58 0 -138014.44 5157.5516 -Loop time of 64.6107 on 1 procs for 100 steps with 32640 atoms + 100 164.05694 -138706.58 0 -138014.44 5157.5517 +Loop time of 111.537 on 1 procs for 100 steps with 32640 atoms -Performance: 0.067 ns/day, 358.948 hours/ns, 1.548 timesteps/s +Performance: 0.039 ns/day, 619.650 hours/ns, 0.897 timesteps/s 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 59.916 | 59.916 | 59.916 | 0.0 | 92.73 -Neigh | 4.6347 | 4.6347 | 4.6347 | 0.0 | 7.17 -Comm | 0.025572 | 0.025572 | 0.025572 | 0.0 | 0.04 -Output | 0.00098896 | 0.00098896 | 0.00098896 | 0.0 | 0.00 -Modify | 0.022327 | 0.022327 | 0.022327 | 0.0 | 0.03 -Other | | 0.01076 | | | 0.02 +Pair | 103.58 | 103.58 | 103.58 | 0.0 | 92.87 +Neigh | 7.8371 | 7.8371 | 7.8371 | 0.0 | 7.03 +Comm | 0.046259 | 0.046259 | 0.046259 | 0.0 | 0.04 +Output | 0.001497 | 0.001497 | 0.001497 | 0.0 | 0.00 +Modify | 0.047151 | 0.047151 | 0.047151 | 0.0 | 0.04 +Other | | 0.02204 | | | 0.02 Nlocal: 32640 ave 32640 max 32640 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -84,4 +86,4 @@ Total # of neighbors = 22210922 Ave neighs/atom = 680.482 Neighbor list builds = 8 Dangerous builds = 0 -Total wall time: 0:01:05 +Total wall time: 0:01:53 diff --git a/examples/airebo/log.27Nov18.airebo-m.g++.4 b/examples/airebo/log.30Apr2019.airebo-m.g++.4 similarity index 64% rename from examples/airebo/log.27Nov18.airebo-m.g++.4 rename to examples/airebo/log.30Apr2019.airebo-m.g++.4 index a4cc55211b..4139c58387 100644 --- a/examples/airebo/log.27Nov18.airebo-m.g++.4 +++ b/examples/airebo/log.30Apr2019.airebo-m.g++.4 @@ -1,36 +1,38 @@ -LAMMPS (27 Nov 2018) +LAMMPS (30 Apr 2019) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88) using 1 OpenMP thread(s) per MPI task # AIREBO polyethelene benchmark -units metal -atom_style atomic +units metal +atom_style atomic -read_data data.airebo +read_data data.airebo orthogonal box = (-2.1 -2.1 0) to (2.1 2.1 25.579) 1 by 1 by 4 MPI processor grid reading atoms ... 60 atoms + read_data CPU = 0.000880957 secs -replicate 17 16 2 +replicate 17 16 2 orthogonal box = (-2.1 -2.1 0) to (69.3 65.1 51.158) 2 by 2 by 1 MPI processor grid 32640 atoms - Time spent = 0.000637531 secs + replicate CPU = 0.00271702 secs -neighbor 0.5 bin -neigh_modify delay 5 every 1 +neighbor 0.5 bin +neigh_modify delay 5 every 1 -pair_style airebo/morse 3.0 1 1 -pair_coeff * * ../../potentials/CH.airebo-m C H -Reading potential file ../../potentials/CH.airebo-m with DATE: 2016-03-15 +pair_style airebo/morse 3.0 1 1 +pair_coeff * * CH.airebo-m C H +Reading potential file CH.airebo-m with DATE: 2016-03-15 -velocity all create 300.0 761341 +velocity all create 300.0 761341 -fix 1 all nve -timestep 0.0005 +fix 1 all nve +timestep 0.0005 -thermo 10 -run 100 +thermo 10 +run 100 Neighbor list info ... update every 1 steps, delay 5 steps, check yes max neighbors/atom: 2000, page size: 100000 @@ -45,7 +47,7 @@ Neighbor list info ... bin: standard Per MPI rank memory allocation (min/avg/max) = 29.37 | 29.75 | 30.13 Mbytes Step Temp E_pair E_mol TotEng Press - 0 300 -139283.82 0 -138018.14 152.25271 + 0 300 -139283.82 0 -138018.14 152.25266 10 166.76148 -138718.75 0 -138015.19 17412.343 20 207.7293 -138891.79 0 -138015.4 -19395.339 30 138.54469 -138596.42 0 -138011.92 -11909.248 @@ -55,21 +57,21 @@ Step Temp E_pair E_mol TotEng Press 70 185.72779 -138799.18 0 -138015.61 -10803.744 80 164.28396 -138709.5 0 -138016.4 -1524.7353 90 180.26403 -138776.42 0 -138015.9 -27143.467 - 100 164.05694 -138706.58 0 -138014.44 5157.5516 -Loop time of 18.1922 on 4 procs for 100 steps with 32640 atoms + 100 164.05694 -138706.58 0 -138014.44 5157.5517 +Loop time of 68.9923 on 4 procs for 100 steps with 32640 atoms -Performance: 0.237 ns/day, 101.068 hours/ns, 5.497 timesteps/s -98.9% CPU use with 4 MPI tasks x 1 OpenMP threads +Performance: 0.063 ns/day, 383.290 hours/ns, 1.449 timesteps/s +96.8% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 15.968 | 16.084 | 16.308 | 3.4 | 88.41 -Neigh | 1.6017 | 1.6334 | 1.7006 | 3.1 | 8.98 -Comm | 0.1603 | 0.45122 | 0.59951 | 26.0 | 2.48 -Output | 0.00042605 | 0.00073195 | 0.0016003 | 0.0 | 0.00 -Modify | 0.0092106 | 0.010544 | 0.014411 | 2.2 | 0.06 -Other | | 0.01193 | | | 0.07 +Pair | 60.09 | 60.276 | 60.515 | 2.1 | 87.37 +Neigh | 6.7521 | 6.8996 | 7.0678 | 4.3 | 10.00 +Comm | 1.5441 | 1.7514 | 2.0838 | 16.9 | 2.54 +Output | 0.0010803 | 0.001972 | 0.0043106 | 3.0 | 0.00 +Modify | 0.031365 | 0.032539 | 0.034404 | 0.7 | 0.05 +Other | | 0.03104 | | | 0.04 Nlocal: 8160 ave 8167 max 8153 min Histogram: 1 0 1 0 0 0 0 1 0 1 @@ -84,4 +86,4 @@ Total # of neighbors = 22210922 Ave neighs/atom = 680.482 Neighbor list builds = 8 Dangerous builds = 0 -Total wall time: 0:00:18 +Total wall time: 0:01:10 diff --git a/examples/airebo/log.27Nov18.airebo.g++.1 b/examples/airebo/log.30Apr2019.airebo.g++.1 similarity index 63% rename from examples/airebo/log.27Nov18.airebo.g++.1 rename to examples/airebo/log.30Apr2019.airebo.g++.1 index 3713c8a8f8..61792e9a7a 100644 --- a/examples/airebo/log.27Nov18.airebo.g++.1 +++ b/examples/airebo/log.30Apr2019.airebo.g++.1 @@ -1,36 +1,38 @@ -LAMMPS (27 Nov 2018) +LAMMPS (30 Apr 2019) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88) using 1 OpenMP thread(s) per MPI task # AIREBO polyethelene benchmark -units metal -atom_style atomic +units metal +atom_style atomic -read_data data.airebo +read_data data.airebo orthogonal box = (-2.1 -2.1 0) to (2.1 2.1 25.579) 1 by 1 by 1 MPI processor grid reading atoms ... 60 atoms + read_data CPU = 0.000217438 secs -replicate 17 16 2 +replicate 17 16 2 orthogonal box = (-2.1 -2.1 0) to (69.3 65.1 51.158) 1 by 1 by 1 MPI processor grid 32640 atoms - Time spent = 0.00144172 secs + replicate CPU = 0.00204968 secs -neighbor 0.5 bin -neigh_modify delay 5 every 1 +neighbor 0.5 bin +neigh_modify delay 5 every 1 -pair_style airebo 3.0 1 1 -pair_coeff * * ../../potentials/CH.airebo C H -Reading potential file ../../potentials/CH.airebo with DATE: 2011-10-25 +pair_style airebo 3.0 1 1 +pair_coeff * * CH.airebo C H +Reading potential file CH.airebo with DATE: 2011-10-25 -velocity all create 300.0 761341 +velocity all create 300.0 761341 -fix 1 all nve -timestep 0.0005 +fix 1 all nve +timestep 0.0005 -thermo 10 -run 100 +thermo 10 +run 100 Neighbor list info ... update every 1 steps, delay 5 steps, check yes max neighbors/atom: 2000, page size: 100000 @@ -45,31 +47,31 @@ Neighbor list info ... bin: standard Per MPI rank memory allocation (min/avg/max) = 106.4 | 106.4 | 106.4 Mbytes Step Temp E_pair E_mol TotEng Press - 0 300 -139300.72 0 -138035.04 7988.6647 + 0 300 -139300.72 0 -138035.04 7988.6646 10 161.34683 -138712.9 0 -138032.19 33228.921 20 208.59504 -138912.79 0 -138032.74 -3211.8806 30 139.7513 -138618.85 0 -138029.25 10878.143 40 142.14562 -138629.02 0 -138029.32 14601.302 - 50 114.23401 -138510.95 0 -138029 24691.125 + 50 114.23401 -138510.95 0 -138029 24691.124 60 164.92002 -138726 0 -138030.21 35125.541 70 162.15256 -138715.9 0 -138031.79 5658.7946 80 157.16184 -138695.77 0 -138032.72 19824.698 - 90 196.15907 -138860.65 0 -138033.07 -7950.8462 + 90 196.15907 -138860.65 0 -138033.07 -7950.8463 100 178.31875 -138784.89 0 -138032.57 30997.671 -Loop time of 57.9914 on 1 procs for 100 steps with 32640 atoms +Loop time of 98.1502 on 1 procs for 100 steps with 32640 atoms -Performance: 0.074 ns/day, 322.174 hours/ns, 1.724 timesteps/s -99.9% CPU use with 1 MPI tasks x 1 OpenMP threads +Performance: 0.044 ns/day, 545.279 hours/ns, 1.019 timesteps/s +99.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 53.275 | 53.275 | 53.275 | 0.0 | 91.87 -Neigh | 4.6548 | 4.6548 | 4.6548 | 0.0 | 8.03 -Comm | 0.026622 | 0.026622 | 0.026622 | 0.0 | 0.05 -Output | 0.00097251 | 0.00097251 | 0.00097251 | 0.0 | 0.00 -Modify | 0.022773 | 0.022773 | 0.022773 | 0.0 | 0.04 -Other | | 0.01089 | | | 0.02 +Pair | 90.237 | 90.237 | 90.237 | 0.0 | 91.94 +Neigh | 7.796 | 7.796 | 7.796 | 0.0 | 7.94 +Comm | 0.048884 | 0.048884 | 0.048884 | 0.0 | 0.05 +Output | 0.0016053 | 0.0016053 | 0.0016053 | 0.0 | 0.00 +Modify | 0.045511 | 0.045511 | 0.045511 | 0.0 | 0.05 +Other | | 0.0217 | | | 0.02 Nlocal: 32640 ave 32640 max 32640 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -84,4 +86,4 @@ Total # of neighbors = 22217840 Ave neighs/atom = 680.694 Neighbor list builds = 8 Dangerous builds = 0 -Total wall time: 0:00:59 +Total wall time: 0:01:39 diff --git a/examples/airebo/log.27Nov18.airebo.g++.4 b/examples/airebo/log.30Apr2019.airebo.g++.4 similarity index 63% rename from examples/airebo/log.27Nov18.airebo.g++.4 rename to examples/airebo/log.30Apr2019.airebo.g++.4 index 335690684a..9857d9c741 100644 --- a/examples/airebo/log.27Nov18.airebo.g++.4 +++ b/examples/airebo/log.30Apr2019.airebo.g++.4 @@ -1,36 +1,38 @@ -LAMMPS (27 Nov 2018) +LAMMPS (30 Apr 2019) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88) using 1 OpenMP thread(s) per MPI task # AIREBO polyethelene benchmark -units metal -atom_style atomic +units metal +atom_style atomic -read_data data.airebo +read_data data.airebo orthogonal box = (-2.1 -2.1 0) to (2.1 2.1 25.579) 1 by 1 by 4 MPI processor grid reading atoms ... 60 atoms + read_data CPU = 0.000266314 secs -replicate 17 16 2 +replicate 17 16 2 orthogonal box = (-2.1 -2.1 0) to (69.3 65.1 51.158) 2 by 2 by 1 MPI processor grid 32640 atoms - Time spent = 0.00262594 secs + replicate CPU = 0.00146151 secs -neighbor 0.5 bin -neigh_modify delay 5 every 1 +neighbor 0.5 bin +neigh_modify delay 5 every 1 -pair_style airebo 3.0 1 1 -pair_coeff * * ../../potentials/CH.airebo C H -Reading potential file ../../potentials/CH.airebo with DATE: 2011-10-25 +pair_style airebo 3.0 1 1 +pair_coeff * * CH.airebo C H +Reading potential file CH.airebo with DATE: 2011-10-25 -velocity all create 300.0 761341 +velocity all create 300.0 761341 -fix 1 all nve -timestep 0.0005 +fix 1 all nve +timestep 0.0005 -thermo 10 -run 100 +thermo 10 +run 100 Neighbor list info ... update every 1 steps, delay 5 steps, check yes max neighbors/atom: 2000, page size: 100000 @@ -45,31 +47,31 @@ Neighbor list info ... bin: standard Per MPI rank memory allocation (min/avg/max) = 29.37 | 29.75 | 30.13 Mbytes Step Temp E_pair E_mol TotEng Press - 0 300 -139300.72 0 -138035.04 7988.6647 + 0 300 -139300.72 0 -138035.04 7988.6646 10 161.34683 -138712.9 0 -138032.19 33228.921 20 208.59504 -138912.79 0 -138032.74 -3211.8806 30 139.7513 -138618.85 0 -138029.25 10878.143 40 142.14562 -138629.02 0 -138029.32 14601.302 - 50 114.23401 -138510.95 0 -138029 24691.125 + 50 114.23401 -138510.95 0 -138029 24691.124 60 164.92002 -138726 0 -138030.21 35125.541 70 162.15256 -138715.9 0 -138031.79 5658.7946 80 157.16184 -138695.77 0 -138032.72 19824.698 - 90 196.15907 -138860.65 0 -138033.07 -7950.8462 + 90 196.15907 -138860.65 0 -138033.07 -7950.8463 100 178.31875 -138784.89 0 -138032.57 30997.671 -Loop time of 16.4395 on 4 procs for 100 steps with 32640 atoms +Loop time of 60.4943 on 4 procs for 100 steps with 32640 atoms -Performance: 0.263 ns/day, 91.331 hours/ns, 6.083 timesteps/s -98.5% CPU use with 4 MPI tasks x 1 OpenMP threads +Performance: 0.071 ns/day, 336.080 hours/ns, 1.653 timesteps/s +97.7% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 14.263 | 14.349 | 14.483 | 2.3 | 87.28 -Neigh | 1.6071 | 1.6283 | 1.6636 | 1.7 | 9.90 -Comm | 0.26261 | 0.43435 | 0.52323 | 16.1 | 2.64 -Output | 0.00042105 | 0.0007121 | 0.001538 | 0.0 | 0.00 -Modify | 0.00898 | 0.009112 | 0.0093675 | 0.2 | 0.06 -Other | | 0.0184 | | | 0.11 +Pair | 51.737 | 52.46 | 52.86 | 6.2 | 86.72 +Neigh | 6.5823 | 6.6605 | 6.726 | 2.0 | 11.01 +Comm | 0.92426 | 1.3125 | 2.0111 | 37.0 | 2.17 +Output | 0.0010669 | 0.0019811 | 0.0043974 | 3.1 | 0.00 +Modify | 0.030364 | 0.031523 | 0.032495 | 0.5 | 0.05 +Other | | 0.028 | | | 0.05 Nlocal: 8160 ave 8174 max 8146 min Histogram: 1 0 1 0 0 0 0 1 0 1 @@ -84,4 +86,4 @@ Total # of neighbors = 22217840 Ave neighs/atom = 680.694 Neighbor list builds = 8 Dangerous builds = 0 -Total wall time: 0:00:16 +Total wall time: 0:01:01 diff --git a/examples/airebo/log.30Apr2019.rebo2.g++.1 b/examples/airebo/log.30Apr2019.rebo2.g++.1 new file mode 100644 index 0000000000..7cd3d65294 --- /dev/null +++ b/examples/airebo/log.30Apr2019.rebo2.g++.1 @@ -0,0 +1,89 @@ +LAMMPS (30 Apr 2019) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88) + using 1 OpenMP thread(s) per MPI task +# REBO polyethelene benchmark + +units metal +atom_style atomic + +read_data data.airebo + orthogonal box = (-2.1 -2.1 0) to (2.1 2.1 25.579) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 60 atoms + read_data CPU = 0.000190735 secs + +replicate 17 16 2 + orthogonal box = (-2.1 -2.1 0) to (69.3 65.1 51.158) + 1 by 1 by 1 MPI processor grid + 32640 atoms + replicate CPU = 0.00197148 secs + +neighbor 0.5 bin +neigh_modify delay 5 every 1 + +pair_style rebo +pair_coeff * * CH.rebo C H +Reading potential file CH.rebo with DATE: 2018-7-3 + +velocity all create 300.0 761341 + +fix 1 all nve +timestep 0.0005 + +thermo 10 +run 100 +Neighbor list info ... + update every 1 steps, delay 5 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6.5 + ghost atom cutoff = 6.5 + binsize = 3.25, bins = 22 21 16 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair rebo, perpetual + attributes: full, newton on, ghost + pair build: full/bin/ghost + stencil: full/ghost/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 34.21 | 34.21 | 34.21 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 300 -138442.83 0 -137177.16 2463.0748 + 10 179.37985 -137931.27 0 -137174.48 15655.936 + 20 206.87654 -138046.99 0 -137174.19 -24042.627 + 30 150.80122 -137807.43 0 -137171.21 -16524.118 + 40 173.24945 -137902.35 0 -137171.42 -5716.9119 + 50 151.80455 -137812.36 0 -137171.91 3480.4584 + 60 199.08777 -138013.82 0 -137173.88 17881.372 + 70 217.85748 -138093.86 0 -137174.73 -12270.999 + 80 202.37482 -138029.39 0 -137175.59 -7622.7319 + 90 194.90628 -137997.05 0 -137174.75 -32267.471 + 100 185.17818 -137954.51 0 -137173.26 -6901.7499 +Loop time of 9.44819 on 1 procs for 100 steps with 32640 atoms + +Performance: 0.457 ns/day, 52.490 hours/ns, 10.584 timesteps/s +99.7% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 7.037 | 7.037 | 7.037 | 0.0 | 74.48 +Neigh | 2.3182 | 2.3182 | 2.3182 | 0.0 | 24.54 +Comm | 0.029898 | 0.029898 | 0.029898 | 0.0 | 0.32 +Output | 0.0014331 | 0.0014331 | 0.0014331 | 0.0 | 0.02 +Modify | 0.043851 | 0.043851 | 0.043851 | 0.0 | 0.46 +Other | | 0.01774 | | | 0.19 + +Nlocal: 32640 ave 32640 max 32640 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 26460 ave 26460 max 26460 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: 4.90213e+06 ave 4.90213e+06 max 4.90213e+06 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 4902134 +Ave neighs/atom = 150.188 +Neighbor list builds = 9 +Dangerous builds = 0 +Total wall time: 0:00:09 diff --git a/examples/airebo/log.30Apr2019.rebo2.g++.4 b/examples/airebo/log.30Apr2019.rebo2.g++.4 new file mode 100644 index 0000000000..14086fbf40 --- /dev/null +++ b/examples/airebo/log.30Apr2019.rebo2.g++.4 @@ -0,0 +1,89 @@ +LAMMPS (30 Apr 2019) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88) + using 1 OpenMP thread(s) per MPI task +# REBO polyethelene benchmark + +units metal +atom_style atomic + +read_data data.airebo + orthogonal box = (-2.1 -2.1 0) to (2.1 2.1 25.579) + 1 by 1 by 4 MPI processor grid + reading atoms ... + 60 atoms + read_data CPU = 0.000682831 secs + +replicate 17 16 2 + orthogonal box = (-2.1 -2.1 0) to (69.3 65.1 51.158) + 2 by 2 by 1 MPI processor grid + 32640 atoms + replicate CPU = 0.00221777 secs + +neighbor 0.5 bin +neigh_modify delay 5 every 1 + +pair_style rebo +pair_coeff * * CH.rebo C H +Reading potential file CH.rebo with DATE: 2018-7-3 + +velocity all create 300.0 761341 + +fix 1 all nve +timestep 0.0005 + +thermo 10 +run 100 +Neighbor list info ... + update every 1 steps, delay 5 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6.5 + ghost atom cutoff = 6.5 + binsize = 3.25, bins = 22 21 16 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair rebo, perpetual + attributes: full, newton on, ghost + pair build: full/bin/ghost + stencil: full/ghost/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 11.75 | 11.94 | 12.13 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 300 -138442.83 0 -137177.16 2463.0748 + 10 179.37985 -137931.27 0 -137174.48 15655.936 + 20 206.87654 -138046.99 0 -137174.19 -24042.627 + 30 150.80122 -137807.43 0 -137171.21 -16524.118 + 40 173.24945 -137902.35 0 -137171.42 -5716.9119 + 50 151.80455 -137812.36 0 -137171.91 3480.4584 + 60 199.08777 -138013.82 0 -137173.88 17881.372 + 70 217.85748 -138093.86 0 -137174.73 -12270.999 + 80 202.37482 -138029.39 0 -137175.59 -7622.7319 + 90 194.90628 -137997.05 0 -137174.75 -32267.471 + 100 185.17818 -137954.51 0 -137173.26 -6901.7499 +Loop time of 6.35645 on 4 procs for 100 steps with 32640 atoms + +Performance: 0.680 ns/day, 35.314 hours/ns, 15.732 timesteps/s +99.0% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 4.4335 | 4.5041 | 4.56 | 2.1 | 70.86 +Neigh | 1.5332 | 1.5919 | 1.6466 | 3.6 | 25.04 +Comm | 0.098299 | 0.20854 | 0.26277 | 14.2 | 3.28 +Output | 0.0011072 | 0.0018047 | 0.0037503 | 2.6 | 0.03 +Modify | 0.028811 | 0.030358 | 0.031516 | 0.6 | 0.48 +Other | | 0.01977 | | | 0.31 + +Nlocal: 8160 ave 8163 max 8157 min +Histogram: 1 1 0 0 0 0 0 0 1 1 +Nghost: 11605.8 ave 11615 max 11593 min +Histogram: 1 0 0 0 0 0 2 0 0 1 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 1.22553e+06 ave 1.22735e+06 max 1.22455e+06 min +Histogram: 2 0 0 1 0 0 0 0 0 1 + +Total # of neighbors = 4902134 +Ave neighs/atom = 150.188 +Neighbor list builds = 9 +Dangerous builds = 0 +Total wall time: 0:00:06 diff --git a/examples/granular/in.pour.drum b/examples/granular/in.pour.drum new file mode 100644 index 0000000000..c30f30b377 --- /dev/null +++ b/examples/granular/in.pour.drum @@ -0,0 +1,98 @@ +# pour two types of particles (cohesive and non-cohesive) into cylinder +# 'turn' cylinder by changing direction of gravity, then rotate it. +# This simulates a rotating drum powder characterization experiment. + +variable name string rotating_drum_two_types + +atom_style sphere +units lj + +############################################### +# Geometry-related parameters +############################################### + +variable boxx equal 30 +variable boxy equal 30 +variable boxz equal 50 + +variable drum_rad equal ${boxx}*0.5 +variable drum_height equal 20 + +variable xc equal 0.5*${boxx} +variable yc equal 0.5*${boxx} +variable zc equal 0.5*${boxz} + +############################################### +# Particle-related parameters +############################################### +variable rlo equal 0.25 +variable rhi equal 0.5 +variable dlo equal 2.0*${rlo} +variable dhi equal 2.0*${rhi} + +variable cyl_rad_inner equal ${drum_rad}-1.1*${rhi} + +variable dens equal 1.0 + +variable skin equal 0.4*${rhi} + +############# +processors * * 1 +region boxreg block 0 ${boxx} 0 ${boxy} 0 ${boxz} +create_box 2 boxreg +change_box all boundary p p f +comm_modify vel yes + +variable theta equal 0 + +region curved_wall cylinder z ${xc} ${yc} ${drum_rad} 0 ${drum_height} side in rotate v_theta ${xc} ${yc} 0 0 0 1 +region bottom_wall plane ${xc} ${yc} 0 0 0 1 side in rotate v_theta ${xc} ${yc} 0 0 0 1 + +region insreg cylinder z ${xc} ${yc} ${cyl_rad_inner} ${drum_height} ${boxz} + +fix 0 all balance 100 1.0 shift xy 5 1.1 +fix 1 all nve/sphere +fix grav all gravity 10 vector 0 0 -1 +fix ins1 all pour 2000 1 1234 region insreg diam range ${dlo} ${dhi} dens ${dens} ${dens} +fix ins2 all pour 2000 2 1234 region insreg diam range ${dlo} ${dhi} dens ${dens} ${dens} + +comm_modify vel yes + +neighbor ${skin} bin +neigh_modify delay 0 every 1 check yes + +pair_style granular +pair_coeff 1 * hertz/material 1e5 0.2 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji +pair_coeff 2 2 jkr 1e5 0.1 0.3 50 tangential mindlin NULL 1.0 0.5 rolling sds 1e3 1e3 0.1 twisting marshall damping tsuji + +fix 3 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji region curved_wall +fix 4 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji region bottom_wall + +thermo_style custom step atoms ke v_theta +thermo_modify lost warn +thermo 100 + +timestep 0.001 + +#dump 1 all custom 100 ${name}.dump id type radius mass x y z + +#For removal later +compute 1 all property/atom radius +variable zmax atom z+c_1>0.5*${drum_height} +group delgroup dynamic all var zmax every 10000 + +run 2000 + +#Remove any particles that are above z > 0.5*drum_height +delete_atoms group delgroup + +#Add top lid +region top_wall plane ${xc} ${yc} ${drum_height} 0 0 -1 side in rotate v_theta ${xc} ${yc} 0 0 0 1 +fix 5 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji region top_wall + +# 'Turn' drum by switching the direction of gravity +unfix grav +fix grav all gravity 10 vector 0 -1 0 + +variable theta equal 2*PI*elapsed/20000.0 +run 3000 diff --git a/examples/granular/in.pour.flatwall b/examples/granular/in.pour.flatwall new file mode 100644 index 0000000000..cfa70e2d84 --- /dev/null +++ b/examples/granular/in.pour.flatwall @@ -0,0 +1,67 @@ +# pour two types of particles (cohesive and non-cohesive) on flat wall + +variable name string pour_two_types + +atom_style sphere +units lj + +############################################### +# Geometry-related parameters +############################################### + +variable boxx equal 20 +variable boxy equal 20 +variable boxz equal 30 + +variable xc1 equal 0.3*${boxx} +variable xc2 equal 0.7*${boxx} +variable yc equal 0.5*${boxy} + +############################################### +# Particle-related parameters +############################################### +variable rlo equal 0.25 +variable rhi equal 0.5 +variable dlo equal 2.0*${rlo} +variable dhi equal 2.0*${rhi} + +variable dens equal 1.0 + +variable skin equal 0.3*${rhi} + +############# +processors * * 1 +region boxreg block 0 ${boxx} 0 ${boxy} 0 ${boxz} +create_box 2 boxreg +change_box all boundary p p f + +comm_modify vel yes + +region insreg1 cylinder z ${xc1} ${yc} 5 15 ${boxz} +region insreg2 cylinder z ${xc2} ${yc} 5 15 ${boxz} + +fix 1 all nve/sphere +fix grav all gravity 10.0 vector 0 0 -1 +fix ins1 all pour 1500 1 3123 region insreg1 diam range ${dlo} ${dhi} dens ${dens} ${dens} +fix ins2 all pour 1500 2 3123 region insreg2 diam range ${dlo} ${dhi} dens ${dens} ${dens} + +comm_modify vel yes + +neighbor ${skin} bin +neigh_modify delay 0 every 1 check yes + +pair_style granular +pair_coeff 1 * jkr 1000.0 50.0 0.3 10 tangential mindlin 800.0 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall +pair_coeff 2 2 hertz 200.0 20.0 tangential linear_history 300.0 1.0 0.1 rolling sds 200.0 100.0 0.1 twisting marshall + +fix 3 all wall/gran granular hertz/material 1e5 1e3 0.3 tangential mindlin NULL 1.0 0.5 zplane 0 NULL + +thermo_style custom step cpu atoms ke +thermo_modify lost warn +thermo 100 + +timestep 0.001 + +#dump 1 all custom 100 ${name}.dump id type radius mass x y z + +run 5000 diff --git a/examples/granular/log.29Mar19.pour.drum.g++.1 b/examples/granular/log.29Mar19.pour.drum.g++.1 new file mode 100644 index 0000000000..71232ed8dd --- /dev/null +++ b/examples/granular/log.29Mar19.pour.drum.g++.1 @@ -0,0 +1,271 @@ +LAMMPS (29 Mar 2019) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:88) + using 1 OpenMP thread(s) per MPI task +# pour two types of particles (cohesive and non-cohesive) into cylinder +# 'turn' cylinder by changing direction of gravity, then rotate it. +# This simulates a rotating drum powder characterization experiment. + +variable name string rotating_drum_two_types + +atom_style sphere +units lj + +############################################### +# Geometry-related parameters +############################################### + +variable boxx equal 30 +variable boxy equal 30 +variable boxz equal 50 + +variable drum_rad equal ${boxx}*0.5 +variable drum_rad equal 30*0.5 +variable drum_height equal 20 + +variable xc equal 0.5*${boxx} +variable xc equal 0.5*30 +variable yc equal 0.5*${boxx} +variable yc equal 0.5*30 +variable zc equal 0.5*${boxz} +variable zc equal 0.5*50 + +############################################### +# Particle-related parameters +############################################### +variable rlo equal 0.25 +variable rhi equal 0.5 +variable dlo equal 2.0*${rlo} +variable dlo equal 2.0*0.25 +variable dhi equal 2.0*${rhi} +variable dhi equal 2.0*0.5 + +variable cyl_rad_inner equal ${drum_rad}-1.1*${rhi} +variable cyl_rad_inner equal 15-1.1*${rhi} +variable cyl_rad_inner equal 15-1.1*0.5 + +variable dens equal 1.0 + +variable skin equal 0.4*${rhi} +variable skin equal 0.4*0.5 + +############# +processors * * 1 +region boxreg block 0 ${boxx} 0 ${boxy} 0 ${boxz} +region boxreg block 0 30 0 ${boxy} 0 ${boxz} +region boxreg block 0 30 0 30 0 ${boxz} +region boxreg block 0 30 0 30 0 50 +create_box 2 boxreg +Created orthogonal box = (0 0 0) to (30 30 50) + 1 by 1 by 1 MPI processor grid +change_box all boundary p p f +comm_modify vel yes + +variable theta equal 0 + +region curved_wall cylinder z ${xc} ${yc} ${drum_rad} 0 ${drum_height} side in rotate v_theta ${xc} ${yc} 0 0 0 1 +region curved_wall cylinder z 15 ${yc} ${drum_rad} 0 ${drum_height} side in rotate v_theta ${xc} ${yc} 0 0 0 1 +region curved_wall cylinder z 15 15 ${drum_rad} 0 ${drum_height} side in rotate v_theta ${xc} ${yc} 0 0 0 1 +region curved_wall cylinder z 15 15 15 0 ${drum_height} side in rotate v_theta ${xc} ${yc} 0 0 0 1 +region curved_wall cylinder z 15 15 15 0 20 side in rotate v_theta ${xc} ${yc} 0 0 0 1 +region curved_wall cylinder z 15 15 15 0 20 side in rotate v_theta 15 ${yc} 0 0 0 1 +region curved_wall cylinder z 15 15 15 0 20 side in rotate v_theta 15 15 0 0 0 1 +region bottom_wall plane ${xc} ${yc} 0 0 0 1 side in rotate v_theta ${xc} ${yc} 0 0 0 1 +region bottom_wall plane 15 ${yc} 0 0 0 1 side in rotate v_theta ${xc} ${yc} 0 0 0 1 +region bottom_wall plane 15 15 0 0 0 1 side in rotate v_theta ${xc} ${yc} 0 0 0 1 +region bottom_wall plane 15 15 0 0 0 1 side in rotate v_theta 15 ${yc} 0 0 0 1 +region bottom_wall plane 15 15 0 0 0 1 side in rotate v_theta 15 15 0 0 0 1 + +region insreg cylinder z ${xc} ${yc} ${cyl_rad_inner} ${drum_height} ${boxz} +region insreg cylinder z 15 ${yc} ${cyl_rad_inner} ${drum_height} ${boxz} +region insreg cylinder z 15 15 ${cyl_rad_inner} ${drum_height} ${boxz} +region insreg cylinder z 15 15 14.45 ${drum_height} ${boxz} +region insreg cylinder z 15 15 14.45 20 ${boxz} +region insreg cylinder z 15 15 14.45 20 50 + +fix 0 all balance 100 1.0 shift xy 5 1.1 +fix 1 all nve/sphere +fix grav all gravity 10 vector 0 0 -1 +fix ins1 all pour 2000 1 1234 region insreg diam range ${dlo} ${dhi} dens ${dens} ${dens} +fix ins1 all pour 2000 1 1234 region insreg diam range 0.5 ${dhi} dens ${dens} ${dens} +fix ins1 all pour 2000 1 1234 region insreg diam range 0.5 1 dens ${dens} ${dens} +fix ins1 all pour 2000 1 1234 region insreg diam range 0.5 1 dens 1 ${dens} +fix ins1 all pour 2000 1 1234 region insreg diam range 0.5 1 dens 1 1 +Particle insertion: 9396 every 490 steps, 2000 by step 1 +fix ins2 all pour 2000 2 1234 region insreg diam range ${dlo} ${dhi} dens ${dens} ${dens} +fix ins2 all pour 2000 2 1234 region insreg diam range 0.5 ${dhi} dens ${dens} ${dens} +fix ins2 all pour 2000 2 1234 region insreg diam range 0.5 1 dens ${dens} ${dens} +fix ins2 all pour 2000 2 1234 region insreg diam range 0.5 1 dens 1 ${dens} +fix ins2 all pour 2000 2 1234 region insreg diam range 0.5 1 dens 1 1 +Particle insertion: 9396 every 490 steps, 2000 by step 1 + +comm_modify vel yes + +neighbor ${skin} bin +neighbor 0.2 bin +neigh_modify delay 0 every 1 check yes + +pair_style granular +pair_coeff 1 * hertz/material 1e5 0.2 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji +pair_coeff 2 2 jkr 1e5 0.1 0.3 50 tangential mindlin NULL 1.0 0.5 rolling sds 1e3 1e3 0.1 twisting marshall damping tsuji + +fix 3 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji region curved_wall +fix 4 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji region bottom_wall + +thermo_style custom step atoms ke v_theta +thermo_modify lost warn +thermo 100 + +timestep 0.001 + +dump 1 all custom 100 ${name}.dump id type radius mass x y z +dump 1 all custom 100 rotating_drum_two_types.dump id type radius mass x y z + +#For removal later +compute 1 all property/atom radius +variable zmax atom z+c_1>0.5*${drum_height} +variable zmax atom z+c_1>0.5*20 +group delgroup dynamic all var zmax every 10000 +dynamic group delgroup defined + +run 2000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.2 + ghost atom cutoff = 1.2 + binsize = 0.6, bins = 50 50 84 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair granular, perpetual + attributes: half, newton on, size, history + pair build: half/size/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 13.02 | 13.02 | 13.02 Mbytes +Step Atoms KinEng v_theta + 0 0 -0 0 + 100 4000 -0 0 + 200 4000 -0 0 + 300 4000 -0 0 + 400 4000 -0 0 + 500 4000 -0 0 + 600 4000 -0 0 + 700 4000 -0 0 + 800 4000 -0 0 + 900 4000 -0 0 + 1000 4000 -0 0 + 1100 4000 -0 0 + 1200 4000 -0 0 + 1300 4000 -0 0 + 1400 4000 -0 0 + 1500 4000 -0 0 + 1600 4000 -0 0 + 1700 4000 -0 0 + 1800 4000 -0 0 + 1900 4000 -0 0 + 2000 4000 -0 0 +Loop time of 3.54461 on 1 procs for 2000 steps with 4000 atoms + +Performance: 48750.057 tau/day, 564.237 timesteps/s +99.5% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.61949 | 0.61949 | 0.61949 | 0.0 | 17.48 +Neigh | 1.2492 | 1.2492 | 1.2492 | 0.0 | 35.24 +Comm | 0.046404 | 0.046404 | 0.046404 | 0.0 | 1.31 +Output | 0.15901 | 0.15901 | 0.15901 | 0.0 | 4.49 +Modify | 1.4165 | 1.4165 | 1.4165 | 0.0 | 39.96 +Other | | 0.05391 | | | 1.52 + +Nlocal: 4000 ave 4000 max 4000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 166 ave 166 max 166 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 8195 ave 8195 max 8195 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 8195 +Ave neighs/atom = 2.04875 +Neighbor list builds = 1004 +Dangerous builds = 3 + +#Remove any particles that are above z > 0.5*drum_height +delete_atoms group delgroup +Deleted 0 atoms, new total = 4000 + +#Add top lid +region top_wall plane ${xc} ${yc} ${drum_height} 0 0 -1 side in rotate v_theta ${xc} ${yc} 0 0 0 1 +region top_wall plane 15 ${yc} ${drum_height} 0 0 -1 side in rotate v_theta ${xc} ${yc} 0 0 0 1 +region top_wall plane 15 15 ${drum_height} 0 0 -1 side in rotate v_theta ${xc} ${yc} 0 0 0 1 +region top_wall plane 15 15 20 0 0 -1 side in rotate v_theta ${xc} ${yc} 0 0 0 1 +region top_wall plane 15 15 20 0 0 -1 side in rotate v_theta 15 ${yc} 0 0 0 1 +region top_wall plane 15 15 20 0 0 -1 side in rotate v_theta 15 15 0 0 0 1 +fix 5 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji region top_wall + +# 'Turn' drum by switching the direction of gravity +unfix grav +fix grav all gravity 10 vector 0 -1 0 + +variable theta equal 2*PI*elapsed/20000.0 +run 3000 +Per MPI rank memory allocation (min/avg/max) = 24.81 | 24.81 | 24.81 Mbytes +Step Atoms KinEng v_theta + 2000 4000 64.333531 0 + 2100 4000 106.69182 0.031415927 + 2200 4000 121.8461 0.062831853 + 2300 4000 88.767952 0.09424778 + 2400 4000 82.850721 0.12566371 + 2500 4000 91.683284 0.15707963 + 2600 4000 31.56344 0.18849556 + 2700 4000 4.5697672 0.21991149 + 2800 4000 3.9879051 0.25132741 + 2900 4000 4.4394235 0.28274334 + 3000 4000 5.1212931 0.31415927 + 3100 4000 5.8608892 0.34557519 + 3200 4000 6.600714 0.37699112 + 3300 4000 7.3497851 0.40840704 + 3400 4000 8.0490988 0.43982297 + 3500 4000 8.6712396 0.4712389 + 3600 4000 9.1328667 0.50265482 + 3700 4000 9.4683561 0.53407075 + 3800 4000 9.5878145 0.56548668 + 3900 4000 9.387745 0.5969026 + 4000 4000 8.9117631 0.62831853 + 4100 4000 8.2344368 0.65973446 + 4200 4000 7.5335088 0.69115038 + 4300 4000 6.8426179 0.72256631 + 4400 4000 6.0567247 0.75398224 + 4500 4000 5.4166132 0.78539816 + 4600 4000 4.6012409 0.81681409 + 4700 4000 3.8314982 0.84823002 + 4800 4000 3.1916415 0.87964594 + 4900 4000 2.7833964 0.91106187 + 5000 4000 2.5051362 0.9424778 +Loop time of 11.9545 on 1 procs for 3000 steps with 4000 atoms + +Performance: 21682.142 tau/day, 250.951 timesteps/s +99.7% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 4.8291 | 4.8291 | 4.8291 | 0.0 | 40.40 +Neigh | 2.7489 | 2.7489 | 2.7489 | 0.0 | 22.99 +Comm | 0.071249 | 0.071249 | 0.071249 | 0.0 | 0.60 +Output | 0.20547 | 0.20547 | 0.20547 | 0.0 | 1.72 +Modify | 4.0179 | 4.0179 | 4.0179 | 0.0 | 33.61 +Other | | 0.0819 | | | 0.69 + +Nlocal: 4000 ave 4000 max 4000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 322 ave 322 max 322 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 14849 ave 14849 max 14849 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 14849 +Ave neighs/atom = 3.71225 +Neighbor list builds = 1290 +Dangerous builds = 672 +Total wall time: 0:00:15 diff --git a/examples/granular/log.29Mar19.pour.drum.g++.4 b/examples/granular/log.29Mar19.pour.drum.g++.4 new file mode 100644 index 0000000000..ccd4365a38 --- /dev/null +++ b/examples/granular/log.29Mar19.pour.drum.g++.4 @@ -0,0 +1,271 @@ +LAMMPS (29 Mar 2019) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:88) + using 1 OpenMP thread(s) per MPI task +# pour two types of particles (cohesive and non-cohesive) into cylinder +# 'turn' cylinder by changing direction of gravity, then rotate it. +# This simulates a rotating drum powder characterization experiment. + +variable name string rotating_drum_two_types + +atom_style sphere +units lj + +############################################### +# Geometry-related parameters +############################################### + +variable boxx equal 30 +variable boxy equal 30 +variable boxz equal 50 + +variable drum_rad equal ${boxx}*0.5 +variable drum_rad equal 30*0.5 +variable drum_height equal 20 + +variable xc equal 0.5*${boxx} +variable xc equal 0.5*30 +variable yc equal 0.5*${boxx} +variable yc equal 0.5*30 +variable zc equal 0.5*${boxz} +variable zc equal 0.5*50 + +############################################### +# Particle-related parameters +############################################### +variable rlo equal 0.25 +variable rhi equal 0.5 +variable dlo equal 2.0*${rlo} +variable dlo equal 2.0*0.25 +variable dhi equal 2.0*${rhi} +variable dhi equal 2.0*0.5 + +variable cyl_rad_inner equal ${drum_rad}-1.1*${rhi} +variable cyl_rad_inner equal 15-1.1*${rhi} +variable cyl_rad_inner equal 15-1.1*0.5 + +variable dens equal 1.0 + +variable skin equal 0.4*${rhi} +variable skin equal 0.4*0.5 + +############# +processors * * 1 +region boxreg block 0 ${boxx} 0 ${boxy} 0 ${boxz} +region boxreg block 0 30 0 ${boxy} 0 ${boxz} +region boxreg block 0 30 0 30 0 ${boxz} +region boxreg block 0 30 0 30 0 50 +create_box 2 boxreg +Created orthogonal box = (0 0 0) to (30 30 50) + 2 by 2 by 1 MPI processor grid +change_box all boundary p p f +comm_modify vel yes + +variable theta equal 0 + +region curved_wall cylinder z ${xc} ${yc} ${drum_rad} 0 ${drum_height} side in rotate v_theta ${xc} ${yc} 0 0 0 1 +region curved_wall cylinder z 15 ${yc} ${drum_rad} 0 ${drum_height} side in rotate v_theta ${xc} ${yc} 0 0 0 1 +region curved_wall cylinder z 15 15 ${drum_rad} 0 ${drum_height} side in rotate v_theta ${xc} ${yc} 0 0 0 1 +region curved_wall cylinder z 15 15 15 0 ${drum_height} side in rotate v_theta ${xc} ${yc} 0 0 0 1 +region curved_wall cylinder z 15 15 15 0 20 side in rotate v_theta ${xc} ${yc} 0 0 0 1 +region curved_wall cylinder z 15 15 15 0 20 side in rotate v_theta 15 ${yc} 0 0 0 1 +region curved_wall cylinder z 15 15 15 0 20 side in rotate v_theta 15 15 0 0 0 1 +region bottom_wall plane ${xc} ${yc} 0 0 0 1 side in rotate v_theta ${xc} ${yc} 0 0 0 1 +region bottom_wall plane 15 ${yc} 0 0 0 1 side in rotate v_theta ${xc} ${yc} 0 0 0 1 +region bottom_wall plane 15 15 0 0 0 1 side in rotate v_theta ${xc} ${yc} 0 0 0 1 +region bottom_wall plane 15 15 0 0 0 1 side in rotate v_theta 15 ${yc} 0 0 0 1 +region bottom_wall plane 15 15 0 0 0 1 side in rotate v_theta 15 15 0 0 0 1 + +region insreg cylinder z ${xc} ${yc} ${cyl_rad_inner} ${drum_height} ${boxz} +region insreg cylinder z 15 ${yc} ${cyl_rad_inner} ${drum_height} ${boxz} +region insreg cylinder z 15 15 ${cyl_rad_inner} ${drum_height} ${boxz} +region insreg cylinder z 15 15 14.45 ${drum_height} ${boxz} +region insreg cylinder z 15 15 14.45 20 ${boxz} +region insreg cylinder z 15 15 14.45 20 50 + +fix 0 all balance 100 1.0 shift xy 5 1.1 +fix 1 all nve/sphere +fix grav all gravity 10 vector 0 0 -1 +fix ins1 all pour 2000 1 1234 region insreg diam range ${dlo} ${dhi} dens ${dens} ${dens} +fix ins1 all pour 2000 1 1234 region insreg diam range 0.5 ${dhi} dens ${dens} ${dens} +fix ins1 all pour 2000 1 1234 region insreg diam range 0.5 1 dens ${dens} ${dens} +fix ins1 all pour 2000 1 1234 region insreg diam range 0.5 1 dens 1 ${dens} +fix ins1 all pour 2000 1 1234 region insreg diam range 0.5 1 dens 1 1 +Particle insertion: 9396 every 490 steps, 2000 by step 1 +fix ins2 all pour 2000 2 1234 region insreg diam range ${dlo} ${dhi} dens ${dens} ${dens} +fix ins2 all pour 2000 2 1234 region insreg diam range 0.5 ${dhi} dens ${dens} ${dens} +fix ins2 all pour 2000 2 1234 region insreg diam range 0.5 1 dens ${dens} ${dens} +fix ins2 all pour 2000 2 1234 region insreg diam range 0.5 1 dens 1 ${dens} +fix ins2 all pour 2000 2 1234 region insreg diam range 0.5 1 dens 1 1 +Particle insertion: 9396 every 490 steps, 2000 by step 1 + +comm_modify vel yes + +neighbor ${skin} bin +neighbor 0.2 bin +neigh_modify delay 0 every 1 check yes + +pair_style granular +pair_coeff 1 * hertz/material 1e5 0.2 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji +pair_coeff 2 2 jkr 1e5 0.1 0.3 50 tangential mindlin NULL 1.0 0.5 rolling sds 1e3 1e3 0.1 twisting marshall damping tsuji + +fix 3 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji region curved_wall +fix 4 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji region bottom_wall + +thermo_style custom step atoms ke v_theta +thermo_modify lost warn +thermo 100 + +timestep 0.001 + +dump 1 all custom 100 ${name}.dump id type radius mass x y z +dump 1 all custom 100 rotating_drum_two_types.dump id type radius mass x y z + +#For removal later +compute 1 all property/atom radius +variable zmax atom z+c_1>0.5*${drum_height} +variable zmax atom z+c_1>0.5*20 +group delgroup dynamic all var zmax every 10000 +dynamic group delgroup defined + +run 2000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.2 + ghost atom cutoff = 1.2 + binsize = 0.6, bins = 50 50 84 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair granular, perpetual + attributes: half, newton on, size, history + pair build: half/size/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 12.25 | 12.25 | 12.25 Mbytes +Step Atoms KinEng v_theta + 0 0 -0 0 + 100 4000 -0 0 + 200 4000 -0 0 + 300 4000 -0 0 + 400 4000 -0 0 + 500 4000 -0 0 + 600 4000 -0 0 + 700 4000 -0 0 + 800 4000 -0 0 + 900 4000 -0 0 + 1000 4000 -0 0 + 1100 4000 -0 0 + 1200 4000 -0 0 + 1300 4000 -0 0 + 1400 4000 -0 0 + 1500 4000 -0 0 + 1600 4000 -0 0 + 1700 4000 -0 0 + 1800 4000 -0 0 + 1900 4000 -0 0 + 2000 4000 -0 0 +Loop time of 2.0709 on 4 procs for 2000 steps with 4000 atoms + +Performance: 83442.024 tau/day, 965.764 timesteps/s +97.7% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.24679 | 0.26336 | 0.28853 | 3.0 | 12.72 +Neigh | 0.52279 | 0.5332 | 0.53858 | 0.9 | 25.75 +Comm | 0.17418 | 0.20253 | 0.23266 | 4.7 | 9.78 +Output | 0.092897 | 0.093531 | 0.09515 | 0.3 | 4.52 +Modify | 0.88151 | 0.89571 | 0.90582 | 0.9 | 43.25 +Other | | 0.08257 | | | 3.99 + +Nlocal: 1000 ave 1001 max 999 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 267.75 ave 276 max 262 min +Histogram: 1 0 1 0 1 0 0 0 0 1 +Neighs: 2031.5 ave 2091 max 1958 min +Histogram: 1 0 0 0 1 0 0 1 0 1 + +Total # of neighbors = 8126 +Ave neighs/atom = 2.0315 +Neighbor list builds = 1004 +Dangerous builds = 3 + +#Remove any particles that are above z > 0.5*drum_height +delete_atoms group delgroup +Deleted 0 atoms, new total = 4000 + +#Add top lid +region top_wall plane ${xc} ${yc} ${drum_height} 0 0 -1 side in rotate v_theta ${xc} ${yc} 0 0 0 1 +region top_wall plane 15 ${yc} ${drum_height} 0 0 -1 side in rotate v_theta ${xc} ${yc} 0 0 0 1 +region top_wall plane 15 15 ${drum_height} 0 0 -1 side in rotate v_theta ${xc} ${yc} 0 0 0 1 +region top_wall plane 15 15 20 0 0 -1 side in rotate v_theta ${xc} ${yc} 0 0 0 1 +region top_wall plane 15 15 20 0 0 -1 side in rotate v_theta 15 ${yc} 0 0 0 1 +region top_wall plane 15 15 20 0 0 -1 side in rotate v_theta 15 15 0 0 0 1 +fix 5 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji region top_wall + +# 'Turn' drum by switching the direction of gravity +unfix grav +fix grav all gravity 10 vector 0 -1 0 + +variable theta equal 2*PI*elapsed/20000.0 +run 3000 +Per MPI rank memory allocation (min/avg/max) = 21.6 | 22.6 | 23.82 Mbytes +Step Atoms KinEng v_theta + 2000 4000 64.255821 0 + 2100 4000 106.47082 0.031415927 + 2200 4000 121.52634 0.062831853 + 2300 4000 87.748818 0.09424778 + 2400 4000 82.712784 0.12566371 + 2500 4000 90.618713 0.15707963 + 2600 4000 30.096031 0.18849556 + 2700 4000 4.0838611 0.21991149 + 2800 4000 3.7485959 0.25132741 + 2900 4000 4.2159774 0.28274334 + 3000 4000 4.8730048 0.31415927 + 3100 4000 5.6109465 0.34557519 + 3200 4000 6.4290528 0.37699112 + 3300 4000 7.2699677 0.40840704 + 3400 4000 8.0895944 0.43982297 + 3500 4000 8.7222781 0.4712389 + 3600 4000 9.133205 0.50265482 + 3700 4000 9.3404584 0.53407075 + 3800 4000 9.3359844 0.56548668 + 3900 4000 9.0916854 0.5969026 + 4000 4000 8.5596424 0.62831853 + 4100 4000 7.9734883 0.65973446 + 4200 4000 7.2154383 0.69115038 + 4300 4000 6.7039232 0.72256631 + 4400 4000 6.1542738 0.75398224 + 4500 4000 5.4049454 0.78539816 + 4600 4000 4.4603192 0.81681409 + 4700 4000 3.6197985 0.84823002 + 4800 4000 2.9895571 0.87964594 + 4900 4000 2.5314553 0.91106187 + 5000 4000 2.2645533 0.9424778 +Loop time of 6.64209 on 4 procs for 3000 steps with 4000 atoms + +Performance: 39023.861 tau/day, 451.665 timesteps/s +96.6% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.8376 | 2.126 | 2.3131 | 12.6 | 32.01 +Neigh | 0.97762 | 1.0518 | 1.1337 | 5.4 | 15.84 +Comm | 0.53699 | 0.84265 | 1.2325 | 27.6 | 12.69 +Output | 0.13922 | 0.14159 | 0.14388 | 0.4 | 2.13 +Modify | 1.8815 | 2.1026 | 2.3368 | 11.2 | 31.66 +Other | | 0.3774 | | | 5.68 + +Nlocal: 1000 ave 1256 max 744 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 579.5 ave 789 max 498 min +Histogram: 2 1 0 0 0 0 0 0 0 1 +Neighs: 3696.25 ave 4853 max 2590 min +Histogram: 2 0 0 0 0 0 0 0 1 1 + +Total # of neighbors = 14785 +Ave neighs/atom = 3.69625 +Neighbor list builds = 1230 +Dangerous builds = 676 +Total wall time: 0:00:08 diff --git a/examples/granular/log.29Mar19.pour.flatwall.g++.1 b/examples/granular/log.29Mar19.pour.flatwall.g++.1 new file mode 100644 index 0000000000..daab5efce3 --- /dev/null +++ b/examples/granular/log.29Mar19.pour.flatwall.g++.1 @@ -0,0 +1,134 @@ +LAMMPS (29 Mar 2019) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:88) + using 1 OpenMP thread(s) per MPI task +# pour two types of particles (cohesive and non-cohesive) on flat wall + +variable name string pour_two_types + +atom_style sphere +units lj + +############################################### +# Geometry-related parameters +############################################### + +variable boxx equal 20 +variable boxy equal 20 +variable boxz equal 30 + +variable xc1 equal 0.3*${boxx} +variable xc1 equal 0.3*20 +variable xc2 equal 0.7*${boxx} +variable xc2 equal 0.7*20 +variable yc equal 0.5*${boxy} +variable yc equal 0.5*20 + +############################################### +# Particle-related parameters +############################################### +variable rlo equal 0.25 +variable rhi equal 0.5 +variable dlo equal 2.0*${rlo} +variable dlo equal 2.0*0.25 +variable dhi equal 2.0*${rhi} +variable dhi equal 2.0*0.5 + +variable dens equal 1.0 + +variable skin equal 0.3*${rhi} +variable skin equal 0.3*0.5 + +############# +processors * * 1 +region boxreg block 0 ${boxx} 0 ${boxy} 0 ${boxz} +region boxreg block 0 20 0 ${boxy} 0 ${boxz} +region boxreg block 0 20 0 20 0 ${boxz} +region boxreg block 0 20 0 20 0 30 +create_box 2 boxreg +Created orthogonal box = (0 0 0) to (20 20 30) + 1 by 1 by 1 MPI processor grid +change_box all boundary p p f + +comm_modify vel yes + +region insreg1 cylinder z ${xc1} ${yc} 5 15 ${boxz} +region insreg1 cylinder z 6 ${yc} 5 15 ${boxz} +region insreg1 cylinder z 6 10 5 15 ${boxz} +region insreg1 cylinder z 6 10 5 15 30 +region insreg2 cylinder z ${xc2} ${yc} 5 15 ${boxz} +region insreg2 cylinder z 14 ${yc} 5 15 ${boxz} +region insreg2 cylinder z 14 10 5 15 ${boxz} +region insreg2 cylinder z 14 10 5 15 30 + +fix 1 all nve/sphere +fix grav all gravity 10.0 vector 0 0 -1 +fix ins1 all pour 1500 1 3123 region insreg1 diam range ${dlo} ${dhi} dens ${dens} ${dens} +fix ins1 all pour 1500 1 3123 region insreg1 diam range 0.5 ${dhi} dens ${dens} ${dens} +fix ins1 all pour 1500 1 3123 region insreg1 diam range 0.5 1 dens ${dens} ${dens} +fix ins1 all pour 1500 1 3123 region insreg1 diam range 0.5 1 dens 1 ${dens} +fix ins1 all pour 1500 1 3123 region insreg1 diam range 0.5 1 dens 1 1 +Particle insertion: 562 every 346 steps, 1500 by step 693 +fix ins2 all pour 1500 2 3123 region insreg2 diam range ${dlo} ${dhi} dens ${dens} ${dens} +fix ins2 all pour 1500 2 3123 region insreg2 diam range 0.5 ${dhi} dens ${dens} ${dens} +fix ins2 all pour 1500 2 3123 region insreg2 diam range 0.5 1 dens ${dens} ${dens} +fix ins2 all pour 1500 2 3123 region insreg2 diam range 0.5 1 dens 1 ${dens} +fix ins2 all pour 1500 2 3123 region insreg2 diam range 0.5 1 dens 1 1 +Particle insertion: 562 every 346 steps, 1500 by step 693 + +comm_modify vel yes + +neighbor ${skin} bin +neighbor 0.15 bin +neigh_modify delay 0 every 1 check yes + +pair_style granular +pair_coeff 1 * jkr 1000.0 50.0 0.3 10 tangential mindlin 800.0 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall +pair_coeff 2 2 hertz 200.0 20.0 tangential linear_history 300.0 1.0 0.1 rolling sds 200.0 100.0 0.1 twisting marshall + +fix 3 all wall/gran granular hertz/material 1e5 1e3 0.3 tangential mindlin NULL 1.0 0.5 zplane 0 NULL + +thermo_style custom step cpu atoms ke +thermo_modify lost warn +thermo 100 + +timestep 0.001 + +#dump 1 all custom 100 ${name}.dump id type radius mass x y z + +run 5000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.15 + ghost atom cutoff = 1.15 + binsize = 0.575, bins = 35 35 53 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair granular, perpetual + attributes: half, newton on, size, history + pair build: half/size/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 12.22 | 12.22 | 12.22 Mbytes +Step CPU Atoms KinEng + 0 0 0 -0 + 100 3.8153191 855 -0 + 200 4.195287 855 -0 + 300 4.5890362 855 -0 + 400 10.636087 1500 -0 + 500 11.306909 1500 -0 + 600 11.968198 1500 -0 + 700 22.631892 2288 -0 + 800 23.711387 2288 -0 + 900 24.754344 2288 -0 + 1000 25.811778 2288 -0 + 1100 35.368869 2845 -0 + 1200 37.149843 2845 -0 + 1300 39.026458 2845 -0 + 1400 41.757583 3000 -0 + 1500 45.155503 3000 -0 + 1600 48.570241 3000 -0 + 1700 52.839322 3000 -0 + 1800 59.772697 3000 -0 + 1900 69.493305 3000 -0 + 2000 114.61886 3000 -0 + 2100 152.89232 3000 -0 diff --git a/examples/granular/log.29Mar19.pour.flatwall.g++.4 b/examples/granular/log.29Mar19.pour.flatwall.g++.4 new file mode 100644 index 0000000000..62a8b96c05 --- /dev/null +++ b/examples/granular/log.29Mar19.pour.flatwall.g++.4 @@ -0,0 +1,191 @@ +LAMMPS (29 Mar 2019) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:88) + using 1 OpenMP thread(s) per MPI task +# pour two types of particles (cohesive and non-cohesive) on flat wall + +variable name string pour_two_types + +atom_style sphere +units lj + +############################################### +# Geometry-related parameters +############################################### + +variable boxx equal 20 +variable boxy equal 20 +variable boxz equal 30 + +variable xc1 equal 0.3*${boxx} +variable xc1 equal 0.3*20 +variable xc2 equal 0.7*${boxx} +variable xc2 equal 0.7*20 +variable yc equal 0.5*${boxy} +variable yc equal 0.5*20 + +############################################### +# Particle-related parameters +############################################### +variable rlo equal 0.25 +variable rhi equal 0.5 +variable dlo equal 2.0*${rlo} +variable dlo equal 2.0*0.25 +variable dhi equal 2.0*${rhi} +variable dhi equal 2.0*0.5 + +variable dens equal 1.0 + +variable skin equal 0.3*${rhi} +variable skin equal 0.3*0.5 + +############# +processors * * 1 +region boxreg block 0 ${boxx} 0 ${boxy} 0 ${boxz} +region boxreg block 0 20 0 ${boxy} 0 ${boxz} +region boxreg block 0 20 0 20 0 ${boxz} +region boxreg block 0 20 0 20 0 30 +create_box 2 boxreg +Created orthogonal box = (0 0 0) to (20 20 30) + 2 by 2 by 1 MPI processor grid +change_box all boundary p p f + +comm_modify vel yes + +region insreg1 cylinder z ${xc1} ${yc} 5 15 ${boxz} +region insreg1 cylinder z 6 ${yc} 5 15 ${boxz} +region insreg1 cylinder z 6 10 5 15 ${boxz} +region insreg1 cylinder z 6 10 5 15 30 +region insreg2 cylinder z ${xc2} ${yc} 5 15 ${boxz} +region insreg2 cylinder z 14 ${yc} 5 15 ${boxz} +region insreg2 cylinder z 14 10 5 15 ${boxz} +region insreg2 cylinder z 14 10 5 15 30 + +fix 1 all nve/sphere +fix grav all gravity 10.0 vector 0 0 -1 +fix ins1 all pour 1500 1 3123 region insreg1 diam range ${dlo} ${dhi} dens ${dens} ${dens} +fix ins1 all pour 1500 1 3123 region insreg1 diam range 0.5 ${dhi} dens ${dens} ${dens} +fix ins1 all pour 1500 1 3123 region insreg1 diam range 0.5 1 dens ${dens} ${dens} +fix ins1 all pour 1500 1 3123 region insreg1 diam range 0.5 1 dens 1 ${dens} +fix ins1 all pour 1500 1 3123 region insreg1 diam range 0.5 1 dens 1 1 +Particle insertion: 562 every 346 steps, 1500 by step 693 +fix ins2 all pour 1500 2 3123 region insreg2 diam range ${dlo} ${dhi} dens ${dens} ${dens} +fix ins2 all pour 1500 2 3123 region insreg2 diam range 0.5 ${dhi} dens ${dens} ${dens} +fix ins2 all pour 1500 2 3123 region insreg2 diam range 0.5 1 dens ${dens} ${dens} +fix ins2 all pour 1500 2 3123 region insreg2 diam range 0.5 1 dens 1 ${dens} +fix ins2 all pour 1500 2 3123 region insreg2 diam range 0.5 1 dens 1 1 +Particle insertion: 562 every 346 steps, 1500 by step 693 + +comm_modify vel yes + +neighbor ${skin} bin +neighbor 0.15 bin +neigh_modify delay 0 every 1 check yes + +pair_style granular +pair_coeff 1 * jkr 1000.0 50.0 0.3 10 tangential mindlin 800.0 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall +pair_coeff 2 2 hertz 200.0 20.0 tangential linear_history 300.0 1.0 0.1 rolling sds 200.0 100.0 0.1 twisting marshall + +fix 3 all wall/gran granular hertz/material 1e5 1e3 0.3 tangential mindlin NULL 1.0 0.5 zplane 0 NULL + +thermo_style custom step cpu atoms ke +thermo_modify lost warn +thermo 100 + +timestep 0.001 + +dump 1 all custom 100 ${name}.dump id type radius mass x y z +dump 1 all custom 100 pour_two_types.dump id type radius mass x y z + +run 5000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.15 + ghost atom cutoff = 1.15 + binsize = 0.575, bins = 35 35 53 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair granular, perpetual + attributes: half, newton on, size, history + pair build: half/size/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 11.98 | 11.98 | 11.98 Mbytes +Step CPU Atoms KinEng + 0 0 0 -0 + 100 0.11584234 855 -0 + 200 0.12743592 855 -0 + 300 0.13925815 855 -0 + 400 0.35203671 1500 -0 + 500 0.37055922 1500 -0 + 600 0.38671875 1500 -0 + 700 0.71736908 2288 -0 + 800 0.74506783 2288 -0 + 900 0.77112222 2288 -0 + 1000 0.79632139 2288 -0 + 1100 1.0384252 2845 -0 + 1200 1.08093 2845 -0 + 1300 1.1224561 2845 -0 + 1400 1.1811485 3000 -0 + 1500 1.2414908 3000 -0 + 1600 1.3105879 3000 -0 + 1700 1.390928 3000 -0 + 1800 1.4869275 3000 -0 + 1900 1.5958266 3000 -0 + 2000 1.7172487 3000 -0 + 2100 1.851155 3000 -0 + 2200 1.9957182 3000 -0 + 2300 2.1593764 3000 -0 + 2400 2.3433132 3000 -0 + 2500 2.532742 3000 -0 + 2600 2.7376895 3000 -0 + 2700 2.9463468 3000 -0 + 2800 3.1645725 3000 -0 + 2900 3.3879526 3000 -0 + 3000 3.6152103 3000 -0 + 3100 3.8467371 3000 -0 + 3200 4.0787683 3000 -0 + 3300 4.3097105 3000 -0 + 3400 4.5423617 3000 -0 + 3500 4.7773693 3000 -0 + 3600 5.0127218 3000 -0 + 3700 5.2519271 3000 -0 + 3800 5.4951298 3000 -0 + 3900 5.7210469 3000 -0 + 4000 5.9432652 3000 -0 + 4100 6.1687591 3000 -0 + 4200 6.3942792 3000 -0 + 4300 6.6331475 3000 -0 + 4400 6.8632154 3000 -0 + 4500 7.0979366 3000 -0 + 4600 7.3305347 3000 -0 + 4700 7.5670528 3000 -0 + 4800 7.8086057 3000 -0 + 4900 8.0407174 3000 -0 + 5000 8.2765219 3000 -0 +Loop time of 8.27669 on 4 procs for 5000 steps with 3000 atoms + +Performance: 52194.788 tau/day, 604.106 timesteps/s +97.7% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.6106 | 3.4073 | 5.4191 | 95.7 | 41.17 +Neigh | 0.51456 | 0.64572 | 0.81542 | 16.6 | 7.80 +Comm | 0.2808 | 2.5222 | 4.4998 | 121.9 | 30.47 +Output | 0.15695 | 0.15919 | 0.16502 | 0.8 | 1.92 +Modify | 1.3517 | 1.4192 | 1.4904 | 4.9 | 17.15 +Other | | 0.123 | | | 1.49 + +Nlocal: 750 ave 1036 max 482 min +Histogram: 2 0 0 0 0 0 0 0 1 1 +Nghost: 429.75 ave 475 max 386 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 4051.75 ave 6274 max 2057 min +Histogram: 2 0 0 0 0 0 0 0 1 1 + +Total # of neighbors = 16207 +Ave neighs/atom = 5.40233 +Neighbor list builds = 1165 +Dangerous builds = 0 +Total wall time: 0:00:08 diff --git a/lib/colvars/colvar.cpp b/lib/colvars/colvar.cpp index 8b28eaa0df..723a54ad39 100644 --- a/lib/colvars/colvar.cpp +++ b/lib/colvars/colvar.cpp @@ -24,12 +24,13 @@ colvar::colvar() { runave_os = NULL; - prev_timestep = -1; + prev_timestep = -1L; after_restart = false; kinetic_energy = 0.0; potential_energy = 0.0; - init_cv_requires(); + description = "uninitialized colvar"; + init_dependencies(); } @@ -193,7 +194,7 @@ int colvar::init(std::string const &conf) { bool homogeneous = is_enabled(f_cv_linear); for (i = 0; i < cvcs.size(); i++) { - if ((std::fabs(cvcs[i]->sup_coeff) - 1.0) > 1.0e-10) { + if ((cvm::fabs(cvcs[i]->sup_coeff) - 1.0) > 1.0e-10) { homogeneous = false; } } @@ -224,7 +225,7 @@ int colvar::init(std::string const &conf) // Allow scripted/custom functions to be defined as periodic if ( (is_enabled(f_cv_scripted) || is_enabled(f_cv_custom_function)) && is_enabled(f_cv_scalar) ) { if (get_keyval(conf, "period", period, 0.)) { - set_enabled(f_cv_periodic, true); + enable(f_cv_periodic); get_keyval(conf, "wrapAround", wrap_center, 0.); } } @@ -471,7 +472,7 @@ int colvar::init_grid_parameters(std::string const &conf) if (get_keyval(conf, "lowerWallConstant", lower_wall_k, 0.0, parse_silent)) { cvm::log("Reading legacy options lowerWall and lowerWallConstant: " - "consider using a harmonicWalls restraint.\n"); + "consider using a harmonicWalls restraint\n(caution: force constant would then be scaled by width^2).\n"); lower_wall.type(value()); if (!get_keyval(conf, "lowerWall", lower_wall, lower_boundary)) { cvm::log("Warning: lowerWall will need to be " @@ -485,7 +486,7 @@ int colvar::init_grid_parameters(std::string const &conf) if (get_keyval(conf, "upperWallConstant", upper_wall_k, 0.0, parse_silent)) { cvm::log("Reading legacy options upperWall and upperWallConstant: " - "consider using a harmonicWalls restraint.\n"); + "consider using a harmonicWalls restraint\n(caution: force constant would then be scaled by width^2).\n"); upper_wall.type(value()); if (!get_keyval(conf, "upperWall", upper_wall, upper_boundary)) { cvm::log("Warning: upperWall will need to be " @@ -562,13 +563,13 @@ int colvar::init_extended_Lagrangian(std::string const &conf) get_keyval_feature(this, conf, "extendedLagrangian", f_cv_extended_Lagrangian, false); if (is_enabled(f_cv_extended_Lagrangian)) { - cvm::real temp, tolerance, period; + cvm::real temp, tolerance, extended_period; cvm::log("Enabling the extended Lagrangian term for colvar \""+ this->name+"\".\n"); - xr.type(value()); - vr.type(value()); + x_ext.type(value()); + v_ext.type(value()); fr.type(value()); const bool found = get_keyval(conf, "extendedTemp", temp, cvm::temperature()); @@ -590,11 +591,11 @@ int colvar::init_extended_Lagrangian(std::string const &conf) ext_force_k = cvm::boltzmann() * temp / (tolerance * tolerance); cvm::log("Computed extended system force constant: " + cvm::to_str(ext_force_k) + " [E]/U^2"); - get_keyval(conf, "extendedTimeConstant", period, 200.0); - if (period <= 0.0) { + get_keyval(conf, "extendedTimeConstant", extended_period, 200.0); + if (extended_period <= 0.0) { cvm::error("Error: \"extendedTimeConstant\" must be positive.\n", INPUT_ERROR); } - ext_mass = (cvm::boltzmann() * temp * period * period) + ext_mass = (cvm::boltzmann() * temp * extended_period * extended_period) / (4.0 * PI * PI * tolerance * tolerance); cvm::log("Computed fictitious mass: " + cvm::to_str(ext_mass) + " [E]/(U/fs)^2 (U: colvar unit)"); @@ -615,7 +616,7 @@ int colvar::init_extended_Lagrangian(std::string const &conf) enable(f_cv_Langevin); ext_gamma *= 1.0e-3; // correct as long as input is required in ps-1 and cvm::dt() is in fs // Adjust Langevin sigma for slow time step if time_step_factor != 1 - ext_sigma = std::sqrt(2.0 * cvm::boltzmann() * temp * ext_gamma * ext_mass / (cvm::dt() * cvm::real(time_step_factor))); + ext_sigma = cvm::sqrt(2.0 * cvm::boltzmann() * temp * ext_gamma * ext_mass / (cvm::dt() * cvm::real(time_step_factor))); } } @@ -761,6 +762,8 @@ int colvar::init_components(std::string const &conf) "weighted by inverse power", "distanceInv"); error_code |= init_components_type(conf, "N1xN2-long vector " "of pairwise distances", "distancePairs"); + error_code |= init_components_type(conf, "dipole magnitude", + "dipoleMagnitude"); error_code |= init_components_type(conf, "coordination " "number", "coordNum"); error_code |= init_components_type(conf, "self-coordination " @@ -831,22 +834,25 @@ void colvar::build_atom_list(void) for (size_t i = 0; i < cvcs.size(); i++) { for (size_t j = 0; j < cvcs[i]->atom_groups.size(); j++) { - cvm::atom_group &ag = *(cvcs[i]->atom_groups[j]); + cvm::atom_group const &ag = *(cvcs[i]->atom_groups[j]); for (size_t k = 0; k < ag.size(); k++) { temp_id_list.push_back(ag[k].id); } + if (ag.is_enabled(f_ag_fitting_group) && ag.is_enabled(f_ag_fit_gradients)) { + cvm::atom_group const &fg = *(ag.fitting_group); + for (size_t k = 0; k < fg.size(); k++) { + temp_id_list.push_back(fg[k].id); + } + } } } temp_id_list.sort(); temp_id_list.unique(); - // atom_ids = std::vector (temp_id_list.begin(), temp_id_list.end()); - unsigned int id_i = 0; std::list::iterator li; for (li = temp_id_list.begin(); li != temp_id_list.end(); ++li) { - atom_ids[id_i] = *li; - id_i++; + atom_ids.push_back(*li); } temp_id_list.clear(); @@ -934,16 +940,153 @@ int colvar::parse_analysis(std::string const &conf) } -void colvar::setup() { - // loop over all components to reset masses of all groups - for (size_t i = 0; i < cvcs.size(); i++) { - for (size_t ig = 0; ig < cvcs[i]->atom_groups.size(); ig++) { - cvm::atom_group &atoms = *(cvcs[i]->atom_groups[ig]); - atoms.setup(); - atoms.reset_mass(name,i,ig); - atoms.read_positions(); +int colvar::init_dependencies() { + size_t i; + if (features().size() == 0) { + for (i = 0; i < f_cv_ntot; i++) { + modify_features().push_back(new feature); + } + + init_feature(f_cv_active, "active", f_type_dynamic); + // Do not require f_cvc_active in children, as some components may be disabled + // Colvars must be either a linear combination, or scalar (and polynomial) or scripted/custom + require_feature_alt(f_cv_active, f_cv_scalar, f_cv_linear, f_cv_scripted, f_cv_custom_function); + + init_feature(f_cv_awake, "awake", f_type_static); + require_feature_self(f_cv_awake, f_cv_active); + + init_feature(f_cv_gradient, "gradient", f_type_dynamic); + require_feature_children(f_cv_gradient, f_cvc_gradient); + + init_feature(f_cv_collect_gradient, "collect gradient", f_type_dynamic); + require_feature_self(f_cv_collect_gradient, f_cv_gradient); + require_feature_self(f_cv_collect_gradient, f_cv_scalar); + // The following exlusion could be lifted by implementing the feature + exclude_feature_self(f_cv_collect_gradient, f_cv_scripted); + require_feature_children(f_cv_collect_gradient, f_cvc_explicit_gradient); + + init_feature(f_cv_fdiff_velocity, "velocity from finite differences", f_type_dynamic); + + // System force: either trivial (spring force); through extended Lagrangian, or calculated explicitly + init_feature(f_cv_total_force, "total force", f_type_dynamic); + require_feature_alt(f_cv_total_force, f_cv_extended_Lagrangian, f_cv_total_force_calc); + + // Deps for explicit total force calculation + init_feature(f_cv_total_force_calc, "total force calculation", f_type_dynamic); + require_feature_self(f_cv_total_force_calc, f_cv_scalar); + require_feature_self(f_cv_total_force_calc, f_cv_linear); + require_feature_children(f_cv_total_force_calc, f_cvc_inv_gradient); + require_feature_self(f_cv_total_force_calc, f_cv_Jacobian); + + init_feature(f_cv_Jacobian, "Jacobian derivative", f_type_dynamic); + require_feature_self(f_cv_Jacobian, f_cv_scalar); + require_feature_self(f_cv_Jacobian, f_cv_linear); + require_feature_children(f_cv_Jacobian, f_cvc_Jacobian); + + init_feature(f_cv_hide_Jacobian, "hide Jacobian force", f_type_user); + require_feature_self(f_cv_hide_Jacobian, f_cv_Jacobian); // can only hide if calculated + + init_feature(f_cv_extended_Lagrangian, "extended Lagrangian", f_type_user); + require_feature_self(f_cv_extended_Lagrangian, f_cv_scalar); + require_feature_self(f_cv_extended_Lagrangian, f_cv_gradient); + + init_feature(f_cv_Langevin, "Langevin dynamics", f_type_user); + require_feature_self(f_cv_Langevin, f_cv_extended_Lagrangian); + + init_feature(f_cv_linear, "linear", f_type_static); + + init_feature(f_cv_scalar, "scalar", f_type_static); + + init_feature(f_cv_output_energy, "output energy", f_type_user); + + init_feature(f_cv_output_value, "output value", f_type_user); + + init_feature(f_cv_output_velocity, "output velocity", f_type_user); + require_feature_self(f_cv_output_velocity, f_cv_fdiff_velocity); + + init_feature(f_cv_output_applied_force, "output applied force", f_type_user); + + init_feature(f_cv_output_total_force, "output total force", f_type_user); + require_feature_self(f_cv_output_total_force, f_cv_total_force); + + init_feature(f_cv_subtract_applied_force, "subtract applied force from total force", f_type_user); + require_feature_self(f_cv_subtract_applied_force, f_cv_total_force); + + init_feature(f_cv_lower_boundary, "lower boundary", f_type_user); + require_feature_self(f_cv_lower_boundary, f_cv_scalar); + + init_feature(f_cv_upper_boundary, "upper boundary", f_type_user); + require_feature_self(f_cv_upper_boundary, f_cv_scalar); + + init_feature(f_cv_grid, "grid", f_type_dynamic); + require_feature_self(f_cv_grid, f_cv_lower_boundary); + require_feature_self(f_cv_grid, f_cv_upper_boundary); + + init_feature(f_cv_runave, "running average", f_type_user); + + init_feature(f_cv_corrfunc, "correlation function", f_type_user); + + init_feature(f_cv_scripted, "scripted", f_type_user); + + init_feature(f_cv_custom_function, "custom function", f_type_user); + exclude_feature_self(f_cv_custom_function, f_cv_scripted); + + init_feature(f_cv_periodic, "periodic", f_type_static); + require_feature_self(f_cv_periodic, f_cv_scalar); + init_feature(f_cv_scalar, "scalar", f_type_static); + init_feature(f_cv_linear, "linear", f_type_static); + init_feature(f_cv_homogeneous, "homogeneous", f_type_static); + + // because total forces are obtained from the previous time step, + // we cannot (currently) have colvar values and total forces for the same timestep + init_feature(f_cv_multiple_ts, "multiple timestep colvar", f_type_static); + exclude_feature_self(f_cv_multiple_ts, f_cv_total_force_calc); + + // check that everything is initialized + for (i = 0; i < colvardeps::f_cv_ntot; i++) { + if (is_not_set(i)) { + cvm::error("Uninitialized feature " + cvm::to_str(i) + " in " + description); + } } } + + // Initialize feature_states for each instance + feature_states.reserve(f_cv_ntot); + for (i = 0; i < f_cv_ntot; i++) { + feature_states.push_back(feature_state(true, false)); + // Most features are available, so we set them so + // and list exceptions below + } + + feature_states[f_cv_fdiff_velocity].available = + cvm::main()->proxy->simulation_running(); + + return COLVARS_OK; +} + + +void colvar::setup() +{ + // loop over all components to update masses and charges of all groups + for (size_t i = 0; i < cvcs.size(); i++) { + for (size_t ig = 0; ig < cvcs[i]->atom_groups.size(); ig++) { + cvm::atom_group *atoms = cvcs[i]->atom_groups[ig]; + atoms->setup(); + atoms->print_properties(name, i, ig); + atoms->read_positions(); + } + } +} + + +std::vector > colvar::get_atom_lists() +{ + std::vector > lists; + for (size_t i = 0; i < cvcs.size(); i++) { + std::vector > li = cvcs[i]->get_atom_lists(); + lists.insert(lists.end(), li.begin(), li.end()); + } + return lists; } @@ -953,8 +1096,8 @@ colvar::~colvar() // because the children are cvcs and will be deleted // just below -// Clear references to this colvar's cvcs as children -// for dependency purposes + // Clear references to this colvar's cvcs as children + // for dependency purposes remove_all_children(); for (std::vector::reverse_iterator ci = cvcs.rbegin(); @@ -1231,7 +1374,6 @@ int colvar::calc_cvc_gradients(int first_cvc, size_t num_cvcs) int colvar::collect_cvc_gradients() { size_t i; - if (is_enabled(f_cv_collect_gradient)) { // Collect the atomic gradients inside colvar object for (unsigned int a = 0; a < atomic_gradients.size(); a++) { @@ -1239,34 +1381,7 @@ int colvar::collect_cvc_gradients() } for (i = 0; i < cvcs.size(); i++) { if (!cvcs[i]->is_enabled()) continue; - // Coefficient: d(a * x^n) = a * n * x^(n-1) * dx - cvm::real coeff = (cvcs[i])->sup_coeff * cvm::real((cvcs[i])->sup_np) * - cvm::integer_power((cvcs[i])->value().real_value, (cvcs[i])->sup_np-1); - - for (size_t j = 0; j < cvcs[i]->atom_groups.size(); j++) { - - cvm::atom_group &ag = *(cvcs[i]->atom_groups[j]); - - // If necessary, apply inverse rotation to get atomic - // gradient in the laboratory frame - if (ag.b_rotate) { - cvm::rotation const rot_inv = ag.rot.inverse(); - - for (size_t k = 0; k < ag.size(); k++) { - size_t a = std::lower_bound(atom_ids.begin(), atom_ids.end(), - ag[k].id) - atom_ids.begin(); - atomic_gradients[a] += coeff * rot_inv.rotate(ag[k].grad); - } - - } else { - - for (size_t k = 0; k < ag.size(); k++) { - size_t a = std::lower_bound(atom_ids.begin(), atom_ids.end(), - ag[k].id) - atom_ids.begin(); - atomic_gradients[a] += coeff * ag[k].grad; - } - } - } + cvcs[i]->collect_gradients(atom_ids, atomic_gradients); } } return COLVARS_OK; @@ -1391,20 +1506,20 @@ int colvar::calc_colvar_properties() // initialize the restraint center in the first step to the value // just calculated from the cvcs if (cvm::step_relative() == 0 && !after_restart) { - xr = x; - vr.reset(); // (already 0; added for clarity) + x_ext = x; + v_ext.reset(); // (already 0; added for clarity) } // Special case of a repeated timestep (eg. multiple NAMD "run" statements) // revert values of the extended coordinate and velocity prior to latest integration - if (cvm::step_relative() == prev_timestep) { - xr = prev_xr; - vr = prev_vr; + if (cvm::proxy->simulation_running() && cvm::step_relative() == prev_timestep) { + x_ext = prev_x_ext; + v_ext = prev_v_ext; } // report the restraint center as "value" - x_reported = xr; - v_reported = vr; + x_reported = x_ext; + v_reported = v_ext; // the "total force" with the extended Lagrangian is // calculated in update_forces_energy() below @@ -1458,77 +1573,86 @@ cvm::real colvar::update_forces_energy() // extended variable if there is one if (is_enabled(f_cv_extended_Lagrangian)) { - if (cvm::debug()) { - cvm::log("Updating extended-Lagrangian degree of freedom.\n"); - } - - if (prev_timestep > -1) { - // Keep track of slow timestep to integrate MTS colvars - // the colvar checks the interval after waking up twice - int n_timesteps = cvm::step_relative() - prev_timestep; - if (n_timesteps != 0 && n_timesteps != time_step_factor) { - cvm::error("Error: extended-Lagrangian " + description + " has timeStepFactor " + - cvm::to_str(time_step_factor) + ", but was activated after " + cvm::to_str(n_timesteps) + - " steps at timestep " + cvm::to_str(cvm::step_absolute()) + " (relative step: " + - cvm::to_str(cvm::step_relative()) + ").\n" + - "Make sure that this colvar is requested by biases at multiples of timeStepFactor.\n"); - return 0.; + if (cvm::proxy->simulation_running()) { + // Only integrate the extended equations of motion in running MD simulations + if (cvm::debug()) { + cvm::log("Updating extended-Lagrangian degree of freedom.\n"); } - } - // Integrate with slow timestep (if time_step_factor != 1) - cvm::real dt = cvm::dt() * cvm::real(time_step_factor); + if (prev_timestep > -1) { + // Keep track of slow timestep to integrate MTS colvars + // the colvar checks the interval after waking up twice + int n_timesteps = cvm::step_relative() - prev_timestep; + if (n_timesteps != 0 && n_timesteps != time_step_factor) { + cvm::error("Error: extended-Lagrangian " + description + " has timeStepFactor " + + cvm::to_str(time_step_factor) + ", but was activated after " + cvm::to_str(n_timesteps) + + " steps at timestep " + cvm::to_str(cvm::step_absolute()) + " (relative step: " + + cvm::to_str(cvm::step_relative()) + ").\n" + + "Make sure that this colvar is requested by biases at multiples of timeStepFactor.\n"); + return 0.; + } + } - colvarvalue f_ext(fr.type()); // force acting on the extended variable - f_ext.reset(); + // Integrate with slow timestep (if time_step_factor != 1) + cvm::real dt = cvm::dt() * cvm::real(time_step_factor); - // the total force is applied to the fictitious mass, while the - // atoms only feel the harmonic force + wall force - // fr: bias force on extended variable (without harmonic spring), for output in trajectory - // f_ext: total force on extended variable (including harmonic spring) - // f: - initially, external biasing force - // - after this code block, colvar force to be applied to atomic coordinates - // ie. spring force (fb_actual will be added just below) - fr = f; - // External force has been scaled for a 1-timestep impulse, scale it back because we will - // integrate it with the colvar's own timestep factor - f_ext = f / cvm::real(time_step_factor); - f_ext += (-0.5 * ext_force_k) * this->dist2_lgrad(xr, x); - f = (-0.5 * ext_force_k) * this->dist2_rgrad(xr, x); - // Coupling force is a slow force, to be applied to atomic coords impulse-style - f *= cvm::real(time_step_factor); + colvarvalue f_ext(fr.type()); // force acting on the extended variable + f_ext.reset(); - if (is_enabled(f_cv_subtract_applied_force)) { - // Report a "system" force without the biases on this colvar - // that is, just the spring force - ft_reported = (-0.5 * ext_force_k) * this->dist2_lgrad(xr, x); + // the total force is applied to the fictitious mass, while the + // atoms only feel the harmonic force + wall force + // fr: bias force on extended variable (without harmonic spring), for output in trajectory + // f_ext: total force on extended variable (including harmonic spring) + // f: - initially, external biasing force + // - after this code block, colvar force to be applied to atomic coordinates + // ie. spring force (fb_actual will be added just below) + fr = f; + // External force has been scaled for a 1-timestep impulse, scale it back because we will + // integrate it with the colvar's own timestep factor + f_ext = f / cvm::real(time_step_factor); + f_ext += (-0.5 * ext_force_k) * this->dist2_lgrad(x_ext, x); + f = (-0.5 * ext_force_k) * this->dist2_rgrad(x_ext, x); + // Coupling force is a slow force, to be applied to atomic coords impulse-style + f *= cvm::real(time_step_factor); + + if (is_enabled(f_cv_subtract_applied_force)) { + // Report a "system" force without the biases on this colvar + // that is, just the spring force + ft_reported = (-0.5 * ext_force_k) * this->dist2_lgrad(x_ext, x); + } else { + // The total force acting on the extended variable is f_ext + // This will be used in the next timestep + ft_reported = f_ext; + } + + // backup in case we need to revert this integration timestep + // if the same MD timestep is re-run + prev_x_ext = x_ext; + prev_v_ext = v_ext; + + // leapfrog: starting from x_i, f_i, v_(i-1/2) + v_ext += (0.5 * dt) * f_ext / ext_mass; + // Because of leapfrog, kinetic energy at time i is approximate + kinetic_energy = 0.5 * ext_mass * v_ext * v_ext; + potential_energy = 0.5 * ext_force_k * this->dist2(x_ext, x); + // leap to v_(i+1/2) + if (is_enabled(f_cv_Langevin)) { + v_ext -= dt * ext_gamma * v_ext; + colvarvalue rnd(x); + rnd.set_random(); + v_ext += dt * ext_sigma * rnd / ext_mass; + } + v_ext += (0.5 * dt) * f_ext / ext_mass; + x_ext += dt * v_ext; + x_ext.apply_constraints(); + this->wrap(x_ext); } else { - // The total force acting on the extended variable is f_ext - // This will be used in the next timestep - ft_reported = f_ext; + // If this is a postprocessing run (eg. in VMD), the extended DOF + // is equal to the actual coordinate + x_ext = x; } - - // backup in case we need to revert this integration timestep - // if the same MD timestep is re-run - prev_xr = xr; - prev_vr = vr; - - // leapfrog: starting from x_i, f_i, v_(i-1/2) - vr += (0.5 * dt) * f_ext / ext_mass; - // Because of leapfrog, kinetic energy at time i is approximate - kinetic_energy = 0.5 * ext_mass * vr * vr; - potential_energy = 0.5 * ext_force_k * this->dist2(xr, x); - // leap to v_(i+1/2) - if (is_enabled(f_cv_Langevin)) { - vr -= dt * ext_gamma * vr; - colvarvalue rnd(x); - rnd.set_random(); - vr += dt * ext_sigma * rnd / ext_mass; - } - vr += (0.5 * dt) * f_ext / ext_mass; - xr += dt * vr; - xr.apply_constraints(); - this->wrap(xr); + // Report extended value + x_reported = x_ext; } // Now adding the force on the actual colvar (for those biases that @@ -1730,7 +1854,7 @@ int colvar::update_cvc_config(std::vector const &confs) // ******************** METRIC FUNCTIONS ******************** -// Use the metrics defined by \link cvc \endlink objects +// Use the metrics defined by \link colvar::cvc \endlink objects bool colvar::periodic_boundaries(colvarvalue const &lb, colvarvalue const &ub) const @@ -1742,7 +1866,7 @@ bool colvar::periodic_boundaries(colvarvalue const &lb, colvarvalue const &ub) c } if (period > 0.0) { - if ( ((std::sqrt(this->dist2(lb, ub))) / this->width) + if ( ((cvm::sqrt(this->dist2(lb, ub))) / this->width) < 1.0E-10 ) { return true; } @@ -1792,21 +1916,21 @@ colvarvalue colvar::dist2_rgrad(colvarvalue const &x1, } } -void colvar::wrap(colvarvalue &x) const + +void colvar::wrap(colvarvalue &x_unwrapped) const { - if ( !is_enabled(f_cv_periodic) ) { + if (!is_enabled(f_cv_periodic)) { return; } if ( is_enabled(f_cv_scripted) || is_enabled(f_cv_custom_function) ) { // Scripted functions do their own wrapping, as cvcs might not be periodic - cvm::real shift = std::floor((x.real_value - wrap_center) / period + 0.5); - x.real_value -= shift * period; + cvm::real shift = cvm::floor((x_unwrapped.real_value - wrap_center) / + period + 0.5); + x_unwrapped.real_value -= shift * period; } else { - cvcs[0]->wrap(x); + cvcs[0]->wrap(x_unwrapped); } - - return; } @@ -1852,15 +1976,15 @@ std::istream & colvar::read_restart(std::istream &is) if (is_enabled(f_cv_extended_Lagrangian)) { - if ( !(get_keyval(conf, "extended_x", xr, + if ( !(get_keyval(conf, "extended_x", x_ext, colvarvalue(x.type()), colvarparse::parse_silent)) && - !(get_keyval(conf, "extended_v", vr, + !(get_keyval(conf, "extended_v", v_ext, colvarvalue(x.type()), colvarparse::parse_silent)) ) { cvm::log("Error: restart file does not contain " "\"extended_x\" or \"extended_v\" for the colvar \""+ name+"\", but you requested \"extendedLagrangian\".\n"); } - x_reported = xr; + x_reported = x_ext; } else { x_reported = x; } @@ -1875,7 +1999,7 @@ std::istream & colvar::read_restart(std::istream &is) } if (is_enabled(f_cv_extended_Lagrangian)) { - v_reported = vr; + v_reported = v_ext; } else { v_reported = v_fdiff; } @@ -1901,8 +2025,8 @@ std::istream & colvar::read_traj(std::istream &is) } if (is_enabled(f_cv_extended_Lagrangian)) { - is >> xr; - x_reported = xr; + is >> x_ext; + x_reported = x_ext; } else { x_reported = x; } @@ -1913,8 +2037,8 @@ std::istream & colvar::read_traj(std::istream &is) is >> v_fdiff; if (is_enabled(f_cv_extended_Lagrangian)) { - is >> vr; - v_reported = vr; + is >> v_ext; + v_reported = v_ext; } else { v_reported = v_fdiff; } @@ -1955,11 +2079,11 @@ std::ostream & colvar::write_restart(std::ostream &os) { os << " extended_x " << std::setprecision(cvm::cv_prec) << std::setw(cvm::cv_width) - << xr << "\n" + << x_ext << "\n" << " extended_v " << std::setprecision(cvm::cv_prec) << std::setw(cvm::cv_width) - << vr << "\n"; + << v_ext << "\n"; } os << "}\n\n"; @@ -2190,6 +2314,7 @@ int colvar::calc_acf() acf_x_history_p = acf_x_history.begin(); break; + case acf_notset: default: break; } @@ -2222,6 +2347,7 @@ int colvar::calc_acf() history_incr(acf_x_history, acf_x_history_p); break; + case acf_notset: default: break; } @@ -2257,7 +2383,7 @@ void colvar::calc_vel_acf(std::list &v_list, void colvar::calc_coor_acf(std::list &x_list, - colvarvalue const &x) + colvarvalue const &x_now) { // same as above but for coordinates if (x_list.size() >= acf_length+acf_offset) { @@ -2269,7 +2395,7 @@ void colvar::calc_coor_acf(std::list &x_list, *(acf_i++) += x.norm2(); - colvarvalue::inner_opt(x, xs_i, x_list.end(), acf_i); + colvarvalue::inner_opt(x_now, xs_i, x_list.end(), acf_i); acf_nframes++; } @@ -2277,7 +2403,7 @@ void colvar::calc_coor_acf(std::list &x_list, void colvar::calc_p2coor_acf(std::list &x_list, - colvarvalue const &x) + colvarvalue const &x_now) { // same as above but with second order Legendre polynomial instead // of just the scalar product @@ -2291,7 +2417,7 @@ void colvar::calc_p2coor_acf(std::list &x_list, // value of P2(0) = 1 *(acf_i++) += 1.0; - colvarvalue::p2leg_opt(x, xs_i, x_list.end(), acf_i); + colvarvalue::p2leg_opt(x_now, xs_i, x_list.end(), acf_i); acf_nframes++; } @@ -2316,6 +2442,9 @@ int colvar::write_acf(std::ostream &os) case acf_p2coor: os << "Coordinate (2nd Legendre poly)"; break; + case acf_notset: + default: + break; } if (acf_colvar_name == name) { @@ -2420,7 +2549,7 @@ int colvar::calc_runave() << std::setprecision(cvm::cv_prec) << std::setw(cvm::cv_width) << runave << " " << std::setprecision(cvm::cv_prec) << std::setw(cvm::cv_width) - << std::sqrt(runave_variance) << "\n"; + << cvm::sqrt(runave_variance) << "\n"; } history_add_value(runave_length, *x_history_p, x); diff --git a/lib/colvars/colvar.h b/lib/colvars/colvar.h index a67749d577..74f7fdee51 100644 --- a/lib/colvars/colvar.h +++ b/lib/colvars/colvar.h @@ -92,7 +92,7 @@ public: static std::vector cv_features; /// \brief Implementation of the feature list accessor for colvar - virtual const std::vector &features() + virtual const std::vector &features() const { return cv_features; } @@ -133,7 +133,7 @@ protected: Here: S(x(t)) = x - s(t) = xr + s(t) = x_ext DS = Ds = delta */ @@ -170,13 +170,13 @@ protected: // Options for extended_lagrangian /// Restraint center - colvarvalue xr; + colvarvalue x_ext; /// Previous value of the restraint center; - colvarvalue prev_xr; + colvarvalue prev_x_ext; /// Velocity of the restraint center - colvarvalue vr; + colvarvalue v_ext; /// Previous velocity of the restraint center - colvarvalue prev_vr; + colvarvalue prev_v_ext; /// Mass of the restraint center cvm::real ext_mass; /// Restraint force constant @@ -273,6 +273,9 @@ public: /// Init output flags int init_output_flags(std::string const &conf); + /// \brief Initialize dependency tree + virtual int init_dependencies(); + private: /// Parse the CVC configuration for all components of a certain type template int init_components_type(std::string const &conf, @@ -373,7 +376,7 @@ protected: void update_active_cvc_square_norm(); /// \brief Absolute timestep number when this colvar was last updated - int prev_timestep; + cvm::step_number prev_timestep; public: @@ -383,32 +386,32 @@ public: /// \brief Return the number of CVC objects with an active flag (as set by update_cvc_flags) inline size_t num_active_cvcs() const { return n_active_cvcs; } - /// \brief Use the internal metrics (as from \link cvc + /// \brief Use the internal metrics (as from \link colvar::cvc /// \endlink objects) to calculate square distances and gradients /// /// Handles correctly symmetries and periodic boundary conditions cvm::real dist2(colvarvalue const &x1, colvarvalue const &x2) const; - /// \brief Use the internal metrics (as from \link cvc + /// \brief Use the internal metrics (as from \link colvar::cvc /// \endlink objects) to calculate square distances and gradients /// /// Handles correctly symmetries and periodic boundary conditions colvarvalue dist2_lgrad(colvarvalue const &x1, colvarvalue const &x2) const; - /// \brief Use the internal metrics (as from \link cvc + /// \brief Use the internal metrics (as from \link colvar::cvc /// \endlink objects) to calculate square distances and gradients /// /// Handles correctly symmetries and periodic boundary conditions colvarvalue dist2_rgrad(colvarvalue const &x1, colvarvalue const &x2) const; - /// \brief Use the internal metrics (as from \link cvc + /// \brief Use the internal metrics (as from \link colvar::cvc /// \endlink objects) to wrap a value into a standard interval /// /// Handles correctly symmetries and periodic boundary conditions - void wrap(colvarvalue &x) const; + void wrap(colvarvalue &x_unwrapped) const; /// Read the analysis tasks @@ -546,6 +549,7 @@ public: class polar_phi; class distance_inv; class distance_pairs; + class dipole_magnitude; class angle; class dipole_angle; class dihedral; @@ -574,7 +578,7 @@ public: protected: - /// \brief Array of \link cvc \endlink objects + /// \brief Array of \link colvar::cvc \endlink objects std::vector cvcs; /// \brief Flags to enable or disable cvcs at next colvar evaluation @@ -619,6 +623,9 @@ public: inline size_t n_components() const { return cvcs.size(); } + + /// \brief Get vector of vectors of atom IDs for all atom groups + virtual std::vector > get_atom_lists(); }; inline cvm::real const & colvar::force_constant() const @@ -655,6 +662,8 @@ inline colvarvalue const & colvar::total_force() const inline void colvar::add_bias_force(colvarvalue const &force) { + check_enabled(f_cv_gradient, + std::string("applying a force to the variable \""+name+"\"")); if (cvm::debug()) { cvm::log("Adding biasing force "+cvm::to_str(force)+" to colvar \""+name+"\".\n"); } diff --git a/lib/colvars/colvar_UIestimator.h b/lib/colvars/colvar_UIestimator.h index 759b8d54a0..365f46148a 100644 --- a/lib/colvars/colvar_UIestimator.h +++ b/lib/colvars/colvar_UIestimator.h @@ -33,24 +33,24 @@ namespace UIestimator { public: n_matrix() {} - n_matrix(const std::vector & lowerboundary, // lowerboundary of x - const std::vector & upperboundary, // upperboundary of - const std::vector & width, // width of x - const int y_size) { // size of y, for example, ysize=7, then when x=1, the distribution of y in [-2,4] is considered + n_matrix(const std::vector & lowerboundary_input, // lowerboundary of x + const std::vector & upperboundary_input, // upperboundary of + const std::vector & width_input, // width of x + const int y_size_input) { // size of y, for example, ysize=7, then when x=1, the distribution of y in [-2,4] is considered int i; - this->lowerboundary = lowerboundary; - this->upperboundary = upperboundary; - this->width = width; - this->dimension = lowerboundary.size(); - this->y_size = y_size; // keep in mind the internal (spare) matrix is stored in diagonal form - this->y_total_size = int(std::pow(double(y_size), double(dimension)) + EPSILON); + this->lowerboundary = lowerboundary_input; + this->upperboundary = upperboundary_input; + this->width = width_input; + this->dimension = lowerboundary_input.size(); + this->y_size = y_size_input; // keep in mind the internal (spare) matrix is stored in diagonal form + this->y_total_size = int(cvm::pow(double(y_size_input), double(dimension)) + EPSILON); // the range of the matrix is [lowerboundary, upperboundary] x_total_size = 1; for (i = 0; i < dimension; i++) { - x_size.push_back(int((upperboundary[i] - lowerboundary[i]) / width[i] + EPSILON)); + x_size.push_back(int((upperboundary_input[i] - lowerboundary_input[i]) / width_input[i] + EPSILON)); x_total_size *= x_size[i]; } @@ -89,9 +89,10 @@ namespace UIestimator { std::vector temp; // this vector is used in convert_x and convert_y to save computational resource - int i, j; - int convert_x(const std::vector & x) { // convert real x value to its interal index + + int i, j; + for (i = 0; i < dimension; i++) { temp[i] = int((x[i] - lowerboundary[i]) / width[i] + EPSILON); } @@ -121,7 +122,7 @@ namespace UIestimator { int index = 0; for (i = 0; i < dimension; i++) { if (i + 1 < dimension) - index += temp[i] * int(std::pow(double(y_size), double(dimension - i - 1)) + EPSILON); + index += temp[i] * int(cvm::pow(double(y_size), double(dimension - i - 1)) + EPSILON); else index += temp[i]; } @@ -139,19 +140,19 @@ namespace UIestimator { public: n_vector() {} - n_vector(const std::vector & lowerboundary, // lowerboundary of x - const std::vector & upperboundary, // upperboundary of - const std::vector & width, // width of x - const int y_size, // size of y, for example, ysize=7, then when x=1, the distribution of y in [-2,4] is considered + n_vector(const std::vector & lowerboundary_input, // lowerboundary of x + const std::vector & upperboundary_input, // upperboundary of + const std::vector & width_input, // width of x + const int y_size_input, // size of y, for example, ysize=7, then when x=1, the distribution of y in [-2,4] is considered const T & default_value) { // the default value of T - this->width = width; - this->dimension = lowerboundary.size(); + this->width = width_input; + this->dimension = lowerboundary_input.size(); x_total_size = 1; for (int i = 0; i < dimension; i++) { - this->lowerboundary.push_back(lowerboundary[i] - (y_size - 1) / 2 * width[i] - EPSILON); - this->upperboundary.push_back(upperboundary[i] + (y_size - 1) / 2 * width[i] + EPSILON); + this->lowerboundary.push_back(lowerboundary_input[i] - (y_size_input - 1) / 2 * width_input[i] - EPSILON); + this->upperboundary.push_back(upperboundary_input[i] + (y_size_input - 1) / 2 * width_input[i] + EPSILON); x_size.push_back(int((this->upperboundary[i] - this->lowerboundary[i]) / this->width[i] + EPSILON)); x_total_size *= x_size[i]; @@ -215,26 +216,26 @@ namespace UIestimator { UIestimator() {} //called when (re)start an eabf simulation - UIestimator(const std::vector & lowerboundary, - const std::vector & upperboundary, - const std::vector & width, - const std::vector & krestr, // force constant in eABF - const std::string & output_filename, // the prefix of output files - const int output_freq, - const bool restart, // whether restart from a .count and a .grad file - const std::vector & input_filename, // the prefixes of input files - const double temperature) { + UIestimator(const std::vector & lowerboundary_input, + const std::vector & upperboundary_input, + const std::vector & width_input, + const std::vector & krestr_input, // force constant in eABF + const std::string & output_filename_input, // the prefix of output files + const int output_freq_input, + const bool restart_input, // whether restart from a .count and a .grad file + const std::vector & input_filename_input, // the prefixes of input files + const double temperature_input) { // initialize variables - this->lowerboundary = lowerboundary; - this->upperboundary = upperboundary; - this->width = width; - this->krestr = krestr; - this->output_filename = output_filename; - this->output_freq = output_freq; - this->restart = restart; - this->input_filename = input_filename; - this->temperature = temperature; + this->lowerboundary = lowerboundary_input; + this->upperboundary = upperboundary_input; + this->width = width_input; + this->krestr = krestr_input; + this->output_filename = output_filename_input; + this->output_freq = output_freq_input; + this->restart = restart_input; + this->input_filename = input_filename_input; + this->temperature = temperature_input; int i, j; @@ -300,7 +301,7 @@ namespace UIestimator { ~UIestimator() {} // called from MD engine every step - bool update(const int step, std::vector x, std::vector y) { + bool update(cvm::step_number step, std::vector x, std::vector y) { int i; @@ -431,7 +432,7 @@ namespace UIestimator { loop_flag_y[k] = loop_flag_x[k] - HALF_Y_SIZE * width[k]; } - int j = 0; + j = 0; while (j >= 0) { norm += distribution_x_y.get_value(loop_flag_x, loop_flag_y); for (k = 0; k < dimension; k++) { @@ -672,7 +673,7 @@ namespace UIestimator { } // read input files - void read_inputfiles(const std::vector input_filename) + void read_inputfiles(const std::vector filename) { char sharp; double nothing; @@ -683,11 +684,11 @@ namespace UIestimator { std::vector position_temp(dimension, 0); std::vector grad_temp(dimension, 0); int count_temp = 0; - for (i = 0; i < int(input_filename.size()); i++) { + for (i = 0; i < int(filename.size()); i++) { int size = 1 , size_temp = 0; - std::string count_filename = input_filename[i] + ".UI.count"; - std::string grad_filename = input_filename[i] + ".UI.grad"; + std::string count_filename = filename[i] + ".UI.count"; + std::string grad_filename = filename[i] + ".UI.grad"; std::ifstream count_file(count_filename.c_str(), std::ios::in); std::ifstream grad_file(grad_filename.c_str(), std::ios::in); diff --git a/lib/colvars/colvaratoms.cpp b/lib/colvars/colvaratoms.cpp index 3315007b54..eeb7985fec 100644 --- a/lib/colvars/colvaratoms.cpp +++ b/lib/colvars/colvaratoms.cpp @@ -22,7 +22,7 @@ cvm::atom::atom() index = -1; id = -1; mass = 1.0; - charge = 1.0; + charge = 0.0; reset_data(); } @@ -107,6 +107,8 @@ cvm::atom_group::~atom_group() delete fitting_group; fitting_group = NULL; } + + cvm::main()->unregister_named_atom_group(this); } @@ -183,10 +185,7 @@ int cvm::atom_group::init() // These may be overwritten by parse(), if a name is provided atoms.clear(); - - // TODO: check with proxy whether atom forces etc are available - init_ag_requires(); - + init_dependencies(); index = -1; b_dummy = false; @@ -207,8 +206,67 @@ int cvm::atom_group::init() } +int cvm::atom_group::init_dependencies() { + size_t i; + // Initialize static array once and for all + if (features().size() == 0) { + for (i = 0; i < f_ag_ntot; i++) { + modify_features().push_back(new feature); + } + + init_feature(f_ag_active, "active", f_type_dynamic); + init_feature(f_ag_center, "translational fit", f_type_static); + init_feature(f_ag_rotate, "rotational fit", f_type_static); + init_feature(f_ag_fitting_group, "fitting group", f_type_static); + init_feature(f_ag_explicit_gradient, "explicit atom gradient", f_type_dynamic); + init_feature(f_ag_fit_gradients, "fit gradients", f_type_user); + require_feature_self(f_ag_fit_gradients, f_ag_explicit_gradient); + + init_feature(f_ag_atom_forces, "atomic forces", f_type_dynamic); + + // parallel calculation implies that we have at least a scalable center of mass, + // but f_ag_scalable is kept as a separate feature to deal with future dependencies + init_feature(f_ag_scalable, "scalable group calculation", f_type_static); + init_feature(f_ag_scalable_com, "scalable group center of mass calculation", f_type_static); + require_feature_self(f_ag_scalable, f_ag_scalable_com); + + // check that everything is initialized + for (i = 0; i < colvardeps::f_ag_ntot; i++) { + if (is_not_set(i)) { + cvm::error("Uninitialized feature " + cvm::to_str(i) + " in " + description); + } + } + } + + // Initialize feature_states for each instance + // default as unavailable, not enabled + feature_states.reserve(f_ag_ntot); + for (i = 0; i < colvardeps::f_ag_ntot; i++) { + feature_states.push_back(feature_state(false, false)); + } + + // Features that are implemented (or not) by all atom groups + feature_states[f_ag_active].available = true; + // f_ag_scalable_com is provided by the CVC iff it is COM-based + feature_states[f_ag_scalable_com].available = false; + // TODO make f_ag_scalable depend on f_ag_scalable_com (or something else) + feature_states[f_ag_scalable].available = true; + feature_states[f_ag_fit_gradients].available = true; + feature_states[f_ag_fitting_group].available = true; + feature_states[f_ag_explicit_gradient].available = true; + + return COLVARS_OK; +} + + int cvm::atom_group::setup() { + if (atoms_ids.size() == 0) { + atoms_ids.reserve(atoms.size()); + for (cvm::atom_iter ai = atoms.begin(); ai != atoms.end(); ai++) { + atoms_ids.push_back(ai->id); + } + } for (cvm::atom_iter ai = atoms.begin(); ai != atoms.end(); ai++) { ai->update_mass(); ai->update_charge(); @@ -237,15 +295,6 @@ void cvm::atom_group::update_total_mass() } -void cvm::atom_group::reset_mass(std::string &name, int i, int j) -{ - update_total_mass(); - cvm::log("Re-initialized atom group "+name+":"+cvm::to_str(i)+"/"+ - cvm::to_str(j)+". "+ cvm::to_str(atoms_ids.size())+ - " atoms: total mass = "+cvm::to_str(total_mass)+".\n"); -} - - void cvm::atom_group::update_total_charge() { if (b_dummy) { @@ -264,6 +313,19 @@ void cvm::atom_group::update_total_charge() } +void cvm::atom_group::print_properties(std::string const &colvar_name, + int i, int j) +{ + if (cvm::proxy->updated_masses() && cvm::proxy->updated_charges()) { + cvm::log("Re-initialized atom group for variable \""+colvar_name+"\":"+ + cvm::to_str(i)+"/"+ + cvm::to_str(j)+". "+ cvm::to_str(atoms_ids.size())+ + " atoms: total mass = "+cvm::to_str(total_mass)+ + ", total charge = "+cvm::to_str(total_charge)+".\n"); + } +} + + int cvm::atom_group::parse(std::string const &group_conf) { cvm::log("Initializing atom group \""+key+"\".\n"); @@ -450,10 +512,21 @@ int cvm::atom_group::parse(std::string const &group_conf) if (cvm::debug()) cvm::log("Done initializing atom group \""+key+"\".\n"); - cvm::log("Atom group \""+key+"\" defined, "+ - cvm::to_str(atoms_ids.size())+" atoms initialized: total mass = "+ - cvm::to_str(total_mass)+", total charge = "+ - cvm::to_str(total_charge)+".\n"); + { + std::string init_msg; + init_msg.append("Atom group \""+key+"\" defined with "+ + cvm::to_str(atoms_ids.size())+" atoms requested"); + if ((cvm::proxy)->updated_masses()) { + init_msg.append(": total mass = "+ + cvm::to_str(total_mass)); + if ((cvm::proxy)->updated_charges()) { + init_msg.append(", total charge = "+ + cvm::to_str(total_charge)); + } + } + init_msg.append(".\n"); + cvm::log(init_msg); + } if (b_print_atom_ids) { cvm::log("Internal definition of the atom group:\n"); @@ -464,7 +537,7 @@ int cvm::atom_group::parse(std::string const &group_conf) } -int cvm::atom_group::add_atoms_of_group(atom_group const * ag) +int cvm::atom_group::add_atoms_of_group(atom_group const *ag) { std::vector const &source_ids = ag->atoms_ids; @@ -696,6 +769,7 @@ int cvm::atom_group::parse_fitting_options(std::string const &group_conf) return INPUT_ERROR; } } + enable(f_ag_fitting_group); } atom_group *group_for_fit = fitting_group ? fitting_group : this; @@ -800,24 +874,24 @@ int cvm::atom_group::create_sorted_ids() // Sort the internal IDs std::list sorted_atoms_ids_list; - for (size_t i = 0; i < this->size(); i++) { + for (size_t i = 0; i < atoms_ids.size(); i++) { sorted_atoms_ids_list.push_back(atoms_ids[i]); } sorted_atoms_ids_list.sort(); sorted_atoms_ids_list.unique(); - if (sorted_atoms_ids_list.size() != this->size()) { + if (sorted_atoms_ids_list.size() != atoms_ids.size()) { return cvm::error("Error: duplicate atom IDs in atom group? (found " + cvm::to_str(sorted_atoms_ids_list.size()) + " unique atom IDs instead of " + - cvm::to_str(this->size()) + ").\n", BUG_ERROR); + cvm::to_str(atoms_ids.size()) + ").\n", BUG_ERROR); } // Compute map between sorted and unsorted elements - sorted_atoms_ids.resize(this->size()); - sorted_atoms_ids_map.resize(this->size()); + sorted_atoms_ids.resize(atoms_ids.size()); + sorted_atoms_ids_map.resize(atoms_ids.size()); std::list::iterator lsii = sorted_atoms_ids_list.begin(); size_t ii = 0; - for ( ; ii < this->size(); lsii++, ii++) { + for ( ; ii < atoms_ids.size(); lsii++, ii++) { sorted_atoms_ids[ii] = *lsii; size_t const pos = std::find(atoms_ids.begin(), atoms_ids.end(), *lsii) - atoms_ids.begin(); @@ -1038,15 +1112,15 @@ int cvm::atom_group::calc_center_of_mass() } -int cvm::atom_group::calc_dipole(cvm::atom_pos const &com) +int cvm::atom_group::calc_dipole(cvm::atom_pos const &dipole_center) { if (b_dummy) { - cvm::error("Error: trying to compute the dipole of an empty group.\n", INPUT_ERROR); - return COLVARS_ERROR; + return cvm::error("Error: trying to compute the dipole " + "of a dummy group.\n", INPUT_ERROR); } dip.reset(); for (cvm::atom_const_iter ai = this->begin(); ai != this->end(); ai++) { - dip += ai->charge * (ai->pos - com); + dip += ai->charge * (ai->pos - dipole_center); } return COLVARS_OK; } @@ -1056,13 +1130,12 @@ void cvm::atom_group::set_weighted_gradient(cvm::rvector const &grad) { if (b_dummy) return; - if (is_enabled(f_ag_scalable)) { - scalar_com_gradient = grad; - return; - } + scalar_com_gradient = grad; - for (cvm::atom_iter ai = this->begin(); ai != this->end(); ai++) { - ai->grad = (ai->mass/total_mass) * grad; + if (!is_enabled(f_ag_scalable)) { + for (cvm::atom_iter ai = this->begin(); ai != this->end(); ai++) { + ai->grad = (ai->mass/total_mass) * grad; + } } } diff --git a/lib/colvars/colvaratoms.h b/lib/colvars/colvaratoms.h index 0b0dd62c70..9756e0e364 100644 --- a/lib/colvars/colvaratoms.h +++ b/lib/colvars/colvaratoms.h @@ -17,7 +17,7 @@ /// \brief Stores numeric id, mass and all mutable data for an atom, -/// mostly used by a \link cvc \endlink +/// mostly used by a \link colvar::cvc \endlink /// /// This class may be used to keep atomic data such as id, mass, /// position and collective variable derivatives) altogether. @@ -63,7 +63,7 @@ public: /// from the \link colvarvalue \endlink class), which is also the /// most frequent case. For more complex types of \link /// colvarvalue \endlink objects, atomic gradients should be - /// defined within the specific \link cvc \endlink + /// defined within the specific \link colvar::cvc \endlink /// implementation cvm::rvector grad; @@ -100,13 +100,19 @@ public: /// Get the latest value of the mass inline void update_mass() { - mass = (cvm::proxy)->get_atom_mass(index); + colvarproxy *p = cvm::proxy; + if (p->updated_masses()) { + mass = p->get_atom_mass(index); + } } /// Get the latest value of the charge inline void update_charge() { - charge = (cvm::proxy)->get_atom_charge(index); + colvarproxy *p = cvm::proxy; + if (p->updated_charges()) { + charge = p->get_atom_charge(index); + } } /// Get the current position @@ -145,7 +151,7 @@ public: /// \brief Group of \link atom \endlink objects, mostly used by a -/// \link cvc \endlink object to gather all atomic data +/// \link colvar::cvc \endlink object to gather all atomic data class colvarmodule::atom_group : public colvarparse, public colvardeps { @@ -174,6 +180,9 @@ public: /// \brief Set default values for common flags int init(); + /// \brief Initialize dependency tree + virtual int init_dependencies(); + /// \brief Update data required to calculate cvc's int setup(); @@ -198,16 +207,16 @@ public: /// \brief Remove an atom object from this group int remove_atom(cvm::atom_iter ai); - /// \brief Re-initialize the total mass of a group. + /// \brief Print the updated the total mass and charge of a group. /// This is needed in case the hosting MD code has an option to /// change atom masses after their initialization. - void reset_mass(std::string &name, int i, int j); + void print_properties(std::string const &colvar_name, int i, int j); /// \brief Implementation of the feature list for atom group static std::vector ag_features; /// \brief Implementation of the feature list accessor for atom group - virtual const std::vector &features() + virtual const std::vector &features() const { return ag_features; } @@ -347,15 +356,19 @@ public: /// Total mass of the atom group cvm::real total_mass; + + /// Update the total mass of the atom group void update_total_mass(); /// Total charge of the atom group cvm::real total_charge; + + /// Update the total mass of the group void update_total_charge(); /// \brief Don't apply any force on this group (use its coordinates /// only to calculate a colvar) - bool noforce; + bool noforce; /// \brief Get the current positions void read_positions(); @@ -423,20 +436,32 @@ public: /// \brief Calculate the center of mass of the atomic positions, assuming that /// they are already pbc-wrapped int calc_center_of_mass(); + private: + /// \brief Center of mass cvm::atom_pos com; + /// \brief The derivative of a scalar variable with respect to the COM // TODO for scalable calculations of more complex variables (e.g. rotation), // use a colvarvalue of vectors to hold the entire derivative cvm::rvector scalar_com_gradient; + public: - /// \brief Return the center of mass of the atomic positions + + /// \brief Return the center of mass (COM) of the atomic positions inline cvm::atom_pos center_of_mass() const { return com; } + /// \brief Return previously gradient of scalar variable with respect to the + /// COM + inline cvm::rvector center_of_mass_scalar_gradient() const + { + return scalar_com_gradient; + } + /// \brief Return a copy of the current atom positions, shifted by a constant vector std::vector positions_shifted(cvm::rvector const &shift) const; @@ -444,10 +469,15 @@ public: std::vector velocities() const; ///\brief Calculate the dipole of the atom group around the specified center - int calc_dipole(cvm::atom_pos const &com); + int calc_dipole(cvm::atom_pos const &dipole_center); + private: + + /// Dipole moment of the atom group cvm::rvector dip; + public: + ///\brief Return the (previously calculated) dipole of the atom group inline cvm::rvector dipole() const { diff --git a/lib/colvars/colvarbias.cpp b/lib/colvars/colvarbias.cpp index 9363fcdcb6..724326d3b4 100644 --- a/lib/colvars/colvarbias.cpp +++ b/lib/colvars/colvarbias.cpp @@ -17,15 +17,14 @@ colvarbias::colvarbias(char const *key) : bias_type(to_lower_cppstr(key)) { - init_cvb_requires(); - + description = "uninitialized " + cvm::to_str(key) + " bias"; + init_dependencies(); rank = 1; has_data = false; b_output_energy = false; reset(); - state_file_step = 0; - description = "uninitialized " + cvm::to_str(key) + " bias"; + state_file_step = 0L; } @@ -76,6 +75,7 @@ int colvarbias::init(std::string const &conf) cvm::error("Error: no collective variables specified.\n", INPUT_ERROR); return INPUT_ERROR; } + } else { cvm::log("Reinitializing bias \""+name+"\".\n"); } @@ -98,6 +98,70 @@ int colvarbias::init(std::string const &conf) } +int colvarbias::init_dependencies() { + int i; + if (features().size() == 0) { + for (i = 0; i < f_cvb_ntot; i++) { + modify_features().push_back(new feature); + } + + init_feature(f_cvb_active, "active", f_type_dynamic); + require_feature_children(f_cvb_active, f_cv_active); + + init_feature(f_cvb_awake, "awake", f_type_static); + require_feature_self(f_cvb_awake, f_cvb_active); + + init_feature(f_cvb_apply_force, "apply force", f_type_user); + require_feature_children(f_cvb_apply_force, f_cv_gradient); + + init_feature(f_cvb_get_total_force, "obtain total force", f_type_dynamic); + require_feature_children(f_cvb_get_total_force, f_cv_total_force); + + init_feature(f_cvb_output_acc_work, "output accumulated work", f_type_user); + require_feature_self(f_cvb_output_acc_work, f_cvb_apply_force); + + init_feature(f_cvb_history_dependent, "history-dependent", f_type_static); + + init_feature(f_cvb_time_dependent, "time-dependent", f_type_static); + + init_feature(f_cvb_scalar_variables, "require scalar variables", f_type_static); + require_feature_children(f_cvb_scalar_variables, f_cv_scalar); + + init_feature(f_cvb_calc_pmf, "calculate a PMF", f_type_static); + + init_feature(f_cvb_calc_ti_samples, "calculate TI samples", f_type_dynamic); + require_feature_self(f_cvb_calc_ti_samples, f_cvb_get_total_force); + require_feature_children(f_cvb_calc_ti_samples, f_cv_grid); + + init_feature(f_cvb_write_ti_samples, "write TI samples ", f_type_user); + require_feature_self(f_cvb_write_ti_samples, f_cvb_calc_ti_samples); + + init_feature(f_cvb_write_ti_pmf, "write TI PMF", f_type_user); + require_feature_self(f_cvb_write_ti_pmf, f_cvb_calc_ti_samples); + + // check that everything is initialized + for (i = 0; i < colvardeps::f_cvb_ntot; i++) { + if (is_not_set(i)) { + cvm::error("Uninitialized feature " + cvm::to_str(i) + " in " + description); + } + } + } + + // Initialize feature_states for each instance + feature_states.reserve(f_cvb_ntot); + for (i = 0; i < f_cvb_ntot; i++) { + feature_states.push_back(feature_state(true, false)); + // Most features are available, so we set them so + // and list exceptions below + } + + // only compute TI samples when deriving from colvarbias_ti + feature_states[f_cvb_calc_ti_samples].available = false; + + return COLVARS_OK; +} + + int colvarbias::reset() { bias_energy = 0.0; @@ -217,6 +281,9 @@ int colvarbias::update() void colvarbias::communicate_forces() { + if (! is_enabled(f_cvb_apply_force)) { + return; + } size_t i = 0; for (i = 0; i < num_variables(); i++) { if (cvm::debug()) { @@ -345,7 +412,8 @@ std::istream & colvarbias::read_state(std::istream &is) (set_state_params(conf) != COLVARS_OK) ) { cvm::error("Error: in reading state configuration for \""+bias_type+"\" bias \""+ this->name+"\" at position "+ - cvm::to_str(is.tellg())+" in stream.\n", INPUT_ERROR); + cvm::to_str(static_cast(is.tellg()))+ + " in stream.\n", INPUT_ERROR); is.clear(); is.seekg(start_pos, std::ios::beg); is.setstate(std::ios::failbit); @@ -355,7 +423,8 @@ std::istream & colvarbias::read_state(std::istream &is) if (!read_state_data(is)) { cvm::error("Error: in reading state data for \""+bias_type+"\" bias \""+ this->name+"\" at position "+ - cvm::to_str(is.tellg())+" in stream.\n", INPUT_ERROR); + cvm::to_str(static_cast(is.tellg()))+ + " in stream.\n", INPUT_ERROR); is.clear(); is.seekg(start_pos, std::ios::beg); is.setstate(std::ios::failbit); @@ -365,7 +434,8 @@ std::istream & colvarbias::read_state(std::istream &is) if (brace != "}") { cvm::error("Error: corrupt restart information for \""+bias_type+"\" bias \""+ this->name+"\": no matching brace at position "+ - cvm::to_str(is.tellg())+" in stream.\n"); + cvm::to_str(static_cast(is.tellg()))+ + " in stream.\n"); is.setstate(std::ios::failbit); } @@ -381,7 +451,8 @@ std::istream & colvarbias::read_state_data_key(std::istream &is, char const *key !(key_in == to_lower_cppstr(std::string(key))) ) { cvm::error("Error: in reading restart configuration for "+ bias_type+" bias \""+this->name+"\" at position "+ - cvm::to_str(is.tellg())+" in stream.\n", INPUT_ERROR); + cvm::to_str(static_cast(is.tellg()))+ + " in stream.\n", INPUT_ERROR); is.clear(); is.seekg(start_pos, std::ios::beg); is.setstate(std::ios::failbit); @@ -640,7 +711,7 @@ int colvarbias_ti::write_output_files() cvm::proxy->close_output_stream(ti_count_file_name); } - std::string const ti_grad_file_name(ti_output_prefix+".ti.grad"); + std::string const ti_grad_file_name(ti_output_prefix+".ti.force"); os = cvm::proxy->output_stream(ti_grad_file_name); if (os) { ti_avg_forces->write_multicol(*os); diff --git a/lib/colvars/colvarbias.h b/lib/colvars/colvarbias.h index 391826e79e..eac88a7f18 100644 --- a/lib/colvars/colvarbias.h +++ b/lib/colvars/colvarbias.h @@ -96,6 +96,9 @@ public: /// \brief Parse config string and (re)initialize virtual int init(std::string const &conf); + /// \brief Initialize dependency tree + virtual int init_dependencies(); + /// \brief Set to zero all mutable data virtual int reset(); @@ -181,7 +184,7 @@ public: static std::vector cvb_features; /// \brief Implementation of the feature list accessor for colvarbias - virtual const std::vector &features() + virtual const std::vector &features() const { return cvb_features; } @@ -220,7 +223,7 @@ protected: bool has_data; /// \brief Step number read from the last state file - size_t state_file_step; + cvm::step_number state_file_step; }; diff --git a/lib/colvars/colvarbias_abf.cpp b/lib/colvars/colvarbias_abf.cpp index e5edd92ae6..bac021be99 100644 --- a/lib/colvars/colvarbias_abf.cpp +++ b/lib/colvars/colvarbias_abf.cpp @@ -191,10 +191,10 @@ int colvarbias_abf::init(std::string const &conf) // Projected ABF get_keyval(conf, "pABFintegrateFreq", pabf_freq, 0); // Parameters for integrating initial (and final) gradient data - get_keyval(conf, "integrateInitSteps", integrate_initial_steps, 1e4); + get_keyval(conf, "integrateInitMaxIterations", integrate_initial_iterations, 1e4); get_keyval(conf, "integrateInitTol", integrate_initial_tol, 1e-6); // for updating the integrated PMF on the fly - get_keyval(conf, "integrateSteps", integrate_steps, 100); + get_keyval(conf, "integrateMaxIterations", integrate_iterations, 100); get_keyval(conf, "integrateTol", integrate_tol, 1e-4); } } else { @@ -366,10 +366,10 @@ int colvarbias_abf::update() if ( b_integrate ) { if ( pabf_freq && cvm::step_relative() % pabf_freq == 0 ) { cvm::real err; - int iter = pmf->integrate(integrate_steps, integrate_tol, err); - if ( iter == integrate_steps ) { + int iter = pmf->integrate(integrate_iterations, integrate_tol, err); + if ( iter == integrate_iterations ) { cvm::log("Warning: PMF integration did not converge to " + cvm::to_str(integrate_tol) - + " in " + cvm::to_str(integrate_steps) + + " in " + cvm::to_str(integrate_iterations) + " steps. Residual error: " + cvm::to_str(err)); } pmf->set_zero_minimum(); // TODO: do this only when necessary @@ -597,7 +597,7 @@ void colvarbias_abf::write_gradients_samples(const std::string &prefix, bool app if (b_integrate) { // Do numerical integration (to high precision) and output a PMF cvm::real err; - pmf->integrate(integrate_initial_steps, integrate_initial_tol, err); + pmf->integrate(integrate_initial_iterations, integrate_initial_tol, err); pmf->set_zero_minimum(); std::string pmf_out_name = prefix + ".pmf"; @@ -661,7 +661,7 @@ void colvarbias_abf::write_gradients_samples(const std::string &prefix, bool app // Do numerical integration (to high precision) and output a PMF cvm::real err; czar_pmf->set_div(); - czar_pmf->integrate(integrate_initial_steps, integrate_initial_tol, err); + czar_pmf->integrate(integrate_initial_iterations, integrate_initial_tol, err); czar_pmf->set_zero_minimum(); std::string czar_pmf_out_name = prefix + ".czar.pmf"; diff --git a/lib/colvars/colvarbias_abf.h b/lib/colvars/colvarbias_abf.h index 52bf2df210..4bcc149da5 100644 --- a/lib/colvars/colvarbias_abf.h +++ b/lib/colvars/colvarbias_abf.h @@ -27,9 +27,13 @@ class colvarbias_abf : public colvarbias { public: + /// Constructor for ABF bias colvarbias_abf(char const *key); + /// Initializer for ABF bias virtual int init(std::string const &conf); + /// Default destructor for ABF bias virtual ~colvarbias_abf(); + /// Per-timestep update of ABF bias virtual int update(); private: @@ -40,11 +44,17 @@ private: /// Base filename(s) for reading previous gradient data (replaces data from restart file) std::vector input_prefix; + /// Adapt the bias at each time step (as opposed to keeping it constant)? bool update_bias; + /// Use normalized definition of PMF for distance functions? (flat at long distances) + /// by including the Jacobian term separately of the recorded PMF bool hide_Jacobian; + /// Integrate gradients into a PMF on output bool b_integrate; + /// Number of samples per bin before applying the full biasing force size_t full_samples; + /// Number of samples per bin before applying a scaled-down biasing force size_t min_samples; /// frequency for updating output files int output_freq; @@ -52,6 +62,7 @@ private: bool b_history_files; /// Write CZAR output file for stratified eABF (.zgrad) bool b_czar_window_file; + /// Number of timesteps between recording data in history files (if non-zero) size_t history_freq; /// Umbrella Integration estimator of free energy from eABF UIestimator::UIestimator eabf_UI; @@ -63,25 +74,30 @@ private: /// Frequency for updating pABF PMF (if zero, pABF is not used) int pabf_freq; /// Max number of CG iterations for integrating PMF at startup and for file output - int integrate_initial_steps; + int integrate_initial_iterations; /// Tolerance for integrating PMF at startup and for file output cvm::real integrate_initial_tol; /// Max number of CG iterations for integrating PMF at on-the-fly pABF updates - int integrate_steps; + int integrate_iterations; /// Tolerance for integrating PMF at on-the-fly pABF updates cvm::real integrate_tol; - /// Cap the biasing force to be applied? + /// Cap the biasing force to be applied? (option maxForce) bool cap_force; + /// Maximum force to be applied std::vector max_force; - // Frequency for updating 2D gradients - int integrate_freq; - // Internal data and methods - std::vector bin, force_bin, z_bin; - gradient_t system_force, applied_force; + /// Current bin in sample grid + std::vector bin; + /// Current bin in force grid + std::vector force_bin; + /// Cuurent bin in "actual" coordinate, when running extended Lagrangian dynamics + std::vector z_bin; + + /// Measured instantaneous system force + gradient_t system_force; /// n-dim grid of free energy gradients colvar_grid_gradient *gradients; @@ -118,7 +134,7 @@ private: // shared ABF bool shared_on; size_t shared_freq; - int shared_last_step; + cvm::step_number shared_last_step; // Share between replicas -- may be called independently of update virtual int replica_share(); diff --git a/lib/colvars/colvarbias_histogram.h b/lib/colvars/colvarbias_histogram.h index b9c1b49950..23565caa5c 100644 --- a/lib/colvars/colvarbias_histogram.h +++ b/lib/colvars/colvarbias_histogram.h @@ -37,7 +37,7 @@ protected: std::string out_name, out_name_dx; size_t output_freq; - /// If one or more of the variables are \link type_vector \endlink, treat them as arrays of this length + /// If one or more of the variables are \link colvarvalue::type_vector \endlink, treat them as arrays of this length size_t colvar_array_size; /// If colvar_array_size is larger than 1, weigh each one by this number before accumulating the histogram std::vector weights; diff --git a/lib/colvars/colvarbias_meta.cpp b/lib/colvars/colvarbias_meta.cpp index f3ae3631a0..27781ec733 100644 --- a/lib/colvars/colvarbias_meta.cpp +++ b/lib/colvars/colvarbias_meta.cpp @@ -11,7 +11,6 @@ #include #include #include -#include #include // used to set the absolute path of a replica file @@ -39,6 +38,8 @@ colvarbias_meta::colvarbias_meta(char const *key) new_hills_begin = hills.end(); hills_traj_os = NULL; replica_hills_os = NULL; + + ebmeta_equil_steps = 0L; } @@ -61,7 +62,7 @@ int colvarbias_meta::init(std::string const &conf) enable(f_cvb_history_dependent); } - get_keyval(conf, "hillWidth", hill_width, std::sqrt(2.0 * PI) / 2.0); + get_keyval(conf, "hillWidth", hill_width, cvm::sqrt(2.0 * PI) / 2.0); cvm::log("Half-widths of the Gaussian hills (sigma's):\n"); for (size_t i = 0; i < num_variables(); i++) { cvm::log(variables(i)->name+std::string(": ")+ @@ -201,6 +202,7 @@ int colvarbias_meta::init_ebmeta_params(std::string const &conf) } target_dist = new colvar_grid_scalar(); target_dist->init_from_colvars(colvars); + std::string target_dist_file; get_keyval(conf, "targetdistfile", target_dist_file); std::ifstream targetdiststream(target_dist_file.c_str()); target_dist->read_multicol(targetdiststream); @@ -221,9 +223,9 @@ int colvarbias_meta::init_ebmeta_params(std::string const &conf) } // normalize target distribution and multiply by effective volume = exp(differential entropy) target_dist->multiply_constant(1.0/target_dist->integral()); - cvm::real volume = std::exp(target_dist->entropy()); + cvm::real volume = cvm::exp(target_dist->entropy()); target_dist->multiply_constant(volume); - get_keyval(conf, "ebMetaEquilSteps", ebmeta_equil_steps, 0); + get_keyval(conf, "ebMetaEquilSteps", ebmeta_equil_steps, ebmeta_equil_steps); } return COLVARS_OK; @@ -291,7 +293,7 @@ colvarbias_meta::create_hill(colvarbias_meta::hill const &h) // need to be computed analytically when the colvar returns // off-grid cvm::real const min_dist = hills_energy->bin_distance_from_boundaries(h.centers, true); - if (min_dist < (3.0 * std::floor(hill_width)) + 1.0) { + if (min_dist < (3.0 * cvm::floor(hill_width)) + 1.0) { hills_off_grid.push_back(h); } } @@ -387,7 +389,7 @@ int colvarbias_meta::update_grid_params() // first of all, expand the grids, if specified bool changed_grids = false; int const min_buffer = - (3 * (size_t) std::floor(hill_width)) + 1; + (3 * (size_t) cvm::floor(hill_width)) + 1; std::vector new_sizes(hills_energy->sizes()); std::vector new_lower_boundaries(hills_energy->lower_boundaries); @@ -492,9 +494,9 @@ int colvarbias_meta::update_bias() if (ebmeta) { hills_scale *= 1.0/target_dist->value(target_dist->get_colvars_index()); - if(cvm::step_absolute() <= long(ebmeta_equil_steps)) { + if(cvm::step_absolute() <= ebmeta_equil_steps) { cvm::real const hills_lambda = - (cvm::real(long(ebmeta_equil_steps) - cvm::step_absolute())) / + (cvm::real(ebmeta_equil_steps - cvm::step_absolute())) / (cvm::real(ebmeta_equil_steps)); hills_scale = hills_lambda + (1-hills_lambda)*hills_scale; } @@ -508,7 +510,7 @@ int colvarbias_meta::update_bias() } else { calc_hills(new_hills_begin, hills.end(), hills_energy_sum_here); } - hills_scale *= std::exp(-1.0*hills_energy_sum_here/(bias_temperature*cvm::boltzmann())); + hills_scale *= cvm::exp(-1.0*hills_energy_sum_here/(bias_temperature*cvm::boltzmann())); } switch (comm) { @@ -710,7 +712,7 @@ void colvarbias_meta::calc_hills(colvarbias_meta::hill_iter h_first, // set it to zero if the exponent is more negative than log(1.0E-05) h->value(0.0); } else { - h->value(std::exp(-0.5*cv_sqdev)); + h->value(cvm::exp(-0.5*cv_sqdev)); } energy += h->energy(); } @@ -904,7 +906,7 @@ void colvarbias_meta::recount_hills_off_grid(colvarbias_meta::hill_iter h_first for (hill_iter h = h_first; h != h_last; h++) { cvm::real const min_dist = hills_energy->bin_distance_from_boundaries(h->centers, true); - if (min_dist < (3.0 * std::floor(hill_width)) + 1.0) { + if (min_dist < (3.0 * cvm::floor(hill_width)) + 1.0) { hills_off_grid.push_back(*h); } } @@ -1427,8 +1429,8 @@ std::istream & colvarbias_meta::read_hill(std::istream &is) return is; } - size_t h_it; - get_keyval(data, "step", h_it, 0, parse_silent); + cvm::step_number h_it; + get_keyval(data, "step", h_it, 0L, parse_silent); if (h_it <= state_file_step) { if (cvm::debug()) cvm::log("Skipping a hill older than the state file for metadynamics bias \""+ @@ -1457,7 +1459,7 @@ std::istream & colvarbias_meta::read_hill(std::istream &is) std::vector h_widths(num_variables()); get_keyval(data, "widths", h_widths, - std::vector(num_variables(), (std::sqrt(2.0 * PI) / 2.0)), + std::vector(num_variables(), (cvm::sqrt(2.0 * PI) / 2.0)), parse_silent); std::string h_replica = ""; @@ -1482,7 +1484,7 @@ std::istream & colvarbias_meta::read_hill(std::istream &is) // be computed analytically cvm::real const min_dist = hills_energy->bin_distance_from_boundaries((hills.back()).centers, true); - if (min_dist < (3.0 * std::floor(hill_width)) + 1.0) { + if (min_dist < (3.0 * cvm::floor(hill_width)) + 1.0) { hills_off_grid.push_back(hills.back()); } } diff --git a/lib/colvars/colvarbias_meta.h b/lib/colvars/colvarbias_meta.h index 78b2d35d41..0ba2bef1c3 100644 --- a/lib/colvars/colvarbias_meta.h +++ b/lib/colvars/colvarbias_meta.h @@ -19,8 +19,8 @@ #include "colvargrid.h" /// Metadynamics bias (implementation of \link colvarbias \endlink) -class colvarbias_meta - : public virtual colvarbias, +class colvarbias_meta + : public virtual colvarbias, public virtual colvarbias_ti { @@ -174,12 +174,14 @@ protected: /// \brief Biasing temperature in well-tempered metadynamics cvm::real bias_temperature; - // EBmeta parameters + /// Ensemble-biased metadynamics (EBmeta) flag bool ebmeta; + + /// Target distribution for EBmeta colvar_grid_scalar* target_dist; - std::string target_dist_file; - cvm::real target_dist_volume; - size_t ebmeta_equil_steps; + + /// Number of equilibration steps for EBmeta + cvm::step_number ebmeta_equil_steps; /// \brief Try to read the restart information by allocating new @@ -285,7 +287,7 @@ public: friend class colvarbias_meta; /// Time step at which this hill was added - size_t it; + cvm::step_number it; /// Identity of the replica who added this hill (only in multiple replica simulations) std::string replica; @@ -296,9 +298,9 @@ public: /// replica (optional) Identity of the replica which creates the /// hill inline hill(cvm::real const &W_in, - std::vector &cv, - cvm::real const &hill_width, - std::string const &replica_in = "") + std::vector &cv, + cvm::real const &hill_width, + std::string const &replica_in = "") : sW(1.0), W(W_in), centers(cv.size()), @@ -325,11 +327,11 @@ public: /// weight Weight of the hill \param centers Center of the hill /// \param widths Width of the hill around centers \param replica /// (optional) Identity of the replica which creates the hill - inline hill(size_t const &it_in, - cvm::real const &W_in, - std::vector const ¢ers_in, - std::vector const &widths_in, - std::string const &replica_in = "") + inline hill(cvm::step_number const &it_in, + cvm::real const &W_in, + std::vector const ¢ers_in, + std::vector const &widths_in, + std::string const &replica_in = "") : sW(1.0), W(W_in), centers(centers_in), diff --git a/lib/colvars/colvarbias_restraint.cpp b/lib/colvars/colvarbias_restraint.cpp index 2daf7a0876..90588f5a1f 100644 --- a/lib/colvars/colvarbias_restraint.cpp +++ b/lib/colvars/colvarbias_restraint.cpp @@ -7,8 +7,6 @@ // If you wish to distribute your changes, please submit them to the // Colvars repository at GitHub. -#include - #include "colvarmodule.h" #include "colvarproxy.h" #include "colvarvalue.h" @@ -179,7 +177,7 @@ int colvarbias_restraint_k::change_configuration(std::string const &conf) colvarbias_restraint_moving::colvarbias_restraint_moving(char const *key) { target_nstages = 0; - target_nsteps = 0; + target_nsteps = 0L; stage = 0; acc_work = 0.0; b_chg_centers = false; @@ -241,8 +239,8 @@ int colvarbias_restraint_moving::set_state_params(std::string const &conf) { if (b_chg_centers || b_chg_force_k) { if (target_nstages) { - if (!get_keyval(conf, "stage", stage)) - cvm::error("Error: current stage is missing from the restart.\n"); + get_keyval(conf, "stage", stage, stage, + colvarparse::parse_restart | colvarparse::parse_required); } } return COLVARS_OK; @@ -436,13 +434,13 @@ int colvarbias_restraint_centers_moving::set_state_params(std::string const &con colvarbias_restraint::set_state_params(conf); if (b_chg_centers) { - // cvm::log ("Reading the updated restraint centers from the restart.\n"); - if (!get_keyval(conf, "centers", colvar_centers)) - cvm::error("Error: restraint centers are missing from the restart.\n"); - if (is_enabled(f_cvb_output_acc_work)) { - if (!get_keyval(conf, "accumulatedWork", acc_work)) - cvm::error("Error: accumulatedWork is missing from the restart.\n"); - } + get_keyval(conf, "centers", colvar_centers, colvar_centers, + colvarparse::parse_restart | colvarparse::parse_required); + } + + if (is_enabled(f_cvb_output_acc_work)) { + get_keyval(conf, "accumulatedWork", acc_work, acc_work, + colvarparse::parse_restart | colvarparse::parse_required); } return COLVARS_OK; @@ -563,7 +561,7 @@ int colvarbias_restraint_k_moving::update() lambda = 0.0; } force_k = starting_force_k + (target_force_k - starting_force_k) - * std::pow(lambda, force_k_exp); + * cvm::pow(lambda, force_k_exp); cvm::log("Restraint " + this->name + ", stage " + cvm::to_str(stage) + " : lambda = " + cvm::to_str(lambda) + ", k = " + cvm::to_str(force_k)); @@ -585,7 +583,7 @@ int colvarbias_restraint_k_moving::update() for (size_t i = 0; i < num_variables(); i++) { dU_dk += d_restraint_potential_dk(i); } - restraint_FE += force_k_exp * std::pow(lambda, force_k_exp - 1.0) + restraint_FE += force_k_exp * cvm::pow(lambda, force_k_exp - 1.0) * (target_force_k - starting_force_k) * dU_dk; } @@ -608,7 +606,7 @@ int colvarbias_restraint_k_moving::update() lambda = cvm::real(stage) / cvm::real(target_nstages); } force_k = starting_force_k + (target_force_k - starting_force_k) - * std::pow(lambda, force_k_exp); + * cvm::pow(lambda, force_k_exp); cvm::log("Restraint " + this->name + ", stage " + cvm::to_str(stage) + " : lambda = " + cvm::to_str(lambda) + ", k = " + cvm::to_str(force_k)); @@ -622,7 +620,7 @@ int colvarbias_restraint_k_moving::update() lambda = cvm::real(cvm::step_absolute()) / cvm::real(target_nsteps); cvm::real const force_k_old = force_k; force_k = starting_force_k + (target_force_k - starting_force_k) - * std::pow(lambda, force_k_exp); + * cvm::pow(lambda, force_k_exp); force_k_incr = force_k - force_k_old; } } @@ -672,13 +670,13 @@ int colvarbias_restraint_k_moving::set_state_params(std::string const &conf) colvarbias_restraint::set_state_params(conf); if (b_chg_force_k) { - // cvm::log ("Reading the updated force constant from the restart.\n"); - if (!get_keyval(conf, "forceConstant", force_k, force_k)) - cvm::error("Error: force constant is missing from the restart.\n"); - if (is_enabled(f_cvb_output_acc_work)) { - if (!get_keyval(conf, "accumulatedWork", acc_work)) - cvm::error("Error: accumulatedWork is missing from the restart.\n"); - } + get_keyval(conf, "forceConstant", force_k, force_k, + colvarparse::parse_restart | colvarparse::parse_required); + } + + if (is_enabled(f_cvb_output_acc_work)) { + get_keyval(conf, "accumulatedWork", acc_work, acc_work, + colvarparse::parse_restart | colvarparse::parse_required); } return COLVARS_OK; @@ -719,7 +717,8 @@ std::istream & colvarbias_restraint::read_state(std::istream &is) (set_state_params(conf) != COLVARS_OK) ) { cvm::error("Error: in reading state configuration for \""+bias_type+"\" bias \""+ this->name+"\" at position "+ - cvm::to_str(is.tellg())+" in stream.\n", INPUT_ERROR); + cvm::to_str(static_cast(is.tellg()))+ + " in stream.\n", INPUT_ERROR); is.clear(); is.seekg(start_pos, std::ios::beg); is.setstate(std::ios::failbit); @@ -729,7 +728,8 @@ std::istream & colvarbias_restraint::read_state(std::istream &is) if (!read_state_data(is)) { cvm::error("Error: in reading state data for \""+bias_type+"\" bias \""+ this->name+"\" at position "+ - cvm::to_str(is.tellg())+" in stream.\n", INPUT_ERROR); + cvm::to_str(static_cast(is.tellg()))+ + " in stream.\n", INPUT_ERROR); is.clear(); is.seekg(start_pos, std::ios::beg); is.setstate(std::ios::failbit); @@ -740,7 +740,7 @@ std::istream & colvarbias_restraint::read_state(std::istream &is) cvm::log("brace = "+brace+"\n"); cvm::error("Error: corrupt restart information for \""+bias_type+"\" bias \""+ this->name+"\": no matching brace at position "+ - cvm::to_str(is.tellg())+" in stream.\n"); + cvm::to_str(static_cast(is.tellg()))+" in stream.\n"); is.setstate(std::ios::failbit); } @@ -787,11 +787,11 @@ int colvarbias_restraint_harmonic::init(std::string const &conf) colvarbias_restraint_k_moving::init(conf); for (size_t i = 0; i < num_variables(); i++) { - if (variables(i)->width != 1.0) - cvm::log("The force constant for colvar \""+variables(i)->name+ - "\" will be rescaled to "+ - cvm::to_str(force_k / (variables(i)->width * variables(i)->width))+ - " according to the specified width.\n"); + cvm::real const w = variables(i)->width; + cvm::log("The force constant for colvar \""+variables(i)->name+ + "\" will be rescaled to "+ + cvm::to_str(force_k/(w*w))+ + " according to the specified width ("+cvm::to_str(w)+").\n"); } return COLVARS_OK; @@ -1014,7 +1014,7 @@ int colvarbias_restraint_harmonic_walls::init(std::string const &conf) INPUT_ERROR); return INPUT_ERROR; } - force_k = std::sqrt(lower_wall_k * upper_wall_k); + force_k = cvm::sqrt(lower_wall_k * upper_wall_k); // transform the two constants to relative values using gemetric mean as ref // to preserve force_k if provided as single parameter // (allow changing both via force_k) @@ -1037,25 +1037,21 @@ int colvarbias_restraint_harmonic_walls::init(std::string const &conf) if (lower_walls.size() > 0) { for (i = 0; i < num_variables(); i++) { - if (variables(i)->width != 1.0) - cvm::log("The lower wall force constant for colvar \""+ - variables(i)->name+ - "\" will be rescaled to "+ - cvm::to_str(lower_wall_k * force_k / - (variables(i)->width * variables(i)->width))+ - " according to the specified width.\n"); + cvm::real const w = variables(i)->width; + cvm::log("The lower wall force constant for colvar \""+ + variables(i)->name+"\" will be rescaled to "+ + cvm::to_str(lower_wall_k * force_k / (w*w))+ + " according to the specified width ("+cvm::to_str(w)+").\n"); } } if (upper_walls.size() > 0) { for (i = 0; i < num_variables(); i++) { - if (variables(i)->width != 1.0) - cvm::log("The upper wall force constant for colvar \""+ - variables(i)->name+ - "\" will be rescaled to "+ - cvm::to_str(upper_wall_k * force_k / - (variables(i)->width * variables(i)->width))+ - " according to the specified width.\n"); + cvm::real const w = variables(i)->width; + cvm::log("The upper wall force constant for colvar \""+ + variables(i)->name+"\" will be rescaled to "+ + cvm::to_str(upper_wall_k * force_k / (w*w))+ + " according to the specified width ("+cvm::to_str(w)+").\n"); } } @@ -1225,11 +1221,11 @@ int colvarbias_restraint_linear::init(std::string const &conf) INPUT_ERROR); return INPUT_ERROR; } - if (variables(i)->width != 1.0) - cvm::log("The force constant for colvar \""+variables(i)->name+ - "\" will be rescaled to "+ - cvm::to_str(force_k / variables(i)->width)+ - " according to the specified width.\n"); + cvm::real const w = variables(i)->width; + cvm::log("The force constant for colvar \""+variables(i)->name+ + "\" will be rescaled to "+ + cvm::to_str(force_k / w)+ + " according to the specified width ("+cvm::to_str(w)+").\n"); } return COLVARS_OK; @@ -1367,6 +1363,7 @@ colvarbias_restraint_histogram::colvarbias_restraint_histogram(char const *key) int colvarbias_restraint_histogram::init(std::string const &conf) { colvarbias::init(conf); + enable(f_cvb_apply_force); get_keyval(conf, "lowerBoundary", lower_boundary, lower_boundary); get_keyval(conf, "upperBoundary", upper_boundary, upper_boundary); @@ -1390,7 +1387,7 @@ int colvarbias_restraint_histogram::init(std::string const &conf) cvm::real const nbins = (upper_boundary - lower_boundary) / width; int const nbins_round = (int)(nbins); - if (std::fabs(nbins - cvm::real(nbins_round)) > 1.0E-10) { + if (cvm::fabs(nbins - cvm::real(nbins_round)) > 1.0E-10) { cvm::log("Warning: grid interval ("+ cvm::to_str(lower_boundary, cvm::cv_width, cvm::cv_prec)+" - "+ cvm::to_str(upper_boundary, cvm::cv_width, cvm::cv_prec)+ @@ -1440,7 +1437,7 @@ int colvarbias_restraint_histogram::init(std::string const &conf) } } cvm::real const ref_integral = ref_p.sum() * width; - if (std::fabs(ref_integral - 1.0) > 1.0e-03) { + if (cvm::fabs(ref_integral - 1.0) > 1.0e-03) { cvm::log("Reference distribution not normalized, normalizing to unity.\n"); ref_p /= ref_integral; } @@ -1471,7 +1468,7 @@ int colvarbias_restraint_histogram::update() vector_size += variables(icv)->value().size(); } - cvm::real const norm = 1.0/(std::sqrt(2.0*PI)*gaussian_width*vector_size); + cvm::real const norm = 1.0/(cvm::sqrt(2.0*PI)*gaussian_width*vector_size); // calculate the histogram p.reset(); @@ -1482,7 +1479,7 @@ int colvarbias_restraint_histogram::update() size_t igrid; for (igrid = 0; igrid < p.size(); igrid++) { cvm::real const x_grid = (lower_boundary + (igrid+0.5)*width); - p[igrid] += norm * std::exp(-1.0 * (x_grid - cv_value) * (x_grid - cv_value) / + p[igrid] += norm * cvm::exp(-1.0 * (x_grid - cv_value) * (x_grid - cv_value) / (2.0 * gaussian_width * gaussian_width)); } } else if (cv.type() == colvarvalue::type_vector) { @@ -1492,7 +1489,7 @@ int colvarbias_restraint_histogram::update() size_t igrid; for (igrid = 0; igrid < p.size(); igrid++) { cvm::real const x_grid = (lower_boundary + (igrid+0.5)*width); - p[igrid] += norm * std::exp(-1.0 * (x_grid - cv_value) * (x_grid - cv_value) / + p[igrid] += norm * cvm::exp(-1.0 * (x_grid - cv_value) * (x_grid - cv_value) / (2.0 * gaussian_width * gaussian_width)); } } @@ -1523,7 +1520,7 @@ int colvarbias_restraint_histogram::update() for (igrid = 0; igrid < p.size(); igrid++) { cvm::real const x_grid = (lower_boundary + (igrid+0.5)*width); force += force_k_cv * p_diff[igrid] * - norm * std::exp(-1.0 * (x_grid - cv_value) * (x_grid - cv_value) / + norm * cvm::exp(-1.0 * (x_grid - cv_value) * (x_grid - cv_value) / (2.0 * gaussian_width * gaussian_width)) * (-1.0 * (x_grid - cv_value) / (gaussian_width * gaussian_width)); } @@ -1536,7 +1533,7 @@ int colvarbias_restraint_histogram::update() for (igrid = 0; igrid < p.size(); igrid++) { cvm::real const x_grid = (lower_boundary + (igrid+0.5)*width); force += force_k_cv * p_diff[igrid] * - norm * std::exp(-1.0 * (x_grid - cv_value) * (x_grid - cv_value) / + norm * cvm::exp(-1.0 * (x_grid - cv_value) * (x_grid - cv_value) / (2.0 * gaussian_width * gaussian_width)) * (-1.0 * (x_grid - cv_value) / (gaussian_width * gaussian_width)); } @@ -1550,7 +1547,7 @@ int colvarbias_restraint_histogram::update() } -std::ostream & colvarbias_restraint_histogram::write_restart(std::ostream &os) +int colvarbias_restraint_histogram::write_output_files() { if (b_write_histogram) { std::string file_name(cvm::output_prefix()+"."+this->name+".hist.dat"); @@ -1558,6 +1555,9 @@ std::ostream & colvarbias_restraint_histogram::write_restart(std::ostream &os) *os << "# " << cvm::wrap_string(variables(0)->name, cvm::cv_width) << " " << "p(" << cvm::wrap_string(variables(0)->name, cvm::cv_width-3) << ")\n"; + + os->setf(std::ios::fixed, std::ios::floatfield); + size_t igrid; for (igrid = 0; igrid < p.size(); igrid++) { cvm::real const x_grid = (lower_boundary + (igrid+1)*width); @@ -1572,13 +1572,7 @@ std::ostream & colvarbias_restraint_histogram::write_restart(std::ostream &os) } cvm::proxy->close_output_stream(file_name); } - return os; -} - - -std::istream & colvarbias_restraint_histogram::read_restart(std::istream &is) -{ - return is; + return COLVARS_OK; } diff --git a/lib/colvars/colvarbias_restraint.h b/lib/colvars/colvarbias_restraint.h index 3ee999c262..6493f7f16b 100644 --- a/lib/colvars/colvarbias_restraint.h +++ b/lib/colvars/colvarbias_restraint.h @@ -132,7 +132,7 @@ protected: /// \brief Number of steps required to reach the target force constant /// or restraint centers - long target_nsteps; + cvm::step_number target_nsteps; /// \brief Accumulated work (computed when outputAccumulatedWork == true) cvm::real acc_work; @@ -328,8 +328,7 @@ public: virtual int update(); - virtual std::istream & read_restart(std::istream &is); - virtual std::ostream & write_restart(std::ostream &os); + virtual int write_output_files(); virtual std::ostream & write_traj_label(std::ostream &os); virtual std::ostream & write_traj(std::ostream &os); diff --git a/lib/colvars/colvarcomp.cpp b/lib/colvars/colvarcomp.cpp index cb272eed05..3075ed82ca 100644 --- a/lib/colvars/colvarcomp.cpp +++ b/lib/colvars/colvarcomp.cpp @@ -20,7 +20,8 @@ colvar::cvc::cvc() b_periodic(false), b_try_scalable(true) { - init_cvc_requires(); + description = "uninitialized colvar component"; + init_dependencies(); sup_coeff = 1.0; period = 0.0; wrap_center = 0.0; @@ -33,7 +34,8 @@ colvar::cvc::cvc(std::string const &conf) b_periodic(false), b_try_scalable(true) { - init_cvc_requires(); + description = "uninitialized colvar component"; + init_dependencies(); sup_coeff = 1.0; period = 0.0; wrap_center = 0.0; @@ -176,6 +178,100 @@ cvm::atom_group *colvar::cvc::parse_group(std::string const &conf, } +int colvar::cvc::init_dependencies() { + size_t i; + // Initialize static array once and for all + if (features().size() == 0) { + for (i = 0; i < colvardeps::f_cvc_ntot; i++) { + modify_features().push_back(new feature); + } + + init_feature(f_cvc_active, "active", f_type_dynamic); +// The dependency below may become useful if we use dynamic atom groups +// require_feature_children(f_cvc_active, f_ag_active); + + init_feature(f_cvc_scalar, "scalar", f_type_static); + + init_feature(f_cvc_gradient, "gradient", f_type_dynamic); + + init_feature(f_cvc_explicit_gradient, "explicit gradient", f_type_static); + require_feature_children(f_cvc_explicit_gradient, f_ag_explicit_gradient); + + init_feature(f_cvc_inv_gradient, "inverse gradient", f_type_dynamic); + require_feature_self(f_cvc_inv_gradient, f_cvc_gradient); + + init_feature(f_cvc_debug_gradient, "debug gradient", f_type_user); + require_feature_self(f_cvc_debug_gradient, f_cvc_gradient); + require_feature_self(f_cvc_debug_gradient, f_cvc_explicit_gradient); + + init_feature(f_cvc_Jacobian, "Jacobian derivative", f_type_dynamic); + require_feature_self(f_cvc_Jacobian, f_cvc_inv_gradient); + + init_feature(f_cvc_com_based, "depends on group centers of mass", f_type_static); + + init_feature(f_cvc_pbc_minimum_image, "use minimum-image distances with PBCs", f_type_user); + + // Compute total force on first site only to avoid unwanted + // coupling to other colvars (see e.g. Ciccotti et al., 2005) + init_feature(f_cvc_one_site_total_force, "compute total force from one group", f_type_user); + require_feature_self(f_cvc_one_site_total_force, f_cvc_com_based); + + init_feature(f_cvc_scalable, "scalable calculation", f_type_static); + require_feature_self(f_cvc_scalable, f_cvc_scalable_com); + + init_feature(f_cvc_scalable_com, "scalable calculation of centers of mass", f_type_static); + require_feature_self(f_cvc_scalable_com, f_cvc_com_based); + + + // TODO only enable this when f_ag_scalable can be turned on for a pre-initialized group + // require_feature_children(f_cvc_scalable, f_ag_scalable); + // require_feature_children(f_cvc_scalable_com, f_ag_scalable_com); + + // check that everything is initialized + for (i = 0; i < colvardeps::f_cvc_ntot; i++) { + if (is_not_set(i)) { + cvm::error("Uninitialized feature " + cvm::to_str(i) + " in " + description); + } + } + } + + // Initialize feature_states for each instance + // default as available, not enabled + // except dynamic features which default as unavailable + feature_states.reserve(f_cvc_ntot); + for (i = 0; i < colvardeps::f_cvc_ntot; i++) { + bool avail = is_dynamic(i) ? false : true; + feature_states.push_back(feature_state(avail, false)); + } + + // Features that are implemented by all cvcs by default + // Each cvc specifies what other features are available + feature_states[f_cvc_active].available = true; + feature_states[f_cvc_gradient].available = true; + + // CVCs are enabled from the start - get disabled based on flags + enable(f_cvc_active); + // feature_states[f_cvc_active].enabled = true; + + // Explicit gradients are implemented in mosts CVCs. Exceptions must be specified explicitly. + // feature_states[f_cvc_explicit_gradient].enabled = true; + enable(f_cvc_explicit_gradient); + + // Use minimum-image distances by default + // feature_states[f_cvc_pbc_minimum_image].enabled = true; + enable(f_cvc_pbc_minimum_image); + + // Features that are implemented by default if their requirements are + feature_states[f_cvc_one_site_total_force].available = true; + + // Features That are implemented only for certain simulation engine configurations + feature_states[f_cvc_scalable_com].available = (cvm::proxy->scalable_group_coms() == COLVARS_OK); + feature_states[f_cvc_scalable].available = feature_states[f_cvc_scalable_com].available; + + return COLVARS_OK; +} + + int colvar::cvc::setup() { description = "cvc " + name; @@ -192,6 +288,7 @@ colvar::cvc::~cvc() } } + void colvar::cvc::read_data() { size_t ig; @@ -214,6 +311,66 @@ void colvar::cvc::read_data() } +std::vector > colvar::cvc::get_atom_lists() +{ + std::vector > lists; + + std::vector::iterator agi = atom_groups.begin(); + for ( ; agi != atom_groups.end(); ++agi) { + (*agi)->create_sorted_ids(); + lists.push_back((*agi)->sorted_ids()); + if ((*agi)->is_enabled(f_ag_fitting_group) && (*agi)->is_enabled(f_ag_fit_gradients)) { + cvm::atom_group &fg = *((*agi)->fitting_group); + fg.create_sorted_ids(); + lists.push_back(fg.sorted_ids()); + } + } + return lists; +} + + +void colvar::cvc::collect_gradients(std::vector const &atom_ids, std::vector &atomic_gradients) +{ + // Coefficient: d(a * x^n) = a * n * x^(n-1) * dx + cvm::real coeff = sup_coeff * cvm::real(sup_np) * + cvm::integer_power(value().real_value, sup_np-1); + + for (size_t j = 0; j < atom_groups.size(); j++) { + + cvm::atom_group &ag = *(atom_groups[j]); + + // If necessary, apply inverse rotation to get atomic + // gradient in the laboratory frame + if (ag.b_rotate) { + cvm::rotation const rot_inv = ag.rot.inverse(); + + for (size_t k = 0; k < ag.size(); k++) { + size_t a = std::lower_bound(atom_ids.begin(), atom_ids.end(), + ag[k].id) - atom_ids.begin(); + atomic_gradients[a] += coeff * rot_inv.rotate(ag[k].grad); + } + + } else { + + for (size_t k = 0; k < ag.size(); k++) { + size_t a = std::lower_bound(atom_ids.begin(), atom_ids.end(), + ag[k].id) - atom_ids.begin(); + atomic_gradients[a] += coeff * ag[k].grad; + } + } + if (ag.is_enabled(f_ag_fitting_group) && ag.is_enabled(f_ag_fit_gradients)) { + cvm::atom_group const &fg = *(ag.fitting_group); + for (size_t k = 0; k < fg.size(); k++) { + size_t a = std::lower_bound(atom_ids.begin(), atom_ids.end(), + fg[k].id) - atom_ids.begin(); + // fit gradients are in the unrotated (simulation) frame + atomic_gradients[a] += coeff * fg.fit_gradients[k]; + } + } + } +} + + void colvar::cvc::calc_force_invgrads() { cvm::error("Error: calculation of inverse gradients is not implemented " @@ -306,8 +463,8 @@ void colvar::cvc::debug_gradients() cvm::log("dx(interp) = "+cvm::to_str(dx_pred, 21, 14)+"\n"); cvm::log("|dx(actual) - dx(interp)|/|dx(actual)| = "+ - cvm::to_str(std::fabs(x_1 - x_0 - dx_pred) / - std::fabs(x_1 - x_0), 12, 5)+"\n"); + cvm::to_str(cvm::fabs(x_1 - x_0 - dx_pred) / + cvm::fabs(x_1 - x_0), 12, 5)+"\n"); } } @@ -341,8 +498,8 @@ void colvar::cvc::debug_gradients() cvm::log("dx(interp) = "+cvm::to_str (dx_pred, 21, 14)+"\n"); cvm::log ("|dx(actual) - dx(interp)|/|dx(actual)| = "+ - cvm::to_str(std::fabs (x_1 - x_0 - dx_pred) / - std::fabs (x_1 - x_0), + cvm::to_str(cvm::fabs (x_1 - x_0 - dx_pred) / + cvm::fabs (x_1 - x_0), 12, 5)+ ".\n"); } @@ -378,7 +535,7 @@ colvarvalue colvar::cvc::dist2_rgrad(colvarvalue const &x1, } -void colvar::cvc::wrap(colvarvalue &x) const +void colvar::cvc::wrap(colvarvalue &x_unwrapped) const { return; } diff --git a/lib/colvars/colvarcomp.h b/lib/colvars/colvarcomp.h index 1a6df3771e..f615680ba6 100644 --- a/lib/colvars/colvarcomp.h +++ b/lib/colvars/colvarcomp.h @@ -27,12 +27,12 @@ /// \brief Colvar component (base class for collective variables) /// -/// A \link cvc \endlink object (or an object of a +/// A \link colvar::cvc \endlink object (or an object of a /// cvc-derived class) implements the calculation of a collective /// variable, its gradients and any other related physical quantities /// that depend on microscopic degrees of freedom. /// -/// No restriction is set to what kind of calculation a \link cvc \endlink +/// No restriction is set to what kind of calculation a \link colvar::cvc \endlink /// object performs (usually an analytical function of atomic coordinates). /// The only constraints are that: \par /// @@ -42,9 +42,9 @@ /// alike, and allows an automatic selection of the applicable algorithms. /// /// - The object provides an implementation \link apply_force() \endlink to -/// apply forces to atoms. Typically, one or more \link cvm::atom_group +/// apply forces to atoms. Typically, one or more \link colvarmodule::atom_group /// \endlink objects are used, but this is not a requirement for as long as -/// the \link cvc \endlink object communicates with the simulation program. +/// the \link colvar::cvc \endlink object communicates with the simulation program. /// /// If you wish to implement a new collective variable component, you /// should write your own class by inheriting directly from \link @@ -75,9 +75,9 @@ public: /// \brief Description of the type of collective variable /// /// Normally this string is set by the parent \link colvar \endlink - /// object within its constructor, when all \link cvc \endlink + /// object within its constructor, when all \link colvar::cvc \endlink /// objects are initialized; therefore the main "config string" - /// constructor does not need to define it. If a \link cvc + /// constructor does not need to define it. If a \link colvar::cvc /// \endlink is initialized and/or a different constructor is used, /// this variable definition should be set within the constructor. std::string function_type; @@ -109,6 +109,9 @@ public: /// cvc \endlink virtual int init(std::string const &conf); + /// \brief Initialize dependency tree + virtual int init_dependencies(); + /// \brief Within the constructor, make a group parse its own /// options from the provided configuration string /// Returns reference to new group @@ -122,7 +125,7 @@ public: /// \brief After construction, set data related to dependency handling int setup(); - /// \brief Default constructor (used when \link cvc \endlink + /// \brief Default constructor (used when \link colvar::cvc \endlink /// objects are declared within other ones) cvc(); @@ -133,7 +136,7 @@ public: static std::vector cvc_features; /// \brief Implementation of the feature list accessor for colvar - virtual const std::vector &features() + virtual const std::vector &features() const { return cvc_features; } @@ -148,6 +151,9 @@ public: cvc_features.clear(); } + /// \brief Get vector of vectors of atom IDs for all atom groups + virtual std::vector > get_atom_lists(); + /// \brief Obtain data needed for the calculation for the backend virtual void read_data(); @@ -164,6 +170,10 @@ public: /// \brief Calculate finite-difference gradients alongside the analytical ones, for each Cartesian component virtual void debug_gradients(); + /// \brief Calculate atomic gradients and add them to the corresponding item in gradient vector + /// May be overridden by CVCs that do not store their gradients in the classic way, see dihedPC + virtual void collect_gradients(std::vector const &atom_ids, std::vector &atomic_gradients); + /// \brief Calculate the total force from the system using the /// inverse atomic gradients virtual void calc_force_invgrads(); @@ -237,7 +247,7 @@ public: colvarvalue const &x2) const; /// \brief Wrap value (for periodic/symmetric cvcs) - virtual void wrap(colvarvalue &x) const; + virtual void wrap(colvarvalue &x_unwrapped) const; /// \brief Pointers to all atom groups, to let colvars collect info /// e.g. atomic gradients @@ -246,7 +256,7 @@ public: /// \brief Store a pointer to new atom group, and list as child for dependencies inline void register_atom_group(cvm::atom_group *ag) { atom_groups.push_back(ag); - add_child((colvardeps *) ag); + add_child(ag); } /// \brief Whether or not this CVC will be computed in parallel whenever possible @@ -415,7 +425,7 @@ public: virtual colvarvalue dist2_rgrad(colvarvalue const &x1, colvarvalue const &x2) const; /// \brief Redefined to make use of the user-provided period - virtual void wrap(colvarvalue &x) const; + virtual void wrap(colvarvalue &x_unwrapped) const; }; @@ -474,7 +484,7 @@ public: virtual colvarvalue dist2_rgrad(colvarvalue const &x1, colvarvalue const &x2) const; /// Redefined to handle the 2*PI periodicity - virtual void wrap(colvarvalue &x) const; + virtual void wrap(colvarvalue &x_unwrapped) const; }; @@ -559,6 +569,35 @@ public: +/// \brief Colvar component: dipole magnitude of a molecule +class colvar::dipole_magnitude + : public colvar::cvc +{ +protected: + /// Dipole atom group + cvm::atom_group *atoms; + cvm::atom_pos dipoleV; +public: + /// Initialize by parsing the configuration + dipole_magnitude (std::string const &conf); + dipole_magnitude (cvm::atom const &a1); + dipole_magnitude(); + virtual inline ~dipole_magnitude() {} + virtual void calc_value(); + virtual void calc_gradients(); + //virtual void calc_force_invgrads(); + //virtual void calc_Jacobian_derivative(); + virtual void apply_force (colvarvalue const &force); + virtual cvm::real dist2 (colvarvalue const &x1, + colvarvalue const &x2) const; + virtual colvarvalue dist2_lgrad (colvarvalue const &x1, + colvarvalue const &x2) const; + virtual colvarvalue dist2_rgrad (colvarvalue const &x1, + colvarvalue const &x2) const; +}; + + + /// \brief Colvar component: Radius of gyration of an atom group /// (colvarvalue::type_scalar type, range [0:*)) class colvar::gyration @@ -818,7 +857,7 @@ public: virtual colvarvalue dist2_rgrad(colvarvalue const &x1, colvarvalue const &x2) const; /// Redefined to handle the 2*PI periodicity - virtual void wrap(colvarvalue &x) const; + virtual void wrap(colvarvalue &x_unwrapped) const; }; @@ -1002,7 +1041,7 @@ public: cvm::atom const &donor, cvm::real r0, int en, int ed); h_bond(); - virtual ~h_bond(); + virtual ~h_bond() {} virtual void calc_value(); virtual void calc_gradients(); virtual void apply_force(colvarvalue const &force); @@ -1090,6 +1129,8 @@ public: virtual ~alpha_angles(); void calc_value(); void calc_gradients(); + /// Re-implementation of cvc::collect_gradients() to carry over atomic gradients of sub-cvcs + void collect_gradients(std::vector const &atom_ids, std::vector &atomic_gradients); void apply_force(colvarvalue const &force); virtual cvm::real dist2(colvarvalue const &x1, colvarvalue const &x2) const; @@ -1120,6 +1161,8 @@ public: virtual ~dihedPC(); void calc_value(); void calc_gradients(); + /// Re-implementation of cvc::collect_gradients() to carry over atomic gradients of sub-cvcs + void collect_gradients(std::vector const &atom_ids, std::vector &atomic_gradients); void apply_force(colvarvalue const &force); virtual cvm::real dist2(colvarvalue const &x1, colvarvalue const &x2) const; @@ -1159,6 +1202,7 @@ public: orientation(std::string const &conf); orientation(); + virtual int init(std::string const &conf); virtual ~orientation() {} virtual void calc_value(); virtual void calc_gradients(); @@ -1183,6 +1227,7 @@ public: orientation_angle(std::string const &conf); orientation_angle(); + virtual int init(std::string const &conf); virtual ~orientation_angle() {} virtual void calc_value(); virtual void calc_gradients(); @@ -1207,6 +1252,7 @@ public: orientation_proj(std::string const &conf); orientation_proj(); + virtual int init(std::string const &conf); virtual ~orientation_proj() {} virtual void calc_value(); virtual void calc_gradients(); @@ -1234,6 +1280,7 @@ public: tilt(std::string const &conf); tilt(); + virtual int init(std::string const &conf); virtual ~tilt() {} virtual void calc_value(); virtual void calc_gradients(); @@ -1261,6 +1308,7 @@ public: spin_angle(std::string const &conf); spin_angle(); + virtual int init(std::string const &conf); virtual ~spin_angle() {} virtual void calc_value(); virtual void calc_gradients(); @@ -1275,7 +1323,7 @@ public: virtual colvarvalue dist2_rgrad(colvarvalue const &x1, colvarvalue const &x2) const; /// Redefined to handle the 2*PI periodicity - virtual void wrap(colvarvalue &x) const; + virtual void wrap(colvarvalue &x_unwrapped) const; }; diff --git a/lib/colvars/colvarcomp_angles.cpp b/lib/colvars/colvarcomp_angles.cpp index 9f879a4c41..97fb23b181 100644 --- a/lib/colvars/colvarcomp_angles.cpp +++ b/lib/colvars/colvarcomp_angles.cpp @@ -11,9 +11,6 @@ #include "colvar.h" #include "colvarcomp.h" -#include - - colvar::angle::angle(std::string const &conf) : cvc(conf) @@ -77,14 +74,14 @@ void colvar::angle::calc_value() cvm::real const cos_theta = (r21*r23)/(r21l*r23l); - x.real_value = (180.0/PI) * std::acos(cos_theta); + x.real_value = (180.0/PI) * cvm::acos(cos_theta); } void colvar::angle::calc_gradients() { cvm::real const cos_theta = (r21*r23)/(r21l*r23l); - cvm::real const dxdcos = -1.0 / std::sqrt(1.0 - cos_theta*cos_theta); + cvm::real const dxdcos = -1.0 / cvm::sqrt(1.0 - cos_theta*cos_theta); dxdr1 = (180.0/PI) * dxdcos * (1.0/r21l) * ( r23/r23l + (-1.0) * cos_theta * r21/r21l ); @@ -126,7 +123,7 @@ void colvar::angle::calc_Jacobian_derivative() // det(J) = (2 pi) r^2 * sin(theta) // hence Jd = cot(theta) const cvm::real theta = x.real_value * PI / 180.0; - jd = PI / 180.0 * (theta != 0.0 ? std::cos(theta) / std::sin(theta) : 0.0); + jd = PI / 180.0 * (theta != 0.0 ? cvm::cos(theta) / cvm::sin(theta) : 0.0); } @@ -202,7 +199,7 @@ void colvar::dipole_angle::calc_value() cvm::real const cos_theta = (r21*r23)/(r21l*r23l); - x.real_value = (180.0/PI) * std::acos(cos_theta); + x.real_value = (180.0/PI) * cvm::acos(cos_theta); } //to be implemented @@ -212,7 +209,7 @@ void colvar::dipole_angle::calc_value() void colvar::dipole_angle::calc_gradients() { cvm::real const cos_theta = (r21*r23)/(r21l*r23l); - cvm::real const dxdcos = -1.0 / std::sqrt(1.0 - cos_theta*cos_theta); + cvm::real const dxdcos = -1.0 / cvm::sqrt(1.0 - cos_theta*cos_theta); dxdr1 = (180.0/PI) * dxdcos * (1.0/r21l)* (r23/r23l + (-1.0) * cos_theta * r21/r21l ); @@ -346,7 +343,7 @@ void colvar::dihedral::calc_value() cvm::real const cos_phi = n1 * n2; cvm::real const sin_phi = n1 * r34 * r23.norm(); - x.real_value = (180.0/PI) * std::atan2(sin_phi, cos_phi); + x.real_value = (180.0/PI) * cvm::atan2(sin_phi, cos_phi); this->wrap(x); } @@ -368,7 +365,7 @@ void colvar::dihedral::calc_gradients() rB = 1.0/rB; B *= rB; - if (std::fabs(sin_phi) > 0.1) { + if (cvm::fabs(sin_phi) > 0.1) { rA = 1.0/rA; A *= rA; cvm::rvector const dcosdA = rA*(cos_phi*A-B); @@ -440,8 +437,8 @@ void colvar::dihedral::calc_force_invgrads() cvm::real const dot1 = u23 * u12; cvm::real const dot4 = u23 * u34; - cvm::real const fact1 = d12 * std::sqrt(1.0 - dot1 * dot1); - cvm::real const fact4 = d34 * std::sqrt(1.0 - dot4 * dot4); + cvm::real const fact1 = d12 * cvm::sqrt(1.0 - dot1 * dot1); + cvm::real const fact4 = d34 * cvm::sqrt(1.0 - dot4 * dot4); group1->read_total_forces(); if (is_enabled(f_cvc_one_site_total_force)) { @@ -508,19 +505,17 @@ colvarvalue colvar::dihedral::dist2_rgrad(colvarvalue const &x1, } -void colvar::dihedral::wrap(colvarvalue &x) const +void colvar::dihedral::wrap(colvarvalue &x_unwrapped) const { - if ((x.real_value - wrap_center) >= 180.0) { - x.real_value -= 360.0; + if ((x_unwrapped.real_value - wrap_center) >= 180.0) { + x_unwrapped.real_value -= 360.0; return; } - if ((x.real_value - wrap_center) < -180.0) { - x.real_value += 360.0; + if ((x_unwrapped.real_value - wrap_center) < -180.0) { + x_unwrapped.real_value += 360.0; return; } - - return; } @@ -548,8 +543,8 @@ void colvar::polar_theta::calc_value() cvm::rvector pos = atoms->center_of_mass(); r = atoms->center_of_mass().norm(); // Internal values of theta and phi are radians - theta = (r > 0.) ? std::acos(pos.z / r) : 0.; - phi = std::atan2(pos.y, pos.x); + theta = (r > 0.) ? cvm::acos(pos.z / r) : 0.; + phi = cvm::atan2(pos.y, pos.x); x.real_value = (180.0/PI) * theta; } @@ -560,9 +555,9 @@ void colvar::polar_theta::calc_gradients() atoms->set_weighted_gradient(cvm::rvector(0., 0., 0.)); else atoms->set_weighted_gradient(cvm::rvector( - (180.0/PI) * std::cos(theta) * std::cos(phi) / r, - (180.0/PI) * std::cos(theta) * std::sin(phi) / r, - (180.0/PI) * -std::sin(theta) / r)); + (180.0/PI) * cvm::cos(theta) * cvm::cos(phi) / r, + (180.0/PI) * cvm::cos(theta) * cvm::sin(phi) / r, + (180.0/PI) * -cvm::sin(theta) / r)); } @@ -602,8 +597,8 @@ void colvar::polar_phi::calc_value() cvm::rvector pos = atoms->center_of_mass(); r = atoms->center_of_mass().norm(); // Internal values of theta and phi are radians - theta = (r > 0.) ? std::acos(pos.z / r) : 0.; - phi = std::atan2(pos.y, pos.x); + theta = (r > 0.) ? cvm::acos(pos.z / r) : 0.; + phi = cvm::atan2(pos.y, pos.x); x.real_value = (180.0/PI) * phi; } @@ -611,8 +606,8 @@ void colvar::polar_phi::calc_value() void colvar::polar_phi::calc_gradients() { atoms->set_weighted_gradient(cvm::rvector( - (180.0/PI) * -std::sin(phi) / (r*std::sin(theta)), - (180.0/PI) * std::cos(phi) / (r*std::sin(theta)), + (180.0/PI) * -cvm::sin(phi) / (r*cvm::sin(theta)), + (180.0/PI) * cvm::cos(phi) / (r*cvm::sin(theta)), 0.)); } @@ -653,15 +648,15 @@ colvarvalue colvar::polar_phi::dist2_rgrad(colvarvalue const &x1, } -void colvar::polar_phi::wrap(colvarvalue &x) const +void colvar::polar_phi::wrap(colvarvalue &x_unwrapped) const { - if ((x.real_value - wrap_center) >= 180.0) { - x.real_value -= 360.0; + if ((x_unwrapped.real_value - wrap_center) >= 180.0) { + x_unwrapped.real_value -= 360.0; return; } - if ((x.real_value - wrap_center) < -180.0) { - x.real_value += 360.0; + if ((x_unwrapped.real_value - wrap_center) < -180.0) { + x_unwrapped.real_value += 360.0; return; } diff --git a/lib/colvars/colvarcomp_coordnums.cpp b/lib/colvars/colvarcomp_coordnums.cpp index ec53391ef5..059b0c825b 100644 --- a/lib/colvars/colvarcomp_coordnums.cpp +++ b/lib/colvars/colvarcomp_coordnums.cpp @@ -7,8 +7,6 @@ // If you wish to distribute your changes, please submit them to the // Colvars repository at GitHub. -#include - #include "colvarmodule.h" #include "colvarparse.h" #include "colvaratoms.h" @@ -102,6 +100,12 @@ colvar::coordnum::coordnum(std::string const &conf) group1 = parse_group(conf, "group1"); group2 = parse_group(conf, "group2"); + if (group1 == NULL || group2 == NULL) { + cvm::error("Error: failed to initialize atom groups.\n", + INPUT_ERROR); + return; + } + if (int atom_number = cvm::atom_group::overlap(*group1, *group2)) { cvm::error("Error: group1 and group2 share a common atom (number: " + cvm::to_str(atom_number) + ")\n", INPUT_ERROR); @@ -408,12 +412,6 @@ colvar::h_bond::h_bond() } -colvar::h_bond::~h_bond() -{ - delete atom_groups[0]; -} - - void colvar::h_bond::calc_value() { int const flags = coordnum::ef_null; @@ -655,8 +653,6 @@ colvar::groupcoordnum::groupcoordnum() void colvar::groupcoordnum::calc_value() { - cvm::rvector const r0_vec(0.0); // TODO enable the flag? - // create fake atoms to hold the com coordinates cvm::atom group1_com_atom; cvm::atom group2_com_atom; @@ -680,8 +676,6 @@ void colvar::groupcoordnum::calc_value() void colvar::groupcoordnum::calc_gradients() { - cvm::rvector const r0_vec(0.0); // TODO enable the flag? - cvm::atom group1_com_atom; cvm::atom group2_com_atom; group1_com_atom.pos = group1->center_of_mass(); diff --git a/lib/colvars/colvarcomp_distances.cpp b/lib/colvars/colvarcomp_distances.cpp index a2b1a5cd23..d9cd9d55e4 100644 --- a/lib/colvars/colvarcomp_distances.cpp +++ b/lib/colvars/colvarcomp_distances.cpp @@ -7,8 +7,6 @@ // If you wish to distribute your changes, please submit them to the // Colvars repository at GitHub. -#include - #include "colvarmodule.h" #include "colvarvalue.h" #include "colvarparse.h" @@ -102,7 +100,7 @@ colvar::distance_vec::distance_vec(std::string const &conf) { function_type = "distance_vec"; enable(f_cvc_com_based); - enable(f_cvc_implicit_gradient); + disable(f_cvc_explicit_gradient); x.type(colvarvalue::type_3vector); } @@ -112,7 +110,7 @@ colvar::distance_vec::distance_vec() { function_type = "distance_vec"; enable(f_cvc_com_based); - enable(f_cvc_implicit_gradient); + disable(f_cvc_explicit_gradient); x.type(colvarvalue::type_3vector); } @@ -320,7 +318,7 @@ cvm::real colvar::distance_z::dist2(colvarvalue const &x1, { cvm::real diff = x1.real_value - x2.real_value; if (b_periodic) { - cvm::real shift = std::floor(diff/period + 0.5); + cvm::real shift = cvm::floor(diff/period + 0.5); diff -= shift * period; } return diff * diff; @@ -332,7 +330,7 @@ colvarvalue colvar::distance_z::dist2_lgrad(colvarvalue const &x1, { cvm::real diff = x1.real_value - x2.real_value; if (b_periodic) { - cvm::real shift = std::floor(diff/period + 0.5); + cvm::real shift = cvm::floor(diff/period + 0.5); diff -= shift * period; } return 2.0 * diff; @@ -344,22 +342,23 @@ colvarvalue colvar::distance_z::dist2_rgrad(colvarvalue const &x1, { cvm::real diff = x1.real_value - x2.real_value; if (b_periodic) { - cvm::real shift = std::floor(diff/period + 0.5); + cvm::real shift = cvm::floor(diff/period + 0.5); diff -= shift * period; } return (-2.0) * diff; } -void colvar::distance_z::wrap(colvarvalue &x) const +void colvar::distance_z::wrap(colvarvalue &x_unwrapped) const { if (!b_periodic) { // don't wrap if the period has not been set return; } - cvm::real shift = std::floor((x.real_value - wrap_center) / period + 0.5); - x.real_value -= shift * period; + cvm::real shift = + cvm::floor((x_unwrapped.real_value - wrap_center) / period + 0.5); + x_unwrapped.real_value -= shift * period; return; } @@ -481,7 +480,7 @@ colvar::distance_dir::distance_dir(std::string const &conf) { function_type = "distance_dir"; enable(f_cvc_com_based); - enable(f_cvc_implicit_gradient); + disable(f_cvc_explicit_gradient); x.type(colvarvalue::type_unit3vector); } @@ -491,7 +490,7 @@ colvar::distance_dir::distance_dir() { function_type = "distance_dir"; enable(f_cvc_com_based); - enable(f_cvc_implicit_gradient); + disable(f_cvc_explicit_gradient); x.type(colvarvalue::type_unit3vector); } @@ -629,7 +628,7 @@ void colvar::distance_inv::calc_value() } x.real_value *= 1.0 / cvm::real(group1->size() * group2->size()); - x.real_value = std::pow(x.real_value, -1.0/cvm::real(exponent)); + x.real_value = cvm::pow(x.real_value, -1.0/cvm::real(exponent)); cvm::real const dxdsum = (-1.0/(cvm::real(exponent))) * cvm::integer_power(x.real_value, exponent+1) / @@ -671,7 +670,7 @@ colvar::distance_pairs::distance_pairs(std::string const &conf) group2 = parse_group(conf, "group2"); x.type(colvarvalue::type_vector); - enable(f_cvc_implicit_gradient); + disable(f_cvc_explicit_gradient); x.vector1d_value.resize(group1->size() * group2->size()); } @@ -679,7 +678,7 @@ colvar::distance_pairs::distance_pairs(std::string const &conf) colvar::distance_pairs::distance_pairs() { function_type = "distance_pairs"; - enable(f_cvc_implicit_gradient); + disable(f_cvc_explicit_gradient); x.type(colvarvalue::type_vector); } @@ -747,6 +746,63 @@ void colvar::distance_pairs::apply_force(colvarvalue const &force) +colvar::dipole_magnitude::dipole_magnitude(std::string const &conf) + : cvc(conf) +{ + function_type = "dipole_magnitude"; + atoms = parse_group(conf, "atoms"); + init_total_force_params(conf); + x.type(colvarvalue::type_scalar); +} + + +colvar::dipole_magnitude::dipole_magnitude(cvm::atom const &a1) +{ + atoms = new cvm::atom_group(std::vector(1, a1)); + register_atom_group(atoms); + x.type(colvarvalue::type_scalar); +} + + +colvar::dipole_magnitude::dipole_magnitude() +{ + function_type = "dipole_magnitude"; + x.type(colvarvalue::type_scalar); +} + + +void colvar::dipole_magnitude::calc_value() +{ + cvm::atom_pos const atomsCom = atoms->center_of_mass(); + atoms->calc_dipole(atomsCom); + dipoleV = atoms->dipole(); + x.real_value = dipoleV.norm(); +} + + +void colvar::dipole_magnitude::calc_gradients() +{ + cvm::real const aux1 = atoms->total_charge/atoms->total_mass; + cvm::atom_pos const dipVunit = dipoleV.unit(); + + for (cvm::atom_iter ai = atoms->begin(); ai != atoms->end(); ai++) { + ai->grad = (ai->charge - aux1*ai->mass) * dipVunit; + } +} + + +void colvar::dipole_magnitude::apply_force(colvarvalue const &force) +{ + if (!atoms->noforce) { + atoms->apply_colvar_force(force.real_value); + } +} + + +simple_scalar_dist_functions(dipole_magnitude) + + + colvar::gyration::gyration(std::string const &conf) : cvc(conf) { @@ -782,7 +838,7 @@ void colvar::gyration::calc_value() for (cvm::atom_iter ai = atoms->begin(); ai != atoms->end(); ai++) { x.real_value += (ai->pos).norm2(); } - x.real_value = std::sqrt(x.real_value / cvm::real(atoms->size())); + x.real_value = cvm::sqrt(x.real_value / cvm::real(atoms->size())); } @@ -1029,7 +1085,7 @@ void colvar::rmsd::calc_value() x.real_value += ((*atoms)[ia].pos - ref_pos[ia]).norm2(); } x.real_value /= cvm::real(atoms->size()); // MSD - x.real_value = std::sqrt(x.real_value); + x.real_value = cvm::sqrt(x.real_value); } @@ -1405,7 +1461,7 @@ void colvar::eigenvector::calc_Jacobian_derivative() } } - jd.real_value = sum * std::sqrt(eigenvec_invnorm2); + jd.real_value = sum * cvm::sqrt(eigenvec_invnorm2); } @@ -1436,7 +1492,7 @@ colvar::cartesian::cartesian(std::string const &conf) } x.type(colvarvalue::type_vector); - enable(f_cvc_implicit_gradient); + disable(f_cvc_explicit_gradient); x.vector1d_value.resize(atoms->size() * axes.size()); } diff --git a/lib/colvars/colvarcomp_protein.cpp b/lib/colvars/colvarcomp_protein.cpp index 91e47f13d9..b9f9c60cdb 100644 --- a/lib/colvars/colvarcomp_protein.cpp +++ b/lib/colvars/colvarcomp_protein.cpp @@ -7,8 +7,6 @@ // If you wish to distribute your changes, please submit them to the // Colvars repository at GitHub. -#include - #include "colvarmodule.h" #include "colvarvalue.h" #include "colvarparse.h" @@ -27,7 +25,7 @@ colvar::alpha_angles::alpha_angles(std::string const &conf) cvm::log("Initializing alpha_angles object.\n"); function_type = "alpha_angles"; - enable(f_cvc_implicit_gradient); + enable(f_cvc_explicit_gradient); x.type(colvarvalue::type_scalar); std::string segment_id; @@ -118,7 +116,7 @@ colvar::alpha_angles::alpha_angles() : cvc() { function_type = "alpha_angles"; - enable(f_cvc_implicit_gradient); + enable(f_cvc_explicit_gradient); x.type(colvarvalue::type_scalar); } @@ -133,6 +131,8 @@ colvar::alpha_angles::~alpha_angles() delete hb.back(); hb.pop_back(); } + // Our references to atom groups have become invalid now that children cvcs are deleted + atom_groups.clear(); } @@ -191,6 +191,58 @@ void colvar::alpha_angles::calc_gradients() } +void colvar::alpha_angles::collect_gradients(std::vector const &atom_ids, std::vector &atomic_gradients) +{ + cvm::real cvc_coeff = sup_coeff * cvm::real(sup_np) * cvm::integer_power(value().real_value, sup_np-1); + + if (theta.size()) { + cvm::real const theta_norm = (1.0-hb_coeff) / cvm::real(theta.size()); + + for (size_t i = 0; i < theta.size(); i++) { + cvm::real const t = ((theta[i])->value().real_value-theta_ref)/theta_tol; + cvm::real const f = ( (1.0 - (t*t)) / + (1.0 - (t*t*t*t)) ); + cvm::real const dfdt = + 1.0/(1.0 - (t*t*t*t)) * + ( (-2.0 * t) + (-1.0*f)*(-4.0 * (t*t*t)) ); + + // Coeficient of this CVC's gradient in the colvar gradient, times coefficient of this + // angle's gradient in the CVC's gradient + cvm::real const coeff = cvc_coeff * theta_norm * dfdt * (1.0/theta_tol); + + for (size_t j = 0; j < theta[i]->atom_groups.size(); j++) { + cvm::atom_group &ag = *(theta[i]->atom_groups[j]); + for (size_t k = 0; k < ag.size(); k++) { + size_t a = std::lower_bound(atom_ids.begin(), atom_ids.end(), + ag[k].id) - atom_ids.begin(); + atomic_gradients[a] += coeff * ag[k].grad; + } + } + } + } + + if (hb.size()) { + + cvm::real const hb_norm = hb_coeff / cvm::real(hb.size()); + + for (size_t i = 0; i < hb.size(); i++) { + // Coeficient of this CVC's gradient in the colvar gradient, times coefficient of this + // hbond's gradient in the CVC's gradient + cvm::real const coeff = cvc_coeff * 0.5 * hb_norm; + + for (size_t j = 0; j < hb[i]->atom_groups.size(); j++) { + cvm::atom_group &ag = *(hb[i]->atom_groups[j]); + for (size_t k = 0; k < ag.size(); k++) { + size_t a = std::lower_bound(atom_ids.begin(), atom_ids.end(), + ag[k].id) - atom_ids.begin(); + atomic_gradients[a] += coeff * ag[k].grad; + } + } + } + } +} + + void colvar::alpha_angles::apply_force(colvarvalue const &force) { @@ -242,7 +294,8 @@ colvar::dihedPC::dihedPC(std::string const &conf) cvm::log("Initializing dihedral PC object.\n"); function_type = "dihedPC"; - enable(f_cvc_implicit_gradient); + // Supported through references to atom groups of children cvcs + enable(f_cvc_explicit_gradient); x.type(colvarvalue::type_scalar); std::string segment_id; @@ -372,7 +425,8 @@ colvar::dihedPC::dihedPC() : cvc() { function_type = "dihedPC"; - enable(f_cvc_implicit_gradient); + // Supported through references to atom groups of children cvcs + enable(f_cvc_explicit_gradient); x.type(colvarvalue::type_scalar); } @@ -383,6 +437,8 @@ colvar::dihedPC::~dihedPC() delete theta.back(); theta.pop_back(); } + // Our references to atom groups have become invalid now that children cvcs are deleted + atom_groups.clear(); } @@ -392,8 +448,8 @@ void colvar::dihedPC::calc_value() for (size_t i = 0; i < theta.size(); i++) { theta[i]->calc_value(); cvm::real const t = (PI / 180.) * theta[i]->value().real_value; - x.real_value += coeffs[2*i ] * std::cos(t) - + coeffs[2*i+1] * std::sin(t); + x.real_value += coeffs[2*i ] * cvm::cos(t) + + coeffs[2*i+1] * cvm::sin(t); } } @@ -406,12 +462,35 @@ void colvar::dihedPC::calc_gradients() } +void colvar::dihedPC::collect_gradients(std::vector const &atom_ids, std::vector &atomic_gradients) +{ + cvm::real cvc_coeff = sup_coeff * cvm::real(sup_np) * cvm::integer_power(value().real_value, sup_np-1); + for (size_t i = 0; i < theta.size(); i++) { + cvm::real const t = (PI / 180.) * theta[i]->value().real_value; + cvm::real const dcosdt = - (PI / 180.) * cvm::sin(t); + cvm::real const dsindt = (PI / 180.) * cvm::cos(t); + // Coeficient of this dihedPC's gradient in the colvar gradient, times coefficient of this + // dihedral's gradient in the dihedPC's gradient + cvm::real const coeff = cvc_coeff * (coeffs[2*i] * dcosdt + coeffs[2*i+1] * dsindt); + + for (size_t j = 0; j < theta[i]->atom_groups.size(); j++) { + cvm::atom_group &ag = *(theta[i]->atom_groups[j]); + for (size_t k = 0; k < ag.size(); k++) { + size_t a = std::lower_bound(atom_ids.begin(), atom_ids.end(), + ag[k].id) - atom_ids.begin(); + atomic_gradients[a] += coeff * ag[k].grad; + } + } + } +} + + void colvar::dihedPC::apply_force(colvarvalue const &force) { for (size_t i = 0; i < theta.size(); i++) { cvm::real const t = (PI / 180.) * theta[i]->value().real_value; - cvm::real const dcosdt = - (PI / 180.) * std::sin(t); - cvm::real const dsindt = (PI / 180.) * std::cos(t); + cvm::real const dcosdt = - (PI / 180.) * cvm::sin(t); + cvm::real const dsindt = (PI / 180.) * cvm::cos(t); theta[i]->apply_force((coeffs[2*i ] * dcosdt + coeffs[2*i+1] * dsindt) * force); diff --git a/lib/colvars/colvarcomp_rotations.cpp b/lib/colvars/colvarcomp_rotations.cpp index 498ef7c2f5..3c8d0b4af6 100644 --- a/lib/colvars/colvarcomp_rotations.cpp +++ b/lib/colvars/colvarcomp_rotations.cpp @@ -7,8 +7,6 @@ // If you wish to distribute your changes, please submit them to the // Colvars repository at GitHub. -#include - #include "colvarmodule.h" #include "colvarvalue.h" #include "colvarparse.h" @@ -18,21 +16,27 @@ colvar::orientation::orientation(std::string const &conf) - : cvc(conf) + : cvc() { function_type = "orientation"; - atoms = parse_group(conf, "atoms"); - enable(f_cvc_implicit_gradient); + disable(f_cvc_explicit_gradient); x.type(colvarvalue::type_quaternion); + init(conf); +} + +int colvar::orientation::init(std::string const &conf) +{ + int error_code = cvc::init(conf); + + atoms = parse_group(conf, "atoms"); ref_pos.reserve(atoms->size()); if (get_keyval(conf, "refPositions", ref_pos, ref_pos)) { cvm::log("Using reference positions from input file.\n"); if (ref_pos.size() != atoms->size()) { - cvm::error("Error: reference positions do not " - "match the number of requested atoms.\n"); - return; + return cvm::error("Error: reference positions do not " + "match the number of requested atoms.\n", INPUT_ERROR); } } @@ -46,9 +50,8 @@ colvar::orientation::orientation(std::string const &conf) // use PDB flags if column is provided bool found = get_keyval(conf, "refPositionsColValue", file_col_value, 0.0); if (found && file_col_value==0.0) { - cvm::error("Error: refPositionsColValue, " - "if provided, must be non-zero.\n"); - return; + return cvm::error("Error: refPositionsColValue, " + "if provided, must be non-zero.\n", INPUT_ERROR); } } @@ -59,9 +62,8 @@ colvar::orientation::orientation(std::string const &conf) } if (!ref_pos.size()) { - cvm::error("Error: must define a set of " - "reference coordinates.\n"); - return; + return cvm::error("Error: must define a set of " + "reference coordinates.\n", INPUT_ERROR); } @@ -85,6 +87,7 @@ colvar::orientation::orientation(std::string const &conf) rot.request_group2_gradients(atoms->size()); } + return error_code; } @@ -92,7 +95,7 @@ colvar::orientation::orientation() : cvc() { function_type = "orientation"; - enable(f_cvc_implicit_gradient); + disable(f_cvc_explicit_gradient); x.type(colvarvalue::type_quaternion); } @@ -158,10 +161,18 @@ colvarvalue colvar::orientation::dist2_rgrad(colvarvalue const &x1, colvar::orientation_angle::orientation_angle(std::string const &conf) - : orientation(conf) + : orientation() { function_type = "orientation_angle"; + enable(f_cvc_explicit_gradient); x.type(colvarvalue::type_scalar); + init(conf); +} + + +int colvar::orientation_angle::init(std::string const &conf) +{ + return orientation::init(conf); } @@ -169,6 +180,7 @@ colvar::orientation_angle::orientation_angle() : orientation() { function_type = "orientation_angle"; + enable(f_cvc_explicit_gradient); x.type(colvarvalue::type_scalar); } @@ -180,9 +192,9 @@ void colvar::orientation_angle::calc_value() rot.calc_optimal_rotation(ref_pos, atoms->positions_shifted(-1.0 * atoms_cog)); if ((rot.q).q0 >= 0.0) { - x.real_value = (180.0/PI) * 2.0 * std::acos((rot.q).q0); + x.real_value = (180.0/PI) * 2.0 * cvm::acos((rot.q).q0); } else { - x.real_value = (180.0/PI) * 2.0 * std::acos(-1.0 * (rot.q).q0); + x.real_value = (180.0/PI) * 2.0 * cvm::acos(-1.0 * (rot.q).q0); } } @@ -191,7 +203,7 @@ void colvar::orientation_angle::calc_gradients() { cvm::real const dxdq0 = ( ((rot.q).q0 * (rot.q).q0 < 1.0) ? - ((180.0 / PI) * (-2.0) / std::sqrt(1.0 - ((rot.q).q0 * (rot.q).q0))) : + ((180.0 / PI) * (-2.0) / cvm::sqrt(1.0 - ((rot.q).q0 * (rot.q).q0))) : 0.0 ); for (size_t ia = 0; ia < atoms->size(); ia++) { @@ -214,10 +226,18 @@ simple_scalar_dist_functions(orientation_angle) colvar::orientation_proj::orientation_proj(std::string const &conf) - : orientation(conf) + : orientation() { function_type = "orientation_proj"; + enable(f_cvc_explicit_gradient); x.type(colvarvalue::type_scalar); + init(conf); +} + + +int colvar::orientation_proj::init(std::string const &conf) +{ + return orientation::init(conf); } @@ -225,6 +245,7 @@ colvar::orientation_proj::orientation_proj() : orientation() { function_type = "orientation_proj"; + enable(f_cvc_explicit_gradient); x.type(colvarvalue::type_scalar); } @@ -261,18 +282,28 @@ simple_scalar_dist_functions(orientation_proj) colvar::tilt::tilt(std::string const &conf) - : orientation(conf) + : orientation() { function_type = "tilt"; + enable(f_cvc_explicit_gradient); + x.type(colvarvalue::type_scalar); + init(conf); +} + + +int colvar::tilt::init(std::string const &conf) +{ + int error_code = COLVARS_OK; + + error_code |= orientation::init(conf); get_keyval(conf, "axis", axis, cvm::rvector(0.0, 0.0, 1.0)); - if (axis.norm2() != 1.0) { axis /= axis.norm(); cvm::log("Normalizing rotation axis to "+cvm::to_str(axis)+".\n"); } - x.type(colvarvalue::type_scalar); + return error_code; } @@ -280,6 +311,7 @@ colvar::tilt::tilt() : orientation() { function_type = "tilt"; + enable(f_cvc_explicit_gradient); x.type(colvarvalue::type_scalar); } @@ -322,20 +354,30 @@ simple_scalar_dist_functions(tilt) colvar::spin_angle::spin_angle(std::string const &conf) - : orientation(conf) + : orientation() { function_type = "spin_angle"; + period = 360.0; + b_periodic = true; + enable(f_cvc_explicit_gradient); + x.type(colvarvalue::type_scalar); + init(conf); +} + + +int colvar::spin_angle::init(std::string const &conf) +{ + int error_code = COLVARS_OK; + + error_code |= orientation::init(conf); get_keyval(conf, "axis", axis, cvm::rvector(0.0, 0.0, 1.0)); - if (axis.norm2() != 1.0) { axis /= axis.norm(); cvm::log("Normalizing rotation axis to "+cvm::to_str(axis)+".\n"); } - period = 360.0; - b_periodic = true; - x.type(colvarvalue::type_scalar); + return error_code; } @@ -345,6 +387,7 @@ colvar::spin_angle::spin_angle() function_type = "spin_angle"; period = 360.0; b_periodic = true; + enable(f_cvc_explicit_gradient); x.type(colvarvalue::type_scalar); } @@ -410,15 +453,15 @@ colvarvalue colvar::spin_angle::dist2_rgrad(colvarvalue const &x1, } -void colvar::spin_angle::wrap(colvarvalue &x) const +void colvar::spin_angle::wrap(colvarvalue &x_unwrapped) const { - if ((x.real_value - wrap_center) >= 180.0) { - x.real_value -= 360.0; + if ((x_unwrapped.real_value - wrap_center) >= 180.0) { + x_unwrapped.real_value -= 360.0; return; } - if ((x.real_value - wrap_center) < -180.0) { - x.real_value += 360.0; + if ((x_unwrapped.real_value - wrap_center) < -180.0) { + x_unwrapped.real_value += 360.0; return; } diff --git a/lib/colvars/colvardeps.cpp b/lib/colvars/colvardeps.cpp index d20ee6e55c..276f2b39e7 100644 --- a/lib/colvars/colvardeps.cpp +++ b/lib/colvars/colvardeps.cpp @@ -122,12 +122,7 @@ bool colvardeps::get_keyval_feature(colvarparse *cvp, int colvardeps::enable(int feature_id, bool dry_run /* default: false */, - // dry_run: fail silently, do not enable if available - // flag is passed recursively to deps of this feature bool toplevel /* default: true */) -// toplevel: false if this is called as part of a chain of dependency resolution -// this is used to diagnose failed dependencies by displaying the full stack -// only the toplevel dependency will throw a fatal error { int res; size_t i, j; @@ -143,8 +138,7 @@ int colvardeps::enable(int feature_id, if (fs->enabled) { if (!(dry_run || toplevel)) { - // This is a dependency - // Prevent disabling this feature as long + // This is a dependency: prevent disabling this feature as long // as requirement is enabled fs->ref_count++; if (cvm::debug()) @@ -173,7 +167,10 @@ int colvardeps::enable(int feature_id, if (!toplevel && !is_dynamic(feature_id)) { if (!dry_run) { cvm::log(feature_type_descr + " feature \"" + f->description - + "\" may not be enabled as a dependency in " + description + ".\n"); + + "\" cannot be enabled automatically in " + description + "."); + if (is_user(feature_id)) { + cvm::log("Try setting it manually.\n"); + } } return COLVARS_ERROR; } @@ -354,6 +351,7 @@ int colvardeps::disable(int feature_id) { return COLVARS_OK; } + int colvardeps::decr_ref_count(int feature_id) { int &rc = feature_states[feature_id].ref_count; feature *f = features()[feature_id]; @@ -379,324 +377,52 @@ int colvardeps::decr_ref_count(int feature_id) { return COLVARS_OK; } -void colvardeps::init_feature(int feature_id, const char *description, feature_type type) { - modify_features()[feature_id]->description = description; + +void colvardeps::init_feature(int feature_id, const char *description_in, feature_type type) { + modify_features()[feature_id]->description = description_in; modify_features()[feature_id]->type = type; } -// Shorthand macros for describing dependencies -#define f_req_self(f, g) features()[f]->requires_self.push_back(g) -// This macro ensures that exclusions are symmetric -#define f_req_exclude(f, g) features()[f]->requires_exclude.push_back(g); \ - features()[g]->requires_exclude.push_back(f) -#define f_req_children(f, g) features()[f]->requires_children.push_back(g) -#define f_req_alt2(f, g, h) features()[f]->requires_alt.push_back(std::vector(2));\ - features()[f]->requires_alt.back()[0] = g; \ - features()[f]->requires_alt.back()[1] = h -#define f_req_alt3(f, g, h, i) features()[f]->requires_alt.push_back(std::vector(3));\ - features()[f]->requires_alt.back()[0] = g; \ - features()[f]->requires_alt.back()[1] = h; \ - features()[f]->requires_alt.back()[2] = i -#define f_req_alt4(f, g, h, i, j) features()[f]->requires_alt.push_back(std::vector(4));\ - features()[f]->requires_alt.back()[0] = g; \ - features()[f]->requires_alt.back()[1] = h; \ - features()[f]->requires_alt.back()[2] = i; \ - features()[f]->requires_alt.back()[3] = j -void colvardeps::init_cvb_requires() { - int i; - if (features().size() == 0) { - for (i = 0; i < f_cvb_ntot; i++) { - modify_features().push_back(new feature); - } - - init_feature(f_cvb_active, "active", f_type_dynamic); - f_req_children(f_cvb_active, f_cv_active); - - init_feature(f_cvb_awake, "awake", f_type_static); - f_req_self(f_cvb_awake, f_cvb_active); - - init_feature(f_cvb_apply_force, "apply force", f_type_user); - f_req_children(f_cvb_apply_force, f_cv_gradient); - - init_feature(f_cvb_get_total_force, "obtain total force", f_type_dynamic); - f_req_children(f_cvb_get_total_force, f_cv_total_force); - - init_feature(f_cvb_output_acc_work, "output accumulated work", f_type_user); - f_req_self(f_cvb_output_acc_work, f_cvb_apply_force); - - init_feature(f_cvb_history_dependent, "history-dependent", f_type_static); - - init_feature(f_cvb_time_dependent, "time-dependent", f_type_static); - - init_feature(f_cvb_scalar_variables, "require scalar variables", f_type_static); - f_req_children(f_cvb_scalar_variables, f_cv_scalar); - - init_feature(f_cvb_calc_pmf, "calculate a PMF", f_type_static); - - init_feature(f_cvb_calc_ti_samples, "calculate TI samples", f_type_dynamic); - f_req_self(f_cvb_calc_ti_samples, f_cvb_get_total_force); - f_req_children(f_cvb_calc_ti_samples, f_cv_grid); - - init_feature(f_cvb_write_ti_samples, "write TI samples ", f_type_user); - f_req_self(f_cvb_write_ti_samples, f_cvb_calc_ti_samples); - - init_feature(f_cvb_write_ti_pmf, "write TI PMF", f_type_user); - f_req_self(f_cvb_write_ti_pmf, f_cvb_calc_ti_samples); - } - - // Initialize feature_states for each instance - feature_states.reserve(f_cvb_ntot); - for (i = 0; i < f_cvb_ntot; i++) { - feature_states.push_back(feature_state(true, false)); - // Most features are available, so we set them so - // and list exceptions below - } - - // only compute TI samples when deriving from colvarbias_ti - feature_states[f_cvb_calc_ti_samples].available = false; +// Shorthand functions for describing dependencies +void colvardeps::require_feature_self(int f, int g) { + features()[f]->requires_self.push_back(g); } -void colvardeps::init_cv_requires() { - size_t i; - if (features().size() == 0) { - for (i = 0; i < f_cv_ntot; i++) { - modify_features().push_back(new feature); - } - - init_feature(f_cv_active, "active", f_type_dynamic); - // Do not require f_cvc_active in children, as some components may be disabled - // Colvars must be either a linear combination, or scalar (and polynomial) or scripted/custom - f_req_alt4(f_cv_active, f_cv_scalar, f_cv_linear, f_cv_scripted, f_cv_custom_function); - - init_feature(f_cv_awake, "awake", f_type_static); - f_req_self(f_cv_awake, f_cv_active); - - init_feature(f_cv_gradient, "gradient", f_type_dynamic); - f_req_children(f_cv_gradient, f_cvc_gradient); - - init_feature(f_cv_collect_gradient, "collect gradient", f_type_dynamic); - f_req_self(f_cv_collect_gradient, f_cv_gradient); - f_req_self(f_cv_collect_gradient, f_cv_scalar); - // The following exlusion could be lifted by implementing the feature - f_req_exclude(f_cv_collect_gradient, f_cv_scripted); - - init_feature(f_cv_fdiff_velocity, "velocity from finite differences", f_type_dynamic); - - // System force: either trivial (spring force); through extended Lagrangian, or calculated explicitly - init_feature(f_cv_total_force, "total force", f_type_dynamic); - f_req_alt2(f_cv_total_force, f_cv_extended_Lagrangian, f_cv_total_force_calc); - - // Deps for explicit total force calculation - init_feature(f_cv_total_force_calc, "total force calculation", f_type_dynamic); - f_req_self(f_cv_total_force_calc, f_cv_scalar); - f_req_self(f_cv_total_force_calc, f_cv_linear); - f_req_children(f_cv_total_force_calc, f_cvc_inv_gradient); - f_req_self(f_cv_total_force_calc, f_cv_Jacobian); - - init_feature(f_cv_Jacobian, "Jacobian derivative", f_type_dynamic); - f_req_self(f_cv_Jacobian, f_cv_scalar); - f_req_self(f_cv_Jacobian, f_cv_linear); - f_req_children(f_cv_Jacobian, f_cvc_Jacobian); - - init_feature(f_cv_hide_Jacobian, "hide Jacobian force", f_type_user); - f_req_self(f_cv_hide_Jacobian, f_cv_Jacobian); // can only hide if calculated - - init_feature(f_cv_extended_Lagrangian, "extended Lagrangian", f_type_user); - f_req_self(f_cv_extended_Lagrangian, f_cv_scalar); - f_req_self(f_cv_extended_Lagrangian, f_cv_gradient); - - init_feature(f_cv_Langevin, "Langevin dynamics", f_type_user); - f_req_self(f_cv_Langevin, f_cv_extended_Lagrangian); - - init_feature(f_cv_linear, "linear", f_type_static); - - init_feature(f_cv_scalar, "scalar", f_type_static); - - init_feature(f_cv_output_energy, "output energy", f_type_user); - - init_feature(f_cv_output_value, "output value", f_type_user); - - init_feature(f_cv_output_velocity, "output velocity", f_type_user); - f_req_self(f_cv_output_velocity, f_cv_fdiff_velocity); - - init_feature(f_cv_output_applied_force, "output applied force", f_type_user); - - init_feature(f_cv_output_total_force, "output total force", f_type_user); - f_req_self(f_cv_output_total_force, f_cv_total_force); - - init_feature(f_cv_subtract_applied_force, "subtract applied force from total force", f_type_user); - f_req_self(f_cv_subtract_applied_force, f_cv_total_force); - - init_feature(f_cv_lower_boundary, "lower boundary", f_type_user); - f_req_self(f_cv_lower_boundary, f_cv_scalar); - - init_feature(f_cv_upper_boundary, "upper boundary", f_type_user); - f_req_self(f_cv_upper_boundary, f_cv_scalar); - - init_feature(f_cv_grid, "grid", f_type_dynamic); - f_req_self(f_cv_grid, f_cv_lower_boundary); - f_req_self(f_cv_grid, f_cv_upper_boundary); - - init_feature(f_cv_runave, "running average", f_type_user); - - init_feature(f_cv_corrfunc, "correlation function", f_type_user); - - init_feature(f_cv_scripted, "scripted", f_type_user); - - init_feature(f_cv_custom_function, "custom function", f_type_user); - f_req_exclude(f_cv_custom_function, f_cv_scripted); - - init_feature(f_cv_periodic, "periodic", f_type_static); - f_req_self(f_cv_periodic, f_cv_scalar); - init_feature(f_cv_scalar, "scalar", f_type_static); - init_feature(f_cv_linear, "linear", f_type_static); - init_feature(f_cv_homogeneous, "homogeneous", f_type_static); - - // because total forces are obtained from the previous time step, - // we cannot (currently) have colvar values and total forces for the same timestep - init_feature(f_cv_multiple_ts, "multiple timestep colvar"); - f_req_exclude(f_cv_multiple_ts, f_cv_total_force_calc); - } - - // Initialize feature_states for each instance - feature_states.reserve(f_cv_ntot); - for (i = 0; i < f_cv_ntot; i++) { - feature_states.push_back(feature_state(true, false)); - // Most features are available, so we set them so - // and list exceptions below - } - - feature_states[f_cv_fdiff_velocity].available = - cvm::main()->proxy->simulation_running(); +// Ensure that exclusions are symmetric +void colvardeps::exclude_feature_self(int f, int g) { + features()[f]->requires_exclude.push_back(g); + features()[g]->requires_exclude.push_back(f); } -void colvardeps::init_cvc_requires() { - size_t i; - // Initialize static array once and for all - if (features().size() == 0) { - for (i = 0; i < colvardeps::f_cvc_ntot; i++) { - modify_features().push_back(new feature); - } - - init_feature(f_cvc_active, "active", f_type_dynamic); -// The dependency below may become useful if we use dynamic atom groups -// f_req_children(f_cvc_active, f_ag_active); - - init_feature(f_cvc_scalar, "scalar", f_type_static); - - init_feature(f_cvc_gradient, "gradient", f_type_dynamic); - - init_feature(f_cvc_implicit_gradient, "implicit gradient", f_type_static); - f_req_children(f_cvc_implicit_gradient, f_ag_implicit_gradient); - - init_feature(f_cvc_inv_gradient, "inverse gradient", f_type_dynamic); - f_req_self(f_cvc_inv_gradient, f_cvc_gradient); - - init_feature(f_cvc_debug_gradient, "debug gradient", f_type_user); - f_req_self(f_cvc_debug_gradient, f_cvc_gradient); - f_req_exclude(f_cvc_debug_gradient, f_cvc_implicit_gradient); - - init_feature(f_cvc_Jacobian, "Jacobian derivative", f_type_dynamic); - f_req_self(f_cvc_Jacobian, f_cvc_inv_gradient); - - init_feature(f_cvc_com_based, "depends on group centers of mass", f_type_static); - - // init_feature(f_cvc_pbc_minimum_image, "use minimum-image distances with PBCs", f_type_user); - - // Compute total force on first site only to avoid unwanted - // coupling to other colvars (see e.g. Ciccotti et al., 2005) - init_feature(f_cvc_one_site_total_force, "compute total force from one group", f_type_user); - f_req_self(f_cvc_one_site_total_force, f_cvc_com_based); - - init_feature(f_cvc_scalable, "scalable calculation", f_type_static); - f_req_self(f_cvc_scalable, f_cvc_scalable_com); - - init_feature(f_cvc_scalable_com, "scalable calculation of centers of mass", f_type_static); - f_req_self(f_cvc_scalable_com, f_cvc_com_based); - - - // TODO only enable this when f_ag_scalable can be turned on for a pre-initialized group - // f_req_children(f_cvc_scalable, f_ag_scalable); - // f_req_children(f_cvc_scalable_com, f_ag_scalable_com); - } - - // Initialize feature_states for each instance - // default as available, not enabled - // except dynamic features which default as unavailable - feature_states.reserve(f_cvc_ntot); - for (i = 0; i < colvardeps::f_cvc_ntot; i++) { - bool avail = is_dynamic(i) ? false : true; - feature_states.push_back(feature_state(avail, false)); - } - - // CVCs are enabled from the start - get disabled based on flags - feature_states[f_cvc_active].enabled = true; - - // Features that are implemented by all cvcs by default - // Each cvc specifies what other features are available - feature_states[f_cvc_active].available = true; - feature_states[f_cvc_gradient].available = true; - - // Use minimum-image distances by default - feature_states[f_cvc_pbc_minimum_image].enabled = true; - - // Features that are implemented by default if their requirements are - feature_states[f_cvc_one_site_total_force].available = true; - - // Features That are implemented only for certain simulation engine configurations - feature_states[f_cvc_scalable_com].available = (cvm::proxy->scalable_group_coms() == COLVARS_OK); - feature_states[f_cvc_scalable].available = feature_states[f_cvc_scalable_com].available; +void colvardeps::require_feature_children(int f, int g) { + features()[f]->requires_children.push_back(g); } -void colvardeps::init_ag_requires() { - size_t i; - // Initialize static array once and for all - if (features().size() == 0) { - for (i = 0; i < f_ag_ntot; i++) { - modify_features().push_back(new feature); - } +void colvardeps::require_feature_alt(int f, int g, int h) { + features()[f]->requires_alt.push_back(std::vector(2)); + features()[f]->requires_alt.back()[0] = g; + features()[f]->requires_alt.back()[1] = h; +} - init_feature(f_ag_active, "active", f_type_dynamic); - init_feature(f_ag_center, "translational fit", f_type_static); - init_feature(f_ag_rotate, "rotational fit", f_type_static); - init_feature(f_ag_fitting_group, "reference positions group", f_type_static); - init_feature(f_ag_implicit_gradient, "implicit atom gradient", f_type_dynamic); - init_feature(f_ag_fit_gradients, "fit gradients", f_type_user); - f_req_exclude(f_ag_fit_gradients, f_ag_implicit_gradient); - init_feature(f_ag_atom_forces, "atomic forces", f_type_dynamic); +void colvardeps::require_feature_alt(int f, int g, int h, int i) { + features()[f]->requires_alt.push_back(std::vector(3)); + features()[f]->requires_alt.back()[0] = g; + features()[f]->requires_alt.back()[1] = h; + features()[f]->requires_alt.back()[2] = i; +} - // parallel calculation implies that we have at least a scalable center of mass, - // but f_ag_scalable is kept as a separate feature to deal with future dependencies - init_feature(f_ag_scalable, "scalable group calculation", f_type_static); - init_feature(f_ag_scalable_com, "scalable group center of mass calculation", f_type_static); - f_req_self(f_ag_scalable, f_ag_scalable_com); -// init_feature(f_ag_min_msd_fit, "minimum MSD fit") -// f_req_self(f_ag_min_msd_fit, f_ag_center) -// f_req_self(f_ag_min_msd_fit, f_ag_rotate) -// f_req_exclude(f_ag_min_msd_fit, f_ag_fitting_group) - } - - // Initialize feature_states for each instance - // default as unavailable, not enabled - feature_states.reserve(f_ag_ntot); - for (i = 0; i < colvardeps::f_ag_ntot; i++) { - feature_states.push_back(feature_state(false, false)); - } - - // Features that are implemented (or not) by all atom groups - feature_states[f_ag_active].available = true; - // f_ag_scalable_com is provided by the CVC iff it is COM-based - feature_states[f_ag_scalable_com].available = false; - // TODO make f_ag_scalable depend on f_ag_scalable_com (or something else) - feature_states[f_ag_scalable].available = true; - feature_states[f_ag_fit_gradients].available = true; - feature_states[f_ag_implicit_gradient].available = true; +void colvardeps::require_feature_alt(int f, int g, int h, int i, int j) { + features()[f]->requires_alt.push_back(std::vector(4)); + features()[f]->requires_alt.back()[0] = g; + features()[f]->requires_alt.back()[1] = h; + features()[f]->requires_alt.back()[2] = i; + features()[f]->requires_alt.back()[3] = j; } @@ -720,7 +446,7 @@ void colvardeps::print_state() { void colvardeps::add_child(colvardeps *child) { children.push_back(child); - child->parents.push_back((colvardeps *)this); + child->parents.push_back(this); // Solve dependencies of already enabled parent features // in the new child diff --git a/lib/colvars/colvardeps.h b/lib/colvars/colvardeps.h index 940eefb01b..198a24f330 100644 --- a/lib/colvars/colvardeps.h +++ b/lib/colvars/colvardeps.h @@ -23,7 +23,11 @@ /// 3. Static features are static properties of the object, determined /// programatically at initialization time. /// -/// In all classes, feature 0 is active. When an object is inactivated +/// The following diagram summarizes the dependency tree at the bias, colvar, and colvarcomp levels. +/// Isolated and atom group features are not shown to save space. +/// @image html deps_2019.svg +/// +/// In all classes, feature 0 is `active`. When an object is inactivated /// all its children dependencies are dereferenced (free_children_deps) /// While the object is inactive, no dependency solving is done on children /// it is done when the object is activated back (restore_children_deps) @@ -72,7 +76,6 @@ protected: /// Unused by lower-level objects (cvcs and atom groups) int time_step_factor; -private: /// List of the states of all features std::vector feature_states; @@ -89,14 +92,14 @@ public: inline int get_time_step_factor() const {return time_step_factor;} /// Pair a numerical feature ID with a description and type - void init_feature(int feature_id, const char *description, feature_type type = f_type_not_set); + void init_feature(int feature_id, const char *description, feature_type type); /// Describes a feature and its dependencies /// used in a static array within each subclass class feature { public: - feature() {} + feature() : type(f_type_not_set) {} ~feature() {} std::string description; // Set by derived object initializer @@ -126,6 +129,7 @@ public: feature_type type; }; + inline bool is_not_set(int id) { return features()[id]->type == f_type_not_set; } inline bool is_dynamic(int id) { return features()[id]->type == f_type_dynamic; } inline bool is_static(int id) { return features()[id]->type == f_type_static; } inline bool is_user(int id) { return features()[id]->type == f_type_user; } @@ -135,7 +139,7 @@ public: // with a non-static array // Intermediate classes (colvarbias and colvarcomp, which are also base classes) // implement this as virtual to allow overriding - virtual const std::vector&features() = 0; + virtual const std::vector &features() const = 0; virtual std::vector&modify_features() = 0; void add_child(colvardeps *child); @@ -188,10 +192,12 @@ protected: public: - /// enable a feature and recursively solve its dependencies - /// for proper reference counting, one should not add - /// spurious calls to enable() - /// dry_run is set to true to recursively test if a feature is available, without enabling it + /// Enable a feature and recursively solve its dependencies. + /// For accurate reference counting, do not add spurious calls to enable() + /// \param dry_run Recursively test if a feature is available, without enabling it + /// \param toplevel False if this is called as part of a chain of dependency resolution. + /// This is used to diagnose failed dependencies by displaying the full stack: + /// only the toplevel dependency will throw a fatal error. int enable(int f, bool dry_run = false, bool toplevel = true); /// Disable a feature, decrease the reference count of its dependencies @@ -318,8 +324,8 @@ public: f_cvc_active, f_cvc_scalar, f_cvc_gradient, - /// \brief CVC doesn't calculate and store explicit atom gradients - f_cvc_implicit_gradient, + /// \brief CVC calculates and stores explicit atom gradients + f_cvc_explicit_gradient, f_cvc_inv_gradient, /// \brief If enabled, calc_gradients() will call debug_gradients() for every group needed f_cvc_debug_gradient, @@ -341,7 +347,7 @@ public: /// ie. not using refpositionsgroup // f_ag_min_msd_fit, /// \brief Does not have explicit atom gradients from parent CVC - f_ag_implicit_gradient, + f_ag_explicit_gradient, f_ag_fit_gradients, f_ag_atom_forces, f_ag_scalable, @@ -349,13 +355,39 @@ public: f_ag_ntot }; - void init_cvb_requires(); - void init_cv_requires(); - void init_cvc_requires(); - void init_ag_requires(); + /// Initialize dependency tree for object of a derived class + virtual int init_dependencies() = 0; + + /// Make feature f require feature g within the same object + void require_feature_self(int f, int g); + + /// Make features f and g mutually exclusive within the same object + void exclude_feature_self(int f, int g); + + /// Make feature f require feature g within children + void require_feature_children(int f, int g); + + /// Make feature f require either g or h within the same object + void require_feature_alt(int f, int g, int h); + + /// Make feature f require any of g, h, or i within the same object + void require_feature_alt(int f, int g, int h, int i); + + /// Make feature f require any of g, h, i, or j within the same object + void require_feature_alt(int f, int g, int h, int i, int j); /// \brief print all enabled features and those of children, for debugging void print_state(); + + /// \brief Check that a feature is enabled, raising BUG_ERROR if not + inline void check_enabled(int f, std::string const &reason) const + { + if (! is_enabled(f)) { + cvm::error("Error: "+reason+" requires that the feature \""+ + features()[f]->description+"\" is active.\n", BUG_ERROR); + } + } + }; #endif diff --git a/lib/colvars/colvargrid.cpp b/lib/colvars/colvargrid.cpp index 407b336afd..dc1a709edb 100644 --- a/lib/colvars/colvargrid.cpp +++ b/lib/colvars/colvargrid.cpp @@ -109,7 +109,7 @@ cvm::real colvar_grid_scalar::entropy() const { cvm::real sum = 0.0; for (size_t i = 0; i < nt; i++) { - sum += -1.0 * data[i] * std::log(data[i]); + sum += -1.0 * data[i] * cvm::logn(data[i]); } cvm::real bin_volume = 1.0; for (size_t id = 0; id < widths.size(); id++) { diff --git a/lib/colvars/colvargrid.h b/lib/colvars/colvargrid.h index 9a0fe4c8ec..2ba0566e49 100644 --- a/lib/colvars/colvargrid.h +++ b/lib/colvars/colvargrid.h @@ -12,7 +12,6 @@ #include #include -#include #include "colvar.h" #include "colvarmodule.h" @@ -53,7 +52,7 @@ protected: std::vector cv; /// Do we request actual value (for extended-system colvars)? - std::vector actual_value; + std::vector use_actual_value; /// Get the low-level index corresponding to an index inline size_t address(std::vector const &ix) const @@ -136,8 +135,8 @@ public: inline void request_actual_value(bool b = true) { size_t i; - for (i = 0; i < actual_value.size(); i++) { - actual_value[i] = b; + for (i = 0; i < use_actual_value.size(); i++) { + use_actual_value[i] = b; } } @@ -215,7 +214,7 @@ public: mult(g.mult), data(), cv(g.cv), - actual_value(g.actual_value), + use_actual_value(g.use_actual_value), lower_boundaries(g.lower_boundaries), upper_boundaries(g.upper_boundaries), periodic(g.periodic), @@ -290,13 +289,13 @@ public: periodic.push_back(cv[i]->periodic_boundaries()); // By default, get reported colvar value (for extended Lagrangian colvars) - actual_value.push_back(false); + use_actual_value.push_back(false); // except if a colvar is specified twice in a row // then the first instance is the actual value // For histograms of extended-system coordinates if (i > 0 && cv[i-1] == cv[i]) { - actual_value[i-1] = true; + use_actual_value[i-1] = true; } if (margin) { @@ -319,8 +318,7 @@ public: return this->setup(); } - int init_from_boundaries(T const &t = T(), - size_t const &mult_i = 1) + int init_from_boundaries() { if (cvm::debug()) { cvm::log("Configuring grid dimensions from colvars boundaries.\n"); @@ -337,7 +335,7 @@ public: lower_boundaries[i].real_value ) / widths[i]; int nbins_round = (int)(nbins+0.5); - if (std::fabs(nbins - cvm::real(nbins_round)) > 1.0E-10) { + if (cvm::fabs(nbins - cvm::real(nbins_round)) > 1.0E-10) { cvm::log("Warning: grid interval("+ cvm::to_str(lower_boundaries[i], cvm::cv_width, cvm::cv_prec)+" - "+ cvm::to_str(upper_boundaries[i], cvm::cv_width, cvm::cv_prec)+ @@ -392,20 +390,20 @@ public: /// \brief Report the bin corresponding to the current value of variable i inline int current_bin_scalar(int const i) const { - return value_to_bin_scalar(actual_value[i] ? cv[i]->actual_value() : cv[i]->value(), i); + return value_to_bin_scalar(use_actual_value[i] ? cv[i]->actual_value() : cv[i]->value(), i); } /// \brief Report the bin corresponding to the current value of variable i /// and assign first or last bin if out of boundaries inline int current_bin_scalar_bound(int const i) const { - return value_to_bin_scalar_bound(actual_value[i] ? cv[i]->actual_value() : cv[i]->value(), i); + return value_to_bin_scalar_bound(use_actual_value[i] ? cv[i]->actual_value() : cv[i]->value(), i); } /// \brief Report the bin corresponding to the current value of item iv in variable i inline int current_bin_scalar(int const i, int const iv) const { - return value_to_bin_scalar(actual_value[i] ? + return value_to_bin_scalar(use_actual_value[i] ? cv[i]->actual_value().vector1d_value[iv] : cv[i]->value().vector1d_value[iv], i); } @@ -414,14 +412,14 @@ public: /// the provided value is in inline int value_to_bin_scalar(colvarvalue const &value, const int i) const { - return (int) std::floor( (value.real_value - lower_boundaries[i].real_value) / widths[i] ); + return (int) cvm::floor( (value.real_value - lower_boundaries[i].real_value) / widths[i] ); } /// \brief Use the lower boundary and the width to report which bin /// the provided value is in and assign first or last bin if out of boundaries inline int value_to_bin_scalar_bound(colvarvalue const &value, const int i) const { - int bin_index = std::floor( (value.real_value - lower_boundaries[i].real_value) / widths[i] ); + int bin_index = cvm::floor( (value.real_value - lower_boundaries[i].real_value) / widths[i] ); if (bin_index < 0) bin_index=0; if (bin_index >=int(nx[i])) bin_index=int(nx[i])-1; return (int) bin_index; @@ -432,7 +430,7 @@ public: colvarvalue const &new_offset, cvm::real const &new_width) const { - return (int) std::floor( (value.real_value - new_offset.real_value) / new_width ); + return (int) cvm::floor( (value.real_value - new_offset.real_value) / new_width ); } /// \brief Use the two boundaries and the width to report the @@ -611,8 +609,8 @@ public: if (periodic[i]) continue; - cvm::real dl = std::sqrt(cv[i]->dist2(values[i], lower_boundaries[i])) / widths[i]; - cvm::real du = std::sqrt(cv[i]->dist2(values[i], upper_boundaries[i])) / widths[i]; + cvm::real dl = cvm::sqrt(cv[i]->dist2(values[i], lower_boundaries[i])) / widths[i]; + cvm::real du = cvm::sqrt(cv[i]->dist2(values[i], upper_boundaries[i])) / widths[i]; if (values[i].real_value < lower_boundaries[i]) dl *= -1.0; @@ -841,7 +839,7 @@ public: if (nd < lower_boundaries.size()) nd = lower_boundaries.size(); - if (! actual_value.size()) actual_value.assign(nd, false); + if (! use_actual_value.size()) use_actual_value.assign(nd, false); if (! periodic.size()) periodic.assign(nd, false); if (! widths.size()) widths.assign(nd, 1.0); @@ -849,7 +847,7 @@ public: if (old_nx.size()) { for (size_t i = 0; i < nd; i++) { if ( (old_nx[i] != nx[i]) || - (std::sqrt(cv[i]->dist2(old_lb[i], + (cvm::sqrt(cv[i]->dist2(old_lb[i], lower_boundaries[i])) > 1.0E-10) ) { new_params = true; } @@ -874,11 +872,11 @@ public: void check_consistency() { for (size_t i = 0; i < nd; i++) { - if ( (std::sqrt(cv[i]->dist2(cv[i]->lower_boundary, + if ( (cvm::sqrt(cv[i]->dist2(cv[i]->lower_boundary, lower_boundaries[i])) > 1.0E-10) || - (std::sqrt(cv[i]->dist2(cv[i]->upper_boundary, + (cvm::sqrt(cv[i]->dist2(cv[i]->upper_boundary, upper_boundaries[i])) > 1.0E-10) || - (std::sqrt(cv[i]->dist2(cv[i]->width, + (cvm::sqrt(cv[i]->dist2(cv[i]->width, widths[i])) > 1.0E-10) ) { cvm::error("Error: restart information for a grid is " "inconsistent with that of its colvars.\n"); @@ -896,11 +894,11 @@ public: // we skip dist2(), because periodicities and the like should // matter: boundaries should be EXACTLY the same (otherwise, // map_grid() should be used) - if ( (std::fabs(other_grid.lower_boundaries[i] - + if ( (cvm::fabs(other_grid.lower_boundaries[i] - lower_boundaries[i]) > 1.0E-10) || - (std::fabs(other_grid.upper_boundaries[i] - + (cvm::fabs(other_grid.upper_boundaries[i] - upper_boundaries[i]) > 1.0E-10) || - (std::fabs(other_grid.widths[i] - + (cvm::fabs(other_grid.widths[i] - widths[i]) > 1.0E-10) || (data.size() != other_grid.data.size()) ) { cvm::error("Error: inconsistency between " @@ -1036,11 +1034,11 @@ public: std::istream & read_multicol(std::istream &is, bool add = false) { // Data in the header: nColvars, then for each - // xiMin, dXi, nPoints, periodic + // xiMin, dXi, nPoints, periodic flag std::string hash; cvm::real lower, width, x; - size_t n, periodic; + size_t n, periodic_flag; bool remap; std::vector new_value; std::vector nx_read; @@ -1053,7 +1051,8 @@ public: if ( !(is >> hash) || (hash != "#") ) { cvm::error("Error reading grid at position "+ - cvm::to_str(is.tellg())+" in stream(read \"" + hash + "\")\n"); + cvm::to_str(static_cast(is.tellg()))+ + " in stream(read \"" + hash + "\")\n"); return is; } @@ -1075,15 +1074,16 @@ public: for (size_t i = 0; i < nd; i++ ) { if ( !(is >> hash) || (hash != "#") ) { cvm::error("Error reading grid at position "+ - cvm::to_str(is.tellg())+" in stream(read \"" + hash + "\")\n"); + cvm::to_str(static_cast(is.tellg()))+ + " in stream(read \"" + hash + "\")\n"); return is; } - is >> lower >> width >> nx_read[i] >> periodic; + is >> lower >> width >> nx_read[i] >> periodic_flag; - if ( (std::fabs(lower - lower_boundaries[i].real_value) > 1.0e-10) || - (std::fabs(width - widths[i] ) > 1.0e-10) || + if ( (cvm::fabs(lower - lower_boundaries[i].real_value) > 1.0e-10) || + (cvm::fabs(width - widths[i] ) > 1.0e-10) || (nx_read[i] != nx[i]) ) { cvm::log("Warning: reading from different grid definition (colvar " + cvm::to_str(i+1) + "); remapping data on new grid.\n"); @@ -1246,7 +1246,7 @@ public: if (A0 * A1 == 0) { return 0.; // can't handle empty bins } else { - return (std::log((cvm::real)A1) - std::log((cvm::real)A0)) + return (cvm::logn((cvm::real)A1) - cvm::logn((cvm::real)A0)) / (widths[n] * 2.); } } else if (ix[n] > 0 && ix[n] < nx[n]-1) { // not an edge @@ -1258,7 +1258,7 @@ public: if (A0 * A1 == 0) { return 0.; // can't handle empty bins } else { - return (std::log((cvm::real)A1) - std::log((cvm::real)A0)) + return (cvm::logn((cvm::real)A1) - cvm::logn((cvm::real)A0)) / (widths[n] * 2.); } } else { @@ -1271,8 +1271,8 @@ public: if (A0 * A1 * A2 == 0) { return 0.; // can't handle empty bins } else { - return (-1.5 * std::log((cvm::real)A0) + 2. * std::log((cvm::real)A1) - - 0.5 * std::log((cvm::real)A2)) * increment / widths[n]; + return (-1.5 * cvm::logn((cvm::real)A0) + 2. * cvm::logn((cvm::real)A1) + - 0.5 * cvm::logn((cvm::real)A2)) * increment / widths[n]; } } } diff --git a/lib/colvars/colvarmodule.cpp b/lib/colvars/colvarmodule.cpp index d88a97a441..baffc25c28 100644 --- a/lib/colvars/colvarmodule.cpp +++ b/lib/colvars/colvarmodule.cpp @@ -28,6 +28,8 @@ colvarmodule::colvarmodule(colvarproxy *proxy_in) { depth_s = 0; + log_level_ = 10; + cv_traj_os = NULL; if (proxy == NULL) { @@ -152,12 +154,12 @@ int colvarmodule::read_config_string(std::string const &config_str) { cvm::log(cvm::line_marker); cvm::log("Reading new configuration:\n"); - std::istringstream config_s(config_str); + std::istringstream new_config_s(config_str); // strip the comments away std::string conf = ""; std::string line; - while (parse->read_config_line(config_s, line)) { + while (parse->read_config_line(new_config_s, line)) { // Delete lines that contain only white space after removing comments if (line.find_first_not_of(colvarparse::white_space) != std::string::npos) conf.append(line+"\n"); @@ -255,13 +257,16 @@ int colvarmodule::append_new_config(std::string const &new_conf) int colvarmodule::parse_global_params(std::string const &conf) { - colvarmodule *cvm = cvm::main(); + // TODO document and then echo this keyword + parse->get_keyval(conf, "logLevel", log_level_, log_level_, + colvarparse::parse_silent); { std::string index_file_name; size_t pos = 0; while (parse->key_lookup(conf, "indexFile", &index_file_name, &pos)) { - cvm->read_index_file(index_file_name.c_str()); + cvm::log("# indexFile = \""+index_file_name+"\"\n"); + read_index_file(index_file_name.c_str()); index_file_name.clear(); } } @@ -580,6 +585,24 @@ cvm::atom_group *colvarmodule::atom_group_by_name(std::string const &name) } +void colvarmodule::register_named_atom_group(atom_group *ag) { + named_atom_groups.push_back(ag); +} + + +void colvarmodule::unregister_named_atom_group(cvm::atom_group *ag) +{ + for (std::vector::iterator agi = named_atom_groups.begin(); + agi != named_atom_groups.end(); + agi++) { + if (*agi == ag) { + named_atom_groups.erase(agi); + break; + } + } +} + + int colvarmodule::change_configuration(std::string const &bias_name, std::string const &conf) { @@ -1034,9 +1057,6 @@ int colvarmodule::analyze() cvm::log("colvarmodule::analyze(), step = "+cvm::to_str(it)+".\n"); } - if (cvm::step_relative() == 0) - cvm::log("Performing analysis.\n"); - // perform colvar-specific analysis for (std::vector::iterator cvi = variables_active()->begin(); cvi != variables_active()->end(); @@ -1089,7 +1109,6 @@ int colvarmodule::end_of_step() int colvarmodule::setup() { if (this->size() == 0) return cvm::get_error(); - // loop over all components of all colvars to reset masses of all groups for (std::vector::iterator cvi = variables()->begin(); cvi != variables()->end(); cvi++) { (*cvi)->setup(); @@ -1248,13 +1267,13 @@ std::istream & colvarmodule::read_restart(std::istream &is) std::string restart_conf; if (is >> colvarparse::read_block("configuration", restart_conf)) { parse->get_keyval(restart_conf, "step", - it_restart, (size_t) 0, - colvarparse::parse_silent); + it_restart, static_cast(0), + colvarparse::parse_restart); it = it_restart; std::string restart_version; parse->get_keyval(restart_conf, "version", restart_version, std::string(""), - colvarparse::parse_silent); + colvarparse::parse_restart); if (restart_version.size() && (restart_version != std::string(COLVARS_VERSION))) { cvm::log("This state file was generated with version "+restart_version+"\n"); } @@ -1600,14 +1619,16 @@ std::ostream & colvarmodule::write_traj(std::ostream &os) } -void cvm::log(std::string const &message) +void cvm::log(std::string const &message, int min_log_level) { + if (cvm::log_level() < min_log_level) return; // allow logging when the module is not fully initialized size_t const d = (cvm::main() != NULL) ? depth() : 0; - if (d > 0) + if (d > 0) { proxy->log((std::string(2*d, ' '))+message); - else + } else { proxy->log(message); + } } @@ -1915,14 +1936,190 @@ int cvm::replica_comm_send(char* msg_data, int msg_len, int dest_rep) +template std::string _to_str(T const &x, + size_t width, size_t prec) +{ + std::ostringstream os; + if (width) os.width(width); + if (prec) { + os.setf(std::ios::scientific, std::ios::floatfield); + os.precision(prec); + } + os << x; + return os.str(); +} + + +template std::string _to_str_vector(std::vector const &x, + size_t width, size_t prec) +{ + if (!x.size()) return std::string(""); + std::ostringstream os; + if (prec) { + os.setf(std::ios::scientific, std::ios::floatfield); + } + os << "{ "; + if (width) os.width(width); + if (prec) os.precision(prec); + os << x[0]; + for (size_t i = 1; i < x.size(); i++) { + os << ", "; + if (width) os.width(width); + if (prec) os.precision(prec); + os << x[i]; + } + os << " }"; + return os.str(); +} + + + +std::string colvarmodule::to_str(std::string const &x) +{ + return std::string("\"")+x+std::string("\""); +} + +std::string colvarmodule::to_str(char const *x) +{ + return std::string("\"")+std::string(x)+std::string("\""); +} + +std::string colvarmodule::to_str(bool x) +{ + return (x ? "on" : "off"); +} + +std::string colvarmodule::to_str(int const &x, + size_t width, size_t prec) +{ + return _to_str(x, width, prec); +} + +std::string colvarmodule::to_str(size_t const &x, + size_t width, size_t prec) +{ + return _to_str(x, width, prec); +} + +std::string colvarmodule::to_str(long int const &x, + size_t width, size_t prec) +{ + return _to_str(x, width, prec); +} + +std::string colvarmodule::to_str(step_number const &x, + size_t width, size_t prec) +{ + return _to_str(x, width, prec); +} + +std::string colvarmodule::to_str(cvm::real const &x, + size_t width, size_t prec) +{ + return _to_str(x, width, prec); +} + +std::string colvarmodule::to_str(cvm::rvector const &x, + size_t width, size_t prec) +{ + return _to_str(x, width, prec); +} + +std::string colvarmodule::to_str(cvm::quaternion const &x, + size_t width, size_t prec) +{ + return _to_str(x, width, prec); +} + +std::string colvarmodule::to_str(colvarvalue const &x, + size_t width, size_t prec) +{ + return _to_str(x, width, prec); +} + +std::string colvarmodule::to_str(cvm::vector1d const &x, + size_t width, size_t prec) +{ + return _to_str< cvm::vector1d >(x, width, prec); +} + +std::string colvarmodule::to_str(cvm::matrix2d const &x, + size_t width, size_t prec) +{ + return _to_str< cvm::matrix2d >(x, width, prec); +} + + +std::string colvarmodule::to_str(std::vector const &x, + size_t width, size_t prec) +{ + return _to_str_vector(x, width, prec); +} + +std::string colvarmodule::to_str(std::vector const &x, + size_t width, size_t prec) +{ + return _to_str_vector(x, width, prec); +} + +std::string colvarmodule::to_str(std::vector const &x, + size_t width, size_t prec) +{ + return _to_str_vector(x, width, prec); +} + +std::string colvarmodule::to_str(std::vector const &x, + size_t width, size_t prec) +{ + return _to_str_vector(x, width, prec); +} + +std::string colvarmodule::to_str(std::vector const &x, + size_t width, size_t prec) +{ + return _to_str_vector(x, width, prec); +} + +std::string colvarmodule::to_str(std::vector const &x, + size_t width, size_t prec) +{ + return _to_str_vector(x, width, prec); +} + +std::string colvarmodule::to_str(std::vector const &x, + size_t width, size_t prec) +{ + return _to_str_vector(x, width, prec); +} + +std::string colvarmodule::to_str(std::vector const &x, + size_t width, size_t prec) +{ + return _to_str_vector(x, width, prec); +} + + +std::string cvm::wrap_string(std::string const &s, size_t nchars) +{ + if (!s.size()) { + return std::string(nchars, ' '); + } else { + return ( (s.size() <= nchars) ? + (s+std::string(nchars-s.size(), ' ')) : + (std::string(s, 0, nchars)) ); + } +} + + // shared pointer to the proxy object colvarproxy *colvarmodule::proxy = NULL; // static runtime data cvm::real colvarmodule::debug_gradients_step_size = 1.0e-07; int colvarmodule::errorCode = 0; -long colvarmodule::it = 0; -long colvarmodule::it_restart = 0; +int colvarmodule::log_level_ = 10; +cvm::step_number colvarmodule::it = 0; +cvm::step_number colvarmodule::it_restart = 0; size_t colvarmodule::restart_out_freq = 0; size_t colvarmodule::cv_traj_freq = 0; bool colvarmodule::use_scripted_forces = false; diff --git a/lib/colvars/colvarmodule.h b/lib/colvars/colvarmodule.h index 99b797627e..30620a2527 100644 --- a/lib/colvars/colvarmodule.h +++ b/lib/colvars/colvarmodule.h @@ -10,6 +10,8 @@ #ifndef COLVARMODULE_H #define COLVARMODULE_H +#include + #include "colvars_version.h" #ifndef COLVARS_DEBUG @@ -55,6 +57,7 @@ class colvar; class colvarbias; class colvarproxy; class colvarscript; +class colvarvalue; /// \brief Collective variables module (main class) @@ -88,10 +91,16 @@ public: // TODO colvarscript should be unaware of colvarmodule's internals friend class colvarscript; + /// Use a 64-bit integer to store the step number + typedef long long step_number; + /// Defining an abstract real number allows to switch precision typedef double real; - /// Override std::pow with a product for n integer + + // Math functions + + /// Override the STL pow() with a product for n integer static inline real integer_power(real const &x, int const n) { // Original code: math_special.h in LAMMPS @@ -105,8 +114,68 @@ public: return (n > 0) ? yy : 1.0/yy; } - /// Residue identifier - typedef int residue_id; + /// Reimplemented to work around MS compiler issues + static inline real pow(real const &x, real const &y) + { + return ::pow(static_cast(x), static_cast(y)); + } + + /// Reimplemented to work around MS compiler issues + static inline real floor(real const &x) + { + return ::floor(static_cast(x)); + } + + /// Reimplemented to work around MS compiler issues + static inline real fabs(real const &x) + { + return ::fabs(static_cast(x)); + } + + /// Reimplemented to work around MS compiler issues + static inline real sqrt(real const &x) + { + return ::sqrt(static_cast(x)); + } + + /// Reimplemented to work around MS compiler issues + static inline real sin(real const &x) + { + return ::sin(static_cast(x)); + } + + /// Reimplemented to work around MS compiler issues + static inline real cos(real const &x) + { + return ::cos(static_cast(x)); + } + + /// Reimplemented to work around MS compiler issues + static inline real acos(real const &x) + { + return ::acos(static_cast(x)); + } + + /// Reimplemented to work around MS compiler issues + static inline real atan2(real const &x, real const &y) + { + return ::atan2(static_cast(x), static_cast(y)); + } + + /// Reimplemented to work around MS compiler issues + static inline real exp(real const &x) + { + return ::exp(static_cast(x)); + } + + /// Reimplemented to work around MS compiler issues. Note: log() is + /// currently defined as the text logging function, but this can be changed + /// at a later time + static inline real logn(real const &x) + { + return ::log(static_cast(x)); + } + class rvector; template class vector1d; @@ -114,6 +183,10 @@ public: class quaternion; class rotation; + + /// Residue identifier + typedef int residue_id; + /// \brief Atom position (different type name from rvector, to make /// possible future PBC-transparent implementations) typedef rvector atom_pos; @@ -150,19 +223,19 @@ public: /// Current step number - static long it; + static step_number it; /// Starting step number for this run - static long it_restart; + static step_number it_restart; /// Return the current step number from the beginning of this run - static inline long step_relative() + static inline step_number step_relative() { return it - it_restart; } /// Return the current step number from the beginning of the whole /// calculation - static inline long step_absolute() + static inline step_number step_absolute() { return it; } @@ -203,9 +276,10 @@ private: std::vector named_atom_groups; public: /// Register a named atom group into named_atom_groups - inline void register_named_atom_group(atom_group * ag) { - named_atom_groups.push_back(ag); - } + void register_named_atom_group(atom_group *ag); + + /// Remove a named atom group from named_atom_groups + void unregister_named_atom_group(atom_group *ag); /// Array of collective variables std::vector *variables(); @@ -254,8 +328,7 @@ public: /// \brief How many objects are configured yet? size_t size() const; - /// \brief Constructor \param config_name Configuration file name - /// \param restart_name (optional) Restart file name + /// \brief Constructor colvarmodule(colvarproxy *proxy); /// Destructor @@ -265,6 +338,7 @@ public: int reset(); /// Open a config file, load its contents, and pass it to config_string() + /// \param config_file_name Configuration file name int read_config_file(char const *config_file_name); /// \brief Parse a config string assuming it is a complete configuration @@ -431,26 +505,92 @@ public: long traj_read_begin, long traj_read_end); - /// Quick conversion of an object to a string - template static std::string to_str(T const &x, - size_t const &width = 0, - size_t const &prec = 0); - /// Quick conversion of a vector of objects to a string - template static std::string to_str(std::vector const &x, - size_t const &width = 0, - size_t const &prec = 0); + /// Convert to string for output purposes + static std::string to_str(char const *s); + + /// Convert to string for output purposes + static std::string to_str(std::string const &s); + + /// Convert to string for output purposes + static std::string to_str(bool x); + + /// Convert to string for output purposes + static std::string to_str(int const &x, + size_t width = 0, size_t prec = 0); + + /// Convert to string for output purposes + static std::string to_str(size_t const &x, + size_t width = 0, size_t prec = 0); + + /// Convert to string for output purposes + static std::string to_str(long int const &x, + size_t width = 0, size_t prec = 0); + + /// Convert to string for output purposes + static std::string to_str(step_number const &x, + size_t width = 0, size_t prec = 0); + + /// Convert to string for output purposes + static std::string to_str(real const &x, + size_t width = 0, size_t prec = 0); + + /// Convert to string for output purposes + static std::string to_str(rvector const &x, + size_t width = 0, size_t prec = 0); + + /// Convert to string for output purposes + static std::string to_str(quaternion const &x, + size_t width = 0, size_t prec = 0); + + /// Convert to string for output purposes + static std::string to_str(colvarvalue const &x, + size_t width = 0, size_t prec = 0); + + /// Convert to string for output purposes + static std::string to_str(vector1d const &x, + size_t width = 0, size_t prec = 0); + + /// Convert to string for output purposes + static std::string to_str(matrix2d const &x, + size_t width = 0, size_t prec = 0); + + + /// Convert to string for output purposes + static std::string to_str(std::vector const &x, + size_t width = 0, size_t prec = 0); + + /// Convert to string for output purposes + static std::string to_str(std::vector const &x, + size_t width = 0, size_t prec = 0); + + /// Convert to string for output purposes + static std::string to_str(std::vector const &x, + size_t width = 0, size_t prec = 0); + + /// Convert to string for output purposes + static std::string to_str(std::vector const &x, + size_t width = 0, size_t prec = 0); + + /// Convert to string for output purposes + static std::string to_str(std::vector const &x, + size_t width = 0, size_t prec = 0); + + /// Convert to string for output purposes + static std::string to_str(std::vector const &x, + size_t width = 0, size_t prec = 0); + + /// Convert to string for output purposes + static std::string to_str(std::vector const &x, + size_t width = 0, size_t prec = 0); + + /// Convert to string for output purposes + static std::string to_str(std::vector const &x, + size_t width = 0, size_t prec = 0); + /// Reduce the number of characters in a string - static inline std::string wrap_string(std::string const &s, - size_t const &nchars) - { - if (!s.size()) - return std::string(nchars, ' '); - else - return ( (s.size() <= size_t(nchars)) ? - (s+std::string(nchars-s.size(), ' ')) : - (std::string(s, 0, nchars)) ); - } + static std::string wrap_string(std::string const &s, + size_t nchars); /// Number of characters to represent a time step static size_t const it_width; @@ -485,7 +625,9 @@ public: static void request_total_force(); /// Print a message to the main log - static void log(std::string const &message); + /// \param message Message to print + /// \param min_log_level Only print if cvm::log_level() >= min_log_level + static void log(std::string const &message, int min_log_level = 10); /// Print a message to the main log and exit with error code static int fatal_error(std::string const &message); @@ -493,6 +635,50 @@ public: /// Print a message to the main log and set global error code static int error(std::string const &message, int code = COLVARS_ERROR); +private: + + /// Level of logging requested by the user + static int log_level_; + +public: + + /// Level of logging requested by the user + static inline int log_level() + { + return log_level_; + } + + /// Level at which initialization messages are logged + static inline int log_init_messages() + { + return 1; + } + + /// Level at which a keyword's user-provided value is logged + static inline int log_user_params() + { + return 2; + } + + /// Level at which a keyword's default value is logged + static inline int log_default_params() + { + return 3; + } + + /// Level at which output-file operations are logged + static inline int log_output_files() + { + return 4; + } + + /// Level at which input-file operations (configuration, state) are logged + static inline int log_input_files() + { + return 5; + } + + // Replica exchange commands. static bool replica_enabled(); static int replica_index(); @@ -630,41 +816,4 @@ std::ostream & operator << (std::ostream &os, cvm::rvector const &v); std::istream & operator >> (std::istream &is, cvm::rvector &v); -template std::string cvm::to_str(T const &x, - size_t const &width, - size_t const &prec) { - std::ostringstream os; - if (width) os.width(width); - if (prec) { - os.setf(std::ios::scientific, std::ios::floatfield); - os.precision(prec); - } - os << x; - return os.str(); -} - - -template std::string cvm::to_str(std::vector const &x, - size_t const &width, - size_t const &prec) { - if (!x.size()) return std::string(""); - std::ostringstream os; - if (prec) { - os.setf(std::ios::scientific, std::ios::floatfield); - } - os << "{ "; - if (width) os.width(width); - if (prec) os.precision(prec); - os << x[0]; - for (size_t i = 1; i < x.size(); i++) { - os << ", "; - if (width) os.width(width); - if (prec) os.precision(prec); - os << x[i]; - } - os << " }"; - return os.str(); -} - - #endif diff --git a/lib/colvars/colvarparse.cpp b/lib/colvars/colvarparse.cpp index d8b3a359cd..10dce911ee 100644 --- a/lib/colvars/colvarparse.cpp +++ b/lib/colvars/colvarparse.cpp @@ -10,6 +10,7 @@ #include #include +#include #include "colvarmodule.h" #include "colvarvalue.h" @@ -20,15 +21,21 @@ char const * const colvarparse::white_space = " \t"; -// definition of single-value keyword parsers +namespace { -template bool colvarparse::_get_keyval_scalar_(std::string const &conf, - char const *key, - TYPE &value, - TYPE const &def_value, - Parse_Mode const parse_mode) + // Avoid having to put the bool assignment in the template :-( + void set_bool(void *p, bool val) + { + bool *v = reinterpret_cast(p); + *v = val; + } + +} + + +bool colvarparse::get_key_string_value(std::string const &conf, + char const *key, std::string &data) { - std::string data; bool b_found = false, b_found_any = false; size_t save_pos = 0, found_count = 0; @@ -48,29 +55,163 @@ template bool colvarparse::_get_keyval_scalar_(std::string const std::string(key)+"\".\n", INPUT_ERROR); } + return b_found_any; +} + + +template +void colvarparse::mark_key_set_user(std::string const &key_str, + TYPE const &value, + Parse_Mode const &parse_mode) +{ + key_set_modes[to_lower_cppstr(key_str)] = key_set_user; + if (parse_mode & parse_echo) { + cvm::log("# "+key_str+" = "+cvm::to_str(value)+"\n", + cvm::log_user_params()); + } +} + + +template +void colvarparse::mark_key_set_default(std::string const &key_str, + TYPE const &def_value, + Parse_Mode const &parse_mode) +{ + key_set_modes[to_lower_cppstr(key_str)] = key_set_default; + if (parse_mode & parse_echo_default) { + cvm::log("# "+key_str+" = "+cvm::to_str(def_value)+ + " [default]\n", cvm::log_default_params()); + } +} + + +void colvarparse::error_key_required(std::string const &key_str, + Parse_Mode const &parse_mode) +{ + if (key_already_set(key_str)) { + return; + } + if (parse_mode & parse_restart) { + cvm::error("Error: keyword \""+key_str+ + "\" is missing from the restart.\n", INPUT_ERROR); + } else { + cvm::error("Error: keyword \""+key_str+ + "\" is required.\n", INPUT_ERROR); + } +} + + +template +int colvarparse::_get_keyval_scalar_value_(std::string const &key_str, + std::string const &data, + TYPE &value, + TYPE const &def_value) +{ + std::istringstream is(data); + size_t value_count = 0; + TYPE x(def_value); + + while (is >> x) { + value = x; + value_count++; + } + + if (value_count == 0) { + return cvm::error("Error: in parsing \""+ + key_str+"\".\n", INPUT_ERROR); + } + + if (value_count > 1) { + return cvm::error("Error: multiple values " + "are not allowed for keyword \""+ + key_str+"\".\n", INPUT_ERROR); + } + + return COLVARS_OK; +} + + +template<> +int colvarparse::_get_keyval_scalar_value_(std::string const &key_str, + std::string const &data, + bool &value, + bool const &def_value) +{ + if ( (data == std::string("on")) || + (data == std::string("yes")) || + (data == std::string("true")) ) { + set_bool(reinterpret_cast(&value), true); + } else if ( (data == std::string("off")) || + (data == std::string("no")) || + (data == std::string("false")) ) { + set_bool(reinterpret_cast(&value), false); + } else { + return cvm::error("Error: boolean values only are allowed " + "for \""+key_str+"\".\n", INPUT_ERROR); + } + return COLVARS_OK; +} + + +template +int colvarparse::_get_keyval_scalar_novalue_(std::string const &key_str, + TYPE &value, + Parse_Mode const &parse_mode) +{ + return cvm::error("Error: improper or missing value " + "for \""+key_str+"\".\n", INPUT_ERROR); +} + +template<> +int colvarparse::_get_keyval_scalar_novalue_(std::string const &key_str, + bool &value, + Parse_Mode const &parse_mode) +{ + set_bool(reinterpret_cast(&value), true); + mark_key_set_user(key_str, value, parse_mode); + return COLVARS_OK; +} + + +template +bool colvarparse::_get_keyval_scalar_(std::string const &conf, + char const *key, + TYPE &value, + TYPE const &def_value, + Parse_Mode const &parse_mode) +{ + std::string const key_str(key); + + std::string data; + bool const b_found_any = get_key_string_value(conf, key, data); + if (data.size()) { - std::istringstream is(data); - TYPE x(def_value); - if (is >> x) { - value = x; + + _get_keyval_scalar_value_(key_str, data, value, def_value); + + mark_key_set_user(key_str, value, parse_mode); + + } else { // No string value + + if (b_found_any) { + + _get_keyval_scalar_novalue_(key_str, value, parse_mode); + } else { - cvm::error("Error: in parsing \""+ - std::string(key)+"\".\n", INPUT_ERROR); - } - if (parse_mode != parse_silent) { - cvm::log("# "+std::string(key)+" = "+ - cvm::to_str(value)+"\n"); - } - } else { - if (b_found_any) { - cvm::error("Error: improper or missing value " - "for \""+std::string(key)+"\".\n", INPUT_ERROR); - } - value = def_value; - if (parse_mode != parse_silent) { - cvm::log("# "+std::string(key)+" = "+ - cvm::to_str(def_value)+" [default]\n"); + if (parse_mode & parse_required) { + if (cvm::debug()) { + cvm::log("get_keyval, parse_required = "+cvm::to_str(parse_mode & parse_required)+ + "\n"); + } + error_key_required(key_str, parse_mode); + return false; + } + + if ( (parse_mode & parse_override) || !(key_already_set(key)) ) { + value = def_value; + mark_key_set_default(key_str, value, parse_mode); + } } } @@ -78,96 +219,17 @@ template bool colvarparse::_get_keyval_scalar_(std::string const } -bool colvarparse::_get_keyval_scalar_string_(std::string const &conf, - char const *key, - std::string &value, - std::string const &def_value, - Parse_Mode const parse_mode) +template +bool colvarparse::_get_keyval_vector_(std::string const &conf, + char const *key, + std::vector &values, + std::vector const &def_values, + Parse_Mode const &parse_mode) { + std::string const key_str(key); + std::string data; - bool b_found = false, b_found_any = false; - size_t save_pos = 0, found_count = 0; - - do { - std::string data_this = ""; - b_found = key_lookup(conf, key, &data_this, &save_pos); - if (b_found) { - if (!b_found_any) - b_found_any = true; - found_count++; - data = data_this; - } - } while (b_found); - - if (found_count > 1) { - cvm::error("Error: found more than one instance of \""+ - std::string(key)+"\".\n", INPUT_ERROR); - } - - if (data.size()) { - std::istringstream is(data); - size_t data_count = 0; - std::string x(def_value); - while (is >> x) { - value = x; - data_count++; - } - if (data_count == 0) - cvm::error("Error: in parsing \""+ - std::string(key)+"\".\n", INPUT_ERROR); - if (data_count > 1) { - cvm::error("Error: multiple values " - "are not allowed for keyword \""+ - std::string(key)+"\".\n", INPUT_ERROR); - } - if (parse_mode != parse_silent) { - cvm::log("# "+std::string(key)+" = \""+ - cvm::to_str(value)+"\"\n"); - } - } else { - - if (b_found_any) { - cvm::error("Error: improper or missing value " - "for \""+std::string(key)+"\".\n", INPUT_ERROR); - } - value = def_value; - if (parse_mode != parse_silent) { - cvm::log("# "+std::string(key)+" = \""+ - cvm::to_str(def_value)+"\" [default]\n"); - } - } - - return b_found_any; -} - - -// multiple-value keyword parsers - -template bool colvarparse::_get_keyval_vector_(std::string const &conf, - char const *key, - std::vector &values, - std::vector const &def_values, - Parse_Mode const parse_mode) -{ - std::string data; - bool b_found = false, b_found_any = false; - size_t save_pos = 0, found_count = 0; - - do { - std::string data_this = ""; - b_found = key_lookup(conf, key, &data_this, &save_pos); - if (b_found) { - if (!b_found_any) - b_found_any = true; - found_count++; - data = data_this; - } - } while (b_found); - - if (found_count > 1) { - cvm::error("Error: found more than one instance of \""+ - std::string(key)+"\".\n", INPUT_ERROR); - } + bool const b_found_any = get_key_string_value(conf, key, data); if (data.size()) { std::istringstream is(data); @@ -175,10 +237,11 @@ template bool colvarparse::_get_keyval_vector_(std::string const if (values.size() == 0) { std::vector x; - if (def_values.size()) + if (def_values.size()) { x = def_values; - else + } else { x.assign(1, TYPE()); + } for (size_t i = 0; ( is >> x[ ((i bool colvarparse::_get_keyval_vector_(std::string const values[i] = x; } else { cvm::error("Error: in parsing \""+ - std::string(key)+"\".\n", INPUT_ERROR); + key_str+"\".\n", INPUT_ERROR); } } } - if (parse_mode != parse_silent) { - cvm::log("# "+std::string(key)+" = "+ - cvm::to_str(values)+"\n"); - } + mark_key_set_user< std::vector >(key_str, values, parse_mode); } else { if (b_found_any) { cvm::error("Error: improper or missing values for \""+ - std::string(key)+"\".\n", INPUT_ERROR); - } + key_str+"\".\n", INPUT_ERROR); + } else { - for (size_t i = 0; i < values.size(); i++) - values[i] = def_values[ (i > def_values.size()) ? 0 : i ]; + if ((values.size() > 0) && (values.size() != def_values.size())) { + cvm::error("Error: the number of default values for \""+ + key_str+"\" is different from the number of " + "current values.\n", BUG_ERROR); + } + + if (parse_mode & parse_required) { + error_key_required(key_str, parse_mode); + return false; + } + + if ( (parse_mode & parse_override) || !(key_already_set(key)) ) { + for (size_t i = 0; i < values.size(); i++) { + values[i] = def_values[i]; + } + mark_key_set_default< std::vector >(key_str, def_values, + parse_mode); + } - if (parse_mode != parse_silent) { - cvm::log("# "+std::string(key)+" = "+ - cvm::to_str(def_values)+" [default]\n"); } } @@ -255,13 +328,22 @@ bool colvarparse::get_keyval(std::string const &conf, return _get_keyval_scalar_(conf, key, value, def_value, parse_mode); } +bool colvarparse::get_keyval(std::string const &conf, + char const *key, + cvm::step_number &value, + cvm::step_number const &def_value, + Parse_Mode const parse_mode) +{ + return _get_keyval_scalar_(conf, key, value, def_value, parse_mode); +} + bool colvarparse::get_keyval(std::string const &conf, char const *key, std::string &value, std::string const &def_value, Parse_Mode const parse_mode) { - return _get_keyval_scalar_string_(conf, key, value, def_value, parse_mode); + return _get_keyval_scalar_(conf, key, value, def_value, parse_mode); } bool colvarparse::get_keyval(std::string const &conf, @@ -300,66 +382,13 @@ bool colvarparse::get_keyval(std::string const &conf, return _get_keyval_scalar_(conf, key, value, def_value, parse_mode); } - bool colvarparse::get_keyval(std::string const &conf, char const *key, bool &value, bool const &def_value, Parse_Mode const parse_mode) { - std::string data; - bool b_found = false, b_found_any = false; - size_t save_pos = 0, found_count = 0; - - do { - std::string data_this = ""; - b_found = key_lookup(conf, key, &data_this, &save_pos); - if (b_found) { - if (!b_found_any) - b_found_any = true; - found_count++; - data = data_this; - } - } while (b_found); - - if (found_count > 1) { - cvm::error("Error: found more than one instance of \""+ - std::string(key)+"\".\n", INPUT_ERROR); - } - - if (data.size()) { - if ( (data == std::string("on")) || - (data == std::string("yes")) || - (data == std::string("true")) ) { - value = true; - } else if ( (data == std::string("off")) || - (data == std::string("no")) || - (data == std::string("false")) ) { - value = false; - } else - cvm::error("Error: boolean values only are allowed " - "for \""+std::string(key)+"\".\n", INPUT_ERROR); - if (parse_mode != parse_silent) { - cvm::log("# "+std::string(key)+" = "+ - (value ? "on" : "off")+"\n"); - } - } else { - - if (b_found_any) { - if (parse_mode != parse_silent) { - cvm::log("# "+std::string(key)+" = on\n"); - } - value = true; - } else { - value = def_value; - if (parse_mode != parse_silent) { - cvm::log("# "+std::string(key)+" = "+ - (def_value ? "on" : "off")+" [default]\n"); - } - } - } - - return b_found_any; + return _get_keyval_scalar_(conf, key, value, def_value, parse_mode); } @@ -440,15 +469,27 @@ bool colvarparse::get_keyval(std::string const &conf, void colvarparse::add_keyword(char const *key) { - for (std::list::iterator ki = allowed_keywords.begin(); - ki != allowed_keywords.end(); ki++) { - if (to_lower_cppstr(std::string(key)) == *ki) - return; + std::string const key_str_lower(to_lower_cppstr(std::string(key))); + + if (key_set_modes.find(key_str_lower) != key_set_modes.end()) { + return; } - // not found in the list - // if (cvm::debug()) - // cvm::log("Registering a new keyword, \""+std::string (key)+"\".\n"); - allowed_keywords.push_back(to_lower_cppstr(std::string(key))); + + key_set_modes[key_str_lower] = key_not_set; + + allowed_keywords.push_back(key_str_lower); +} + + +bool colvarparse::key_already_set(std::string const &key_str) +{ + std::string const key_str_lower(to_lower_cppstr(key_str)); + + if (key_set_modes.find(key_str_lower) == key_set_modes.end()) { + return false; + } + + return (key_set_modes[key_str_lower] > 0); } @@ -457,6 +498,10 @@ void colvarparse::strip_values(std::string &conf) size_t offset = 0; data_begin_pos.sort(); data_end_pos.sort(); + std::list::iterator data_begin_pos_last = std::unique(data_begin_pos.begin(), data_begin_pos.end()); + data_begin_pos.erase(data_begin_pos_last, data_begin_pos.end()); + std::list::iterator data_end_pos_last = std::unique(data_end_pos.begin(), data_end_pos.end()); + data_end_pos.erase(data_end_pos_last, data_end_pos.end()); std::list::iterator data_begin = data_begin_pos.begin(); std::list::iterator data_end = data_end_pos.begin(); @@ -464,28 +509,16 @@ void colvarparse::strip_values(std::string &conf) for ( ; (data_begin != data_begin_pos.end()) && (data_end != data_end_pos.end()) ; data_begin++, data_end++) { - - // std::cerr << "data_begin, data_end " - // << *data_begin << ", " << *data_end - // << "\n"; - size_t const nchars = *data_end-*data_begin; - - // std::cerr << "conf[data_begin:data_end] = \"" - // << std::string (conf, *data_begin - offset, nchars) - // << "\"\n"; - conf.erase(*data_begin - offset, nchars); offset += nchars; - - // std::cerr << ("Stripped config = \"\n"+conf+"\"\n"); - } } void colvarparse::clear_keyword_registry() { + key_set_modes.clear(); allowed_keywords.clear(); data_begin_pos.clear(); data_end_pos.clear(); diff --git a/lib/colvars/colvarparse.h b/lib/colvars/colvarparse.h index 28ad3c052b..8501ee8c14 100644 --- a/lib/colvars/colvarparse.h +++ b/lib/colvars/colvarparse.h @@ -12,6 +12,7 @@ #include #include +#include #include "colvarmodule.h" #include "colvarvalue.h" @@ -24,35 +25,9 @@ /// need to parse input inherit from this class colvarparse { -protected: - - /// \brief List of legal keywords for this object: this is updated - /// by each call to colvarparse::get_keyval() or - /// colvarparse::key_lookup() - std::list allowed_keywords; - - /// \brief List of delimiters for the values of each keyword in the - /// configuration string; all keywords will be stripped of their - /// values before the keyword check is performed - std::list data_begin_pos; - - /// \brief List of delimiters for the values of each keyword in the - /// configuration string; all keywords will be stripped of their - /// values before the keyword check is performed - std::list data_end_pos; - - /// \brief Add a new valid keyword to the list - void add_keyword(char const *key); - - /// \brief Remove all the values from the config string - void strip_values(std::string &conf); - - /// \brief Configuration string of the object (includes comments) - std::string config_string; - public: - + /// Default constructor inline colvarparse() { init(); @@ -88,14 +63,23 @@ public: /// How a keyword is parsed in a string enum Parse_Mode { - /// \brief(default) Read the first instance of a keyword (if - /// any), report its value, and print a warning when there is more - /// than one - parse_normal, - /// \brief Like parse_normal, but don't send any message to the log - /// (useful e.g. in restart files when such messages are very - /// numerous and redundant) - parse_silent + /// Zero for all flags + parse_null = 0, + /// Print the value of a keyword if it is given + parse_echo = (1<<1), + /// Print the default value of a keyword, if it is NOT given + parse_echo_default = (1<<2), + /// Do not print the keyword + parse_silent = 0, + /// Raise error if the keyword is not provided + parse_required = (1<<16), + /// Successive calls to get_keyval() will override the previous values + /// when the keyword is not given any more + parse_override = (1<<17), + /// The call is being executed from a read_restart() function + parse_restart = (1<<18), + /// Alias for old default behavior (should be phased out) + parse_normal = (1<<2) | (1<<1) | (1<<17) }; /// \brief Check that all the keywords within "conf" are in the list @@ -146,6 +130,11 @@ public: long &value, long const &def_value = 0, Parse_Mode const parse_mode = parse_normal); + bool get_keyval(std::string const &conf, + char const *key, + cvm::step_number &value, + cvm::step_number const &def_value = 0, + Parse_Mode const parse_mode = parse_normal); bool get_keyval(std::string const &conf, char const *key, std::string &value, @@ -219,23 +208,57 @@ public: protected: - // Templates - template bool _get_keyval_scalar_(std::string const &conf, - char const *key, - TYPE &value, - TYPE const &def_value, - Parse_Mode const parse_mode); - bool _get_keyval_scalar_string_(std::string const &conf, - char const *key, - std::string &value, - std::string const &def_value, - Parse_Mode const parse_mode); + /// Get the string value of a keyword, and save it for later parsing + bool get_key_string_value(std::string const &conf, + char const *key, std::string &data); - template bool _get_keyval_vector_(std::string const &conf, - char const *key, - std::vector &values, - std::vector const &def_values, - Parse_Mode const parse_mode); + /// Template for single-value keyword parsers + template + bool _get_keyval_scalar_(std::string const &conf, + char const *key, + TYPE &value, + TYPE const &def_value, + Parse_Mode const &parse_mode); + + /// Template for multiple-value keyword parsers + template + bool _get_keyval_vector_(std::string const &conf, + char const *key, + std::vector &values, + std::vector const &def_values, + Parse_Mode const &parse_mode); + + /// Extract the value of a variable from a string + template + int _get_keyval_scalar_value_(std::string const &key_str, + std::string const &data, + TYPE &value, + TYPE const &def_value); + + /// Handle the case where the user provides a keyword without value + template + int _get_keyval_scalar_novalue_(std::string const &key_str, + TYPE &value, + Parse_Mode const &parse_mode); + + /// Record that the keyword has just been user-defined + template + void mark_key_set_user(std::string const &key_str, + TYPE const &value, + Parse_Mode const &parse_mode); + + /// Record that the keyword has just been set to its default value + template + void mark_key_set_default(std::string const &key_str, + TYPE const &def_value, + Parse_Mode const &parse_mode); + + /// Raise error condition due to the keyword being required! + void error_key_required(std::string const &key_str, + Parse_Mode const &parse_mode); + + /// True if the keyword has been set already + bool key_already_set(std::string const &key_str); public: @@ -286,7 +309,7 @@ public: size_t *save_pos = NULL); /// \brief Reads a configuration line, adds it to config_string, and returns - /// the stream \param is Input stream \param s String that will hold the + /// the stream \param is Input stream \param line String that will hold the /// configuration line, with comments stripped std::istream & read_config_line(std::istream &is, std::string &line); @@ -299,7 +322,51 @@ public: /// from this position static int check_braces(std::string const &conf, size_t const start_pos); +protected: + + /// \brief List of legal keywords for this object: this is updated + /// by each call to colvarparse::get_keyval() or + /// colvarparse::key_lookup() + std::list allowed_keywords; + + /// How a keyword has been set + enum key_set_mode { + key_not_set = 0, + key_set_user = 1, + key_set_default = 2 + }; + + /// Track which keywords have been already set, and how + std::map key_set_modes; + + /// \brief List of delimiters for the values of each keyword in the + /// configuration string; all keywords will be stripped of their + /// values before the keyword check is performed + std::list data_begin_pos; + + /// \brief List of delimiters for the values of each keyword in the + /// configuration string; all keywords will be stripped of their + /// values before the keyword check is performed + std::list data_end_pos; + + /// \brief Add a new valid keyword to the list + void add_keyword(char const *key); + + /// \brief Remove all the values from the config string + void strip_values(std::string &conf); + + /// \brief Configuration string of the object (includes comments) + std::string config_string; + }; +/// Bitwise OR between two Parse_mode flags +inline colvarparse::Parse_Mode operator | (colvarparse::Parse_Mode const &mode1, + colvarparse::Parse_Mode const &mode2) +{ + return static_cast(static_cast(mode1) | + static_cast(mode2)); +} + #endif diff --git a/lib/colvars/colvarproxy.cpp b/lib/colvars/colvarproxy.cpp index da9257eee2..5f8e82d30a 100644 --- a/lib/colvars/colvarproxy.cpp +++ b/lib/colvars/colvarproxy.cpp @@ -60,7 +60,7 @@ bool colvarproxy_system::total_forces_same_step() const inline int round_to_integer(cvm::real x) { - return std::floor(x+0.5); + return cvm::floor(x+0.5); } @@ -129,7 +129,10 @@ cvm::rvector colvarproxy_system::position_distance(cvm::atom_pos const &pos1, -colvarproxy_atoms::colvarproxy_atoms() {} +colvarproxy_atoms::colvarproxy_atoms() +{ + updated_masses_ = updated_charges_ = false; +} colvarproxy_atoms::~colvarproxy_atoms() @@ -544,7 +547,7 @@ int colvarproxy_script::run_colvar_gradient_callback( colvarproxy_tcl::colvarproxy_tcl() { - _tcl_interp = NULL; + tcl_interp_ = NULL; } @@ -573,7 +576,7 @@ char const *colvarproxy_tcl::tcl_obj_to_str(unsigned char *obj) int colvarproxy_tcl::tcl_run_force_callback() { #if defined(COLVARS_TCL) - Tcl_Interp *const tcl_interp = reinterpret_cast(_tcl_interp); + Tcl_Interp *const tcl_interp = reinterpret_cast(tcl_interp_); std::string cmd = std::string("calc_colvar_forces ") + cvm::to_str(cvm::step_absolute()); int err = Tcl_Eval(tcl_interp, cmd.c_str()); @@ -596,7 +599,7 @@ int colvarproxy_tcl::tcl_run_colvar_callback( { #if defined(COLVARS_TCL) - Tcl_Interp *const tcl_interp = reinterpret_cast(_tcl_interp); + Tcl_Interp *const tcl_interp = reinterpret_cast(tcl_interp_); size_t i; std::string cmd = std::string("calc_") + name; for (i = 0; i < cvc_values.size(); i++) { @@ -633,7 +636,7 @@ int colvarproxy_tcl::tcl_run_colvar_gradient_callback( { #if defined(COLVARS_TCL) - Tcl_Interp *const tcl_interp = reinterpret_cast(_tcl_interp); + Tcl_Interp *const tcl_interp = reinterpret_cast(tcl_interp_); size_t i; std::string cmd = std::string("calc_") + name + "_gradient"; for (i = 0; i < cvc_values.size(); i++) { diff --git a/lib/colvars/colvarproxy.h b/lib/colvars/colvarproxy.h index 3ff5f3c697..3bbdfe522e 100644 --- a/lib/colvars/colvarproxy.h +++ b/lib/colvars/colvarproxy.h @@ -29,7 +29,7 @@ /// /// To interface to a new MD engine, the simplest solution is to derive a new /// class from \link colvarproxy \endlink. Currently implemented are: \link -/// colvarproxy_lammps, \endlink, \link colvarproxy_namd, \endlink, \link +/// colvarproxy_lammps \endlink, \link colvarproxy_namd \endlink, \link /// colvarproxy_vmd \endlink. @@ -227,11 +227,15 @@ public: inline std::vector *modify_atom_masses() { + // assume that we are requesting masses to change them + updated_masses_ = true; return &atoms_masses; } inline std::vector *modify_atom_charges() { + // assume that we are requesting charges to change them + updated_charges_ = true; return &atoms_charges; } @@ -250,6 +254,18 @@ public: return &atoms_new_colvar_forces; } + /// Record whether masses have been updated + inline bool updated_masses() const + { + return updated_masses_; + } + + /// Record whether masses have been updated + inline bool updated_charges() const + { + return updated_charges_; + } + protected: /// \brief Array of 0-based integers used to uniquely associate atoms @@ -268,6 +284,9 @@ protected: /// \brief Forces applied from colvars, to be communicated to the MD integrator std::vector atoms_new_colvar_forces; + /// Whether the masses and charges have been updated from the host code + bool updated_masses_, updated_charges_; + /// Used by all init_atom() functions: create a slot for an atom not /// requested yet; returns the index in the arrays int add_atom_slot(int atom_id); @@ -522,7 +541,7 @@ public: protected: /// Pointer to Tcl interpreter object - void *_tcl_interp; + void *tcl_interp_; /// Set Tcl pointers virtual void init_tcl_pointers(); diff --git a/lib/colvars/colvars_version.h b/lib/colvars/colvars_version.h index bd84d077d7..2521fdf872 100644 --- a/lib/colvars/colvars_version.h +++ b/lib/colvars/colvars_version.h @@ -1,5 +1,5 @@ #ifndef COLVARS_VERSION -#define COLVARS_VERSION "2018-11-16" +#define COLVARS_VERSION "2019-04-26" // This file is part of the Collective Variables module (Colvars). // The original version of Colvars and its updates are located at: // https://github.com/colvars/colvars diff --git a/lib/colvars/colvarscript.cpp b/lib/colvars/colvarscript.cpp index c9fe0497a9..1ad3283337 100644 --- a/lib/colvars/colvarscript.cpp +++ b/lib/colvars/colvarscript.cpp @@ -137,6 +137,10 @@ int colvarscript::run(int objc, unsigned char *const objv[]) if (cmd == "update") { error_code |= proxy->update_input(); + if (error_code) { + result += "Error updating the Colvars module.\n"; + return error_code; + } error_code |= colvars->calc(); error_code |= proxy->update_output(); if (error_code) { @@ -273,6 +277,10 @@ int colvarscript::run(int objc, unsigned char *const objv[]) int colvarscript::proc_colvar(colvar *cv, int objc, unsigned char *const objv[]) { + if (objc < 3) { + result = "Missing arguments"; + return COLVARSCRIPT_ERROR; + } std::string const subcmd(obj_to_str(objv[2])); if (subcmd == "value") { @@ -323,6 +331,47 @@ int colvarscript::proc_colvar(colvar *cv, int objc, unsigned char *const objv[]) return COLVARS_OK; } + if (subcmd == "getatomgroups") { + std::vector > lists = cv->get_atom_lists(); + std::vector >::iterator li = lists.begin(); + + for ( ; li != lists.end(); ++li) { + result += "{"; + std::vector::iterator lj = (*li).begin(); + for ( ; lj != (*li).end(); ++lj) { + result += cvm::to_str(*lj); + result += " "; + } + result += "} "; + } + return COLVARS_OK; + } + + if (subcmd == "getatomids") { + std::vector::iterator li = cv->atom_ids.begin(); + + for ( ; li != cv->atom_ids.end(); ++li) { + result += cvm::to_str(*li); + result += " "; + } + return COLVARS_OK; + } + + if (subcmd == "getgradients") { + std::vector::iterator li = cv->atomic_gradients.begin(); + + for ( ; li != cv->atomic_gradients.end(); ++li) { + result += "{"; + int j; + for (j = 0; j < 3; ++j) { + result += cvm::to_str((*li)[j]); + result += " "; + } + result += "} "; + } + return COLVARS_OK; + } + if (subcmd == "getappliedforce") { result = (cv->applied_force()).to_simple_string(); return COLVARS_OK; @@ -410,6 +459,10 @@ int colvarscript::proc_colvar(colvar *cv, int objc, unsigned char *const objv[]) int colvarscript::proc_bias(colvarbias *b, int objc, unsigned char *const objv[]) { + if (objc < 3) { + result = "Missing arguments"; + return COLVARSCRIPT_ERROR; + } std::string const subcmd(obj_to_str(objv[2])); if (subcmd == "energy") { diff --git a/lib/colvars/colvarscript.h b/lib/colvars/colvarscript.h index 313dbd661b..341cb1f72c 100644 --- a/lib/colvars/colvarscript.h +++ b/lib/colvars/colvarscript.h @@ -191,8 +191,9 @@ inline static colvarbias *colvarbias_obj(void *pobj) #ifdef COLVARSCRIPT_CPP #define CVSCRIPT_COMM_FN(COMM,N_ARGS_MIN,N_ARGS_MAX,ARGS,FN_BODY) \ - int CVSCRIPT_COMM_FNAME(COMM)(void *pobj, \ - int objc, unsigned char *const objv[]) \ + extern "C" int CVSCRIPT_COMM_FNAME(COMM)(void *pobj, \ + int objc, \ + unsigned char *const objv[]) \ { \ colvarscript *script = colvarscript_obj(); \ script->clear_results(); \ diff --git a/lib/colvars/colvartypes.cpp b/lib/colvars/colvartypes.cpp index 2b45d77e07..b81a943eab 100644 --- a/lib/colvars/colvartypes.cpp +++ b/lib/colvars/colvartypes.cpp @@ -19,6 +19,8 @@ bool colvarmodule::rotation::monitor_crossings = false; cvm::real colvarmodule::rotation::crossing_threshold = 1.0E-02; +namespace { + /// Numerical recipes diagonalization static int jacobi(cvm::real **a, cvm::real *d, cvm::real **v, int *nrot); @@ -28,6 +30,7 @@ static int eigsrt(cvm::real *d, cvm::real **v); /// Transpose the matrix static int transpose(cvm::real **v); +} std::string cvm::rvector::to_simple_string() const @@ -245,13 +248,11 @@ cvm::quaternion::position_derivative_inner(cvm::rvector const &pos, // Seok C, Dill KA. Using quaternions to calculate RMSD. J Comput // Chem. 25(15):1849-57 (2004) DOI: 10.1002/jcc.20110 PubMed: 15376254 -void colvarmodule::rotation::build_matrix(std::vector const &pos1, - std::vector const &pos2, - cvm::matrix2d &S) +void colvarmodule::rotation::build_correlation_matrix( + std::vector const &pos1, + std::vector const &pos2) { // build the correlation matrix - C.resize(3, 3); - C.reset(); size_t i; for (i = 0; i < pos1.size(); i++) { C.xx() += pos1[i].x * pos2[i].x; @@ -264,7 +265,11 @@ void colvarmodule::rotation::build_matrix(std::vector const &pos1 C.zy() += pos1[i].z * pos2[i].y; C.zz() += pos1[i].z * pos2[i].z; } +} + +void colvarmodule::rotation::compute_overlap_matrix() +{ // build the "overlap" matrix, whose eigenvectors are stationary // points of the RMSD in the space of rotations S[0][0] = C.xx() + C.yy() + C.zz(); @@ -286,37 +291,38 @@ void colvarmodule::rotation::build_matrix(std::vector const &pos1 } -void colvarmodule::rotation::diagonalize_matrix(cvm::matrix2d &S, - cvm::vector1d &S_eigval, - cvm::matrix2d &S_eigvec) +void colvarmodule::rotation::diagonalize_matrix( + cvm::matrix2d &m, + cvm::vector1d &eigval, + cvm::matrix2d &eigvec) { - S_eigval.resize(4); - S_eigval.reset(); - S_eigvec.resize(4,4); - S_eigvec.reset(); + eigval.resize(4); + eigval.reset(); + eigvec.resize(4, 4); + eigvec.reset(); // diagonalize int jac_nrot = 0; - if (jacobi(S.c_array(), S_eigval.c_array(), S_eigvec.c_array(), &jac_nrot) != + if (jacobi(m.c_array(), eigval.c_array(), eigvec.c_array(), &jac_nrot) != COLVARS_OK) { cvm::error("Too many iterations in routine jacobi.\n" "This is usually the result of an ill-defined set of atoms for " "rotational alignment (RMSD, rotateReference, etc).\n"); } - eigsrt(S_eigval.c_array(), S_eigvec.c_array()); + eigsrt(eigval.c_array(), eigvec.c_array()); // jacobi saves eigenvectors by columns - transpose(S_eigvec.c_array()); + transpose(eigvec.c_array()); // normalize eigenvectors for (size_t ie = 0; ie < 4; ie++) { cvm::real norm2 = 0.0; size_t i; for (i = 0; i < 4; i++) { - norm2 += S_eigvec[ie][i] * S_eigvec[ie][i]; + norm2 += eigvec[ie][i] * eigvec[ie][i]; } - cvm::real const norm = std::sqrt(norm2); + cvm::real const norm = cvm::sqrt(norm2); for (i = 0; i < 4; i++) { - S_eigvec[ie][i] /= norm; + eigvec[ie][i] /= norm; } } } @@ -324,23 +330,26 @@ void colvarmodule::rotation::diagonalize_matrix(cvm::matrix2d &S, // Calculate the rotation, plus its derivatives -void colvarmodule::rotation::calc_optimal_rotation(std::vector const &pos1, - std::vector const &pos2) +void colvarmodule::rotation::calc_optimal_rotation( + std::vector const &pos1, + std::vector const &pos2) { - S.resize(4,4); + C.resize(3, 3); + C.reset(); + build_correlation_matrix(pos1, pos2); + + S.resize(4, 4); S.reset(); + compute_overlap_matrix(); - build_matrix(pos1, pos2, S); - - S_backup.resize(4,4); + S_backup.resize(4, 4); S_backup = S; if (b_debug_gradients) { - cvm::log("S = "+cvm::to_str(cvm::to_str(S_backup), cvm::cv_width, cvm::cv_prec)+"\n"); + cvm::log("S = "+cvm::to_str(S_backup, cvm::cv_width, cvm::cv_prec)+"\n"); } diagonalize_matrix(S, S_eigval, S_eigvec); - // eigenvalues and eigenvectors cvm::real const L0 = S_eigval[0]; cvm::real const L1 = S_eigval[1]; @@ -524,7 +533,7 @@ void colvarmodule::rotation::calc_optimal_rotation(std::vector co dq0_2[3][comp] * colvarmodule::debug_gradients_step_size); cvm::log( "|(l_0+dl_0) - l_0^new|/l_0 = "+ - cvm::to_str(std::fabs(L0+DL0 - L0_new)/L0, cvm::cv_width, cvm::cv_prec)+ + cvm::to_str(cvm::fabs(L0+DL0 - L0_new)/L0, cvm::cv_width, cvm::cv_prec)+ ", |(q_0+dq_0) - q_0^new| = "+ cvm::to_str((Q0+DQ0 - Q0_new).norm(), cvm::cv_width, cvm::cv_prec)+ "\n"); @@ -544,6 +553,9 @@ void colvarmodule::rotation::calc_optimal_rotation(std::vector co #define n 4 + +namespace { + int jacobi(cvm::real **a, cvm::real *d, cvm::real **v, int *nrot) { int j,iq,ip,i; @@ -567,7 +579,7 @@ int jacobi(cvm::real **a, cvm::real *d, cvm::real **v, int *nrot) sm=0.0; for (ip=0;ip 4 && (cvm::real)(std::fabs(d[ip])+g) == (cvm::real)std::fabs(d[ip]) - && (cvm::real)(std::fabs(d[iq])+g) == (cvm::real)std::fabs(d[iq])) + g=100.0*cvm::fabs(a[ip][iq]); + if (i > 4 && (cvm::real)(cvm::fabs(d[ip])+g) == (cvm::real)cvm::fabs(d[ip]) + && (cvm::real)(cvm::fabs(d[iq])+g) == (cvm::real)cvm::fabs(d[iq])) a[ip][iq]=0.0; - else if (std::fabs(a[ip][iq]) > tresh) { + else if (cvm::fabs(a[ip][iq]) > tresh) { h=d[iq]-d[ip]; - if ((cvm::real)(std::fabs(h)+g) == (cvm::real)std::fabs(h)) + if ((cvm::real)(cvm::fabs(h)+g) == (cvm::real)cvm::fabs(h)) t=(a[ip][iq])/h; else { theta=0.5*h/(a[ip][iq]); - t=1.0/(std::fabs(theta)+std::sqrt(1.0+theta*theta)); + t=1.0/(cvm::fabs(theta)+cvm::sqrt(1.0+theta*theta)); if (theta < 0.0) t = -t; } - c=1.0/std::sqrt(1+t*t); + c=1.0/cvm::sqrt(1+t*t); s=t*c; tau=s/(1.0+c); h=t*a[ip][iq]; @@ -663,5 +675,7 @@ int transpose(cvm::real **v) return COLVARS_OK; } +} + #undef n #undef ROTATE diff --git a/lib/colvars/colvartypes.h b/lib/colvars/colvartypes.h index 4ef9557dcb..9973d92e98 100644 --- a/lib/colvars/colvartypes.h +++ b/lib/colvars/colvartypes.h @@ -10,7 +10,6 @@ #ifndef COLVARTYPES_H #define COLVARTYPES_H -#include #include #include "colvarmodule.h" @@ -220,7 +219,7 @@ public: inline cvm::real norm() const { - return std::sqrt(this->norm2()); + return cvm::sqrt(this->norm2()); } inline cvm::real sum() const @@ -801,7 +800,7 @@ public: inline cvm::real norm() const { - return std::sqrt(this->norm2()); + return cvm::sqrt(this->norm2()); } inline cvm::rvector unit() const @@ -1008,17 +1007,17 @@ public: cvm::real theta_in, cvm::real psi_in) { - q0 = ( (std::cos(phi_in/2.0)) * (std::cos(theta_in/2.0)) * (std::cos(psi_in/2.0)) + - (std::sin(phi_in/2.0)) * (std::sin(theta_in/2.0)) * (std::sin(psi_in/2.0)) ); + q0 = ( (cvm::cos(phi_in/2.0)) * (cvm::cos(theta_in/2.0)) * (cvm::cos(psi_in/2.0)) + + (cvm::sin(phi_in/2.0)) * (cvm::sin(theta_in/2.0)) * (cvm::sin(psi_in/2.0)) ); - q1 = ( (std::sin(phi_in/2.0)) * (std::cos(theta_in/2.0)) * (std::cos(psi_in/2.0)) - - (std::cos(phi_in/2.0)) * (std::sin(theta_in/2.0)) * (std::sin(psi_in/2.0)) ); + q1 = ( (cvm::sin(phi_in/2.0)) * (cvm::cos(theta_in/2.0)) * (cvm::cos(psi_in/2.0)) - + (cvm::cos(phi_in/2.0)) * (cvm::sin(theta_in/2.0)) * (cvm::sin(psi_in/2.0)) ); - q2 = ( (std::cos(phi_in/2.0)) * (std::sin(theta_in/2.0)) * (std::cos(psi_in/2.0)) + - (std::sin(phi_in/2.0)) * (std::cos(theta_in/2.0)) * (std::sin(psi_in/2.0)) ); + q2 = ( (cvm::cos(phi_in/2.0)) * (cvm::sin(theta_in/2.0)) * (cvm::cos(psi_in/2.0)) + + (cvm::sin(phi_in/2.0)) * (cvm::cos(theta_in/2.0)) * (cvm::sin(psi_in/2.0)) ); - q3 = ( (std::cos(phi_in/2.0)) * (std::cos(theta_in/2.0)) * (std::sin(psi_in/2.0)) - - (std::sin(phi_in/2.0)) * (std::sin(theta_in/2.0)) * (std::cos(psi_in/2.0)) ); + q3 = ( (cvm::cos(phi_in/2.0)) * (cvm::cos(theta_in/2.0)) * (cvm::sin(psi_in/2.0)) - + (cvm::sin(phi_in/2.0)) * (cvm::sin(theta_in/2.0)) * (cvm::cos(psi_in/2.0)) ); } /// \brief Default constructor @@ -1115,7 +1114,7 @@ public: /// Norm of the quaternion inline cvm::real norm() const { - return std::sqrt(this->norm2()); + return cvm::sqrt(this->norm2()); } /// Return the conjugate quaternion @@ -1177,7 +1176,7 @@ public: } /// \brief Provides the quaternion product. \b NOTE: for the inner - /// product use: \code h.inner (q); \endcode + /// product use: `h.inner (q);` friend inline cvm::quaternion operator * (cvm::quaternion const &h, cvm::quaternion const &q) { @@ -1263,7 +1262,7 @@ public: cvm::real const cos_omega = this->q0*Q2.q0 + this->q1*Q2.q1 + this->q2*Q2.q2 + this->q3*Q2.q3; - cvm::real const omega = std::acos( (cos_omega > 1.0) ? 1.0 : + cvm::real const omega = cvm::acos( (cos_omega > 1.0) ? 1.0 : ( (cos_omega < -1.0) ? -1.0 : cos_omega) ); // get the minimum distance: x and -x are the same quaternion @@ -1278,11 +1277,11 @@ public: inline cvm::quaternion dist2_grad(cvm::quaternion const &Q2) const { cvm::real const cos_omega = this->q0*Q2.q0 + this->q1*Q2.q1 + this->q2*Q2.q2 + this->q3*Q2.q3; - cvm::real const omega = std::acos( (cos_omega > 1.0) ? 1.0 : + cvm::real const omega = cvm::acos( (cos_omega > 1.0) ? 1.0 : ( (cos_omega < -1.0) ? -1.0 : cos_omega) ); - cvm::real const sin_omega = std::sin(omega); + cvm::real const sin_omega = cvm::sin(omega); - if (std::fabs(sin_omega) < 1.0E-14) { + if (cvm::fabs(sin_omega) < 1.0E-14) { // return a null 4d vector return cvm::quaternion(0.0, 0.0, 0.0, 0.0); } @@ -1338,14 +1337,16 @@ public: /// \brief Perform gradient tests bool b_debug_gradients; - /// \brief Positions to superimpose: the rotation should brings pos1 - /// into pos2 - std::vector pos1, pos2; - + /// Correlation matrix C (3, 3) cvm::rmatrix C; + /// Overlap matrix S (4, 4) cvm::matrix2d S; + + /// Eigenvalues of S cvm::vector1d S_eigval; + + /// Eigenvectors of S cvm::matrix2d S_eigvec; /// Used for debugging gradients @@ -1404,8 +1405,8 @@ public: : b_debug_gradients(false) { cvm::rvector const axis_n = axis.unit(); - cvm::real const sina = std::sin(angle/2.0); - q = cvm::quaternion(std::cos(angle/2.0), + cvm::real const sina = cvm::sin(angle/2.0); + q = cvm::quaternion(cvm::cos(angle/2.0), sina * axis_n.x, sina * axis_n.y, sina * axis_n.z); } @@ -1437,7 +1438,7 @@ public: inline cvm::real spin_angle(cvm::rvector const &axis) const { cvm::rvector const q_vec = q.get_vector(); - cvm::real alpha = (180.0/PI) * 2.0 * std::atan2(axis * q_vec, q.q0); + cvm::real alpha = (180.0/PI) * 2.0 * cvm::atan2(axis * q_vec, q.q0); while (alpha > 180.0) alpha -= 360; while (alpha < -180.0) alpha += 360; return alpha; @@ -1473,9 +1474,9 @@ public: { cvm::rvector const q_vec = q.get_vector(); cvm::real const alpha = - (180.0/PI) * 2.0 * std::atan2(axis * q_vec, q.q0); + (180.0/PI) * 2.0 * cvm::atan2(axis * q_vec, q.q0); - cvm::real const cos_spin_2 = std::cos(alpha * (PI/180.0) * 0.5); + cvm::real const cos_spin_2 = cvm::cos(alpha * (PI/180.0) * 0.5); cvm::real const cos_theta_2 = ( (cos_spin_2 != 0.0) ? (q.q0 / cos_spin_2) : (0.0) ); @@ -1489,7 +1490,7 @@ public: cvm::rvector const q_vec = q.get_vector(); cvm::real const iprod = axis * q_vec; - cvm::real const cos_spin_2 = std::cos(std::atan2(iprod, q.q0)); + cvm::real const cos_spin_2 = cvm::cos(cvm::atan2(iprod, q.q0)); if (q.q0 != 0.0) { @@ -1529,15 +1530,17 @@ protected: /// eigenvalue crossing) cvm::quaternion q_old; - /// Build the overlap matrix S (used by calc_optimal_rotation()) - void build_matrix(std::vector const &pos1, - std::vector const &pos2, - cvm::matrix2d &S); + /// Build the correlation matrix C (used by calc_optimal_rotation()) + void build_correlation_matrix(std::vector const &pos1, + std::vector const &pos2); - /// Diagonalize the overlap matrix S (used by calc_optimal_rotation()) - void diagonalize_matrix(cvm::matrix2d &S, - cvm::vector1d &S_eigval, - cvm::matrix2d &S_eigvec); + /// Compute the overlap matrix S (used by calc_optimal_rotation()) + void compute_overlap_matrix(); + + /// Diagonalize a given matrix m (used by calc_optimal_rotation()) + static void diagonalize_matrix(cvm::matrix2d &m, + cvm::vector1d &eigval, + cvm::matrix2d &eigvec); }; diff --git a/lib/colvars/colvarvalue.cpp b/lib/colvars/colvarvalue.cpp index 86b99ed3d6..accc5defec 100644 --- a/lib/colvars/colvarvalue.cpp +++ b/lib/colvars/colvarvalue.cpp @@ -144,10 +144,10 @@ void colvarvalue::apply_constraints() case colvarvalue::type_quaternionderiv: break; case colvarvalue::type_unit3vector: - rvector_value /= std::sqrt(rvector_value.norm2()); + rvector_value /= cvm::sqrt(rvector_value.norm2()); break; case colvarvalue::type_quaternion: - quaternion_value /= std::sqrt(quaternion_value.norm2()); + quaternion_value /= cvm::sqrt(quaternion_value.norm2()); break; case colvarvalue::type_vector: if (elem_types.size() > 0) { @@ -579,7 +579,7 @@ colvarvalue colvarvalue::dist2_grad(colvarvalue const &x2) const cvm::rvector const &v1 = this->rvector_value; cvm::rvector const &v2 = x2.rvector_value; cvm::real const cos_t = v1 * v2; - cvm::real const sin_t = std::sqrt(1.0 - cos_t*cos_t); + cvm::real const sin_t = cvm::sqrt(1.0 - cos_t*cos_t); return colvarvalue( 2.0 * sin_t * cvm::rvector((-1.0) * sin_t * v2.x + cos_t/sin_t * (v1.x - cos_t*v2.x), @@ -630,7 +630,7 @@ colvarvalue const colvarvalue::interpolate(colvarvalue const &x1, break; case colvarvalue::type_unit3vector: case colvarvalue::type_quaternion: - if (interp.norm()/std::sqrt(d2) < 1.0e-6) { + if (interp.norm()/cvm::sqrt(d2) < 1.0e-6) { cvm::error("Error: interpolation between "+cvm::to_str(x1)+" and "+ cvm::to_str(x2)+" with lambda = "+cvm::to_str(lambda)+ " is undefined: result = "+cvm::to_str(interp)+"\n", diff --git a/lib/colvars/colvarvalue.h b/lib/colvars/colvarvalue.h index 25255e2f7c..29b535a1a8 100644 --- a/lib/colvars/colvarvalue.h +++ b/lib/colvars/colvarvalue.h @@ -17,22 +17,22 @@ /// \brief Value of a collective variable: this is a metatype which /// can be set at runtime. By default it is set to be a scalar /// number, and can be treated as such in all operations (this is -/// done by most \link cvc \endlink implementations). +/// done by most \link colvar::cvc \endlink implementations). /// /// \link colvarvalue \endlink allows \link colvar \endlink to be /// treat different data types. By default, a \link colvarvalue /// \endlink variable is a scalar number. To use it as /// another type, declare and initialize it as -/// \code colvarvalue x(colvarvalue::type_xxx)\endcode, use \link x.type -/// (colvarvalue::type_xxx) \endlink at a later stage, or if unset, -/// assign the type with \code x = y; \endcode, provided y is correctly set. +/// `colvarvalue x(colvarvalue::type_xxx)`, use `x.type (colvarvalue::type_xxx)` +/// at a later stage, or if unset, +/// assign the type with `x = y;`, provided y is correctly set. /// /// All operators (either unary or binary) on a \link /// colvarvalue \endlink object performs one or more checks on the /// \link Type \endlink, except when reading from a stream, when there is no way to -/// detect the \link Type \endlink. To use \code is >> x; \endcode x \b MUST +/// detect the \link Type \endlink. To use `is >> x;` x \b MUST /// already have a type correcly set up for properly parsing the -/// stream. No problem of course with the output streams: \code os << x; \endcode +/// stream. No problem of course with the output streams: `os << x;` /// /// \em Note \em on \em performance: to avoid type checks in a long array of \link /// colvarvalue \endlink objects, use one of the existing "_opt" functions or implement a new one @@ -159,7 +159,7 @@ public: /// \brief If the variable has constraints (e.g. unitvector or /// quaternion), transform it to satisfy them; this function needs /// to be called only when the \link colvarvalue \endlink - /// is calculated outside of \link cvc \endlink objects + /// is calculated outside of \link colvar::cvc \endlink objects void apply_constraints(); /// Get the current type @@ -184,7 +184,7 @@ public: /// Norm of this colvarvalue inline cvm::real norm() const { - return std::sqrt(this->norm2()); + return cvm::sqrt(this->norm2()); } /// Sum of the components of this colvarvalue (if more than one dimension) @@ -728,7 +728,7 @@ inline cvm::real colvarvalue::dist2(colvarvalue const &x2) const case colvarvalue::type_unit3vector: case colvarvalue::type_unit3vectorderiv: // angle between (*this) and x2 is the distance - return std::acos(this->rvector_value * x2.rvector_value) * std::acos(this->rvector_value * x2.rvector_value); + return cvm::acos(this->rvector_value * x2.rvector_value) * cvm::acos(this->rvector_value * x2.rvector_value); case colvarvalue::type_quaternion: case colvarvalue::type_quaternionderiv: // angle between (*this) and x2 is the distance, the quaternion diff --git a/lib/gpu/lal_dpd.cu b/lib/gpu/lal_dpd.cu index e32404ff5c..462401ad70 100644 --- a/lib/gpu/lal_dpd.cu +++ b/lib/gpu/lal_dpd.cu @@ -42,9 +42,9 @@ texture vel_tex; // 2. C. L. Phillips, J. A. Anderson, S. C. Glotzer, Comput. Phys. Comm. 230 (2011), 7191-7201. // PRNG period = 3666320093*2^32 ~ 2^64 ~ 10^19 -#define LCGA 0x4beb5d59 // Full period 32 bit LCG +#define LCGA 0x4beb5d59 /* Full period 32 bit LCG */ #define LCGC 0x2600e1f7 -#define oWeylPeriod 0xda879add // Prime period 3666320093 +#define oWeylPeriod 0xda879add /* Prime period 3666320093 */ #define oWeylOffset 0x8009d14b #define TWO_N32 0.232830643653869628906250e-9f /* 2^-32 */ diff --git a/lib/gpu/lal_lj_cubic.cu b/lib/gpu/lal_lj_cubic.cu index a4b1992f33..683c6b2aac 100644 --- a/lib/gpu/lal_lj_cubic.cu +++ b/lib/gpu/lal_lj_cubic.cu @@ -27,9 +27,9 @@ texture pos_tex; // LJ quantities scaled by epsilon and rmin = sigma*2^1/6 (see src/pair_lj_cubic.h) #define _RT6TWO (numtyp)1.1224621 -#define _PHIS (numtyp)-0.7869823 // energy at s -#define _DPHIDS (numtyp)2.6899009 // gradient at s -#define _A3 (numtyp)27.93357 // cubic coefficient +#define _PHIS (numtyp)-0.7869823 /* energy at s */ +#define _DPHIDS (numtyp)2.6899009 /* gradient at s */ +#define _A3 (numtyp)27.93357 /* cubic coefficient */ __kernel void k_lj_cubic(const __global numtyp4 *restrict x_, const __global numtyp4 *restrict lj1, diff --git a/potentials/C.drip b/potentials/C.drip new file mode 100644 index 0000000000..435efe40a9 --- /dev/null +++ b/potentials/C.drip @@ -0,0 +1,19 @@ +# DATE: 2019-04-19 CONTRIBUTOR: Mingjian Wen, wenxx151@umn.edu +# +# Parameters of the Dihedral-angle-corrected registry-dependent interlayer (DRIP) +# potential for multilayer graphene structures. +# +# Cite as M. Wen, S. Carr, S. Fang, E. Kaxiras, and E. B. Tadmor, Phys. Rev. B, 98, 235404 (2018). + + +# C0 C2 C4 C delta lambda A z0 B eta rho_cut r_cut normal_cut +C C 1.1598e-02 1.2981e-02 3.2515e-02 7.8151e-03 8.3679e-01 2.7158 2.2216e-02 3.34 7.6799e-03 1.1432 1.562 12.0 3.7 + + +# C0, C2, C4, C, A, and B in [eV] +# delta, z0, eta, rho_cut, r_cut, and normal_cut in [Angstrom] +# lambda in [1/Angstrom] +# +# normal_cut is a parameter not present in the Wen paper, but specific to the +# LAMMPS implementation, which is used to find the 3 nearest neighbors of an +# atom to construct the normal. diff --git a/potentials/CH.rebo b/potentials/CH.rebo new file mode 100644 index 0000000000..08b1b19dc2 --- /dev/null +++ b/potentials/CH.rebo @@ -0,0 +1,37595 @@ +# DATE: 2018-7-3 CONTRIBUTOR: Cyril Falvo, cyril.falvo@u-psud.fr +# REBO2 Brenner potential modified from CH.airebo +# Cite as D. W. Brenner, O. A. Shenderova, J. A. Harrison, S. J. Stuart, B. Ni, and S. B. Sinnott, +# "A second- generation reactive empirical bond order (rebo) potential energy expression for hydrocarbons.", +# J. Phys. Cond. Mat., 14:783, 2002. + +1.7 rcmin_CC +1.3 rcmin_CH +1.1 rcmin_HH +2.0 rcmax_CC +1.8 rcmax_CH +1.7 rcmax_HH +2.0 rcmaxp_CC +1.6 rcmaxp_CH +1.7 rcmaxp_HH +0.1 smin +2.0 Nmin +3.0 Nmax +3.2 NCmin +3.7 NCmax +0.3134602960833 Q_CC +0.340775728 Q_CH +0.370471487045 Q_HH +4.7465390606595 alpha_CC +4.10254983 alpha_CH +3.536298648 alpha_HH +10953.544162170 A_CC +149.94098723 A_CH +32.817355747 A_HH +12388.79197798 BIJc_CC1 +17.56740646509 BIJc_CC2 +30.71493208065 BIJc_CC3 +32.3551866587 BIJc_CH1 +0.0 BIJc_CH2 +0.0 BIJc_CH3 +29.632593 BIJc_HH1 +0.0 BIJc_HH2 +0.0 BIJc_HH3 +4.7204523127 Beta_CC1 +1.4332132499 Beta_CC2 +1.3826912506 Beta_CC3 +1.434458059249837 Beta_CH1 +0.0 Beta_CH2 +0.0 Beta_CH3 +1.71589217 Beta_HH1 +1.0 Beta_HH2 +1.0 Beta_HH3 +0.0 rho_CC +1.09 rho_CH +0.7415887 rho_HH +3.4 rcLJmin_CC +3.025 rcLJmin_CH +2.65 rcLJmin_HH +3.816370964 rcLJmax_CC +3.395447696 rcLJmax_CH +2.974524428 rcLJmax_HH +0.77 bLJmin_CC +0.75 bLJmin_CH +0.32 bLJmin_HH +0.81 bLJmax_CC +0.9 bLJmax_CH +0.42 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27f4f8a64c..1e073bb657 100644 --- a/src/.gitignore +++ b/src/.gitignore @@ -150,10 +150,18 @@ /compute_spin.h /fix_langevin_spin.cpp /fix_langevin_spin.h +/fix_neb_spin.cpp +/fix_neb_spin.h /fix_nve_spin.cpp /fix_nve_spin.h /fix_precession_spin.cpp /fix_precession_spin.h +/fix_setforce_spin.cpp +/fix_setforce_spin.h +/min_spin.cpp +/min_spin.h +/neb_spin.cpp +/neb_spin.h /pair_spin.cpp /pair_spin.h /pair_spin_dmi.cpp @@ -187,6 +195,8 @@ /angle_cosine_shift_exp.h /angle_cosine_squared.cpp /angle_cosine_squared.h +/angle_cross.cpp +/angle_cross.h /angle_dipole.cpp /angle_dipole.h /angle_fourier.cpp @@ -195,6 +205,8 @@ /angle_fourier_simple.h /angle_harmonic.cpp /angle_harmonic.h +/angle_mm3.cpp +/angle_mm3.h /angle_quartic.cpp /angle_quartic.h /angle_sdk.cpp @@ -249,6 +261,8 @@ /bond_harmonic_shift.h /bond_harmonic_shift_cut.cpp /bond_harmonic_shift_cut.h +/bond_mm3.cpp +/bond_mm3.h /bond_morse.cpp /bond_morse.h /bond_nonlinear.cpp @@ -377,6 +391,8 @@ /dihedral_table.h /dihedral_table_cut.cpp /dihedral_table_cut.h +/dump_atom_adios.cpp +/dump_atom_adios.h /dump_atom_gz.cpp /dump_atom_gz.h /dump_xyz_gz.cpp @@ -387,6 +403,8 @@ /dump_cfg_gz.h /dump_cfg_mpiio.cpp /dump_cfg_mpiio.h +/dump_custom_adios.cpp +/dump_custom_adios.h /dump_custom_gz.cpp /dump_custom_gz.h /dump_custom_mpiio.cpp @@ -403,6 +421,8 @@ /dump_xtc.h /dump_xyz_mpiio.cpp /dump_xyz_mpiio.h +/dynamical_matrix.cpp +/dynamical_matrix.h /ewald.cpp /ewald.h /ewald_cg.cpp @@ -445,6 +465,8 @@ /fix_dpd_energy.h /fix_efield.cpp /fix_efield.h +/fix_electron_stopping.cpp +/fix_electron_stopping.h /fix_eos_cv.cpp /fix_eos_cv.h /fix_eos_table.cpp @@ -683,6 +705,10 @@ /improper_cvff.h /improper_distance.cpp /improper_distance.h +/improper_distharm.cpp +/improper_distharm.h +/improper_sqdistharm.cpp +/improper_sqdistharm.h /improper_fourier.cpp /improper_fourier.h /improper_harmonic.cpp @@ -782,6 +808,10 @@ /pair_dpd_mt.h /pair_dsmc.cpp /pair_dsmc.h +/pair_e3b.cpp +/pair_e3b.h +/pair_drip.cpp +/pair_drip.h /pair_eam.cpp /pair_eam.h /pair_eam_alloy.cpp @@ -790,6 +820,10 @@ /pair_eam_cd.h /pair_eam_fs.cpp /pair_eam_fs.h +/fix_electron_stopping.cpp +/fix_electron_stopping.h +/pair_lebedeva_z.cpp +/pair_lebedeva_z.h /pair_lj_expand_coul_long.cpp /pair_lj_expand_coul_long.h /pair_edip.cpp @@ -805,6 +839,8 @@ /pair_gauss_cut.h /pair_gayberne.cpp /pair_gayberne.h +/pair_granular.cpp +/pair_granular.h /pair_gran_easy.cpp /pair_gran_easy.h /pair_gran_hertz_history.cpp @@ -829,6 +865,8 @@ /pair_kolmogorov_crespi_z.h /pair_lcbop.cpp /pair_lcbop.h +/pair_lebedeva_z.cpp +/pair_lebedeva_z.h /pair_line_lj.cpp /pair_line_lj.h /pair_list.cpp @@ -847,8 +885,14 @@ /pair_lj_class2.h /pair_lj_class2_coul_cut.cpp /pair_lj_class2_coul_cut.h +/pair_lj_class2_coul_cut_soft.cpp +/pair_lj_class2_coul_cut_soft.h /pair_lj_class2_coul_long.cpp /pair_lj_class2_coul_long.h +/pair_lj_class2_coul_long_soft.cpp +/pair_lj_class2_coul_long_soft.h +/pair_lj_class2_soft.cpp +/pair_lj_class2_soft.h /pair_lj_coul.cpp /pair_lj_coul.h /pair_coul_cut_soft.cpp @@ -893,6 +937,8 @@ /pair_lj_sdk_coul_msm.h /pair_lj_sf_dipole_sf.cpp /pair_lj_sf_dipole_sf.h +/pair_lj_switch3_coulgauss_long.cpp +/pair_lj_switch3_coulgauss_long.h /pair_lubricateU.cpp /pair_lubricateU.h /pair_lubricateU_poly.cpp @@ -901,12 +947,12 @@ /pair_lubricate_poly.h /pair_lubricate.cpp /pair_lubricate.h -/pair_meam.cpp -/pair_meam.h /pair_meam_spline.cpp /pair_meam_spline.h /pair_meam_sw_spline.cpp /pair_meam_sw_spline.h +/pair_mm3_switch3_coulgauss_long.cpp +/pair_mm3_switch3_coulgauss_long.h /pair_morse_soft.cpp /pair_morse_soft.h /pair_nb3b_harmonic.cpp @@ -1238,4 +1284,3 @@ /pair_smtbq.h /pair_vashishta*.cpp /pair_vashishta*.h - diff --git a/src/GRANULAR/fix_wall_gran.cpp b/src/GRANULAR/fix_wall_gran.cpp index 555c5071e7..8513fc702b 100644 --- a/src/GRANULAR/fix_wall_gran.cpp +++ b/src/GRANULAR/fix_wall_gran.cpp @@ -53,7 +53,7 @@ enum{NONE,CONSTANT,EQUAL}; #define EPSILON 1e-10 enum {NORMAL_HOOKE, NORMAL_HERTZ, HERTZ_MATERIAL, DMT, JKR}; -enum {VELOCITY, VISCOELASTIC, TSUJI}; +enum {VELOCITY, MASS_VELOCITY, VISCOELASTIC, TSUJI}; enum {TANGENTIAL_NOHISTORY, TANGENTIAL_HISTORY, TANGENTIAL_MINDLIN, TANGENTIAL_MINDLIN_RESCALE}; enum {TWIST_NONE, TWIST_SDS, TWIST_MARSHALL}; @@ -122,6 +122,7 @@ FixWallGran::FixWallGran(LAMMPS *lmp, int narg, char **arg) : iarg = 4; damping_model = VISCOELASTIC; roll_model = twist_model = NONE; + tangential_history = roll_history = twist_history = 0; while (iarg < narg) { if (strcmp(arg[iarg], "hooke") == 0) { if (iarg + 2 >= narg) @@ -183,6 +184,9 @@ FixWallGran::FixWallGran(LAMMPS *lmp, int narg, char **arg) : if (strcmp(arg[iarg+1], "velocity") == 0) { damping_model = VELOCITY; iarg += 1; + } else if (strcmp(arg[iarg+1], "mass_velocity") == 0) { + damping_model = MASS_VELOCITY; + iarg += 1; } else if (strcmp(arg[iarg+1], "viscoelastic") == 0) { damping_model = VISCOELASTIC; iarg += 1; @@ -226,7 +230,7 @@ FixWallGran::FixWallGran(LAMMPS *lmp, int narg, char **arg) : "stiffness requires a normal contact model " "that specifies material properties"); } - tangential_coeffs[0] = 4*(2-poiss)*(1+poiss)/Emod; + tangential_coeffs[0] = Emod/4*(2-poiss)*(1+poiss); } else { tangential_coeffs[0] = force->numeric(FLERR,arg[iarg+2]); //kt } @@ -1061,7 +1065,7 @@ void FixWallGran::granular(double rsq, double dx, double dy, double dz, double *contact) { double fx,fy,fz,nx,ny,nz; - double radsum,r,rinv; + double r,rinv; double Reff, delta, dR, dR2; double vr1,vr2,vr3,vnnr,vn1,vn2,vn3,vt1,vt2,vt3; @@ -1095,11 +1099,8 @@ void FixWallGran::granular(double rsq, double dx, double dy, double dz, double shrmag,rsht; r = sqrt(rsq); - radsum = rwall + radius; - E = normal_coeffs[0]; - radsum = radius + rwall; if (rwall == 0) Reff = radius; else Reff = radius*rwall/(radius+rwall); @@ -1122,7 +1123,7 @@ void FixWallGran::granular(double rsq, double dx, double dy, double dz, vn2 = ny*vnnr; vn3 = nz*vnnr; - delta = radsum - r; + delta = radius - r; dR = delta*Reff; if (normal_model == JKR) { history[0] = 1.0; @@ -1160,6 +1161,9 @@ void FixWallGran::granular(double rsq, double dx, double dy, double dz, if (damping_model == VELOCITY) { damp_normal = 1; } + else if (damping_model == MASS_VELOCITY) { + damp_normal = meff; + } else if (damping_model == VISCOELASTIC) { damp_normal = a*meff; } @@ -1182,9 +1186,9 @@ void FixWallGran::granular(double rsq, double dx, double dy, double dz, vt3 = vr3 - vn3; // relative rotational velocity - wr1 = radius*omega[0] * rinv; - wr2 = radius*omega[1] * rinv; - wr3 = radius*omega[2] * rinv; + wr1 = radius*omega[0]; + wr2 = radius*omega[1]; + wr3 = radius*omega[2]; // relative tangential velocities vtr1 = vt1 - (nz*wr2-ny*wr3); diff --git a/src/GRANULAR/fix_wall_gran_region.cpp b/src/GRANULAR/fix_wall_gran_region.cpp index 7702967504..72798bf7b7 100644 --- a/src/GRANULAR/fix_wall_gran_region.cpp +++ b/src/GRANULAR/fix_wall_gran_region.cpp @@ -121,7 +121,7 @@ void FixWallGranRegion::init() region->reset_vel(); } - if (motion_resetflag){ + if (motion_resetflag) { char str[256]; snprintf(str,256,"Region properties for region %s are inconsistent " "with restart file, resetting its motion",idregion); @@ -190,7 +190,7 @@ void FixWallGranRegion::post_force(int /*vflag*/) if (mask[i] & groupbit) { if (!region->match(x[i][0],x[i][1],x[i][2])) continue; - if (pairstyle == GRANULAR && normal_model == JKR){ + if (pairstyle == GRANULAR && normal_model == JKR) { nc = region->surface(x[i][0],x[i][1],x[i][2], radius[i]+pulloff_distance(radius[i])); } @@ -232,8 +232,8 @@ void FixWallGranRegion::post_force(int /*vflag*/) rsq = region->contact[ic].r*region->contact[ic].r; - if (pairstyle == GRANULAR && normal_model == JKR){ - if (history_many[i][c2r[ic]][0] == 0.0 && rsq > radius[i]*radius[i]){ + if (pairstyle == GRANULAR && normal_model == JKR) { + if (history_many[i][c2r[ic]][0] == 0.0 && rsq > radius[i]*radius[i]) { for (m = 0; m < size_history; m++) history_many[i][0][m] = 0.0; continue; @@ -253,7 +253,7 @@ void FixWallGranRegion::post_force(int /*vflag*/) if (fix_rigid && mass_rigid[i] > 0.0) meff = mass_rigid[i]; // store contact info - if (peratom_flag){ + if (peratom_flag) { array_atom[i][0] = (double)atom->tag[i]; array_atom[i][4] = x[i][0] - dx; array_atom[i][5] = x[i][1] - dy; @@ -382,7 +382,7 @@ void FixWallGranRegion::copy_arrays(int i, int j, int /*delflag*/) { int m,n,iwall; - if (use_history){ + if (use_history) { n = ncontact[i]; for (iwall = 0; iwall < n; iwall++) { walls[j][iwall] = walls[i][iwall]; @@ -392,7 +392,7 @@ void FixWallGranRegion::copy_arrays(int i, int j, int /*delflag*/) ncontact[j] = ncontact[i]; } - if (peratom_flag){ + if (peratom_flag) { for (int m = 0; m < size_peratom_cols; m++) array_atom[j][m] = array_atom[i][m]; } @@ -406,7 +406,7 @@ void FixWallGranRegion::set_arrays(int i) { if (use_history) ncontact[i] = 0; - if (peratom_flag){ + if (peratom_flag) { for (int m = 0; m < size_peratom_cols; m++) array_atom[i][m] = 0; } @@ -421,7 +421,7 @@ int FixWallGranRegion::pack_exchange(int i, double *buf) int m; int n = 0; - if (use_history){ + if (use_history) { int count = ncontact[i]; buf[n++] = ubuf(count).d; for (int iwall = 0; iwall < count; iwall++) { @@ -430,7 +430,7 @@ int FixWallGranRegion::pack_exchange(int i, double *buf) buf[n++] = history_many[i][iwall][m]; } } - if (peratom_flag){ + if (peratom_flag) { for (int m = 0; m < size_peratom_cols; m++) buf[n++] = array_atom[i][m]; } @@ -448,7 +448,7 @@ int FixWallGranRegion::unpack_exchange(int nlocal, double *buf) int n = 0; - if (use_history){ + if (use_history) { int count = ncontact[nlocal] = (int) ubuf(buf[n++]).i; for (int iwall = 0; iwall < count; iwall++) { walls[nlocal][iwall] = (int) ubuf(buf[n++]).i; @@ -456,7 +456,7 @@ int FixWallGranRegion::unpack_exchange(int nlocal, double *buf) history_many[nlocal][iwall][m] = buf[n++]; } } - if (peratom_flag){ + if (peratom_flag) { for (int m = 0; m < size_peratom_cols; m++) array_atom[nlocal][m] = buf[n++]; } diff --git a/src/GRANULAR/pair_granular.cpp b/src/GRANULAR/pair_granular.cpp index ce6cae75e4..903ed303b0 100644 --- a/src/GRANULAR/pair_granular.cpp +++ b/src/GRANULAR/pair_granular.cpp @@ -52,7 +52,7 @@ using namespace MathSpecial; #define EPSILON 1e-10 enum {HOOKE, HERTZ, HERTZ_MATERIAL, DMT, JKR}; -enum {VELOCITY, VISCOELASTIC, TSUJI}; +enum {VELOCITY, MASS_VELOCITY, VISCOELASTIC, TSUJI}; enum {TANGENTIAL_NOHISTORY, TANGENTIAL_HISTORY, TANGENTIAL_MINDLIN, TANGENTIAL_MINDLIN_RESCALE}; enum {TWIST_NONE, TWIST_SDS, TWIST_MARSHALL}; @@ -345,6 +345,8 @@ void PairGranular::compute(int eflag, int vflag) if (damping_model[itype][jtype] == VELOCITY) { damp_normal = 1; + } else if (damping_model[itype][jtype] == MASS_VELOCITY) { + damp_normal = meff; } else if (damping_model[itype][jtype] == VISCOELASTIC) { damp_normal = a*meff; } else if (damping_model[itype][jtype] == TSUJI) { @@ -589,7 +591,7 @@ void PairGranular::compute(int eflag, int vflag) tor2 = nz*fs1 - nx*fs3; tor3 = nx*fs2 - ny*fs1; - dist_to_contact = radi-0.5*delta; + dist_to_contact = radi-0.5*delta; torque[i][0] -= dist_to_contact*tor1; torque[i][1] -= dist_to_contact*tor2; torque[i][2] -= dist_to_contact*tor3; @@ -619,7 +621,7 @@ void PairGranular::compute(int eflag, int vflag) f[j][1] -= fy; f[j][2] -= fz; - dist_to_contact = radj-0.5*delta; + dist_to_contact = radj-0.5*delta; torque[j][0] -= dist_to_contact*tor1; torque[j][1] -= dist_to_contact*tor2; torque[j][2] -= dist_to_contact*tor3; @@ -735,24 +737,22 @@ void PairGranular::coeff(int narg, char **arg) normal_coeffs_one[1] = force->numeric(FLERR,arg[iarg+2]); // damping iarg += 3; } else if (strcmp(arg[iarg], "hertz") == 0) { - int num_coeffs = 2; - if (iarg + num_coeffs >= narg) + if (iarg + 2 >= narg) error->all(FLERR,"Illegal pair_coeff command, " "not enough parameters provided for Hertz option"); normal_model_one = HERTZ; normal_coeffs_one[0] = force->numeric(FLERR,arg[iarg+1]); // kn normal_coeffs_one[1] = force->numeric(FLERR,arg[iarg+2]); // damping - iarg += num_coeffs+1; + iarg += 3; } else if (strcmp(arg[iarg], "hertz/material") == 0) { - int num_coeffs = 3; - if (iarg + num_coeffs >= narg) + if (iarg + 3 >= narg) error->all(FLERR,"Illegal pair_coeff command, " "not enough parameters provided for Hertz/material option"); normal_model_one = HERTZ_MATERIAL; normal_coeffs_one[0] = force->numeric(FLERR,arg[iarg+1]); // E normal_coeffs_one[1] = force->numeric(FLERR,arg[iarg+2]); // damping normal_coeffs_one[2] = force->numeric(FLERR,arg[iarg+3]); // Poisson's ratio - iarg += num_coeffs+1; + iarg += 4; } else if (strcmp(arg[iarg], "dmt") == 0) { if (iarg + 4 >= narg) error->all(FLERR,"Illegal pair_coeff command, " @@ -781,6 +781,9 @@ void PairGranular::coeff(int narg, char **arg) if (strcmp(arg[iarg+1], "velocity") == 0) { damping_model_one = VELOCITY; iarg += 1; + } else if (strcmp(arg[iarg+1], "mass_velocity") == 0) { + damping_model_one = MASS_VELOCITY; + iarg += 1; } else if (strcmp(arg[iarg+1], "viscoelastic") == 0) { damping_model_one = VISCOELASTIC; iarg += 1; @@ -955,7 +958,7 @@ void PairGranular::coeff(int narg, char **arg) } /* ---------------------------------------------------------------------- - init specific to this pair style + init specific to this pair style ------------------------------------------------------------------------- */ void PairGranular::init_style() @@ -1723,9 +1726,9 @@ double PairGranular::pulloff_distance(double radi, double radj, double E, coh, a, Reff; Reff = radi*radj/(radi+radj); if (Reff <= 0) return 0; - coh = normal_coeffs[itype][itype][3]; + coh = normal_coeffs[itype][jtype][3]; E = normal_coeffs[itype][jtype][0]*THREEQUARTERS; - a = cbrt(9*MY_PI*coh*Reff/(4*E)); + a = cbrt(9*MY_PI*coh*Reff*Reff/(4*E)); return a*a/Reff - 2*sqrt(MY_PI*coh*a/E); } diff --git a/src/KOKKOS/atom_vec_bond_kokkos.cpp b/src/KOKKOS/atom_vec_bond_kokkos.cpp index 825b141b8b..21768c6009 100644 --- a/src/KOKKOS/atom_vec_bond_kokkos.cpp +++ b/src/KOKKOS/atom_vec_bond_kokkos.cpp @@ -43,6 +43,8 @@ AtomVecBondKokkos::AtomVecBondKokkos(LAMMPS *lmp) : AtomVecKokkos(lmp) size_data_vel = 4; xcol_data = 4; + atom->molecule_flag = 1; + k_count = DAT::tdual_int_1d("atom::k_count",1); atomKK = (AtomKokkos *) atom; commKK = (CommKokkos *) comm; diff --git a/src/KOKKOS/pair_reaxc_kokkos.cpp b/src/KOKKOS/pair_reaxc_kokkos.cpp index dda75782b2..64651be270 100644 --- a/src/KOKKOS/pair_reaxc_kokkos.cpp +++ b/src/KOKKOS/pair_reaxc_kokkos.cpp @@ -143,7 +143,7 @@ template void PairReaxCKokkos::init_style() { PairReaxC::init_style(); - if (fix_reax) modify->delete_fix("REAXC"); // not needed in the Kokkos version + if (fix_reax) modify->delete_fix(fix_id); // not needed in the Kokkos version fix_reax = NULL; // irequest = neigh request made by parent class @@ -340,6 +340,7 @@ void PairReaxCKokkos::init_md() { // init_taper() F_FLOAT d1, d7, swa, swa2, swa3, swb, swb2, swb3; + LR_lookup_table ** & LR = system->LR; swa = control->nonb_low; swb = control->nonb_cut; @@ -437,6 +438,7 @@ int PairReaxCKokkos::Init_Lookup_Tables() double dr; double *h, *fh, *fvdw, *fele, *fCEvd, *fCEclmb; double v0_vdw, v0_ele, vlast_vdw, vlast_ele; + LR_lookup_table ** & LR = system->LR; /* initializations */ v0_vdw = 0; @@ -541,6 +543,7 @@ void PairReaxCKokkos::Deallocate_Lookup_Tables() { int i, j; int ntypes; + LR_lookup_table ** & LR = system->LR; ntypes = atom->ntypes; diff --git a/src/KSPACE/pair_lj_charmmfsw_coul_long.cpp b/src/KSPACE/pair_lj_charmmfsw_coul_long.cpp index 4aecc8453a..cdde211157 100644 --- a/src/KSPACE/pair_lj_charmmfsw_coul_long.cpp +++ b/src/KSPACE/pair_lj_charmmfsw_coul_long.cpp @@ -501,6 +501,7 @@ void PairLJCharmmfswCoulLong::compute_outer(int eflag, int vflag) if (rsq < cut_bothsq) { r2inv = 1.0/rsq; + r6inv = r2inv*r2inv*r2inv; if (rsq < cut_coulsq) { if (!ncoultablebits || rsq <= tabinnersq) { @@ -541,7 +542,6 @@ void PairLJCharmmfswCoulLong::compute_outer(int eflag, int vflag) } else forcecoul = 0.0; if (rsq < cut_ljsq && rsq > cut_in_off_sq) { - r6inv = r2inv*r2inv*r2inv; forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]); if (rsq > cut_lj_innersq) { switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) * @@ -582,11 +582,10 @@ void PairLJCharmmfswCoulLong::compute_outer(int eflag, int vflag) } else ecoul = 0.0; if (rsq < cut_ljsq) { - r6inv = r2inv*r2inv*r2inv; evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]); if (rsq > cut_lj_innersq) { - rinv = 1.0/r; - r3inv = rinv*rinv*rinv; + rinv = sqrt(r2inv); + r3inv = r2inv*rinv; evdwl12 = lj3[itype][jtype]*cut_lj6*denom_lj12 * (r6inv - cut_lj6inv)*(r6inv - cut_lj6inv); evdwl6 = -lj4[itype][jtype]*cut_lj3*denom_lj6 * @@ -620,7 +619,6 @@ void PairLJCharmmfswCoulLong::compute_outer(int eflag, int vflag) } else forcecoul = 0.0; if (rsq <= cut_in_off_sq) { - r6inv = r2inv*r2inv*r2inv; forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]); if (rsq > cut_lj_innersq) { switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) * diff --git a/src/MANYBODY/pair_airebo.cpp b/src/MANYBODY/pair_airebo.cpp index 4502bd9a82..e3c5a1627b 100644 --- a/src/MANYBODY/pair_airebo.cpp +++ b/src/MANYBODY/pair_airebo.cpp @@ -50,7 +50,8 @@ using namespace MathSpecial; /* ---------------------------------------------------------------------- */ -PairAIREBO::PairAIREBO(LAMMPS *lmp) : Pair(lmp) +PairAIREBO::PairAIREBO(LAMMPS *lmp) + : Pair(lmp), variant(AIREBO) { single_enable = 0; restartinfo = 0; @@ -168,10 +169,6 @@ void PairAIREBO::settings(int narg, char **arg) sigwid = sigcut - sigmin; } - // this one parameter for C-C interactions is different in AIREBO vs REBO - // see Favata, Micheletti, Ryu, Pugno, Comp Phys Comm (2016) - - PCCf_2_0 = -0.0276030; } /* ---------------------------------------------------------------------- @@ -3376,14 +3373,38 @@ void PairAIREBO::read_file(char *filename) fp = force->open_potential(filename); if (fp == NULL) { char str[128]; - if (morseflag) - snprintf(str,128,"Cannot open AIREBO-M potential file %s",filename); - else + switch (variant) { + + case AIREBO: snprintf(str,128,"Cannot open AIREBO potential file %s",filename); + break; + + case REBO_2: + snprintf(str,128,"Cannot open REBO2 potential file %s",filename); + break; + + case AIREBO_M: + snprintf(str,128,"Cannot open AIREBO-M potential file %s",filename); + break; + + default: + snprintf(str,128,"Unknown REBO style variant %d",variant); + } error->one(FLERR,str); } - // skip initial comment lines + // skip initial comment line and check for potential file style identifier comment + + fgets(s,MAXLINE,fp); + fgets(s,MAXLINE,fp); + + if (((variant == AIREBO) && (strncmp(s,"# AIREBO ",9) != 0)) + || ((variant == REBO_2) && (strncmp(s,"# REBO2 ",8) != 0)) + || ((variant == AIREBO_M) && (strncmp(s,"# AIREBO-M ",11) != 0))) { + error->one(FLERR,"Potential file does not match AIREBO/REBO style variant"); + } + + // skip remaining comments while (1) { utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); @@ -4502,19 +4523,18 @@ void PairAIREBO::spline_init() // this one parameter for C-C interactions is different in REBO vs AIREBO // see Favata, Micheletti, Ryu, Pugno, Comp Phys Comm (2016) - PCCf[2][0] = PCCf_2_0; - + PCCf[2][0] = -0.0276030; PCCf[2][1] = 0.00317953083; - PCHf[0][1] = 0.209336733; - PCHf[0][2] = -0.0644496154; - PCHf[0][3] = -0.303927546; + PCHf[0][1] = 0.2093367328250380; + PCHf[0][2] = -0.064449615432525; + PCHf[0][3] = -0.303927546346162; PCHf[1][0] = 0.010; - PCHf[1][1] = -0.125123401; - PCHf[1][2] = -0.298905246; - PCHf[2][0] = -0.122042146; - PCHf[2][1] = -0.300529172; - PCHf[3][0] = -0.307584705; + PCHf[1][1] = -0.1251234006287090; + PCHf[1][2] = -0.298905245783; + PCHf[2][0] = -0.1220421462782555; + PCHf[2][1] = -0.3005291724067579; + PCHf[3][0] = -0.307584705066; for (int nH = 0; nH < 4; nH++) { for (int nC = 0; nC < 4; nC++) { diff --git a/src/MANYBODY/pair_airebo.h b/src/MANYBODY/pair_airebo.h index c7c9b07357..8e92807afb 100644 --- a/src/MANYBODY/pair_airebo.h +++ b/src/MANYBODY/pair_airebo.h @@ -38,10 +38,12 @@ class PairAIREBO : public Pair { double init_one(int, int); double memory_usage(); - protected: + enum { AIREBO, REBO_2, AIREBO_M }; // for telling class variants apart in shared code + +protected: int *map; // 0 (C), 1 (H), or -1 (NULL) for each type - int me; + int me,variant; int ljflag,torflag; // 0/1 if LJ/Morse,torsion terms included int morseflag; // 1 if Morse instead of LJ for non-bonded @@ -84,7 +86,6 @@ class PairAIREBO : public Pair { // spline knot values - double PCCf_2_0; double PCCf[5][5],PCCdfdx[5][5],PCCdfdy[5][5],PCHf[5][5]; double PCHdfdx[5][5],PCHdfdy[5][5]; double piCCf[5][5][11],piCCdfdx[5][5][11]; @@ -120,7 +121,7 @@ class PairAIREBO : public Pair { void Spbicubic_patch_adjust(double *, double, double, char); void Spbicubic_patch_coeffs(double, double, double, double, double *, double *, double *, double *); - void spline_init(); + virtual void spline_init(); void allocate(); diff --git a/src/MANYBODY/pair_airebo_morse.cpp b/src/MANYBODY/pair_airebo_morse.cpp index b501ed0982..a39f7df82e 100644 --- a/src/MANYBODY/pair_airebo_morse.cpp +++ b/src/MANYBODY/pair_airebo_morse.cpp @@ -19,7 +19,9 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -PairAIREBOMorse::PairAIREBOMorse(LAMMPS *lmp) : PairAIREBO(lmp) {} +PairAIREBOMorse::PairAIREBOMorse(LAMMPS *lmp) : PairAIREBO(lmp) { + variant = AIREBO_M; +} /* ---------------------------------------------------------------------- global settings diff --git a/src/MANYBODY/pair_rebo.cpp b/src/MANYBODY/pair_rebo.cpp index 1f31c0b0cd..e07a1b3495 100644 --- a/src/MANYBODY/pair_rebo.cpp +++ b/src/MANYBODY/pair_rebo.cpp @@ -18,7 +18,9 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -PairREBO::PairREBO(LAMMPS *lmp) : PairAIREBO(lmp) {} +PairREBO::PairREBO(LAMMPS *lmp) : PairAIREBO(lmp) { + variant = REBO_2; +} /* ---------------------------------------------------------------------- global settings @@ -30,9 +32,35 @@ void PairREBO::settings(int narg, char **/*arg*/) cutlj = 0.0; ljflag = torflag = 0; - - // this one parameter for C-C interactions is different in REBO vs AIREBO - // see Favata, Micheletti, Ryu, Pugno, Comp Phys Comm (2016) - - PCCf_2_0 = 0.0; +} + +/* ---------------------------------------------------------------------- + initialize spline knot values +------------------------------------------------------------------------- */ + +void PairREBO::spline_init() { + PairAIREBO::spline_init(); + + PCCf[0][2] = 0.007860700254745; + PCCf[0][3] = 0.016125364564267; + PCCf[1][1] = 0.003026697473481; + PCCf[1][2] = 0.006326248241119; + PCCf[2][0] = 0.; + PCCf[2][1] = 0.003179530830731; + + for (int nH = 0; nH < 4; nH++) { + for (int nC = 0; nC < 4; nC++) { + double y[4] = {0}, y1[4] = {0}, y2[4] = {0}; + y[0] = PCCf[nC][nH]; + y[1] = PCCf[nC][nH+1]; + y[2] = PCCf[nC+1][nH]; + y[3] = PCCf[nC+1][nH+1]; + Spbicubic_patch_coeffs(nC, nC+1, nH, nH+1, y, y1, y2, &pCC[nC][nH][0]); + y[0] = PCHf[nC][nH]; + y[1] = PCHf[nC][nH+1]; + y[2] = PCHf[nC+1][nH]; + y[3] = PCHf[nC+1][nH+1]; + Spbicubic_patch_coeffs(nC, nC+1, nH, nH+1, y, y1, y2, &pCH[nC][nH][0]); + } + } } diff --git a/src/MANYBODY/pair_rebo.h b/src/MANYBODY/pair_rebo.h index be1e1f0b55..9c1a12d4de 100644 --- a/src/MANYBODY/pair_rebo.h +++ b/src/MANYBODY/pair_rebo.h @@ -28,6 +28,7 @@ class PairREBO : public PairAIREBO { public: PairREBO(class LAMMPS *); void settings(int, char **); + void spline_init(); }; } diff --git a/src/MOLECULE/angle_table.cpp b/src/MOLECULE/angle_table.cpp index 7dd56ffb76..c18b4c43b0 100644 --- a/src/MOLECULE/angle_table.cpp +++ b/src/MOLECULE/angle_table.cpp @@ -500,7 +500,7 @@ void AngleTable::param_extract(Table *tb, char *line) { tb->ninput = 0; tb->fpflag = 0; - tb->theta0 = 180.0; + tb->theta0 = MY_PI; char *word = strtok(line," \t\n\r\f"); while (word) { @@ -517,7 +517,7 @@ void AngleTable::param_extract(Table *tb, char *line) tb->fphi *= (180.0/MY_PI)*(180.0/MY_PI); } else if (strcmp(word,"EQ") == 0) { word = strtok(NULL," \t\n\r\f"); - tb->theta0 = atof(word); + tb->theta0 = atof(word)/180.0*MY_PI; } else { error->one(FLERR,"Invalid keyword in angle table parameters"); } diff --git a/src/PYTHON/Install.sh b/src/PYTHON/Install.sh index 9d2783ba0c..8c394d43ad 100755 --- a/src/PYTHON/Install.sh +++ b/src/PYTHON/Install.sh @@ -28,7 +28,7 @@ action () { # force rebuild of files using python header -touch ../python.h +touch ../lmppython.h # all package files with no dependencies diff --git a/src/SPIN/README b/src/SPIN/README index 53e456bacb..a4eb4ff22b 100644 --- a/src/SPIN/README +++ b/src/SPIN/README @@ -8,6 +8,8 @@ atom in the system * integrating the equations of motion for the coupled spin-lattice system * implementing magnetic pair interactions and magnetic forces * thermostating and applying a transverse damping to the magnetic spins +* minimizing spin configurations with an adaptive timestep scheme +* performing geodesic NEB calculations * computing and outputing magnetic quantities * minimizing the energy or total torque of a magnetic system @@ -15,7 +17,8 @@ The different options provided by this package are explained in the LAMMPS documentation. Once you have successfully built LAMMPS with this package, you can test -it using one of the input files provided from the examples/SPIN dir: +it using one of the input files provided from the examples/SPIN dir. +For example: ./lmp_serial < lammps/examples/SPIN/cobalt_hcp/in.spin.cobalt_hcp diff --git a/src/SPIN/atom_vec_spin.cpp b/src/SPIN/atom_vec_spin.cpp index 24c4480e04..a6c0430940 100644 --- a/src/SPIN/atom_vec_spin.cpp +++ b/src/SPIN/atom_vec_spin.cpp @@ -943,6 +943,10 @@ bigint AtomVecSpin::memory_usage() return bytes; } +/* ---------------------------------------------------------------------- + clear all forces (mech and mag) +------------------------------------------------------------------------- */ + void AtomVecSpin::force_clear(int /*n*/, size_t nbytes) { memset(&atom->f[0][0],0,3*nbytes); diff --git a/src/SPIN/fix_neb_spin.cpp b/src/SPIN/fix_neb_spin.cpp new file mode 100644 index 0000000000..a8cb0cd2ca --- /dev/null +++ b/src/SPIN/fix_neb_spin.cpp @@ -0,0 +1,1014 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + 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: Julien Tranchida (SNL) + + Please cite the related publication: + Bessarab, P. F., Uzdin, V. M., & Jónsson, H. (2015). + Method for finding mechanism and activation energy of magnetic transitions, + applied to skyrmion and antivortex annihilation. + Computer Physics Communications, 196, 335-347. +------------------------------------------------------------------------- */ + +#include +#include +#include +#include +#include "fix_neb_spin.h" +#include "universe.h" +#include "update.h" +#include "atom.h" +#include "domain.h" +#include "comm.h" +#include "modify.h" +#include "compute.h" +#include "group.h" +#include "memory.h" +#include "error.h" +#include "force.h" +#include "math_const.h" + +using namespace LAMMPS_NS; +using namespace FixConst; +using namespace MathConst; + +enum{SINGLE_PROC_DIRECT,SINGLE_PROC_MAP,MULTI_PROC}; + +#define BUFSIZE 8 + +/* ---------------------------------------------------------------------- */ + +FixNEBSpin::FixNEBSpin(LAMMPS *lmp, int narg, char **arg) : + Fix(lmp, narg, arg), id_pe(NULL), pe(NULL), nlenall(NULL), xprev(NULL), + xnext(NULL), fnext(NULL), spprev(NULL), spnext(NULL), fmnext(NULL), springF(NULL), + tangent(NULL), xsend(NULL), xrecv(NULL), fsend(NULL), frecv(NULL), spsend(NULL), + sprecv(NULL), fmsend(NULL), fmrecv(NULL), tagsend(NULL), tagrecv(NULL), + xsendall(NULL), xrecvall(NULL), fsendall(NULL), frecvall(NULL), spsendall(NULL), + sprecvall(NULL), fmsendall(NULL), fmrecvall(NULL), tagsendall(NULL), tagrecvall(NULL), + counts(NULL), displacements(NULL) +{ + + if (narg < 4) error->all(FLERR,"Illegal fix neb_spin command"); + + kspring = force->numeric(FLERR,arg[3]); + if (kspring <= 0.0) error->all(FLERR,"Illegal fix neb command"); + + // optional params + + NEBLongRange = false; // see if needed (comb. with pppm/spin?) + StandardNEB = true; // only option for now + PerpSpring = FreeEndIni = FreeEndFinal = false; + FreeEndFinalWithRespToEIni = FinalAndInterWithRespToEIni = false; + kspringPerp = 0.0; + kspringIni = 1.0; + kspringFinal = 1.0; + SpinLattice = false; // no spin-lattice neb for now + + // no available fix neb/spin options for now + + int iarg = 4; + while (iarg < narg) { + if (strcmp(arg[iarg],"parallel") == 0) { + error->all(FLERR,"Illegal fix neb command"); + iarg += 2; + } else if (strcmp(arg[iarg],"perp") == 0) { + error->all(FLERR,"Illegal fix neb command"); + iarg += 2; + } else if (strcmp (arg[iarg],"end") == 0) { + iarg += 3; + } else if (strcmp (arg[iarg],"lattice") == 0) { + iarg += 2; + } else error->all(FLERR,"Illegal fix neb command"); + } + + // nreplica = number of partitions + // ireplica = which world I am in universe + // nprocs_universe = # of procs in all replicase + // procprev,procnext = root proc in adjacent replicas + + me = comm->me; + nprocs = comm->nprocs; + + nprocs_universe = universe->nprocs; + nreplica = universe->nworlds; + ireplica = universe->iworld; + + if (ireplica > 0) procprev = universe->root_proc[ireplica-1]; + else procprev = -1; + if (ireplica < nreplica-1) procnext = universe->root_proc[ireplica+1]; + else procnext = -1; + + uworld = universe->uworld; + int *iroots = new int[nreplica]; + MPI_Group uworldgroup,rootgroup; + if (NEBLongRange) { + for (int i=0; iroot_proc[i]; + MPI_Comm_group(uworld, &uworldgroup); + MPI_Group_incl(uworldgroup, nreplica, iroots, &rootgroup); + MPI_Comm_create(uworld, rootgroup, &rootworld); + } + delete [] iroots; + + // create a new compute pe style + // id = fix-ID + pe, compute group = all + + int n = strlen(id) + 4; + id_pe = new char[n]; + strcpy(id_pe,id); + strcat(id_pe,"_pe"); + + char **newarg = new char*[3]; + newarg[0] = id_pe; + newarg[1] = (char *) "all"; + newarg[2] = (char *) "pe"; + modify->add_compute(3,newarg); + delete [] newarg; + + // initialize local storage + + maxlocal = -1; + ntotal = -1; +} + +/* ---------------------------------------------------------------------- */ + +FixNEBSpin::~FixNEBSpin() +{ + modify->delete_compute(id_pe); + delete [] id_pe; + + // memory destroy of all spin and lattice arrays + + memory->destroy(xprev); + memory->destroy(xnext); + memory->destroy(tangent); + memory->destroy(fnext); + memory->destroy(spprev); + memory->destroy(spnext); + memory->destroy(fmnext); + memory->destroy(springF); + memory->destroy(xsend); + memory->destroy(xrecv); + memory->destroy(fsend); + memory->destroy(frecv); + memory->destroy(spsend); + memory->destroy(sprecv); + memory->destroy(fmsend); + memory->destroy(fmrecv); + memory->destroy(tagsend); + memory->destroy(tagrecv); + + memory->destroy(xsendall); + memory->destroy(xrecvall); + memory->destroy(fsendall); + memory->destroy(frecvall); + memory->destroy(spsendall); + memory->destroy(sprecvall); + memory->destroy(fmsendall); + memory->destroy(fmrecvall); + memory->destroy(tagsendall); + memory->destroy(tagrecvall); + + memory->destroy(counts); + memory->destroy(displacements); + + if (NEBLongRange) { + if (rootworld != MPI_COMM_NULL) MPI_Comm_free(&rootworld); + memory->destroy(nlenall); + } +} + +/* ---------------------------------------------------------------------- */ + +int FixNEBSpin::setmask() +{ + int mask = 0; + mask |= MIN_POST_FORCE; + return mask; +} + +/* ---------------------------------------------------------------------- */ + +void FixNEBSpin::init() +{ + int icompute = modify->find_compute(id_pe); + if (icompute < 0) + error->all(FLERR,"Potential energy ID for fix neb does not exist"); + pe = modify->compute[icompute]; + + // turn off climbing mode, NEB command turns it on after init() + + rclimber = -1; + + // nebatoms = # of atoms in fix group = atoms with inter-replica forces + + bigint count = group->count(igroup); + if (count > MAXSMALLINT) error->all(FLERR,"Too many active NEB atoms"); + nebatoms = count; + + // comm mode for inter-replica exchange of coords + + if (nreplica == nprocs_universe && + nebatoms == atom->natoms && atom->sortfreq == 0) + cmode = SINGLE_PROC_DIRECT; + else if (nreplica == nprocs_universe) cmode = SINGLE_PROC_MAP; + else cmode = MULTI_PROC; + + // ntotal = total # of atoms in system, NEB atoms or not + + if (atom->natoms > MAXSMALLINT) error->all(FLERR,"Too many atoms for NEB"); + ntotal = atom->natoms; + + if (atom->nmax > maxlocal) reallocate(); + + if (MULTI_PROC && counts == NULL) { + memory->create(xsendall,ntotal,3,"neb:xsendall"); + memory->create(xrecvall,ntotal,3,"neb:xrecvall"); + memory->create(fsendall,ntotal,3,"neb:fsendall"); + memory->create(frecvall,ntotal,3,"neb:frecvall"); + memory->create(tagsendall,ntotal,"neb:tagsendall"); + memory->create(tagrecvall,ntotal,"neb:tagrecvall"); + memory->create(spsendall,ntotal,3,"neb:xsendall"); + memory->create(sprecvall,ntotal,3,"neb:xrecvall"); + memory->create(fmsendall,ntotal,3,"neb:fsendall"); + memory->create(fmrecvall,ntotal,3,"neb:frecvall"); + memory->create(counts,nprocs,"neb:counts"); + memory->create(displacements,nprocs,"neb:displacements"); + } +} + +/* ---------------------------------------------------------------------- */ + +void FixNEBSpin::min_setup(int vflag) +{ + min_post_force(vflag); + + // trigger potential energy computation on next timestep + + pe->addstep(update->ntimestep+1); +} + +/* ---------------------------------------------------------------------- */ + +void FixNEBSpin::min_post_force(int /*vflag*/) +{ + double vprev,vnext; + double delspxp,delspyp,delspzp; + double delspxn,delspyn,delspzn; + double templen; + double vIni=0.0; + double spi[3],spj[3]; + + vprev = vnext = veng = pe->compute_scalar(); + + if (ireplica < nreplica-1 && me == 0) + MPI_Send(&veng,1,MPI_DOUBLE,procnext,0,uworld); + if (ireplica > 0 && me == 0) + MPI_Recv(&vprev,1,MPI_DOUBLE,procprev,0,uworld,MPI_STATUS_IGNORE); + + if (ireplica > 0 && me == 0) + MPI_Send(&veng,1,MPI_DOUBLE,procprev,0,uworld); + if (ireplica < nreplica-1 && me == 0) + MPI_Recv(&vnext,1,MPI_DOUBLE,procnext,0,uworld,MPI_STATUS_IGNORE); + + if (cmode == MULTI_PROC) { + MPI_Bcast(&vprev,1,MPI_DOUBLE,0,world); + MPI_Bcast(&vnext,1,MPI_DOUBLE,0,world); + } + + if (FreeEndFinal && ireplica == nreplica-1 && (update->ntimestep == 0)) + error->all(FLERR,"NEBSpin Free End option not yet active"); + + if (ireplica == 0) vIni=veng; + + if (FreeEndFinalWithRespToEIni) + error->all(FLERR,"NEBSpin Free End option not yet active"); + + if (FreeEndIni && ireplica == 0 && (update->ntimestep == 0)) + error->all(FLERR,"NEBSpin Free End option not yet active"); + + + // communicate atoms to/from adjacent replicas to fill xprev,xnext + + inter_replica_comm(); + + // trigger potential energy computation on next timestep + + pe->addstep(update->ntimestep+1); + + int nlocal = atom->nlocal; + int *mask = atom->mask; + double **sp = atom->sp; + double dot = 0.0; + double prefactor = 0.0; + double **fm = atom->fm; + + //calculating separation between images + + plen = 0.0; + nlen = 0.0; + double tlen = 0.0; + double gradnextlen = 0.0; + double delndots = 0.0; + double delpdots = 0.0; + + dotgrad = gradlen = dotpath = dottangrad = 0.0; + + // computation of the tangent vector + + if (ireplica == nreplica-1) { // final replica + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit) { + + // tangent vector + + delspxp = sp[i][0] - spprev[i][0]; + delspyp = sp[i][1] - spprev[i][1]; + delspzp = sp[i][2] - spprev[i][2]; + + // project delp vector on tangent space + + delpdots = delspxp*sp[i][0]+delspyp*sp[i][1]+delspzp*sp[i][2]; + delspxp -= delpdots*sp[i][0]; + delspyp -= delpdots*sp[i][1]; + delspzp -= delpdots*sp[i][2]; + + // calc. geodesic length + + spi[0] = sp[i][0]; + spi[1] = sp[i][1]; + spi[2] = sp[i][2]; + spj[0] = spprev[i][0]; + spj[1] = spprev[i][1]; + spj[2] = spprev[i][2]; + templen = geodesic_distance(spi,spj); + plen += templen*templen; + dottangrad += delspxp*fm[i][0]+ delspyp*fm[i][1]+delspzp*fm[i][2]; + gradlen += fm[i][0]*fm[i][0] + fm[i][1]*fm[i][1] + fm[i][2]*fm[i][2]; + + // no free end option for now + + if (FreeEndFinal||FreeEndFinalWithRespToEIni) + error->all(FLERR,"Free End option not yet active"); + + } + } else if (ireplica == 0) { // initial replica + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit) { + + // tangent vector + + delspxn = spnext[i][0]- sp[i][0]; + delspyn = spnext[i][1]- sp[i][1]; + delspzn = spnext[i][2]- sp[i][2]; + + // project deln vector on tangent space + + delndots = delspxn*sp[i][0]+delspyn*sp[i][1]+delspzn*sp[i][2]; + delspxn -= delndots*sp[i][0]; + delspyn -= delndots*sp[i][1]; + delspzn -= delndots*sp[i][2]; + + // calc. geodesic length + + spi[0]=sp[i][0]; + spi[1]=sp[i][1]; + spi[2]=sp[i][2]; + spj[0]=spnext[i][0]; + spj[1]=spnext[i][1]; + spj[2]=spnext[i][2]; + templen = geodesic_distance(spi,spj); + nlen += templen*templen; + dottangrad += delspxn*fm[i][0] + delspyn*fm[i][1] + delspzn*fm[i][2]; + gradlen += fm[i][0]*fm[i][0] + fm[i][1]*fm[i][1] + fm[i][2]*fm[i][2]; + + // no free end option for now + + if (FreeEndIni) + error->all(FLERR,"Free End option not yet active"); + + } + } else { // intermediate replica + + double vmax = MAX(fabs(vnext-veng),fabs(vprev-veng)); + double vmin = MIN(fabs(vnext-veng),fabs(vprev-veng)); + + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit) { + + // calc. delp vector + + delspxp = sp[i][0] - spprev[i][0]; + delspyp = sp[i][1] - spprev[i][1]; + delspzp = sp[i][2] - spprev[i][2]; + + // project delp vector on tangent space + + delndots = delspxp*sp[i][0]+delspyp*sp[i][1]+delspzp*sp[i][2]; + delspxp -= delpdots*sp[i][0]; + delspyp -= delpdots*sp[i][1]; + delspzp -= delpdots*sp[i][2]; + + // calc. prev. geodesic length + + spi[0]=sp[i][0]; + spi[1]=sp[i][1]; + spi[2]=sp[i][2]; + spj[0]=spprev[i][0]; + spj[1]=spprev[i][1]; + spj[2]=spprev[i][2]; + templen = geodesic_distance(spi, spj); + plen += templen*templen; + + // calc. deln vector + + delspxn = spnext[i][0] - sp[i][0]; + delspyn = spnext[i][1] - sp[i][1]; + delspzn = spnext[i][2] - sp[i][2]; + + // project deln vector on tangent space + + delndots = delspxn*sp[i][0]+delspyn*sp[i][1]+delspzn*sp[i][2]; + delspxn -= delndots*sp[i][0]; + delspyn -= delndots*sp[i][1]; + delspzn -= delndots*sp[i][2]; + + // evaluate best path tangent + + if (vnext > veng && veng > vprev) { + tangent[i][0] = delspxn; + tangent[i][1] = delspyn; + tangent[i][2] = delspzn; + } else if (vnext < veng && veng < vprev) { + tangent[i][0] = delspxp; + tangent[i][1] = delspyp; + tangent[i][2] = delspzp; + } else { + if (vnext > vprev) { + tangent[i][0] = vmax*delspxn + vmin*delspxp; + tangent[i][1] = vmax*delspyn + vmin*delspyp; + tangent[i][2] = vmax*delspzn + vmin*delspzp; + } else if (vnext < vprev) { + tangent[i][0] = vmin*delspxn + vmax*delspxp; + tangent[i][1] = vmin*delspyn + vmax*delspyp; + tangent[i][2] = vmin*delspzn + vmax*delspzp; + } else { // vnext == vprev, e.g. for potentials that do not compute an energy + tangent[i][0] = delspxn + delspxp; + tangent[i][1] = delspyn + delspyp; + tangent[i][2] = delspzn + delspzp; + } + } + + // project tangent vector on tangent space + + double sdottan; + sdottan = sp[i][0]*tangent[i][0] + sp[i][1]*tangent[i][1] + + sp[i][2]*tangent[i][2]; + tangent[i][0] -= sdottan*sp[i][0]; + tangent[i][1] -= sdottan*sp[i][1]; + tangent[i][2] -= sdottan*sp[i][2]; + + // calc. next geodesic length + + spi[0]=sp[i][0]; + spi[1]=sp[i][1]; + spi[2]=sp[i][2]; + spj[0]=spnext[i][0]; + spj[1]=spnext[i][1]; + spj[2]=spnext[i][2]; + templen = geodesic_distance(spi, spj); + nlen += templen*templen; + + tlen += tangent[i][0]*tangent[i][0] + tangent[i][1]*tangent[i][1] + + tangent[i][2]*tangent[i][2]; + gradlen += fm[i][0]*fm[i][0] + fm[i][1]*fm[i][1] + fm[i][2]*fm[i][2]; + dotpath += delspxp*delspxn + delspyp*delspyn + delspzp*delspzn; + dottangrad += tangent[i][0]*fm[i][0] + tangent[i][1]*fm[i][1] + + tangent[i][2]*fm[i][2]; + gradnextlen += fnext[i][0]*fnext[i][0] + fnext[i][1]*fnext[i][1] + + fnext[i][2]*fnext[i][2]; + dotgrad += fm[i][0]*fnext[i][0] + fm[i][1]*fnext[i][1] + + fm[i][2]*fnext[i][2]; + + // no Perpendicular nudging force option active yet + + if (kspringPerp != 0.0) + error->all(FLERR,"NEBSpin Perpendicular spring force not yet active"); + + } + } + + // MPI reduce if more than one proc for world + + double bufin[BUFSIZE], bufout[BUFSIZE]; + bufin[0] = nlen; + bufin[1] = plen; + bufin[2] = tlen; + bufin[3] = gradlen; + bufin[4] = gradnextlen; + bufin[5] = dotpath; + bufin[6] = dottangrad; + bufin[7] = dotgrad; + MPI_Allreduce(bufin,bufout,BUFSIZE,MPI_DOUBLE,MPI_SUM,world); + nlen = sqrt(bufout[0]); + plen = sqrt(bufout[1]); + tlen = sqrt(bufout[2]); + gradlen = sqrt(bufout[3]); + gradnextlen = sqrt(bufout[4]); + dotpath = bufout[5]; + dottangrad = bufout[6]; + dotgrad = bufout[7]; + + // check projection of tangent vector on tangent space + // and normalize it + + double buftan[3]; + double tandots; + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit) { + tandots = tangent[i][0]*sp[i][0]+tangent[i][1]*sp[i][1]+ + tangent[i][2]*sp[i][2]; + buftan[0] = tangent[i][0]-tandots*sp[i][0]; + buftan[1] = tangent[i][1]-tandots*sp[i][1]; + buftan[2] = tangent[i][2]-tandots*sp[i][2]; + tangent[i][0] = buftan[0]; + tangent[i][1] = buftan[1]; + tangent[i][2] = buftan[2]; + + if (tlen > 0.0) { + double tleninv = 1.0/tlen; + tangent[i][0] *= tleninv; + tangent[i][1] *= tleninv; + tangent[i][2] *= tleninv; + } + } + + // first or last replica has no change to forces, just return + + if (ireplica > 0 && ireplica < nreplica-1) + dottangrad = dottangrad/(tlen*gradlen); + if (ireplica == 0) + dottangrad = dottangrad/(nlen*gradlen); + if (ireplica == nreplica-1) + dottangrad = dottangrad/(plen*gradlen); + if (ireplica < nreplica-1) + dotgrad = dotgrad /(gradlen*gradnextlen); + + // no Free End options active yet + + if (FreeEndIni && ireplica == 0) + error->all(FLERR,"NEBSpin Free End option not yet active"); + if (FreeEndFinal && ireplica == nreplica -1) + error->all(FLERR,"NEBSpin Free End option not yet active"); + if (FreeEndFinalWithRespToEIni&&ireplica == nreplica -1) + error->all(FLERR,"NEBSpin Free End option not yet active"); + + // no NEBSpin long range option + + if (NEBLongRange) + error->all(FLERR,"NEBSpin long range option not yet active"); + + // exit calc. if first or last replica (no gneb force) + + if (ireplica == 0 || ireplica == nreplica-1) return ; + + dotpath = dotpath/(plen*nlen); + + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit) { + dot += fm[i][0]*tangent[i][0] + fm[i][1]*tangent[i][1] + + fm[i][2]*tangent[i][2]; + } + + // gather all dot for this replica + + double dotall; + MPI_Allreduce(&dot,&dotall,1,MPI_DOUBLE,MPI_SUM,world); + dot=dotall; + + // for intermediate replica + // calc. GNEB force prefactor + + if (ireplica == rclimber) prefactor = -2.0*dot; // for climbing replica + else { + if (NEBLongRange) { + error->all(FLERR,"Long Range NEBSpin climber option not yet active"); + } else if (StandardNEB) { + prefactor = -dot + kspring*(nlen-plen); + } + + if (FinalAndInterWithRespToEIni && vengall(FLERR,"Incorrect calc. of geodesic_distance in Fix NEB/spin"); + + dist = atan2(normcross,dots); + + return dist; +} + +/* ---------------------------------------------------------------------- + send/recv NEB atoms to/from adjacent replicas + received atoms matching my local atoms are stored in xprev,xnext + replicas 0 and N-1 send but do not receive any atoms +------------------------------------------------------------------------- */ + +void FixNEBSpin::inter_replica_comm() +{ + int i,m; + MPI_Request request; + MPI_Request requests[2]; + MPI_Status statuses[2]; + + // reallocate memory if necessary + + if (atom->nmax > maxlocal) reallocate(); + + double **x = atom->x; + double **f = atom->f; + double **sp = atom->sp; + double **fm = atom->fm; + tagint *tag = atom->tag; + int *mask = atom->mask; + int nlocal = atom->nlocal; + + // ----------------------------------------------------- + // 3 cases: two for single proc per replica + // one for multiple procs per replica + // ----------------------------------------------------- + + + // case 1 => to be done + + // single proc per replica + // all atoms are NEB atoms and no atom sorting + // direct comm of x -> xprev and x -> xnext + + if (cmode == SINGLE_PROC_DIRECT) { + if (ireplica > 0) { + MPI_Irecv(xprev[0],3*nlocal,MPI_DOUBLE,procprev,0,uworld,&request); + MPI_Irecv(spprev[0],3*nlocal,MPI_DOUBLE,procprev,0,uworld,&request); + } + if (ireplica < nreplica-1) { + MPI_Send(x[0],3*nlocal,MPI_DOUBLE,procnext,0,uworld); + MPI_Send(sp[0],3*nlocal,MPI_DOUBLE,procnext,0,uworld); + } + if (ireplica > 0) MPI_Wait(&request,MPI_STATUS_IGNORE); + if (ireplica < nreplica-1) { + MPI_Irecv(xnext[0],3*nlocal,MPI_DOUBLE,procnext,0,uworld,&request); + MPI_Irecv(spnext[0],3*nlocal,MPI_DOUBLE,procnext,0,uworld,&request); + } + if (ireplica > 0) { + MPI_Send(x[0],3*nlocal,MPI_DOUBLE,procprev,0,uworld); + MPI_Send(sp[0],3*nlocal,MPI_DOUBLE,procprev,0,uworld); + } + if (ireplica < nreplica-1) MPI_Wait(&request,MPI_STATUS_IGNORE); + + if (ireplica < nreplica-1) { + MPI_Irecv(fnext[0],3*nlocal,MPI_DOUBLE,procnext,0,uworld,&request); + MPI_Irecv(fmnext[0],3*nlocal,MPI_DOUBLE,procnext,0,uworld,&request); + } + if (ireplica > 0) { + MPI_Send(f[0],3*nlocal,MPI_DOUBLE,procprev,0,uworld); + MPI_Send(fm[0],3*nlocal,MPI_DOUBLE,procprev,0,uworld); + } + if (ireplica < nreplica-1) MPI_Wait(&request,MPI_STATUS_IGNORE); + + return; + } + + // single proc per replica + // but only some atoms are NEB atoms or atom sorting is enabled + // send atom IDs and coords of only NEB atoms to prev/next proc + // recv procs use atom->map() to match received coords to owned atoms + + if (cmode == SINGLE_PROC_MAP) { + m = 0; + for (i = 0; i < nlocal; i++) + if (mask[i] & groupbit) { + tagsend[m] = tag[i]; + xsend[m][0] = x[i][0]; + xsend[m][1] = x[i][1]; + xsend[m][2] = x[i][2]; + fsend[m][0] = f[i][0]; + fsend[m][1] = f[i][1]; + fsend[m][2] = f[i][2]; + spsend[m][0] = sp[i][0]; + spsend[m][1] = sp[i][1]; + spsend[m][2] = sp[i][2]; + fmsend[m][0] = fm[i][0]; + fmsend[m][1] = fm[i][1]; + fmsend[m][2] = fm[i][2]; + m++; + } + + if (ireplica > 0) { + MPI_Irecv(xrecv[0],3*nebatoms,MPI_DOUBLE,procprev,0,uworld,&requests[0]); + MPI_Irecv(sprecv[0],3*nebatoms,MPI_DOUBLE,procprev,0,uworld,&requests[0]); + MPI_Irecv(tagrecv,nebatoms,MPI_LMP_TAGINT,procprev,0,uworld,&requests[1]); + } + if (ireplica < nreplica-1) { + MPI_Send(xsend[0],3*nebatoms,MPI_DOUBLE,procnext,0,uworld); + MPI_Send(spsend[0],3*nebatoms,MPI_DOUBLE,procnext,0,uworld); + MPI_Send(tagsend,nebatoms,MPI_LMP_TAGINT,procnext,0,uworld); + } + + if (ireplica > 0) { + MPI_Waitall(2,requests,statuses); + for (i = 0; i < nebatoms; i++) { + m = atom->map(tagrecv[i]); + xprev[m][0] = xrecv[i][0]; + xprev[m][1] = xrecv[i][1]; + xprev[m][2] = xrecv[i][2]; + spprev[m][0] = sprecv[i][0]; + spprev[m][1] = sprecv[i][1]; + spprev[m][2] = sprecv[i][2]; + } + } + if (ireplica < nreplica-1) { + MPI_Irecv(xrecv[0],3*nebatoms,MPI_DOUBLE,procnext,0,uworld,&requests[0]); + MPI_Irecv(frecv[0],3*nebatoms,MPI_DOUBLE,procnext,0,uworld,&requests[0]); + MPI_Irecv(sprecv[0],3*nebatoms,MPI_DOUBLE,procnext,0,uworld,&requests[0]); + MPI_Irecv(fmrecv[0],3*nebatoms,MPI_DOUBLE,procnext,0,uworld,&requests[0]); + MPI_Irecv(tagrecv,nebatoms,MPI_LMP_TAGINT,procnext,0,uworld,&requests[1]); + } + if (ireplica > 0) { + MPI_Send(xsend[0],3*nebatoms,MPI_DOUBLE,procprev,0,uworld); + MPI_Send(fsend[0],3*nebatoms,MPI_DOUBLE,procprev,0,uworld); + MPI_Send(spsend[0],3*nebatoms,MPI_DOUBLE,procprev,0,uworld); + MPI_Send(fmsend[0],3*nebatoms,MPI_DOUBLE,procprev,0,uworld); + MPI_Send(tagsend,nebatoms,MPI_LMP_TAGINT,procprev,0,uworld); + } + + if (ireplica < nreplica-1) { + MPI_Waitall(2,requests,statuses); + for (i = 0; i < nebatoms; i++) { + m = atom->map(tagrecv[i]); + xnext[m][0] = xrecv[i][0]; + xnext[m][1] = xrecv[i][1]; + xnext[m][2] = xrecv[i][2]; + fnext[m][0] = frecv[i][0]; + fnext[m][1] = frecv[i][1]; + fnext[m][2] = frecv[i][2]; + spnext[m][0] = sprecv[i][0]; + spnext[m][1] = sprecv[i][1]; + spnext[m][2] = sprecv[i][2]; + fmnext[m][0] = fmrecv[i][0]; + fmnext[m][1] = fmrecv[i][1]; + fmnext[m][2] = fmrecv[i][2]; + } + } + + return; + } + + // multiple procs per replica + // MPI_Gather all coords and atom IDs to root proc of each replica + // send to root of adjacent replicas + // bcast within each replica + // each proc extracts info for atoms it owns via atom->map() + + m = 0; + for (i = 0; i < nlocal; i++) + if (mask[i] & groupbit) { + tagsend[m] = tag[i]; + xsend[m][0] = x[i][0]; + xsend[m][1] = x[i][1]; + xsend[m][2] = x[i][2]; + fsend[m][0] = f[i][0]; + fsend[m][1] = f[i][1]; + fsend[m][2] = f[i][2]; + spsend[m][0] = sp[i][0]; + spsend[m][1] = sp[i][1]; + spsend[m][2] = sp[i][2]; + fmsend[m][0] = fm[i][0]; + fmsend[m][1] = fm[i][1]; + fmsend[m][2] = fm[i][2]; + m++; + } + + MPI_Gather(&m,1,MPI_INT,counts,1,MPI_INT,0,world); + displacements[0] = 0; + for (i = 0; i < nprocs-1; i++) + displacements[i+1] = displacements[i] + counts[i]; + MPI_Gatherv(tagsend,m,MPI_LMP_TAGINT, + tagsendall,counts,displacements,MPI_LMP_TAGINT,0,world); + for (i = 0; i < nprocs; i++) counts[i] *= 3; + for (i = 0; i < nprocs-1; i++) + displacements[i+1] = displacements[i] + counts[i]; + if (xsend) { + MPI_Gatherv(xsend[0],3*m,MPI_DOUBLE, + xsendall[0],counts,displacements,MPI_DOUBLE,0,world); + MPI_Gatherv(fsend[0],3*m,MPI_DOUBLE, + fsendall[0],counts,displacements,MPI_DOUBLE,0,world); + } else { + MPI_Gatherv(NULL,3*m,MPI_DOUBLE, + xsendall[0],counts,displacements,MPI_DOUBLE,0,world); + MPI_Gatherv(NULL,3*m,MPI_DOUBLE, + fsendall[0],counts,displacements,MPI_DOUBLE,0,world); + } + if (spsend) { + MPI_Gatherv(spsend[0],3*m,MPI_DOUBLE, + spsendall[0],counts,displacements,MPI_DOUBLE,0,world); + MPI_Gatherv(fmsend[0],3*m,MPI_DOUBLE, + fmsendall[0],counts,displacements,MPI_DOUBLE,0,world); + } else { + MPI_Gatherv(NULL,3*m,MPI_DOUBLE, + spsendall[0],counts,displacements,MPI_DOUBLE,0,world); + MPI_Gatherv(NULL,3*m,MPI_DOUBLE, + fmsendall[0],counts,displacements,MPI_DOUBLE,0,world); + } + + if (ireplica > 0 && me == 0) { + MPI_Irecv(xrecvall[0],3*nebatoms,MPI_DOUBLE,procprev,0,uworld,&requests[0]); + MPI_Irecv(sprecvall[0],3*nebatoms,MPI_DOUBLE,procprev,0,uworld,&requests[0]); + MPI_Irecv(tagrecvall,nebatoms,MPI_LMP_TAGINT,procprev,0,uworld, + &requests[1]); + } + if (ireplica < nreplica-1 && me == 0) { + MPI_Send(xsendall[0],3*nebatoms,MPI_DOUBLE,procnext,0,uworld); + MPI_Send(spsendall[0],3*nebatoms,MPI_DOUBLE,procnext,0,uworld); + MPI_Send(tagsendall,nebatoms,MPI_LMP_TAGINT,procnext,0,uworld); + } + + if (ireplica > 0) { + if (me == 0) MPI_Waitall(2,requests,statuses); + + MPI_Bcast(tagrecvall,nebatoms,MPI_INT,0,world); + MPI_Bcast(xrecvall[0],3*nebatoms,MPI_DOUBLE,0,world); + MPI_Bcast(sprecvall[0],3*nebatoms,MPI_DOUBLE,0,world); + + for (i = 0; i < nebatoms; i++) { + m = atom->map(tagrecvall[i]); + if (m < 0 || m >= nlocal) continue; + xprev[m][0] = xrecvall[i][0]; + xprev[m][1] = xrecvall[i][1]; + xprev[m][2] = xrecvall[i][2]; + spprev[m][0] = sprecvall[i][0]; + spprev[m][1] = sprecvall[i][1]; + spprev[m][2] = sprecvall[i][2]; + } + } + + if (ireplica < nreplica-1 && me == 0) { + MPI_Irecv(xrecvall[0],3*nebatoms,MPI_DOUBLE,procnext,0,uworld,&requests[0]); + MPI_Irecv(frecvall[0],3*nebatoms,MPI_DOUBLE,procnext,0,uworld,&requests[0]); + MPI_Irecv(sprecvall[0],3*nebatoms,MPI_DOUBLE,procnext,0,uworld,&requests[0]); + MPI_Irecv(sprecvall[0],3*nebatoms,MPI_DOUBLE,procnext,0,uworld,&requests[0]); + MPI_Irecv(tagrecvall,nebatoms,MPI_LMP_TAGINT,procnext,0,uworld, + &requests[1]); + } + if (ireplica > 0 && me == 0) { + MPI_Send(xsendall[0],3*nebatoms,MPI_DOUBLE,procprev,0,uworld); + MPI_Send(fsendall[0],3*nebatoms,MPI_DOUBLE,procprev,0,uworld); + MPI_Send(spsendall[0],3*nebatoms,MPI_DOUBLE,procprev,0,uworld); + MPI_Send(fmsendall[0],3*nebatoms,MPI_DOUBLE,procprev,0,uworld); + MPI_Send(tagsendall,nebatoms,MPI_LMP_TAGINT,procprev,0,uworld); + } + + if (ireplica < nreplica-1) { + if (me == 0) MPI_Waitall(2,requests,statuses); + + MPI_Bcast(tagrecvall,nebatoms,MPI_INT,0,world); + MPI_Bcast(xrecvall[0],3*nebatoms,MPI_DOUBLE,0,world); + MPI_Bcast(frecvall[0],3*nebatoms,MPI_DOUBLE,0,world); + MPI_Bcast(sprecvall[0],3*nebatoms,MPI_DOUBLE,0,world); + MPI_Bcast(fmrecvall[0],3*nebatoms,MPI_DOUBLE,0,world); + + for (i = 0; i < nebatoms; i++) { + m = atom->map(tagrecvall[i]); + if (m < 0 || m >= nlocal) continue; + xnext[m][0] = xrecvall[i][0]; + xnext[m][1] = xrecvall[i][1]; + xnext[m][2] = xrecvall[i][2]; + fnext[m][0] = frecvall[i][0]; + fnext[m][1] = frecvall[i][1]; + fnext[m][2] = frecvall[i][2]; + spnext[m][0] = sprecvall[i][0]; + spnext[m][1] = sprecvall[i][1]; + spnext[m][2] = sprecvall[i][2]; + fmnext[m][0] = fmrecvall[i][0]; + fmnext[m][1] = fmrecvall[i][1]; + fmnext[m][2] = fmrecvall[i][2]; + } + } +} + +/* ---------------------------------------------------------------------- + reallocate xprev,xnext,tangent arrays if necessary + reallocate communication arrays if necessary +------------------------------------------------------------------------- */ + +void FixNEBSpin::reallocate() +{ + maxlocal = atom->nmax; + + memory->destroy(xprev); + memory->destroy(xnext); + memory->destroy(tangent); + memory->destroy(fnext); + memory->destroy(springF); + memory->destroy(spprev); + memory->destroy(spnext); + memory->destroy(fmnext); + + memory->create(xprev,maxlocal,3,"neb:xprev"); + memory->create(xnext,maxlocal,3,"neb:xnext"); + memory->create(tangent,maxlocal,3,"neb:tangent"); + memory->create(fnext,maxlocal,3,"neb:fnext"); + memory->create(springF,maxlocal,3,"neb:springF"); + memory->create(spprev,maxlocal,3,"neb:xprev"); + memory->create(spnext,maxlocal,3,"neb:xnext"); + memory->create(fmnext,maxlocal,3,"neb:fnext"); + + if (cmode != SINGLE_PROC_DIRECT) { + memory->destroy(xsend); + memory->destroy(fsend); + memory->destroy(xrecv); + memory->destroy(frecv); + memory->destroy(spsend); + memory->destroy(fmsend); + memory->destroy(sprecv); + memory->destroy(fmrecv); + memory->destroy(tagsend); + memory->destroy(tagrecv); + memory->create(xsend,maxlocal,3,"neb:xsend"); + memory->create(fsend,maxlocal,3,"neb:fsend"); + memory->create(xrecv,maxlocal,3,"neb:xrecv"); + memory->create(frecv,maxlocal,3,"neb:frecv"); + memory->create(spsend,maxlocal,3,"neb:xsend"); + memory->create(fmsend,maxlocal,3,"neb:fsend"); + memory->create(sprecv,maxlocal,3,"neb:xrecv"); + memory->create(fmrecv,maxlocal,3,"neb:frecv"); + memory->create(tagsend,maxlocal,"neb:tagsend"); + memory->create(tagrecv,maxlocal,"neb:tagrecv"); + } + + if (NEBLongRange) { + memory->destroy(nlenall); + memory->create(nlenall,nreplica,"neb:nlenall"); + } +} diff --git a/src/SPIN/fix_neb_spin.h b/src/SPIN/fix_neb_spin.h new file mode 100644 index 0000000000..7ac83ddce7 --- /dev/null +++ b/src/SPIN/fix_neb_spin.h @@ -0,0 +1,112 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef FIX_CLASS + +FixStyle(neb/spin,FixNEBSpin) + +#else + +#ifndef LMP_FIX_NEB_SPIN_H +#define LMP_FIX_NEB_SPIN_H + +#include "fix.h" + +namespace LAMMPS_NS { + +class FixNEBSpin : public Fix { + public: + double veng,plen,nlen,dotpath,dottangrad,gradlen,dotgrad; + int rclimber; + + FixNEBSpin(class LAMMPS *, int, char **); + ~FixNEBSpin(); + int setmask(); + void init(); + void min_setup(int); + void min_post_force(int); + + private: + int me,nprocs,nprocs_universe; + double kspring,kspringIni,kspringFinal,kspringPerp,EIniIni,EFinalIni; + bool StandardNEB,NEBLongRange,PerpSpring,FreeEndIni,FreeEndFinal; + bool FreeEndFinalWithRespToEIni,FinalAndInterWithRespToEIni; + bool SpinLattice; + int ireplica,nreplica; + int procnext,procprev; + int cmode; + MPI_Comm uworld; + MPI_Comm rootworld; + + + char *id_pe; + class Compute *pe; + + int nebatoms; + int ntotal; // total # of atoms, NEB or not + int maxlocal; // size of xprev,xnext,tangent arrays + double *nlenall; + double **xprev,**xnext,**fnext; + double **spprev,**spnext,**fmnext; + double **springF; + double **tangent; + double **xsend,**xrecv; // coords to send/recv to/from other replica + double **fsend,**frecv; // coords to send/recv to/from other replica + double **spsend,**sprecv; // sp to send/recv to/from other replica + double **fmsend,**fmrecv; // fm to send/recv to/from other replica + tagint *tagsend,*tagrecv; // ditto for atom IDs + + // info gathered from all procs in my replica + double **xsendall,**xrecvall; // coords to send/recv to/from other replica + double **fsendall,**frecvall; // force to send/recv to/from other replica + double **spsendall,**sprecvall; // sp to send/recv to/from other replica + double **fmsendall,**fmrecvall; // fm to send/recv to/from other replica + tagint *tagsendall,*tagrecvall; // ditto for atom IDs + + int *counts,*displacements; // used for MPI_Gather + + double geodesic_distance(double *, double *); + void inter_replica_comm(); + void reallocate(); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +E: Potential energy ID for fix neb does not exist + +Self-explanatory. + +E: Too many active GNEB atoms + +UNDOCUMENTED + +E: Too many atoms for GNEB + +UNDOCUMENTED + +U: Atom count changed in fix neb + +This is not allowed in a GNEB calculation. + +*/ diff --git a/src/SPIN/fix_nve_spin.cpp b/src/SPIN/fix_nve_spin.cpp index 8d549ed64a..9b67b29492 100644 --- a/src/SPIN/fix_nve_spin.cpp +++ b/src/SPIN/fix_nve_spin.cpp @@ -31,9 +31,10 @@ #include "comm.h" #include "domain.h" #include "error.h" -#include "fix_precession_spin.h" #include "fix_nve_spin.h" +#include "fix_precession_spin.h" #include "fix_langevin_spin.h" +#include "fix_setforce_spin.h" #include "force.h" #include "math_vector.h" #include "math_extra.h" @@ -88,7 +89,6 @@ FixNVESpin::FixNVESpin(LAMMPS *lmp, int narg, char **arg) : npairs = 0; npairspin = 0; - // checking if map array or hash is defined if (atom->map_style == 0) @@ -132,6 +132,7 @@ FixNVESpin::FixNVESpin(LAMMPS *lmp, int narg, char **arg) : precession_spin_flag = 0; maglangevin_flag = 0; tdamp_flag = temp_flag = 0; + setforce_spin_flag = 0; } @@ -238,6 +239,15 @@ void FixNVESpin::init() if (locklangevinspin->temp_flag == 1) temp_flag = 1; } + // ptrs FixSetForceSpin classes + + for (iforce = 0; iforce < modify->nfix; iforce++) { + if (strstr(modify->fix[iforce]->style,"setforce/spin")) { + setforce_spin_flag = 1; + locksetforcespin = (FixSetForceSpin *) modify->fix[iforce]; + } + } + // setting the sector variables/lists nsectors = 0; @@ -250,13 +260,10 @@ void FixNVESpin::init() // init. size of stacking lists (sectoring) nlocal_max = atom->nlocal; - stack_head = memory->grow(stack_head,nsectors,"NVE/spin:stack_head"); - stack_foot = memory->grow(stack_foot,nsectors,"NVE/spin:stack_foot"); - backward_stacks = memory->grow(backward_stacks,nlocal_max,"NVE/spin:backward_stacks"); - forward_stacks = memory->grow(forward_stacks,nlocal_max,"NVE/spin:forward_stacks"); - if (nlocal_max == 0) - error->all(FLERR,"Incorrect value of nlocal_max"); - + memory->grow(stack_head,nsectors,"NVE/spin:stack_head"); + memory->grow(stack_foot,nsectors,"NVE/spin:stack_foot"); + memory->grow(backward_stacks,nlocal_max,"NVE/spin:backward_stacks"); + memory->grow(forward_stacks,nlocal_max,"NVE/spin:forward_stacks"); } /* ---------------------------------------------------------------------- */ @@ -389,8 +396,8 @@ void FixNVESpin::pre_neighbor() if (nlocal_max < nlocal) { // grow linked lists if necessary nlocal_max = nlocal; - backward_stacks = memory->grow(backward_stacks,nlocal_max,"NVE/spin:backward_stacks"); - forward_stacks = memory->grow(forward_stacks,nlocal_max,"NVE/spin:forward_stacks"); + memory->grow(backward_stacks,nlocal_max,"NVE/spin:backward_stacks"); + memory->grow(forward_stacks,nlocal_max,"NVE/spin:forward_stacks"); } for (int j = 0; j < nsectors; j++) { @@ -462,6 +469,12 @@ void FixNVESpin::ComputeInteractionsSpin(int i) } } + // update setforce of magnetic interactions + + if (setforce_spin_flag) { + locksetforcespin->single_setforce_spin(i,fmi); + } + // replace the magnetic force fm[i] by its new value fmi fm[i][0] = fmi[0]; @@ -560,7 +573,7 @@ void FixNVESpin::AdvanceSingleSpin(int i) int *sametag = atom->sametag; double **sp = atom->sp; double **fm = atom->fm; - double msq,scale,fm2,energy,dts2; + double fm2,energy,dts2; double cp[3],g[3]; cp[0] = cp[1] = cp[2] = 0.0; @@ -569,21 +582,21 @@ void FixNVESpin::AdvanceSingleSpin(int i) energy = (sp[i][0]*fm[i][0])+(sp[i][1]*fm[i][1])+(sp[i][2]*fm[i][2]); dts2 = dts*dts; - cp[0] = fm[i][1]*sp[i][2]-fm[i][2]*sp[i][1]; - cp[1] = fm[i][2]*sp[i][0]-fm[i][0]*sp[i][2]; - cp[2] = fm[i][0]*sp[i][1]-fm[i][1]*sp[i][0]; + cp[0] = fm[i][1]*sp[i][2] - fm[i][2]*sp[i][1]; + cp[1] = fm[i][2]*sp[i][0] - fm[i][0]*sp[i][2]; + cp[2] = fm[i][0]*sp[i][1] - fm[i][1]*sp[i][0]; - g[0] = sp[i][0]+cp[0]*dts; - g[1] = sp[i][1]+cp[1]*dts; - g[2] = sp[i][2]+cp[2]*dts; + g[0] = sp[i][0] + cp[0]*dts; + g[1] = sp[i][1] + cp[1]*dts; + g[2] = sp[i][2] + cp[2]*dts; - g[0] += (fm[i][0]*energy-0.5*sp[i][0]*fm2)*0.5*dts2; - g[1] += (fm[i][1]*energy-0.5*sp[i][1]*fm2)*0.5*dts2; - g[2] += (fm[i][2]*energy-0.5*sp[i][2]*fm2)*0.5*dts2; + g[0] += (fm[i][0]*energy - 0.5*sp[i][0]*fm2)*0.5*dts2; + g[1] += (fm[i][1]*energy - 0.5*sp[i][1]*fm2)*0.5*dts2; + g[2] += (fm[i][2]*energy - 0.5*sp[i][2]*fm2)*0.5*dts2; - g[0] /= (1+0.25*fm2*dts2); - g[1] /= (1+0.25*fm2*dts2); - g[2] /= (1+0.25*fm2*dts2); + g[0] /= (1.0 + 0.25*fm2*dts2); + g[1] /= (1.0 + 0.25*fm2*dts2); + g[2] /= (1.0 + 0.25*fm2*dts2); sp[i][0] = g[0]; sp[i][1] = g[1]; @@ -591,11 +604,11 @@ void FixNVESpin::AdvanceSingleSpin(int i) // renormalization (check if necessary) - msq = g[0]*g[0] + g[1]*g[1] + g[2]*g[2]; - scale = 1.0/sqrt(msq); - sp[i][0] *= scale; - sp[i][1] *= scale; - sp[i][2] *= scale; + //msq = g[0]*g[0] + g[1]*g[1] + g[2]*g[2]; + //scale = 1.0/sqrt(msq); + //sp[i][0] *= scale; + //sp[i][1] *= scale; + //sp[i][2] *= scale; // comm. sp[i] to atoms with same tag (for serial algo) diff --git a/src/SPIN/fix_nve_spin.h b/src/SPIN/fix_nve_spin.h index afc1db14d6..4e135e3c2f 100644 --- a/src/SPIN/fix_nve_spin.h +++ b/src/SPIN/fix_nve_spin.h @@ -27,7 +27,7 @@ FixStyle(nve/spin,FixNVESpin) namespace LAMMPS_NS { class FixNVESpin : public Fix { -friend class PairSpin; +friend class PairSpin; public: FixNVESpin(class LAMMPS *, int, char **); virtual ~FixNVESpin(); @@ -58,14 +58,16 @@ friend class PairSpin; int nlocal_max; // max value of nlocal (for lists size) int pair_spin_flag; // magnetic pair flags - int precession_spin_flag; // magnetic precession flags + int precession_spin_flag; // magnetic precession flags int maglangevin_flag; // magnetic langevin flags int tdamp_flag, temp_flag; + int setforce_spin_flag; // pointers to magnetic fixes class FixPrecessionSpin *lockprecessionspin; class FixLangevinSpin *locklangevinspin; + class FixSetForceSpin *locksetforcespin; // pointers to magnetic pair styles diff --git a/src/SPIN/fix_precession_spin.cpp b/src/SPIN/fix_precession_spin.cpp index 9ee691c227..1ea134d367 100644 --- a/src/SPIN/fix_precession_spin.cpp +++ b/src/SPIN/fix_precession_spin.cpp @@ -25,8 +25,8 @@ #include #include #include - #include "atom.h" +#include "error.h" #include "domain.h" #include "error.h" #include "fix_precession_spin.h" @@ -35,6 +35,7 @@ #include "math_const.h" #include "memory.h" #include "modify.h" +#include "neigh_list.h" #include "respa.h" #include "update.h" #include "variable.h" @@ -71,8 +72,12 @@ FixPrecessionSpin::FixPrecessionSpin(LAMMPS *lmp, int narg, char **arg) : Fix(lm Ka = 0.0; nax = nay = naz = 0.0; Kax = Kay = Kaz = 0.0; + k1c = k2c = 0.0; + nc1x = nc1y = nc1z = 0.0; + nc2x = nc2y = nc2z = 0.0; + nc3x = nc3y = nc3z = 0.0; - zeeman_flag = aniso_flag = 0; + zeeman_flag = aniso_flag = cubic_flag = 0; int iarg = 3; while (iarg < narg) { @@ -92,14 +97,61 @@ FixPrecessionSpin::FixPrecessionSpin(LAMMPS *lmp, int narg, char **arg) : Fix(lm nay = force->numeric(FLERR,arg[iarg+3]); naz = force->numeric(FLERR,arg[iarg+4]); iarg += 5; + } else if (strcmp(arg[iarg],"cubic") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal fix precession/spin command"); + cubic_flag = 1; + k1c = force->numeric(FLERR,arg[iarg+1]); + k2c = force->numeric(FLERR,arg[iarg+2]); + nc1x = force->numeric(FLERR,arg[iarg+3]); + nc1y = force->numeric(FLERR,arg[iarg+4]); + nc1z = force->numeric(FLERR,arg[iarg+5]); + nc2x = force->numeric(FLERR,arg[iarg+6]); + nc2y = force->numeric(FLERR,arg[iarg+7]); + nc2z = force->numeric(FLERR,arg[iarg+8]); + nc3x = force->numeric(FLERR,arg[iarg+9]); + nc3y = force->numeric(FLERR,arg[iarg+10]); + nc3z = force->numeric(FLERR,arg[iarg+11]); + iarg += 12; } else error->all(FLERR,"Illegal precession/spin command"); } + // normalize vectors + + double inorm; + if (zeeman_flag) { + inorm = 1.0/sqrt(nhx*nhx + nhy*nhy + nhz*nhz); + nhx *= inorm; + nhy *= inorm; + nhz *= inorm; + } + + if (aniso_flag) { + inorm = 1.0/sqrt(nax*nax + nay*nay + naz*naz); + nax *= inorm; + nay *= inorm; + naz *= inorm; + } + + if (cubic_flag) { + inorm = 1.0/sqrt(nc1x*nc1x + nc1y*nc1y + nc1z*nc1z); + nc1x *= inorm; + nc1y *= inorm; + nc1z *= inorm; + inorm = 1.0/sqrt(nc2x*nc2x + nc2y*nc2y + nc2z*nc2z); + nc2x *= inorm; + nc2y *= inorm; + nc2z *= inorm; + inorm = 1.0/sqrt(nc3x*nc3x + nc3y*nc3y + nc3z*nc3z); + nc3x *= inorm; + nc3y *= inorm; + nc3z *= inorm; + } + degree2rad = MY_PI/180.0; time_origin = update->ntimestep; eflag = 0; - emag = 0.0; + eprec = 0.0; } /* ---------------------------------------------------------------------- */ @@ -130,8 +182,12 @@ void FixPrecessionSpin::init() const double mub = 5.78901e-5; // in eV/T const double gyro = mub/hbar; // in rad.THz/T - H_field *= gyro; // in rad.THz - Ka /= hbar; // in rad.THz + // convert field quantities to rad.THz + + H_field *= gyro; + Kah = Ka/hbar; + k1ch = k1c/hbar; + k2ch = k2c/hbar; if (strstr(update->integrate_style,"respa")) { ilevel_respa = ((Respa *) update->integrate)->nlevels-1; @@ -185,53 +241,60 @@ void FixPrecessionSpin::post_force(int /* vflag */) if (varflag != CONSTANT) { modify->clearstep_compute(); modify->addstep_compute(update->ntimestep + 1); - set_magneticprecession(); // update mag. field if time-dep. + set_magneticprecession(); // update mag. field if time-dep. } - double **sp = atom->sp; + int *mask = atom->mask; double **fm = atom->fm; - double spi[3], fmi[3]; + double **sp = atom->sp; const int nlocal = atom->nlocal; - + double spi[3], fmi[3], epreci; + eflag = 0; - emag = 0.0; - + eprec = 0.0; for (int i = 0; i < nlocal; i++) { - spi[0] = sp[i][0]; - spi[1] = sp[i][1]; - spi[2] = sp[i][2]; - fmi[0] = fmi[1] = fmi[2] = 0.0; + if (mask[i] & groupbit) { + epreci = 0.0; + spi[0] = sp[i][0]; + spi[1] = sp[i][1]; + spi[2] = sp[i][2]; + fmi[0] = fmi[1] = fmi[2] = 0.0; - if (zeeman_flag) { // compute Zeeman interaction - compute_zeeman(i,fmi); - emag -= (spi[0]*fmi[0] + spi[1]*fmi[1] + spi[2]*fmi[2]); + if (zeeman_flag) { // compute Zeeman interaction + compute_zeeman(i,fmi); + epreci -= hbar*(spi[0]*fmi[0] + spi[1]*fmi[1] + spi[2]*fmi[2]); + } + + if (aniso_flag) { // compute magnetic anisotropy + compute_anisotropy(spi,fmi); + epreci -= compute_anisotropy_energy(spi); + } + + if (cubic_flag) { // compute cubic anisotropy + compute_cubic(spi,fmi); + epreci -= compute_cubic_energy(spi); + } + + eprec += epreci; + fm[i][0] += fmi[0]; + fm[i][1] += fmi[1]; + fm[i][2] += fmi[2]; } - - if (aniso_flag) { // compute magnetic anisotropy - compute_anisotropy(spi,fmi); - emag -= 0.5*(spi[0]*fmi[0] + spi[1]*fmi[1] + spi[2]*fmi[2]); - } - - fm[i][0] += fmi[0]; - fm[i][1] += fmi[1]; - fm[i][2] += fmi[2]; } - emag *= hbar; } /* ---------------------------------------------------------------------- */ void FixPrecessionSpin::compute_single_precession(int i, double spi[3], double fmi[3]) { - if (zeeman_flag) { - compute_zeeman(i,fmi); - } - if (aniso_flag) { - compute_anisotropy(spi,fmi); + int *mask = atom->mask; + if (mask[i] & groupbit) { + if (zeeman_flag) compute_zeeman(i,fmi); + if (aniso_flag) compute_anisotropy(spi,fmi); + if (cubic_flag) compute_cubic(spi,fmi); } } - /* ---------------------------------------------------------------------- */ void FixPrecessionSpin::compute_zeeman(int i, double fmi[3]) @@ -254,6 +317,16 @@ void FixPrecessionSpin::compute_anisotropy(double spi[3], double fmi[3]) /* ---------------------------------------------------------------------- */ +double FixPrecessionSpin::compute_anisotropy_energy(double spi[3]) +{ + double energy = 0.0; + double scalar = nax*spi[0] + nay*spi[1] + naz*spi[2]; + energy = Ka*scalar*scalar; + return energy; +} + +/* ---------------------------------------------------------------------- */ + void FixPrecessionSpin::post_force_respa(int vflag, int ilevel, int /*iloop*/) { if (ilevel == ilevel_respa) post_force(vflag); @@ -264,17 +337,75 @@ void FixPrecessionSpin::post_force_respa(int vflag, int ilevel, int /*iloop*/) void FixPrecessionSpin::set_magneticprecession() { if (zeeman_flag) { - hx = H_field*nhx; - hy = H_field*nhy; - hz = H_field*nhz; + hx = H_field*nhx; + hy = H_field*nhy; + hz = H_field*nhz; } if (aniso_flag) { - Kax = 2.0*Ka*nax; - Kay = 2.0*Ka*nay; - Kaz = 2.0*Ka*naz; + Kax = 2.0*Kah*nax; + Kay = 2.0*Kah*nay; + Kaz = 2.0*Kah*naz; } } +/* ---------------------------------------------------------------------- + compute cubic aniso energy of spin i +------------------------------------------------------------------------- */ + +double FixPrecessionSpin::compute_cubic_energy(double spi[3]) +{ + double energy = 0.0; + double skx,sky,skz; + + skx = spi[0]*nc1x+spi[1]*nc1y+spi[2]*nc1z; + sky = spi[0]*nc2x+spi[1]*nc2y+spi[2]*nc2z; + skz = spi[0]*nc3x+spi[1]*nc3y+spi[2]*nc3z; + + energy = k1c*(skx*skx*sky*sky + sky*sky*skz*skz + skx*skx*skz*skz); + energy += k2c*skx*skx*sky*sky*skz*skz; + + return energy; +} + +/* ---------------------------------------------------------------------- + compute cubic anisotropy interaction for spin i +------------------------------------------------------------------------- */ + +void FixPrecessionSpin::compute_cubic(double spi[3], double fmi[3]) +{ + double skx,sky,skz,skx2,sky2,skz2; + double four1,four2,four3,fourx,foury,fourz; + double six1,six2,six3,sixx,sixy,sixz; + + skx = spi[0]*nc1x+spi[1]*nc1y+spi[2]*nc1z; + sky = spi[0]*nc2x+spi[1]*nc2y+spi[2]*nc2z; + skz = spi[0]*nc3x+spi[1]*nc3y+spi[2]*nc3z; + + skx2 = skx*skx; + sky2 = sky*sky; + skz2 = skz*skz; + + four1 = 2.0*skx*(sky2+skz2); + four2 = 2.0*sky*(skx2+skz2); + four3 = 2.0*skz*(skx2+sky2); + + fourx = k1ch*(nc1x*four1 + nc2x*four2 + nc3x*four3); + foury = k1ch*(nc1y*four1 + nc2y*four2 + nc3y*four3); + fourz = k1ch*(nc1z*four1 + nc2z*four2 + nc3z*four3); + + six1 = 2.0*skx*sky2*skz2; + six2 = 2.0*sky*skx2*skz2; + six3 = 2.0*skz*skx2*sky2; + + sixx = k2ch*(nc1x*six1 + nc2x*six2 + nc3x*six3); + sixy = k2ch*(nc1y*six1 + nc2y*six2 + nc3y*six3); + sixz = k2ch*(nc1z*six1 + nc2z*six2 + nc3z*six3); + + fmi[0] += fourx + sixx; + fmi[1] += foury + sixy; + fmi[2] += fourz + sixz; +} + /* ---------------------------------------------------------------------- potential energy in magnetic field ------------------------------------------------------------------------- */ @@ -284,10 +415,10 @@ double FixPrecessionSpin::compute_scalar() // only sum across procs one time if (eflag == 0) { - MPI_Allreduce(&emag,&emag_all,1,MPI_DOUBLE,MPI_SUM,world); + MPI_Allreduce(&eprec,&eprec_all,1,MPI_DOUBLE,MPI_SUM,world); eflag = 1; } - return emag_all; + return eprec_all; } /* ---------------------------------------------------------------------- */ diff --git a/src/SPIN/fix_precession_spin.h b/src/SPIN/fix_precession_spin.h index 1db4d32ae9..0037784a48 100644 --- a/src/SPIN/fix_precession_spin.h +++ b/src/SPIN/fix_precession_spin.h @@ -39,11 +39,20 @@ class FixPrecessionSpin : public Fix { void min_post_force(int); double compute_scalar(); - int zeeman_flag, aniso_flag; + int zeeman_flag, aniso_flag, cubic_flag; void compute_single_precession(int, double *, double *); void compute_zeeman(int, double *); - void compute_anisotropy(double *, double *); + + // uniaxial aniso calculations + void compute_anisotropy(double *, double *); + double compute_anisotropy_energy(double *); + + // cubic aniso calculations + + void compute_cubic(double *, double *); + double compute_cubic_energy(double *); + protected: int style; // style of the magnetic precession @@ -52,7 +61,7 @@ class FixPrecessionSpin : public Fix { int ilevel_respa; int time_origin; int eflag; - double emag, emag_all; + double eprec, eprec_all; int varflag; int magfieldstyle; @@ -67,10 +76,19 @@ class FixPrecessionSpin : public Fix { // magnetic anisotropy intensity and direction - double Ka; + double Ka; // aniso const. in eV + double Kah; // aniso const. in rad.THz double nax, nay, naz; double Kax, Kay, Kaz; // temp. force variables + // cubic anisotropy intensity + + double k1c,k2c; // cubic const. in eV + double k1ch,k2ch; // cubic const. in rad.THz + double nc1x,nc1y,nc1z; + double nc2x,nc2y,nc2z; + double nc3x,nc3y,nc3z; + void set_magneticprecession(); }; diff --git a/src/SPIN/fix_setforce_spin.cpp b/src/SPIN/fix_setforce_spin.cpp new file mode 100644 index 0000000000..c2807418ec --- /dev/null +++ b/src/SPIN/fix_setforce_spin.cpp @@ -0,0 +1,222 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + 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: Julien Tranchida (SNL) + Aidan Thompson (SNL) + + Please cite the related publication: + Tranchida, J., Plimpton, S. J., Thibaudeau, P., & Thompson, A. P. (2018). + Massively parallel symplectic algorithm for coupled magnetic spin dynamics + and molecular dynamics. Journal of Computational Physics. +------------------------------------------------------------------------- */ + +#include +#include +#include "fix_setforce_spin.h" +#include "atom.h" +#include "update.h" +#include "modify.h" +#include "domain.h" +#include "region.h" +#include "respa.h" +#include "input.h" +#include "variable.h" +#include "memory.h" +#include "error.h" +#include "force.h" + +using namespace LAMMPS_NS; +using namespace FixConst; + +enum{NONE,CONSTANT,EQUAL,ATOM}; + +/* ---------------------------------------------------------------------- */ + +FixSetForceSpin::FixSetForceSpin(LAMMPS *lmp, int narg, char **arg) : + FixSetForce(lmp, narg, arg) {} + +/* ---------------------------------------------------------------------- */ + +void FixSetForceSpin::post_force(int /*vflag*/) +{ + double **x = atom->x; + double **fm = atom->fm; + int *mask = atom->mask; + int nlocal = atom->nlocal; + + // update region if necessary + + Region *region = NULL; + if (iregion >= 0) { + region = domain->regions[iregion]; + region->prematch(); + } + + // reallocate sforce array if necessary + + if (varflag == ATOM && atom->nmax > maxatom) { + maxatom = atom->nmax; + memory->destroy(sforce); + memory->create(sforce,maxatom,3,"setforce:sforce"); + } + + foriginal[0] = foriginal[1] = foriginal[2] = 0.0; + force_flag = 0; + + if (varflag == CONSTANT) { + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit) { + if (region && !region->match(x[i][0],x[i][1],x[i][2])) continue; + foriginal[0] += fm[i][0]; + foriginal[1] += fm[i][1]; + foriginal[2] += fm[i][2]; + if (xstyle) fm[i][0] = xvalue; + if (ystyle) fm[i][1] = yvalue; + if (zstyle) fm[i][2] = zvalue; + } + + // variable force, wrap with clear/add + + } else { + + modify->clearstep_compute(); + + if (xstyle == EQUAL) xvalue = input->variable->compute_equal(xvar); + else if (xstyle == ATOM) + input->variable->compute_atom(xvar,igroup,&sforce[0][0],3,0); + if (ystyle == EQUAL) yvalue = input->variable->compute_equal(yvar); + else if (ystyle == ATOM) + input->variable->compute_atom(yvar,igroup,&sforce[0][1],3,0); + if (zstyle == EQUAL) zvalue = input->variable->compute_equal(zvar); + else if (zstyle == ATOM) + input->variable->compute_atom(zvar,igroup,&sforce[0][2],3,0); + + modify->addstep_compute(update->ntimestep + 1); + + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit) { + if (region && !region->match(x[i][0],x[i][1],x[i][2])) continue; + foriginal[0] += fm[i][0]; + foriginal[1] += fm[i][1]; + foriginal[2] += fm[i][2]; + if (xstyle == ATOM) fm[i][0] = sforce[i][0]; + else if (xstyle) fm[i][0] = xvalue; + if (ystyle == ATOM) fm[i][1] = sforce[i][1]; + else if (ystyle) fm[i][1] = yvalue; + if (zstyle == ATOM) fm[i][2] = sforce[i][2]; + else if (zstyle) fm[i][2] = zvalue; + } + } +} + +/* ---------------------------------------------------------------------- */ + +void FixSetForceSpin::single_setforce_spin(int i, double fmi[3]) +{ + double **x = atom->x; + int *mask = atom->mask; + + // update region if necessary + + Region *region = NULL; + if (iregion >= 0) { + region = domain->regions[iregion]; + region->prematch(); + } + + // reallocate sforce array if necessary + + if (varflag == ATOM && atom->nmax > maxatom) { + maxatom = atom->nmax; + memory->destroy(sforce); + memory->create(sforce,maxatom,3,"setforce:sforce"); + } + + foriginal[0] = foriginal[1] = foriginal[2] = 0.0; + force_flag = 0; + + // constant force + + if (varflag == CONSTANT) { + if (mask[i] & groupbit) { + if (region && !region->match(x[i][0],x[i][1],x[i][2])) return; + foriginal[0] += fmi[0]; + foriginal[1] += fmi[1]; + foriginal[2] += fmi[2]; + if (xstyle) fmi[0] = xvalue; + if (ystyle) fmi[1] = yvalue; + if (zstyle) fmi[2] = zvalue; + } + + // variable force, wrap with clear/add + + } else { + + modify->clearstep_compute(); + + if (xstyle == EQUAL) xvalue = input->variable->compute_equal(xvar); + else if (xstyle == ATOM) + input->variable->compute_atom(xvar,igroup,&sforce[0][0],3,0); + if (ystyle == EQUAL) yvalue = input->variable->compute_equal(yvar); + else if (ystyle == ATOM) + input->variable->compute_atom(yvar,igroup,&sforce[0][1],3,0); + if (zstyle == EQUAL) zvalue = input->variable->compute_equal(zvar); + else if (zstyle == ATOM) + input->variable->compute_atom(zvar,igroup,&sforce[0][2],3,0); + + modify->addstep_compute(update->ntimestep + 1); + + if (mask[i] & groupbit) { + if (region && !region->match(x[i][0],x[i][1],x[i][2])) return; + foriginal[0] += fmi[0]; + foriginal[1] += fmi[1]; + foriginal[2] += fmi[2]; + if (xstyle == ATOM) fmi[0] = sforce[i][0]; + else if (xstyle) fmi[0] = xvalue; + if (ystyle == ATOM) fmi[1] = sforce[i][1]; + else if (ystyle) fmi[1] = yvalue; + if (zstyle == ATOM) fmi[2] = sforce[i][2]; + else if (zstyle) fmi[2] = zvalue; + } + } +} + +/* ---------------------------------------------------------------------- */ + +void FixSetForceSpin::post_force_respa(int vflag, int ilevel, int /*iloop*/) +{ + // set force to desired value on requested level, 0.0 on other levels + + if (ilevel == ilevel_respa) post_force(vflag); + else { + Region *region = NULL; + if (iregion >= 0) { + region = domain->regions[iregion]; + region->prematch(); + } + + double **x = atom->x; + double **fm = atom->fm; + int *mask = atom->mask; + int nlocal = atom->nlocal; + + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit) { + if (region && !region->match(x[i][0],x[i][1],x[i][2])) continue; + if (xstyle) fm[i][0] = 0.0; + if (ystyle) fm[i][1] = 0.0; + if (zstyle) fm[i][2] = 0.0; + } + } +} diff --git a/src/SPIN/fix_setforce_spin.h b/src/SPIN/fix_setforce_spin.h new file mode 100644 index 0000000000..a836911d85 --- /dev/null +++ b/src/SPIN/fix_setforce_spin.h @@ -0,0 +1,65 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef FIX_CLASS + +FixStyle(setforce/spin,FixSetForceSpin) + +#else + +#ifndef LMP_FIX_SET_FORCE_SPIN_H +#define LMP_FIX_SET_FORCE_SPIN_H + +#include "fix_setforce.h" + +namespace LAMMPS_NS { + +class FixSetForceSpin : public FixSetForce { + public: + FixSetForceSpin(class LAMMPS *, int, char **); + virtual void post_force(int); + void post_force_respa(int, int, int); + void single_setforce_spin(int, double *); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +E: Region ID for fix setforce does not exist + +Self-explanatory. + +E: Variable name for fix setforce does not exist + +Self-explanatory. + +E: Variable for fix setforce is invalid style + +Only equal-style variables can be used. + +E: Cannot use non-zero forces in an energy minimization + +Fix setforce cannot be used in this manner. Use fix addforce +instead. + +*/ diff --git a/src/SPIN/min_spin.h b/src/SPIN/min_spin.h index 224d205000..fbc624a9cc 100644 --- a/src/SPIN/min_spin.h +++ b/src/SPIN/min_spin.h @@ -40,7 +40,7 @@ class MinSpin : public Min { private: // global and spin timesteps - + double dt; double dts; diff --git a/src/SPIN/neb_spin.cpp b/src/SPIN/neb_spin.cpp new file mode 100644 index 0000000000..126cfb09e3 --- /dev/null +++ b/src/SPIN/neb_spin.cpp @@ -0,0 +1,853 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + 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: Julien Tranchida (SNL) + + Please cite the related publication: + Bessarab, P. F., Uzdin, V. M., & Jónsson, H. (2015). + Method for finding mechanism and activation energy of magnetic transitions, + applied to skyrmion and antivortex annihilation. + Computer Physics Communications, 196, 335-347. +------------------------------------------------------------------------- */ + +// lmptype.h must be first b/c this file uses MAXBIGINT and includes mpi.h +// due to OpenMPI bug which sets INT64_MAX via its mpi.h +// before lmptype.h can set flags to insure it is done correctly + +#include "lmptype.h" +#include +#include +#include +#include +#include "neb_spin.h" +#include "citeme.h" +#include "compute.h" +#include "force.h" +#include "universe.h" +#include "atom.h" +#include "update.h" +#include "domain.h" +#include "comm.h" +#include "min.h" +#include "modify.h" +#include "fix.h" +#include "fix_neb_spin.h" +#include "output.h" +#include "thermo.h" +#include "finish.h" +#include "timer.h" +#include "memory.h" +#include "error.h" +#include "math_const.h" + +using namespace LAMMPS_NS; +using namespace MathConst; + +static const char cite_neb_spin[] = + "neb/spin command:\n\n" + "@article{bessarab2015method,\n" + "title={Method for finding mechanism and activation energy of " + "magnetic transitions, applied to skyrmion and antivortex " + "annihilation},\n" + "author={Bessarab, P.F. and Uzdin, V.M. and J{\'o}nsson, H.},\n" + "journal={Computer Physics Communications},\n" + "volume={196},\n" + "pages={335--347},\n" + "year={2015},\n" + "publisher={Elsevier}\n" + "doi={10.1016/j.cpc.2015.07.001}\n" + "}\n\n"; + +#define MAXLINE 256 +#define CHUNK 1024 +// 8 attributes: tag, spin norm, position (3), spin direction (3) +#define ATTRIBUTE_PERLINE 8 + +/* ---------------------------------------------------------------------- */ + +NEBSpin::NEBSpin(LAMMPS *lmp) : Pointers(lmp) { + if (lmp->citeme) lmp->citeme->add(cite_neb_spin); +} + +/* ---------------------------------------------------------------------- */ + +NEBSpin::~NEBSpin() +{ + MPI_Comm_free(&roots); + memory->destroy(all); + delete [] rdist; +} + +/* ---------------------------------------------------------------------- + perform NEBSpin on multiple replicas +------------------------------------------------------------------------- */ + +void NEBSpin::command(int narg, char **arg) +{ + if (domain->box_exist == 0) + error->all(FLERR,"NEBSpin command before simulation box is defined"); + + if (narg < 6) error->universe_all(FLERR,"Illegal NEBSpin command"); + + etol = force->numeric(FLERR,arg[0]); + ttol = force->numeric(FLERR,arg[1]); + n1steps = force->inumeric(FLERR,arg[2]); + n2steps = force->inumeric(FLERR,arg[3]); + nevery = force->inumeric(FLERR,arg[4]); + + // error checks + + if (etol < 0.0) error->all(FLERR,"Illegal NEBSpin command"); + if (ttol < 0.0) error->all(FLERR,"Illegal NEBSpin command"); + if (nevery <= 0) error->universe_all(FLERR,"Illegal NEBSpin command"); + if (n1steps % nevery || n2steps % nevery) + error->universe_all(FLERR,"Illegal NEBSpin command"); + + // replica info + + nreplica = universe->nworlds; + ireplica = universe->iworld; + me_universe = universe->me; + uworld = universe->uworld; + MPI_Comm_rank(world,&me); + + // check metal units and spin atom/style + + if (!atom->sp_flag) + error->all(FLERR,"neb/spin requires atom/spin style"); + if (strcmp(update->unit_style,"metal") != 0) + error->all(FLERR,"neb/spin simulation requires metal unit style"); + + // error checks + + if (nreplica == 1) error->all(FLERR,"Cannot use NEBSpin with a single replica"); + if (atom->map_style == 0) + error->all(FLERR,"Cannot use NEBSpin unless atom map exists"); + + // process file-style setting to setup initial configs for all replicas + + if (strcmp(arg[5],"final") == 0) { + if (narg != 7 && narg !=8) error->universe_all(FLERR,"Illegal NEBSpin command"); + infile = arg[6]; + readfile(infile,0); + } else if (strcmp(arg[5],"each") == 0) { + if (narg != 7 && narg !=8) error->universe_all(FLERR,"Illegal NEBSpin command"); + infile = arg[6]; + readfile(infile,1); + } else if (strcmp(arg[5],"none") == 0) { + if (narg != 6 && narg !=7) error->universe_all(FLERR,"Illegal NEBSpin command"); + } else error->universe_all(FLERR,"Illegal NEBSpin command"); + + verbose=false; + if (strcmp(arg[narg-1],"verbose") == 0) verbose=true; + + run(); +} + +/* ---------------------------------------------------------------------- + run NEBSpin on multiple replicas +------------------------------------------------------------------------- */ + +void NEBSpin::run() +{ + // create MPI communicator for root proc from each world + + int color; + if (me == 0) color = 0; + else color = 1; + MPI_Comm_split(uworld,color,0,&roots); + + // search for neb_spin fix, allocate it + + int ineb; + for (ineb = 0; ineb < modify->nfix; ineb++) + if (strcmp(modify->fix[ineb]->style,"neb/spin") == 0) break; + if (ineb == modify->nfix) error->all(FLERR,"NEBSpin requires use of fix neb/spin"); + + fneb = (FixNEBSpin *) modify->fix[ineb]; + if (verbose) numall =7; + else numall = 4; + memory->create(all,nreplica,numall,"neb:all"); + rdist = new double[nreplica]; + + // initialize LAMMPS + + update->whichflag = 2; + update->etol = etol; + update->ftol = ttol; // update->ftol is a torque tolerance + update->multireplica = 1; + + lmp->init(); + + // check if correct minimizer is setup + + if (update->minimize->searchflag) + error->all(FLERR,"NEBSpin requires damped dynamics minimizer"); + if (strcmp(update->minimize_style,"spin") != 0) + error->all(FLERR,"NEBSpin requires spin minimizer"); + + // setup regular NEBSpin minimization + + FILE *uscreen = universe->uscreen; + FILE *ulogfile = universe->ulogfile; + + if (me_universe == 0 && uscreen) + fprintf(uscreen,"Setting up regular NEBSpin ...\n"); + + update->beginstep = update->firststep = update->ntimestep; + update->endstep = update->laststep = update->firststep + n1steps; + update->nsteps = n1steps; + update->max_eval = n1steps; + if (update->laststep < 0) + error->all(FLERR,"Too many timesteps for NEBSpin"); + + update->minimize->setup(); + + if (me_universe == 0) { + if (uscreen) { + if (verbose) { + fprintf(uscreen,"Step MaxReplicaTorque MaxAtomTorque " + "GradV0 GradV1 GradVc EBF EBR RDT " + "RD1 PE1 RD2 PE2 ... RDN PEN " + "GradV0dottan DN0 ... GradVNdottan DNN\n"); + } else { + fprintf(uscreen,"Step MaxReplicaTorque MaxAtomTorque " + "GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... " + "RDN PEN\n"); + } + } + + if (ulogfile) { + if (verbose) { + fprintf(ulogfile,"Step MaxReplicaTorque MaxAtomTorque " + "GradV0 GradV1 GradVc EBF EBR RDT " + "RD1 PE1 RD2 PE2 ... RDN PEN " + "GradV0dottan DN0 ... GradVNdottan DNN\n"); + } else { + fprintf(ulogfile,"Step MaxReplicaTorque MaxAtomTorque " + "GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... " + "RDN PEN\n"); + } + } + } + print_status(); + + // perform regular NEBSpin for n1steps or until replicas converge + // retrieve PE values from fix NEBSpin and print every nevery iterations + // break out of while loop early if converged + // damped dynamic min styles insure all replicas converge together + + timer->init(); + timer->barrier_start(); + + while (update->minimize->niter < n1steps) { + update->minimize->run(nevery); + print_status(); + if (update->minimize->stop_condition) break; + } + + timer->barrier_stop(); + + update->minimize->cleanup(); + + Finish finish(lmp); + finish.end(1); + + // switch fix NEBSpin to climbing mode + // top = replica that becomes hill climber + + double vmax = all[0][0]; + int top = 0; + for (int m = 1; m < nreplica; m++) + if (vmax < all[m][0]) { + vmax = all[m][0]; + top = m; + } + + // setup climbing NEBSpin minimization + // must reinitialize minimizer so it re-creates its fix MINIMIZE + + if (me_universe == 0 && uscreen) + fprintf(uscreen,"Setting up climbing ...\n"); + + if (me_universe == 0) { + if (uscreen) + fprintf(uscreen,"Climbing replica = %d\n",top+1); + if (ulogfile) + fprintf(ulogfile,"Climbing replica = %d\n",top+1); + } + + update->beginstep = update->firststep = update->ntimestep; + update->endstep = update->laststep = update->firststep + n2steps; + update->nsteps = n2steps; + update->max_eval = n2steps; + if (update->laststep < 0) + error->all(FLERR,"Too many timesteps"); + + update->minimize->init(); + fneb->rclimber = top; + update->minimize->setup(); + + if (me_universe == 0) { + if (uscreen) { + if (verbose) { + fprintf(uscreen,"Step MaxReplicaTorque MaxAtomTorque " + "GradV0 GradV1 GradVc EBF EBR RDT " + "RD1 PE1 RD2 PE2 ... RDN PEN " + "GradV0dottan DN0... GradVNdottan DNN\n"); + } else { + fprintf(uscreen,"Step MaxReplicaTorque MaxAtomTorque " + "GradV0 GradV1 GradVc " + "EBF EBR RDT " + "RD1 PE1 RD2 PE2 ... RDN PEN\n"); + } + } + if (ulogfile) { + if (verbose) { + fprintf(ulogfile,"Step MaxReplicaTorque MaxAtomTorque " + "GradV0 GradV1 GradVc EBF EBR RDT " + "RD1 PE1 RD2 PE2 ... RDN PEN " + "GradV0dottan DN0 ... GradVNdottan DNN\n"); + } else { + fprintf(ulogfile,"Step MaxReplicaTorque MaxAtomTorque " + "GradV0 GradV1 GradVc " + "EBF EBR RDT " + "RD1 PE1 RD2 PE2 ... RDN PEN\n"); + } + } + } + print_status(); + + // perform climbing NEBSpin for n2steps or until replicas converge + // retrieve PE values from fix NEBSpin and print every nevery iterations + // break induced if converged + // damped dynamic min styles insure all replicas converge together + + timer->init(); + timer->barrier_start(); + + while (update->minimize->niter < n2steps) { + update->minimize->run(nevery); + print_status(); + if (update->minimize->stop_condition) break; + } + + timer->barrier_stop(); + + update->minimize->cleanup(); + + finish.end(1); + + update->whichflag = 0; + update->multireplica = 0; + update->firststep = update->laststep = 0; + update->beginstep = update->endstep = 0; +} + +/* ---------------------------------------------------------------------- + read initial config atom coords from file + flag = 0 + only first replica opens file and reads it + first replica bcasts lines to all replicas + final replica stores coords + intermediate replicas interpolate from coords + new coord = replica fraction between current and final state + initial replica does nothing + flag = 1 + each replica (except first) opens file and reads it + each replica stores coords + initial replica does nothing +------------------------------------------------------------------------- */ + +void NEBSpin::readfile(char *file, int flag) +{ + int i,j,m,nchunk,eofflag,nlines; + tagint tag; + char *eof,*start,*next,*buf; + char line[MAXLINE]; + double xx,yy,zz; + double musp,spx,spy,spz; + + if (me_universe == 0 && screen) + fprintf(screen,"Reading NEBSpin coordinate file(s) ...\n"); + + // flag = 0, universe root reads header of file, bcast to universe + // flag = 1, each replica's root reads header of file, bcast to world + // but explicitly skip first replica + + if (flag == 0) { + if (me_universe == 0) { + open(file); + while (1) { + eof = fgets(line,MAXLINE,fp); + if (eof == NULL) error->one(FLERR,"Unexpected end of neb/spin file"); + start = &line[strspn(line," \t\n\v\f\r")]; + if (*start != '\0' && *start != '#') break; + } + sscanf(line,"%d",&nlines); + } + MPI_Bcast(&nlines,1,MPI_INT,0,uworld); + + } else { + if (me == 0) { + if (ireplica) { + open(file); + while (1) { + eof = fgets(line,MAXLINE,fp); + if (eof == NULL) error->one(FLERR,"Unexpected end of neb/spin file"); + start = &line[strspn(line," \t\n\v\f\r")]; + if (*start != '\0' && *start != '#') break; + } + sscanf(line,"%d",&nlines); + } else nlines = 0; + } + MPI_Bcast(&nlines,1,MPI_INT,0,world); + } + + char *buffer = new char[CHUNK*MAXLINE]; + char **values = new char*[ATTRIBUTE_PERLINE]; + + double fraction = ireplica/(nreplica-1.0); + + double **x = atom->x; + double **sp = atom->sp; + double spinit[3],spfinal[3]; + int nlocal = atom->nlocal; + + // loop over chunks of lines read from file + // two versions of read_lines_from_file() for world vs universe bcast + // count # of atom coords changed so can check for invalid atom IDs in file + + int ncount = 0; + + int temp_flag,rot_flag; + temp_flag = rot_flag = 0; + int nread = 0; + while (nread < nlines) { + nchunk = MIN(nlines-nread,CHUNK); + if (flag == 0) + eofflag = comm->read_lines_from_file_universe(fp,nchunk,MAXLINE,buffer); + else + eofflag = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer); + if (eofflag) error->all(FLERR,"Unexpected end of neb/spin file"); + + buf = buffer; + next = strchr(buf,'\n'); + *next = '\0'; + int nwords = atom->count_words(buf); + *next = '\n'; + + if (nwords != ATTRIBUTE_PERLINE) + error->all(FLERR,"Incorrect atom format in neb/spin file"); + + // loop over lines of atom coords + // tokenize the line into values + + for (i = 0; i < nchunk; i++) { + next = strchr(buf,'\n'); + + values[0] = strtok(buf," \t\n\r\f"); + for (j = 1; j < nwords; j++) + values[j] = strtok(NULL," \t\n\r\f"); + + // adjust spin coord based on replica fraction + // for flag = 0, interpolate for intermediate and final replicas + // for flag = 1, replace existing coord with new coord + // ignore image flags of final x + // for interpolation: + // new x is displacement from old x via minimum image convention + // if final x is across periodic boundary: + // new x may be outside box + // will be remapped back into box when simulation starts + // its image flags will then be adjusted + + tag = ATOTAGINT(values[0]); + m = atom->map(tag); + if (m >= 0 && m < nlocal) { + ncount++; + musp = atof(values[1]); + xx = atof(values[2]); + yy = atof(values[3]); + zz = atof(values[4]); + spx = atof(values[5]); + spy = atof(values[6]); + spz = atof(values[7]); + + if (flag == 0) { + + spinit[0] = sp[m][0]; + spinit[1] = sp[m][1]; + spinit[2] = sp[m][2]; + spfinal[0] = spx; + spfinal[1] = spy; + spfinal[2] = spz; + + // interpolate intermediate spin states + + sp[m][3] = musp; + if (fraction == 0.0) { + sp[m][0] = spinit[0]; + sp[m][1] = spinit[1]; + sp[m][2] = spinit[2]; + } else if (fraction == 1.0) { + sp[m][0] = spfinal[0]; + sp[m][1] = spfinal[1]; + sp[m][2] = spfinal[2]; + } else { + temp_flag = initial_rotation(spinit,spfinal,fraction); + rot_flag = MAX(temp_flag,rot_flag); + sp[m][0] = spfinal[0]; + sp[m][1] = spfinal[1]; + sp[m][2] = spfinal[2]; + } + } else { + sp[m][3] = musp; + x[m][0] = xx; + x[m][1] = yy; + x[m][2] = zz; + sp[m][0] = spx; + sp[m][1] = spy; + sp[m][2] = spz; + } + } + + buf = next + 1; + } + + nread += nchunk; + } + + // warning message if one or more couples (spi,spf) were aligned + // this breaks Rodrigues' formula, and an arbitrary rotation + // vector has to be chosen + + if ((rot_flag > 0) && (comm->me == 0)) + error->warning(FLERR,"arbitrary initial rotation of one or more spin(s)"); + + // check that all atom IDs in file were found by a proc + + if (flag == 0) { + int ntotal; + MPI_Allreduce(&ncount,&ntotal,1,MPI_INT,MPI_SUM,uworld); + if (ntotal != nreplica*nlines) + error->universe_all(FLERR,"Invalid atom IDs in neb/spin file"); + } else { + int ntotal; + MPI_Allreduce(&ncount,&ntotal,1,MPI_INT,MPI_SUM,world); + if (ntotal != nlines) + error->all(FLERR,"Invalid atom IDs in neb/spin file"); + } + + // clean up + + delete [] buffer; + delete [] values; + + if (flag == 0) { + if (me_universe == 0) { + if (compressed) pclose(fp); + else fclose(fp); + } + } else { + if (me == 0 && ireplica) { + if (compressed) pclose(fp); + else fclose(fp); + } + } +} + +/* ---------------------------------------------------------------------- + initial configuration of intermediate spins using Rodrigues' formula + interpolates between initial (spi) and final (stored in sploc) +------------------------------------------------------------------------- */ + +int NEBSpin::initial_rotation(double *spi, double *sploc, double fraction) +{ + + // no interpolation for initial and final replica + + if (fraction == 0.0 || fraction == 1.0) return 0; + + int rot_flag = 0; + double kx,ky,kz; + double spix,spiy,spiz,spfx,spfy,spfz; + double kcrossx,kcrossy,kcrossz,knormsq; + double kdots; + double spkx,spky,spkz; + double sidotsf,omega,iknorm,isnorm; + + spix = spi[0]; + spiy = spi[1]; + spiz = spi[2]; + + spfx = sploc[0]; + spfy = sploc[1]; + spfz = sploc[2]; + + kx = spiy*spfz - spiz*spfy; + ky = spiz*spfx - spix*spfz; + kz = spix*spfy - spiy*spfx; + + knormsq = kx*kx+ky*ky+kz*kz; + sidotsf = spix*spfx + spiy*spfy + spiz*spfz; + + // if knormsq == 0.0, init and final spins are aligned + // Rodrigues' formula breaks, needs to define another axis k + + if (knormsq == 0.0) { + if (sidotsf > 0.0) { // spins aligned and in same direction + return 0; + } else if (sidotsf < 0.0) { // spins aligned and in opposite directions + + // defining a rotation axis + // first guess, k = spi x [100] + // second guess, k = spi x [010] + + if (spiy*spiy + spiz*spiz != 0.0) { // spin not along [100] + kx = 0.0; + ky = spiz; + kz = -spiy; + knormsq = ky*ky + kz*kz; + } else if (spix*spix + spiz*spiz != 0.0) { // spin not along [010] + kx = -spiz; + ky = 0.0; + kz = spix; + knormsq = kx*kx + kz*kz; + } else error->all(FLERR,"Incorrect initial rotation operation"); + rot_flag = 1; + } + } + + // knormsq should not be 0 + + if (knormsq == 0.0) + error->all(FLERR,"Incorrect initial rotation operation"); + + // normalize k vector + + iknorm = 1.0/sqrt(knormsq); + kx *= iknorm; + ky *= iknorm; + kz *= iknorm; + + // calc. k x spi and total rotation angle + + kcrossx = ky*spiz - kz*spiy; + kcrossy = kz*spix - kx*spiz; + kcrossz = kx*spiy - ky*spix; + + kdots = kx*spix + ky*spiz + kz*spiz; + + omega = acos(sidotsf); + omega *= fraction; + + // apply Rodrigues' formula + + spkx = spix*cos(omega); + spky = spiy*cos(omega); + spkz = spiz*cos(omega); + + spkx += kcrossx*sin(omega); + spky += kcrossy*sin(omega); + spkz += kcrossz*sin(omega); + + spkx += kx*kdots*(1.0-cos(omega)); + spky += ky*kdots*(1.0-cos(omega)); + spkz += kz*kdots*(1.0-cos(omega)); + + // normalizing resulting spin vector + + isnorm = 1.0/sqrt(spkx*spkx+spky*spky+spkz*spkz); + if (isnorm == 0.0) + error->all(FLERR,"Incorrect initial rotation operation"); + + spkx *= isnorm; + spky *= isnorm; + spkz *= isnorm; + + // returns rotated spin + + sploc[0] = spkx; + sploc[1] = spky; + sploc[2] = spkz; + + return rot_flag; +} + +/* ---------------------------------------------------------------------- + universe proc 0 opens NEBSpin data file + test if gzipped +------------------------------------------------------------------------- */ + +void NEBSpin::open(char *file) +{ + compressed = 0; + char *suffix = file + strlen(file) - 3; + if (suffix > file && strcmp(suffix,".gz") == 0) compressed = 1; + if (!compressed) fp = fopen(file,"r"); + else { +#ifdef LAMMPS_GZIP + char gunzip[128]; + snprintf(gunzip,128,"gzip -c -d %s",file); + +#ifdef _WIN32 + fp = _popen(gunzip,"rb"); +#else + fp = popen(gunzip,"r"); +#endif + +#else + error->one(FLERR,"Cannot open gzipped file"); +#endif + } + + if (fp == NULL) { + char str[128]; + snprintf(str,128,"Cannot open file %s",file); + error->one(FLERR,str); + } +} + +/* ---------------------------------------------------------------------- + query fix NEBSpin for info on each replica + universe proc 0 prints current NEBSpin status +------------------------------------------------------------------------- */ + +void NEBSpin::print_status() +{ + int nlocal = atom->nlocal; + double tx,ty,tz; + double tnorm2,local_norm_inf,temp_inf; + double **sp = atom->sp; + double **fm = atom->fm; + + // calc. magnetic torques + + tnorm2 = local_norm_inf = temp_inf = 0.0; + for (int i = 0; i < nlocal; i++) { + tx = (fm[i][1]*sp[i][2] - fm[i][2]*sp[i][1]); + ty = (fm[i][2]*sp[i][0] - fm[i][0]*sp[i][2]); + tz = (fm[i][0]*sp[i][1] - fm[i][1]*sp[i][0]); + tnorm2 += tx*tx + ty*ty + tz*tz; + temp_inf = MAX(fabs(tx),fabs(ty)); + temp_inf = MAX(fabs(tz),temp_inf); + local_norm_inf = MAX(temp_inf,local_norm_inf); + } + + double fmaxreplica; + MPI_Allreduce(&tnorm2,&fmaxreplica,1,MPI_DOUBLE,MPI_MAX,roots); + + double fnorminf = 0.0; + MPI_Allreduce(&local_norm_inf,&fnorminf,1,MPI_DOUBLE,MPI_MAX,world); + double fmaxatom; + MPI_Allreduce(&fnorminf,&fmaxatom,1,MPI_DOUBLE,MPI_MAX,roots); + + if (verbose) { + freplica = new double[nreplica]; + MPI_Allgather(&tnorm2,1,MPI_DOUBLE,&freplica[0],1,MPI_DOUBLE,roots); + fmaxatomInRepl = new double[nreplica]; + MPI_Allgather(&fnorminf,1,MPI_DOUBLE,&fmaxatomInRepl[0],1,MPI_DOUBLE,roots); + } + + double one[7]; + one[0] = fneb->veng; + one[1] = fneb->plen; + one[2] = fneb->nlen; + one[3] = fneb->gradlen; + + if (verbose) { + one[4] = fneb->dotpath; + one[5] = fneb->dottangrad; + one[6] = fneb->dotgrad; + } + + if (output->thermo->normflag) one[0] /= atom->natoms; + if (me == 0) + MPI_Allgather(one,numall,MPI_DOUBLE,&all[0][0],numall,MPI_DOUBLE,roots); + MPI_Bcast(&all[0][0],numall*nreplica,MPI_DOUBLE,0,world); + + rdist[0] = 0.0; + for (int i = 1; i < nreplica; i++) + rdist[i] = rdist[i-1] + all[i][1]; + double endpt = rdist[nreplica-1] = rdist[nreplica-2] + all[nreplica-2][2]; + for (int i = 1; i < nreplica; i++) + rdist[i] /= endpt; + + // look up GradV for the initial, final, and climbing replicas + // these are identical to fnorm2, but to be safe we + // take them straight from fix_neb + + double gradvnorm0, gradvnorm1, gradvnormc; + + int irep; + irep = 0; + gradvnorm0 = all[irep][3]; + irep = nreplica-1; + gradvnorm1 = all[irep][3]; + irep = fneb->rclimber; + if (irep > -1) { + gradvnormc = all[irep][3]; + ebf = all[irep][0]-all[0][0]; + ebr = all[irep][0]-all[nreplica-1][0]; + } else { + double vmax = all[0][0]; + int top = 0; + for (int m = 1; m < nreplica; m++) + if (vmax < all[m][0]) { + vmax = all[m][0]; + top = m; + } + irep = top; + gradvnormc = all[irep][3]; + ebf = all[irep][0]-all[0][0]; + ebr = all[irep][0]-all[nreplica-1][0]; + } + + if (me_universe == 0) { + FILE *uscreen = universe->uscreen; + FILE *ulogfile = universe->ulogfile; + if (uscreen) { + fprintf(uscreen,BIGINT_FORMAT " %12.8g %12.8g ", + update->ntimestep,fmaxreplica,fmaxatom); + fprintf(uscreen,"%12.8g %12.8g %12.8g ", + gradvnorm0,gradvnorm1,gradvnormc); + fprintf(uscreen,"%12.8g %12.8g %12.8g ",ebf,ebr,endpt); + for (int i = 0; i < nreplica; i++) + fprintf(uscreen,"%12.8g %12.8g ",rdist[i],all[i][0]); + if (verbose) { + for (int i = 0; i < nreplica-1; i++) + fprintf(uscreen,"%12.8g %12.8g ",all[i][2],all[i][5]); + fprintf(uscreen,"%12.8g %12.8g ",NAN,all[nreplica-1][5]); + } + fprintf(uscreen,"\n"); + } + + if (ulogfile) { + fprintf(ulogfile,BIGINT_FORMAT " %12.8g %12.8g ", + update->ntimestep,fmaxreplica,fmaxatom); + fprintf(ulogfile,"%12.8g %12.8g %12.8g ", + gradvnorm0,gradvnorm1,gradvnormc); + fprintf(ulogfile,"%12.8g %12.8g %12.8g ",ebf,ebr,endpt); + for (int i = 0; i < nreplica; i++) + fprintf(ulogfile,"%12.8g %12.8g ",rdist[i],all[i][0]); + if (verbose) { + for (int i = 0; i < nreplica-1; i++) + fprintf(ulogfile,"%12.8g %12.8g ",all[i][2],all[i][5]); + fprintf(ulogfile,"%12.8g %12.8g ",NAN,all[nreplica-1][5]); + } + fprintf(ulogfile,"\n"); + fflush(ulogfile); + } + } +} diff --git a/src/SPIN/neb_spin.h b/src/SPIN/neb_spin.h new file mode 100644 index 0000000000..5acd034e95 --- /dev/null +++ b/src/SPIN/neb_spin.h @@ -0,0 +1,137 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + 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 COMMAND_CLASS + +CommandStyle(neb/spin,NEBSpin) + +#else + +#ifndef LMP_NEB_SPIN_H +#define LMP_NEB_SPIN_H + +#include +#include "pointers.h" + +namespace LAMMPS_NS { + +class NEBSpin : protected Pointers { + public: + NEBSpin(class LAMMPS *); + ~NEBSpin(); + void command(int, char **); // process neb/spin command + void run(); // run NEBSpin + + double ebf,ebr; // forward and reverse energy barriers + + private: + int me,me_universe; // my proc ID in world and universe + int ireplica,nreplica; + bool verbose; + MPI_Comm uworld; + MPI_Comm roots; // MPI comm with 1 root proc from each world + FILE *fp; + int compressed; + double etol; // energy tolerance convergence criterion + double ttol; // torque tolerance convergence criterion + int n1steps, n2steps; // number of steps in stage 1 and 2 + int nevery; // output interval + char *infile; // name of file containing final state + + class FixNEBSpin *fneb; + int numall; // per-replica dimension of array all + double **all; // PE,plen,nlen,gradvnorm from each replica + double *rdist; // normalize reaction distance, 0 to 1 + double *freplica; // force on an image + double *fmaxatomInRepl; // force on an image + + void readfile(char *, int); + int initial_rotation(double *, double *, double); + void open(char *); + void print_status(); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: NEBSpin command before simulation box is defined + +Self-explanatory. + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +E: Cannot use NEBSpin with a single replica + +Self-explanatory. + +E: Cannot use NEBSpin unless atom map exists + +Use the atom_modify command to create an atom map. + +E: NEBSpin requires use of fix neb + +Self-explanatory. + +E: NEBSpin requires damped dynamics minimizer + +Use a different minimization style. + +E: Too many timesteps for NEBSpin + +You must use a number of timesteps that fit in a 32-bit integer +for NEBSpin. + +E: Too many timesteps + +The cumulative timesteps must fit in a 64-bit integer. + +E: Unexpected end of neb/spin file + +A read operation from the file failed. + +E: Incorrect atom format in neb/spin file + +The number of fields per line is not what expected. + +E: Invalid atom IDs in neb/spin file + +An ID in the file was not found in the system. + +E: Cannot open gzipped file + +LAMMPS was compiled without support for reading and writing gzipped +files through a pipeline to the gzip program with -DLAMMPS_GZIP. + +E: Cannot open file %s + +The specified file cannot be opened. Check that the path and name are +correct. If the file is a compressed file, also check that the gzip +executable can be found and run. + +U: Can only use NEBSpin with 1-processor replicas + +This is current restriction for NEBSpin as implemented in LAMMPS. + +U: Cannot use NEBSpin with atom_modify sort enabled + +This is current restriction for NEBSpin implemented in LAMMPS. + +*/ diff --git a/src/SPIN/pair_spin_dmi.cpp b/src/SPIN/pair_spin_dmi.cpp index d0506e972d..41430d230f 100644 --- a/src/SPIN/pair_spin_dmi.cpp +++ b/src/SPIN/pair_spin_dmi.cpp @@ -171,10 +171,11 @@ void PairSpinDmi::init_style() int ifix = 0; while (ifix < modify->nfix) { if (strcmp(modify->fix[ifix]->style,"nve/spin") == 0) break; + if (strcmp(modify->fix[ifix]->style,"neb/spin") == 0) break; ifix++; } if ((ifix == modify->nfix) && (comm->me == 0)) - error->warning(FLERR,"Using pair/spin style without nve/spin"); + error->warning(FLERR,"Using pair/spin style without nve/spin or neb/spin"); // get the lattice_flag from nve/spin @@ -430,9 +431,9 @@ void PairSpinDmi::compute_dmi(int i, int j, double eij[3], double fmi[3], double dmiy = eij[2]*v_dmx[itype][jtype] - eij[0]*v_dmz[itype][jtype]; dmiz = eij[0]*v_dmy[itype][jtype] - eij[1]*v_dmx[itype][jtype]; - fmi[0] -= (spj[1]*dmiz - spj[2]*dmiy); - fmi[1] -= (spj[2]*dmix - spj[0]*dmiz); - fmi[2] -= (spj[0]*dmiy - spj[1]*dmix); + fmi[0] -= (dmiy*spj[2] - dmiz*spj[1]); + fmi[1] -= (dmiz*spj[0] - dmix*spj[2]); + fmi[2] -= (dmix*spj[1] - dmiy*spj[0]); } /* ---------------------------------------------------------------------- diff --git a/src/SPIN/pair_spin_exchange.cpp b/src/SPIN/pair_spin_exchange.cpp index cb3242c711..0260a611cf 100644 --- a/src/SPIN/pair_spin_exchange.cpp +++ b/src/SPIN/pair_spin_exchange.cpp @@ -153,15 +153,16 @@ void PairSpinExchange::init_style() neighbor->requests[irequest]->half = 0; neighbor->requests[irequest]->full = 1; - // checking if nve/spin is a listed fix + // checking if nve/spin or neb/spin are a listed fix int ifix = 0; while (ifix < modify->nfix) { if (strcmp(modify->fix[ifix]->style,"nve/spin") == 0) break; + if (strcmp(modify->fix[ifix]->style,"neb/spin") == 0) break; ifix++; } if ((ifix == modify->nfix) && (comm->me == 0)) - error->warning(FLERR,"Using pair/spin style without nve/spin"); + error->warning(FLERR,"Using pair/spin style without nve/spin or neb/spin"); // get the lattice_flag from nve/spin diff --git a/src/SPIN/pair_spin_magelec.cpp b/src/SPIN/pair_spin_magelec.cpp index 6ff003521d..1f1488b93c 100644 --- a/src/SPIN/pair_spin_magelec.cpp +++ b/src/SPIN/pair_spin_magelec.cpp @@ -164,10 +164,11 @@ void PairSpinMagelec::init_style() int ifix = 0; while (ifix < modify->nfix) { if (strcmp(modify->fix[ifix]->style,"nve/spin") == 0) break; + if (strcmp(modify->fix[ifix]->style,"neb/spin") == 0) break; ifix++; } if ((ifix == modify->nfix) && (comm->me == 0)) - error->warning(FLERR,"Using pair/spin style without nve/spin"); + error->warning(FLERR,"Using pair/spin style without nve/spin or neb/spin"); // get the lattice_flag from nve/spin diff --git a/src/SPIN/pair_spin_neel.cpp b/src/SPIN/pair_spin_neel.cpp index a39d6f3461..03041da17f 100644 --- a/src/SPIN/pair_spin_neel.cpp +++ b/src/SPIN/pair_spin_neel.cpp @@ -171,10 +171,11 @@ void PairSpinNeel::init_style() int ifix = 0; while (ifix < modify->nfix) { if (strcmp(modify->fix[ifix]->style,"nve/spin") == 0) break; + if (strcmp(modify->fix[ifix]->style,"neb/spin") == 0) break; ifix++; } if ((ifix == modify->nfix) && (comm->me == 0)) - error->warning(FLERR,"Using pair/spin style without nve/spin"); + error->warning(FLERR,"Using pair/spin style without nve/spin or neb/spin"); // get the lattice_flag from nve/spin diff --git a/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp b/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp index f54197aea7..dfea97f0bf 100644 --- a/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp +++ b/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp @@ -62,9 +62,9 @@ PairOxdna2Coaxstk::~PairOxdna2Coaxstk() memory->destroy(cut_cxst_hi); memory->destroy(cut_cxst_lc); memory->destroy(cut_cxst_hc); + memory->destroy(cutsq_cxst_hc); memory->destroy(b_cxst_lo); memory->destroy(b_cxst_hi); - memory->destroy(cutsq_cxst_hc); memory->destroy(a_cxst1); memory->destroy(theta_cxst1_0); diff --git a/src/USER-CGDNA/pair_oxdna2_dh.cpp b/src/USER-CGDNA/pair_oxdna2_dh.cpp index 10e7121427..b4afad12db 100644 --- a/src/USER-CGDNA/pair_oxdna2_dh.cpp +++ b/src/USER-CGDNA/pair_oxdna2_dh.cpp @@ -225,8 +225,8 @@ void PairOxdna2Dh::compute(int eflag, int vflag) // increment energy and virial - if (evflag) ev_tally(a,b,nlocal,newton_pair, - evdwl,0.0,fpair,delr[0],delr[1],delr[2]); + if (evflag) ev_tally(a,b,nlocal,newton_pair, + evdwl,0.0,fpair,delr[0],delr[1],delr[2]); } } diff --git a/src/USER-CGDNA/pair_oxdna_coaxstk.cpp b/src/USER-CGDNA/pair_oxdna_coaxstk.cpp index 6d3061620d..6f3fa4fa4e 100644 --- a/src/USER-CGDNA/pair_oxdna_coaxstk.cpp +++ b/src/USER-CGDNA/pair_oxdna_coaxstk.cpp @@ -62,9 +62,9 @@ PairOxdnaCoaxstk::~PairOxdnaCoaxstk() memory->destroy(cut_cxst_hi); memory->destroy(cut_cxst_lc); memory->destroy(cut_cxst_hc); + memory->destroy(cutsq_cxst_hc); memory->destroy(b_cxst_lo); memory->destroy(b_cxst_hi); - memory->destroy(cutsq_cxst_hc); memory->destroy(a_cxst1); memory->destroy(theta_cxst1_0); diff --git a/src/USER-CGDNA/pair_oxdna_hbond.cpp b/src/USER-CGDNA/pair_oxdna_hbond.cpp index d2aa236a05..8cd28f10c8 100644 --- a/src/USER-CGDNA/pair_oxdna_hbond.cpp +++ b/src/USER-CGDNA/pair_oxdna_hbond.cpp @@ -40,7 +40,7 @@ using namespace MFOxdna; // sequence-specific base-pairing strength // A:0 C:1 G:2 T:3, 5'- (i,j) -3' -static const double alpha[4][4] = +static const double alpha_hb[4][4] = {{1.00000,1.00000,1.00000,0.82915}, {1.00000,1.00000,1.15413,1.00000}, {1.00000,1.15413,1.00000,1.00000}, @@ -71,10 +71,10 @@ PairOxdnaHbond::~PairOxdnaHbond() memory->destroy(cut_hb_hi); memory->destroy(cut_hb_lc); memory->destroy(cut_hb_hc); + memory->destroy(cutsq_hb_hc); memory->destroy(b_hb_lo); memory->destroy(b_hb_hi); memory->destroy(shift_hb); - memory->destroy(cutsq_hb_hc); memory->destroy(a_hb1); memory->destroy(theta_hb1_0); @@ -732,7 +732,7 @@ void PairOxdnaHbond::coeff(int narg, char **arg) for (int j = MAX(jlo,i); j <= jhi; j++) { epsilon_hb[i][j] = epsilon_hb_one; - if (seqdepflag) epsilon_hb[i][j] *= alpha[i-1][j-1]; + if (seqdepflag) epsilon_hb[i][j] *= alpha_hb[i-1][j-1]; a_hb[i][j] = a_hb_one; cut_hb_0[i][j] = cut_hb_0_one; cut_hb_c[i][j] = cut_hb_c_one; @@ -743,7 +743,7 @@ void PairOxdnaHbond::coeff(int narg, char **arg) b_hb_lo[i][j] = b_hb_lo_one; b_hb_hi[i][j] = b_hb_hi_one; shift_hb[i][j] = shift_hb_one; - if (seqdepflag) shift_hb[i][j] *= alpha[i-1][j-1]; + if (seqdepflag) shift_hb[i][j] *= alpha_hb[i-1][j-1]; a_hb1[i][j] = a_hb1_one; theta_hb1_0[i][j] = theta_hb1_0_one; @@ -831,7 +831,7 @@ double PairOxdnaHbond::init_one(int i, int j) } if (seqdepflag) { - epsilon_hb[j][i] = epsilon_hb[i][j] / alpha[i-1][j-1] * alpha[j-1][i-1]; + epsilon_hb[j][i] = epsilon_hb[i][j] / alpha_hb[i-1][j-1] * alpha_hb[j-1][i-1]; } else { epsilon_hb[j][i] = epsilon_hb[i][j]; @@ -846,7 +846,7 @@ double PairOxdnaHbond::init_one(int i, int j) cut_hb_lc[j][i] = cut_hb_lc[i][j]; cut_hb_hc[j][i] = cut_hb_hc[i][j]; if (seqdepflag) { - shift_hb[j][i] = shift_hb[i][j] / alpha[i-1][j-1] * alpha[j-1][i-1]; + shift_hb[j][i] = shift_hb[i][j] / alpha_hb[i-1][j-1] * alpha_hb[j-1][i-1]; } else { shift_hb[j][i] = shift_hb[i][j]; diff --git a/src/USER-CGDNA/pair_oxdna_stk.cpp b/src/USER-CGDNA/pair_oxdna_stk.cpp index 4cbc0317dd..93c65979ac 100644 --- a/src/USER-CGDNA/pair_oxdna_stk.cpp +++ b/src/USER-CGDNA/pair_oxdna_stk.cpp @@ -40,7 +40,7 @@ using namespace MFOxdna; // sequence-specific stacking strength // A:0 C:1 G:2 T:3, 5'- (i,j) -3' -static const double alpha[4][4] = +static const double eta_st[4][4] = {{1.11960,1.00852,0.96950,0.99632}, {1.01889,0.97804,1.02681,0.96950}, {0.98169,1.05913,0.97804,1.00852}, @@ -156,7 +156,7 @@ void PairOxdnaStk::compute(int eflag, int vflag) evdwl = 0.0; ev_init(eflag,vflag); - // loop over stacking interaction neighours using bond topology + // loop over stacking interaction neighbors using bond topology for (in = 0; in < nbondlist; in++) { @@ -774,7 +774,7 @@ void PairOxdnaStk::coeff(int narg, char **arg) for (int j = MAX(jlo,i); j <= jhi; j++) { epsilon_st[i][j] = epsilon_st_one; - if (seqdepflag) epsilon_st[i][j] *= alpha[i-1][j-1]; + if (seqdepflag) epsilon_st[i][j] *= eta_st[i-1][j-1]; a_st[i][j] = a_st_one; cut_st_0[i][j] = cut_st_0_one; cut_st_c[i][j] = cut_st_c_one; @@ -785,7 +785,7 @@ void PairOxdnaStk::coeff(int narg, char **arg) b_st_lo[i][j] = b_st_lo_one; b_st_hi[i][j] = b_st_hi_one; shift_st[i][j] = shift_st_one; - if (seqdepflag) shift_st[i][j] *= alpha[i-1][j-1]; + if (seqdepflag) shift_st[i][j] *= eta_st[i-1][j-1]; a_st4[i][j] = a_st4_one; theta_st4_0[i][j] = theta_st4_0_one; @@ -865,7 +865,7 @@ double PairOxdnaStk::init_one(int i, int j) } if (seqdepflag) { - epsilon_st[j][i] = epsilon_st[i][j] / alpha[i-1][j-1] * alpha[j-1][i-1]; + epsilon_st[j][i] = epsilon_st[i][j] / eta_st[i-1][j-1] * eta_st[j-1][i-1]; } else { epsilon_st[j][i] = epsilon_st[i][j]; @@ -880,7 +880,7 @@ double PairOxdnaStk::init_one(int i, int j) cut_st_lc[j][i] = cut_st_lc[i][j]; cut_st_hc[j][i] = cut_st_hc[i][j]; if (seqdepflag) { - shift_st[j][i] = shift_st[i][j] / alpha[i-1][j-1] * alpha[j-1][i-1]; + shift_st[j][i] = shift_st[i][j] / eta_st[i-1][j-1] * eta_st[j-1][i-1]; } else { shift_st[j][i] = shift_st[i][j]; diff --git a/src/USER-CGDNA/pair_oxdna_xstk.cpp b/src/USER-CGDNA/pair_oxdna_xstk.cpp index 071886556c..1365d0d2b2 100644 --- a/src/USER-CGDNA/pair_oxdna_xstk.cpp +++ b/src/USER-CGDNA/pair_oxdna_xstk.cpp @@ -62,9 +62,9 @@ PairOxdnaXstk::~PairOxdnaXstk() memory->destroy(cut_xst_hi); memory->destroy(cut_xst_lc); memory->destroy(cut_xst_hc); + memory->destroy(cutsq_xst_hc); memory->destroy(b_xst_lo); memory->destroy(b_xst_hi); - memory->destroy(cutsq_xst_hc); memory->destroy(a_xst1); memory->destroy(theta_xst1_0); diff --git a/src/USER-COLVARS/colvarproxy_lammps.cpp b/src/USER-COLVARS/colvarproxy_lammps.cpp index ff74602b41..651999f79c 100644 --- a/src/USER-COLVARS/colvarproxy_lammps.cpp +++ b/src/USER-COLVARS/colvarproxy_lammps.cpp @@ -153,18 +153,29 @@ void colvarproxy_lammps::init(const char *conf_file) if (_lmp->update->ntimestep != 0) { cvm::log("Setting initial step number from LAMMPS: "+ cvm::to_str(_lmp->update->ntimestep)+"\n"); - colvars->it = colvars->it_restart = _lmp->update->ntimestep; + colvars->it = colvars->it_restart = + static_cast(_lmp->update->ntimestep); } if (cvm::debug()) { - log("atoms_ids = "+cvm::to_str(atoms_ids)+"\n"); - log("atoms_ncopies = "+cvm::to_str(atoms_ncopies)+"\n"); - log("atoms_positions = "+cvm::to_str(atoms_positions)+"\n"); - log(cvm::line_marker); - log("Info: done initializing the colvars proxy object.\n"); + cvm::log("atoms_ids = "+cvm::to_str(atoms_ids)+"\n"); + cvm::log("atoms_ncopies = "+cvm::to_str(atoms_ncopies)+"\n"); + cvm::log("atoms_positions = "+cvm::to_str(atoms_positions)+"\n"); + cvm::log(cvm::line_marker); + cvm::log("Info: done initializing the colvars proxy object.\n"); } } +void colvarproxy_lammps::add_config_file(const char *conf_file) +{ + colvars->read_config_file(conf_file); +} + +void colvarproxy_lammps::add_config_string(const std::string &conf) +{ + colvars->read_config_string(conf); +} + colvarproxy_lammps::~colvarproxy_lammps() { delete _random; @@ -185,7 +196,7 @@ int colvarproxy_lammps::setup() double colvarproxy_lammps::compute() { if (cvm::debug()) { - log(std::string(cvm::line_marker)+ + cvm::log(std::string(cvm::line_marker)+ "colvarproxy_lammps step no. "+ cvm::to_str(_lmp->update->ntimestep)+" [first - last = "+ cvm::to_str(_lmp->update->beginstep)+" - "+ @@ -238,20 +249,20 @@ double colvarproxy_lammps::compute() bias_energy = 0.0; if (cvm::debug()) { - log("atoms_ids = "+cvm::to_str(atoms_ids)+"\n"); - log("atoms_ncopies = "+cvm::to_str(atoms_ncopies)+"\n"); - log("atoms_positions = "+cvm::to_str(atoms_positions)+"\n"); - log("atoms_new_colvar_forces = "+cvm::to_str(atoms_new_colvar_forces)+"\n"); + cvm::log("atoms_ids = "+cvm::to_str(atoms_ids)+"\n"); + cvm::log("atoms_ncopies = "+cvm::to_str(atoms_ncopies)+"\n"); + cvm::log("atoms_positions = "+cvm::to_str(atoms_positions)+"\n"); + cvm::log("atoms_new_colvar_forces = "+cvm::to_str(atoms_new_colvar_forces)+"\n"); } // call the collective variable module colvars->calc(); if (cvm::debug()) { - log("atoms_ids = "+cvm::to_str(atoms_ids)+"\n"); - log("atoms_ncopies = "+cvm::to_str(atoms_ncopies)+"\n"); - log("atoms_positions = "+cvm::to_str(atoms_positions)+"\n"); - log("atoms_new_colvar_forces = "+cvm::to_str(atoms_new_colvar_forces)+"\n"); + cvm::log("atoms_ids = "+cvm::to_str(atoms_ids)+"\n"); + cvm::log("atoms_ncopies = "+cvm::to_str(atoms_ncopies)+"\n"); + cvm::log("atoms_positions = "+cvm::to_str(atoms_positions)+"\n"); + cvm::log("atoms_new_colvar_forces = "+cvm::to_str(atoms_new_colvar_forces)+"\n"); } return bias_energy; diff --git a/src/USER-COLVARS/colvarproxy_lammps.h b/src/USER-COLVARS/colvarproxy_lammps.h index cdd86cbd16..c3d9dbb35f 100644 --- a/src/USER-COLVARS/colvarproxy_lammps.h +++ b/src/USER-COLVARS/colvarproxy_lammps.h @@ -103,6 +103,11 @@ class colvarproxy_lammps : public colvarproxy { // Write files expected from Colvars (called by post_run()) void write_output_files(); + // read additional config from file + void add_config_file(char const *config_filename); + + // read additional config from string + void add_config_string(const std::string &config); // implementation of pure methods from base class public: diff --git a/src/USER-COLVARS/colvarproxy_lammps_version.h b/src/USER-COLVARS/colvarproxy_lammps_version.h index edd6778c64..0a4f9fdf4f 100644 --- a/src/USER-COLVARS/colvarproxy_lammps_version.h +++ b/src/USER-COLVARS/colvarproxy_lammps_version.h @@ -1,5 +1,5 @@ #ifndef COLVARPROXY_VERSION -#define COLVARPROXY_VERSION "2018-08-29" +#define COLVARPROXY_VERSION "2019-04-09" // This file is part of the Collective Variables module (Colvars). // The original version of Colvars and its updates are located at: // https://github.com/colvars/colvars diff --git a/src/USER-COLVARS/fix_colvars.cpp b/src/USER-COLVARS/fix_colvars.cpp index 545ceb7b0e..ff0e8fb334 100644 --- a/src/USER-COLVARS/fix_colvars.cpp +++ b/src/USER-COLVARS/fix_colvars.cpp @@ -480,6 +480,31 @@ void FixColvars::one_time_init() /* ---------------------------------------------------------------------- */ +int FixColvars::modify_param(int narg, char **arg) +{ + if (strcmp(arg[0],"configfile") == 0) { + if (narg < 2) error->all(FLERR,"Illegal fix_modify command"); + if (me == 0) { + if (! proxy) + error->one(FLERR,"Cannot use fix_modify before initialization"); + proxy->add_config_file(arg[1]); + } + return 2; + } else if (strcmp(arg[0],"config") == 0) { + if (narg < 2) error->all(FLERR,"Illegal fix_modify command"); + if (me == 0) { + if (! proxy) + error->one(FLERR,"Cannot use fix_modify before initialization"); + std::string conf(arg[1]); + proxy->add_config_string(conf); + } + return 2; + } + return 0; +} + +/* ---------------------------------------------------------------------- */ + void FixColvars::setup(int vflag) { const tagint * const tag = atom->tag; diff --git a/src/USER-COLVARS/fix_colvars.h b/src/USER-COLVARS/fix_colvars.h index 3029ba9db5..a0c197fca4 100644 --- a/src/USER-COLVARS/fix_colvars.h +++ b/src/USER-COLVARS/fix_colvars.h @@ -50,6 +50,7 @@ class FixColvars : public Fix { virtual int setmask(); virtual void init(); virtual void setup(int); + virtual int modify_param(int, char **); virtual void min_setup(int vflag) {setup(vflag);}; virtual void min_post_force(int); virtual void post_force(int); diff --git a/src/USER-INTEL/fix_intel.cpp b/src/USER-INTEL/fix_intel.cpp index 67bf33e751..bdc47827ab 100644 --- a/src/USER-INTEL/fix_intel.cpp +++ b/src/USER-INTEL/fix_intel.cpp @@ -34,10 +34,6 @@ #include #include -#ifdef LAMMPS_BIGBIG -#error "The USER-INTEL package is not compatible with -DLAMMPS_BIGBIG" -#endif - #ifdef _LMP_INTEL_OFFLOAD #ifndef INTEL_OFFLOAD_NOAFFINITY #include @@ -378,13 +374,13 @@ void FixIntel::setup(int vflag) if (neighbor->style != Neighbor::BIN) error->all(FLERR, "Currently, neighbor style BIN must be used with Intel package."); - if (neighbor->exclude_setting() != 0) - error->all(FLERR, - "Currently, cannot use neigh_modify exclude with Intel package."); - if (vflag_atom) + if (vflag > 3) error->all(FLERR, "Cannot currently get per-atom virials with Intel package."); #ifdef _LMP_INTEL_OFFLOAD + if (neighbor->exclude_setting() != 0) + error->all(FLERR, + "Currently, cannot use neigh_modify exclude with Intel package offload."); post_force(vflag); #endif } diff --git a/src/USER-INTEL/fix_intel.h b/src/USER-INTEL/fix_intel.h index 3810b57355..f23e305ca7 100644 --- a/src/USER-INTEL/fix_intel.h +++ b/src/USER-INTEL/fix_intel.h @@ -495,9 +495,9 @@ E: Currently, neighbor style BIN must be used with Intel package. This is the only neighbor style that has been implemented for the Intel package. -E: Currently, cannot use neigh_modify exclude with Intel package. +E: Currently, cannot use neigh_modify exclude with Intel package offload. -This is a current restriction of the Intel package. +This is a current restriction of the Intel package when built for offload. W: Unknown Intel Compiler Version diff --git a/src/USER-INTEL/intel_buffers.cpp b/src/USER-INTEL/intel_buffers.cpp index c0995b6a9c..ec3c233542 100644 --- a/src/USER-INTEL/intel_buffers.cpp +++ b/src/USER-INTEL/intel_buffers.cpp @@ -186,8 +186,8 @@ void IntelBuffers::free_nmax() { #ifdef _LMP_INTEL_OFFLOAD if (_off_map_nmax > 0) { - const int * tag = _off_map_tag; - const int * special = _off_map_special; + const tagint * tag = _off_map_tag; + const tagint * special = _off_map_special; const int * nspecial = _off_map_nspecial; #pragma offload_transfer target(mic:_cop) \ nocopy(tag:alloc_if(0) free_if(1)) \ @@ -209,7 +209,8 @@ void IntelBuffers::_grow_nmax(const int offload_end) _host_nmax = size; if (!offload_end) return; - int *special, *nspecial; + tagint *special; + int *nspecial; int tag_length, special_length, nspecial_length; if (lmp->atom->molecular) { special = lmp->atom->special[0]; @@ -226,7 +227,7 @@ void IntelBuffers::_grow_nmax(const int offload_end) tag_length = size; else tag_length = 1; - int *tag = lmp->atom->tag; + tagint *tag = lmp->atom->tag; #pragma offload_transfer target(mic:_cop) \ nocopy(tag:length(tag_length) alloc_if(1) free_if(0)) \ nocopy(special:length(special_length) alloc_if(1) free_if(0)) \ @@ -523,7 +524,7 @@ void IntelBuffers::free_ncache() flt_t *ncachez = _ncachez; int *ncachej = _ncachej; int *ncachejtype = _ncachejtype; - int *ncachetag = _ncachetag; + tagint *ncachetag = _ncachetag; #ifdef _LMP_INTEL_OFFLOAD if (_off_ncache) { @@ -603,7 +604,7 @@ void IntelBuffers::grow_ncache(const int off_flag, tsize = 16; lmp->memory->create(_ncachetag, tsize, "_ncachetag"); } - int *ncachetag = _ncachetag; + tagint *ncachetag = _ncachetag; #pragma offload_transfer target(mic:_cop) \ nocopy(ncachetag:length(tsize) alloc_if(1) free_if(0)) _off_ncache = 1; diff --git a/src/USER-INTEL/intel_buffers.h b/src/USER-INTEL/intel_buffers.h index 276b87ec5f..f3c07da7c2 100644 --- a/src/USER-INTEL/intel_buffers.h +++ b/src/USER-INTEL/intel_buffers.h @@ -132,7 +132,7 @@ class IntelBuffers { inline flt_t * get_ncachez() { return _ncachez; } inline int * get_ncachej() { return _ncachej; } inline int * get_ncachejtype() { return _ncachejtype; } - inline int * get_ncachetag() { return _ncachetag; } + inline tagint * get_ncachetag() { return _ncachetag; } inline int get_max_nbors() { int mn = lmp->neighbor->oneatom * sizeof(int) / @@ -336,7 +336,8 @@ class IntelBuffers { int _ncache_stride, _ncache_alloc; flt_t *_ncachex, *_ncachey, *_ncachez; - int *_ncachej, *_ncachejtype, *_ncachetag; + int *_ncachej, *_ncachejtype; + tagint *_ncachetag; int _need_tag, _host_nmax; @@ -352,8 +353,8 @@ class IntelBuffers { quat_t *_host_quat; vec3_acc_t *_off_f; int _off_map_nmax, _cop, _off_ccache, _off_ncache; - int *_off_map_ilist; - int *_off_map_special, *_off_map_nspecial, *_off_map_tag; + int *_off_map_ilist, *_off_map_nspecial; + tagint *_off_map_tag, *_off_map_special; int **_off_map_firstneigh, *_off_map_numneigh; bool _off_list_alloc; #endif diff --git a/src/USER-INTEL/npair_full_bin_ghost_intel.cpp b/src/USER-INTEL/npair_full_bin_ghost_intel.cpp index db4b0c50a4..e1e09fd3da 100644 --- a/src/USER-INTEL/npair_full_bin_ghost_intel.cpp +++ b/src/USER-INTEL/npair_full_bin_ghost_intel.cpp @@ -194,7 +194,7 @@ void NPairFullBinGhostIntel::fbi(const int offload, NeighList * list, flt_t * _noalias const ncachez = buffers->get_ncachez(); int * _noalias const ncachej = buffers->get_ncachej(); int * _noalias const ncachejtype = buffers->get_ncachejtype(); - int * _noalias const ncachetag = buffers->get_ncachetag(); + tagint * _noalias const ncachetag = buffers->get_ncachetag(); const int ncache_stride = buffers->ncache_stride(); const int mbinx = this->mbinx; @@ -304,7 +304,7 @@ void NPairFullBinGhostIntel::fbi(const int offload, NeighList * list, flt_t * _noalias const tz = ncachez + toffs; int * _noalias const tj = ncachej + toffs; int * _noalias const tjtype = ncachejtype + toffs; - int * _noalias const ttag = ncachetag + toffs; + tagint * _noalias const ttag = ncachetag + toffs; // loop over all atoms in other bins in stencil, store every pair int ncount, oldbin = -9999999; @@ -392,7 +392,7 @@ void NPairFullBinGhostIntel::fbi(const int offload, NeighList * list, const flt_t dely = ytmp - ty[u]; const flt_t delz = ztmp - tz[u]; const int jtype = tjtype[u]; - const int jtag = ttag[u]; + const tagint jtag = ttag[u]; const flt_t rsq = delx * delx + dely * dely + delz * delz; if (rsq > cutsq[ioffset + jtype]) addme = 0; diff --git a/src/USER-INTEL/npair_intel.cpp b/src/USER-INTEL/npair_intel.cpp index e20c437cb7..ad9ec6e7d3 100644 --- a/src/USER-INTEL/npair_intel.cpp +++ b/src/USER-INTEL/npair_intel.cpp @@ -191,7 +191,7 @@ void NPairIntel::bin_newton(const int offload, NeighList *list, flt_t * _noalias const ncachez = buffers->get_ncachez(); int * _noalias const ncachej = buffers->get_ncachej(); int * _noalias const ncachejtype = buffers->get_ncachejtype(); - int * _noalias const ncachetag = buffers->get_ncachetag(); + tagint * _noalias const ncachetag = buffers->get_ncachetag(); const int ncache_stride = buffers->ncache_stride(); int sb = 1; @@ -308,7 +308,7 @@ void NPairIntel::bin_newton(const int offload, NeighList *list, flt_t * _noalias const tz = ncachez + toffs; int * _noalias const tj = ncachej + toffs; int * _noalias const tjtype = ncachejtype + toffs; - int * _noalias const ttag = ncachetag + toffs; + tagint * _noalias const ttag = ncachetag + toffs; flt_t * _noalias itx; flt_t * _noalias ity; @@ -501,7 +501,7 @@ void NPairIntel::bin_newton(const int offload, NeighList *list, } if (THREE) { - const int jtag = ttag[u]; + const tagint jtag = ttag[u]; int flist = 0; if (itag > jtag) { if (((itag+jtag) & 1) == 0) flist = 1; diff --git a/src/USER-INTEL/pair_airebo_intel.h b/src/USER-INTEL/pair_airebo_intel.h index 95e054fc0f..675fda8fe3 100644 --- a/src/USER-INTEL/pair_airebo_intel.h +++ b/src/USER-INTEL/pair_airebo_intel.h @@ -27,7 +27,6 @@ PairStyle(airebo/intel,PairAIREBOIntel) #include "pair.h" #include "fix_intel.h" #include "pair_airebo.h" -//#include "airebo_common.h" namespace LAMMPS_NS { diff --git a/src/USER-INTEL/pair_airebo_morse_intel.cpp b/src/USER-INTEL/pair_airebo_morse_intel.cpp index 21de29e1a7..f68e299fa0 100644 --- a/src/USER-INTEL/pair_airebo_morse_intel.cpp +++ b/src/USER-INTEL/pair_airebo_morse_intel.cpp @@ -23,7 +23,9 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ PairAIREBOMorseIntel::PairAIREBOMorseIntel(LAMMPS *lmp) - : PairAIREBOIntel(lmp) {} + : PairAIREBOIntel(lmp) { + variant = AIREBO_M; +} /* ---------------------------------------------------------------------- global settings diff --git a/src/USER-INTEL/pair_rebo_intel.cpp b/src/USER-INTEL/pair_rebo_intel.cpp index b7cc3d1c71..d067005cfd 100644 --- a/src/USER-INTEL/pair_rebo_intel.cpp +++ b/src/USER-INTEL/pair_rebo_intel.cpp @@ -22,7 +22,9 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -PairREBOIntel::PairREBOIntel(LAMMPS *lmp) : PairAIREBOIntel(lmp) {} +PairREBOIntel::PairREBOIntel(LAMMPS *lmp) : PairAIREBOIntel(lmp) { + variant = REBO_2; +} /* ---------------------------------------------------------------------- global settings @@ -34,9 +36,4 @@ void PairREBOIntel::settings(int narg, char ** /* arg */) cutlj = 0.0; ljflag = torflag = 0; - // - // this one parameter for C-C interactions is different in REBO vs AIREBO - // see Favata, Micheletti, Ryu, Pugno, Comp Phys Comm (2016) - - PCCf_2_0 = 0.0; } diff --git a/src/USER-MISC/README b/src/USER-MISC/README index 9adc817986..219e19673d 100644 --- a/src/USER-MISC/README +++ b/src/USER-MISC/README @@ -70,6 +70,8 @@ pair_style buck/mdf, Paolo Raiteri, p.raiteri at curtin.edu.au, 2 Dec 15 pair_style coul/diel, Axel Kohlmeyer, akohlmey at gmail.com, 1 Dec 11 pair_style coul/shield, Wengen Ouyang (Tel Aviv University), w.g.ouyang at gmail dot com, 30 Mar 18 pair_style dipole/sf, Mario Orsi, orsimario at gmail.com, 8 Aug 11 +pair_style e3b, Steven Strong (U Chicago), stevene.strong at gmail dot com, 16 Apr 19 +pair_style drip, Mingjian Wen, University of Minnesota, wenxx151 at umn.edu, 17 Apr 19 pair_style edip, Luca Ferraro, luca.ferraro at caspur.it, 15 Sep 11 pair_style extep, Jaap Kroes (Radboud U), jaapkroes at gmail dot com, 28 Nov 17 pair_style gauss/cut, Axel Kohlmeyer, akohlmey at gmail.com, 1 Dec 11 diff --git a/src/USER-MISC/pair_buck_mdf.cpp b/src/USER-MISC/pair_buck_mdf.cpp index b5e81417ee..afd15d7fdb 100644 --- a/src/USER-MISC/pair_buck_mdf.cpp +++ b/src/USER-MISC/pair_buck_mdf.cpp @@ -52,7 +52,6 @@ PairBuckMDF::~PairBuckMDF() memory->destroy(rhoinv); memory->destroy(buck1); memory->destroy(buck2); - memory->destroy(offset); } } @@ -177,7 +176,6 @@ void PairBuckMDF::allocate() memory->create(rhoinv,n+1,n+1,"pair:rhoinv"); memory->create(buck1,n+1,n+1,"pair:buck1"); memory->create(buck2,n+1,n+1,"pair:buck2"); - memory->create(offset,n+1,n+1,"pair:offset"); } /* ---------------------------------------------------------------------- @@ -207,7 +205,8 @@ void PairBuckMDF::settings(int narg, char **arg) void PairBuckMDF::coeff(int narg, char **arg) { - if (narg != 5 && narg != 7) error->all(FLERR,"Incorrect args for pair coefficients"); + if (narg != 5 && narg != 7) + error->all(FLERR,"Incorrect args for pair coefficients"); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -258,11 +257,6 @@ double PairBuckMDF::init_one(int i, int j) buck1[i][j] = a[i][j]/rho[i][j]; buck2[i][j] = 6.0*c[i][j]; - if (offset_flag && (cut[i][j] > 0.0)) { - double rexp = exp(-cut[i][j]/rho[i][j]); - offset[i][j] = a[i][j]*rexp - c[i][j]/pow(cut[i][j],6.0); - } else offset[i][j] = 0.0; - cut_inner[j][i] = cut_inner[i][j]; cut_inner_sq[i][j] = cut_inner[i][j]*cut_inner[i][j]; cut_inner_sq[j][i] = cut_inner_sq[i][j]; @@ -272,36 +266,6 @@ double PairBuckMDF::init_one(int i, int j) rhoinv[j][i] = rhoinv[i][j]; buck1[j][i] = buck1[i][j]; buck2[j][i] = buck2[i][j]; - offset[j][i] = offset[i][j]; - - // compute I,J contribution to long-range tail correction - // count total # of atoms of type I and J via Allreduce - - if (tail_flag) { - int *type = atom->type; - int nlocal = atom->nlocal; - - double count[2],all[2]; - count[0] = count[1] = 0.0; - for (int k = 0; k < nlocal; k++) { - if (type[k] == i) count[0] += 1.0; - if (type[k] == j) count[1] += 1.0; - } - MPI_Allreduce(count,all,2,MPI_DOUBLE,MPI_SUM,world); - - double rho1 = rho[i][j]; - double rho2 = rho1*rho1; - double rho3 = rho2*rho1; - double rc = cut[i][j]; - double rc2 = rc*rc; - double rc3 = rc2*rc; - etail_ij = 2.0*MY_PI*all[0]*all[1]* - (a[i][j]*exp(-rc/rho1)*rho1*(rc2 + 2.0*rho1*rc + 2.0*rho2) - - c[i][j]/(3.0*rc3)); - ptail_ij = (-1/3.0)*2.0*MY_PI*all[0]*all[1]* - (-a[i][j]*exp(-rc/rho1)* - (rc3 + 3.0*rho1*rc2 + 6.0*rho2*rc + 6.0*rho3) + 2.0*c[i][j]/rc3); - } return cut[i][j]; } diff --git a/src/USER-MISC/pair_drip.cpp b/src/USER-MISC/pair_drip.cpp new file mode 100644 index 0000000000..118c033b5c --- /dev/null +++ b/src/USER-MISC/pair_drip.cpp @@ -0,0 +1,1107 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + 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 author: Mingjian Wen (University of Minnesota) + e-mail: wenxx151@umn.edu, wenxx151@gmail.com + + This implements the DRIP model as described in + M. Wen, S. Carr, S. Fang, E. Kaxiras, and E. B. Tadmor, + Phys. Rev. B, 98, 235404 (2018). +------------------------------------------------------------------------- */ + +#include +#include +#include +#include +#include +#include "pair_drip.h" +#include "atom.h" +#include "comm.h" +#include "force.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "my_page.h" +#include "memory.h" +#include "error.h" + +using namespace LAMMPS_NS; + +#define MAXLINE 1024 +#define DELTA 4 +#define HALF 0.5 + +/* ---------------------------------------------------------------------- */ + +PairDRIP::PairDRIP(LAMMPS *lmp) : Pair(lmp) +{ + single_enable = 0; + restartinfo = 0; + manybody_flag = 1; + + params = NULL; + nearest3neigh = NULL; + elements = NULL; + elem2param = NULL; + map = NULL; + nelements = 0; + cutmax = 0.0; +} + +/* ---------------------------------------------------------------------- */ + +PairDRIP::~PairDRIP() +{ + if (allocated) { + memory->destroy(setflag); + memory->destroy(cutsq); + delete [] map; + } + + if (elements != NULL) { + for (int i = 0; i < nelements; i++) delete [] elements[i]; + delete [] elements; + elements = NULL; + } + memory->destroy(params); + memory->destroy(elem2param); + memory->destroy(nearest3neigh); +} + +/* ---------------------------------------------------------------------- + init specific to this pair style +------------------------------------------------------------------------- */ + +void PairDRIP::init_style() +{ + if (force->newton_pair == 0) + error->all(FLERR,"Pair style drip requires newton pair on"); + if (!atom->molecule_flag) + error->all(FLERR,"Pair style drip requires atom attribute molecule"); + + // need a full neighbor list, including neighbors of ghosts + int irequest = neighbor->request(this,instance_me); + neighbor->requests[irequest]->half = 0; + neighbor->requests[irequest]->full = 1; + neighbor->requests[irequest]->ghost = 1; +} + +/* ---------------------------------------------------------------------- + allocate all arrays +------------------------------------------------------------------------- */ + +void PairDRIP::allocate() +{ + allocated = 1; + int n = atom->ntypes; + + memory->create(setflag,n+1,n+1,"pair:setflag"); + memory->create(cutsq,n+1,n+1,"pair:cutsq"); + map = new int[n+1]; +} + +/* ---------------------------------------------------------------------- + global settings +------------------------------------------------------------------------- */ + +void PairDRIP::settings(int narg, char ** /* arg */) +{ + if (narg != 0) error->all(FLERR,"Illegal pair_style command"); + if (strcmp(force->pair_style,"hybrid/overlay")!=0) + error->all(FLERR,"ERROR: requires hybrid/overlay pair_style"); +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more type pairs +------------------------------------------------------------------------- */ + +void PairDRIP::coeff(int narg, char **arg) +{ + int i,j,n; + + if (!allocated) allocate(); + + if (narg != 3 + atom->ntypes) + error->all(FLERR,"Incorrect args for pair coefficients"); + + // insure I,J args are * * + if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0) + error->all(FLERR,"Incorrect args for pair coefficients"); + + // read args that map atom types to elements in potential file + // map[i] = which element the Ith atom type is, -1 if NULL + // nelements = # of unique elements + // elements = list of element names + + if (elements) { + for (i = 0; i < nelements; i++) delete [] elements[i]; + delete [] elements; + } + elements = new char*[atom->ntypes]; + for (i = 0; i < atom->ntypes; i++) elements[i] = NULL; + + nelements = 0; + for (i = 3; i < narg; i++) { + if (strcmp(arg[i],"NULL") == 0) { + map[i-2] = -1; + continue; + } + for (j = 0; j < nelements; j++) + if (strcmp(arg[i],elements[j]) == 0) break; + map[i-2] = j; + if (j == nelements) { + n = strlen(arg[i]) + 1; + elements[j] = new char[n]; + strcpy(elements[j],arg[i]); + nelements++; + } + } + + read_file(arg[2]); + + + // clear setflag since coeff() called once with I,J = * * + n = atom->ntypes; + for (i = 1; i <= n; i++) + for (j = i; j <= n; j++) + setflag[i][j] = 0; + + int count = 0; + for (i = 1; i <= n; i++) + for (j = i; j <= n; j++) + if (map[i] >= 0 && map[j] >= 0) { + setflag[i][j] = 1; + count++; + } + + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); +} + + +/* ---------------------------------------------------------------------- + init for one type pair i,j and corresponding j,i +------------------------------------------------------------------------- */ + +double PairDRIP::init_one(int i, int j) +{ + if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set"); + + int itype = map[i]; + int jtype = map[j]; + int iparam_ij = elem2param[itype][jtype]; + Param& p = params[iparam_ij]; + + // max cutoff is the main cutoff plus the normal cutoff such that + double cutmax = p.rcut + p.ncut; + + return cutmax; +} + +/* ---------------------------------------------------------------------- + read DRIP file +------------------------------------------------------------------------- */ + +void PairDRIP::read_file(char *filename) +{ + int params_per_line = 15; + char **words = new char*[params_per_line+1]; + memory->sfree(params); + int nparams = 0; + int maxparam = 0; + + // open file on proc 0 + + FILE *fp; + if (comm->me == 0) { + fp = force->open_potential(filename); + if (fp == NULL) { + char str[128]; + snprintf(str,128,"Cannot open DRIP potential file %s",filename); + error->one(FLERR,str); + } + } + + // read each line out of file, skipping blank lines or leading '#' + // store line of params if all 3 element tags are in element list + + int i,j,n,m,nwords,ielement,jelement; + char line[MAXLINE],*ptr; + int eof = 0; + + while (1) { + if (comm->me == 0) { + ptr = fgets(line,MAXLINE,fp); + if (ptr == NULL) { + eof = 1; + fclose(fp); + } else n = strlen(line) + 1; + } + MPI_Bcast(&eof,1,MPI_INT,0,world); + if (eof) break; + MPI_Bcast(&n,1,MPI_INT,0,world); + MPI_Bcast(line,n,MPI_CHAR,0,world); + + // strip comment, skip line if blank + + if ((ptr = strchr(line,'#'))) *ptr = '\0'; + nwords = atom->count_words(line); + if (nwords == 0) continue; + + // concatenate additional lines until have params_per_line words + + while (nwords < params_per_line) { + n = strlen(line); + if (comm->me == 0) { + ptr = fgets(&line[n],MAXLINE-n,fp); + if (ptr == NULL) { + eof = 1; + fclose(fp); + } else n = strlen(line) + 1; + } + MPI_Bcast(&eof,1,MPI_INT,0,world); + if (eof) break; + MPI_Bcast(&n,1,MPI_INT,0,world); + MPI_Bcast(line,n,MPI_CHAR,0,world); + if ((ptr = strchr(line,'#'))) *ptr = '\0'; + nwords = atom->count_words(line); + } + + if (nwords != params_per_line) + error->all(FLERR,"Insufficient format in DRIP potential file"); + + // words = ptrs to all words in line + + nwords = 0; + words[nwords++] = strtok(line," \t\n\r\f"); + while ((words[nwords++] = strtok(NULL," \t\n\r\f"))) continue; + + // ielement,jelement = 1st args + // if these 2 args are in element list, then parse this line + // else skip to next line (continue) + + for (ielement = 0; ielement < nelements; ielement++) + if (strcmp(words[0],elements[ielement]) == 0) break; + if (ielement == nelements) continue; + for (jelement = 0; jelement < nelements; jelement++) + if (strcmp(words[1],elements[jelement]) == 0) break; + if (jelement == nelements) continue; + + // load up parameter settings and error check their values + + if (nparams == maxparam) { + maxparam += DELTA; + params = (Param *) memory->srealloc(params,maxparam*sizeof(Param), + "pair:params"); + } + + params[nparams].ielement = ielement; + params[nparams].jelement = jelement; + params[nparams].C0 = atof(words[2]); + params[nparams].C2 = atof(words[3]); + params[nparams].C4 = atof(words[4]); + params[nparams].C = atof(words[5]); + params[nparams].delta = atof(words[6]); + params[nparams].lambda = atof(words[7]); + params[nparams].A = atof(words[8]); + params[nparams].z0 = atof(words[9]); + params[nparams].B = atof(words[10]); + params[nparams].eta = atof(words[11]); + params[nparams].rhocut = atof(words[12]); + params[nparams].rcut = atof(words[13]); + params[nparams].ncut = atof(words[14]); + + // convenient precomputations + params[nparams].rhocutsq = params[nparams].rhocut * params[nparams].rhocut; + params[nparams].rcutsq = params[nparams].rcut * params[nparams].rcut; + params[nparams].ncutsq = params[nparams].ncut * params[nparams].ncut; + + nparams++; + } + + memory->destroy(elem2param); + memory->create(elem2param,nelements,nelements,"pair:elem2param"); + for (i = 0; i < nelements; i++) { + for (j = 0; j < nelements; j++) { + n = -1; + for (m = 0; m < nparams; m++) { + if (i == params[m].ielement && j == params[m].jelement) { + if (n >= 0) error->all(FLERR,"Potential file has duplicate entry"); + n = m; + } + } + if (n < 0) error->all(FLERR,"Potential file is missing an entry"); + elem2param[i][j] = n; + } + } + delete [] words; +} + +/* ---------------------------------------------------------------------- */ + +void PairDRIP::compute(int eflag, int vflag) +{ + int i,j,ii,jj,inum,jnum,itype,jtype; + double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,rsq; + int *ilist,*jlist,*numneigh,**firstneigh; + + double ni[DIM]; + double dni_dri[DIM][DIM], dni_drnb1[DIM][DIM]; + double dni_drnb2[DIM][DIM], dni_drnb3[DIM][DIM]; + + ev_init(eflag,vflag); + + double **x = atom->x; + double **f = atom->f; + int *type = atom->type; + int nlocal = atom->nlocal; + int newton_pair = force->newton_pair; + + inum = list->inum; + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + find_nearest3neigh(); + + for (ii = 0; ii < inum; ii++) { + i = ilist[ii]; + if (nearest3neigh[i][0] == -1) { + continue; + } + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + itype = map[type[i]]; + jlist = firstneigh[i]; + jnum = numneigh[i]; + + // normal and its derivatives w.r.t. atom i and its 3 nearest neighbors + calc_normal(i, ni, dni_dri,dni_drnb1, dni_drnb2, dni_drnb3); + + double fi[DIM] = {0., 0., 0.}; + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + j &= NEIGHMASK; + if (nearest3neigh[j][0] == -1) { + continue; + } + jtype = map[type[j]]; + + delx = x[j][0] - xtmp; + dely = x[j][1] - ytmp; + delz = x[j][2] - ztmp; + rsq = delx*delx + dely*dely + delz*delz; + int iparam_ij = elem2param[itype][jtype]; + Param& p = params[iparam_ij]; + double rcutsq = p.rcutsq; + + // only include the interation between different layers + if (rsq < rcutsq && atom->molecule[i] != atom->molecule[j]) { + + double fj[DIM] = {0., 0., 0.}; + double rvec[DIM] = {delx, dely, delz}; + + double phi_attr = calc_attractive(p, rsq, rvec, fi, fj); + + double phi_repul = calc_repulsive(i, j, p, rsq, rvec, + ni, dni_dri, dni_drnb1, dni_drnb2, dni_drnb3, fi, fj); + + if (eflag) evdwl = HALF * (phi_repul + phi_attr); + else evdwl = 0.0; + if (evflag) ev_tally(i,j,nlocal,newton_pair, evdwl,0.0,0,0,0,0); + + f[j][0] += fj[0]; + f[j][1] += fj[1]; + f[j][2] += fj[2]; + + // multiply 2 since v_tally has a 0.5 coeff + fj[0] *= 2; fj[1] *= 2; fj[2] *= 2; + if (vflag_atom) v_tally(j, fj, x[j]); + + } + } //loop over jj + + f[i][0] += fi[0]; + f[i][1] += fi[1]; + f[i][2] += fi[2]; + + // multiply 2 since v_tally has a 0.5 coeff + fi[0] *= 2; fi[1] *= 2; fi[2] *= 2; + if (vflag_atom) v_tally(i, fi, x[i]); + + } // loop over ii + + +if (vflag_fdotr) + virial_fdotr_compute(); + +} + +/* ---------------------------------------------------------------------- + Attractive part, i.e. the r^(-6) part +------------------------------------------------------------------------- */ + +double PairDRIP::calc_attractive(Param& p, double const rsq, double const *rvec, + double *const fi, double *const fj) +{ + double const z0 = p.z0; + double const A = p.A; + double const cutoff = p.rcut; + double const r = sqrt(rsq); + + double roz0_sq = rsq / (z0 * z0); + double dtp; + double tp = tap(r, cutoff, dtp); + double r6 = A / (roz0_sq * roz0_sq * roz0_sq); + double dr6 = -6 * r6 / r; + double phi = -r6 * tp; + + double fpair = -HALF * (r6 * dtp + dr6 * tp); + + fi[0] += rvec[0] * fpair / r; + fi[1] += rvec[1] * fpair / r; + fi[2] += rvec[2] * fpair / r; + fj[0] -= rvec[0] * fpair / r; + fj[1] -= rvec[1] * fpair / r; + fj[2] -= rvec[2] * fpair / r; + + return phi; +} + +/* ---------------------------------------------------------------------- + Repulsive part that depends on transverse distance and dihedral angle +------------------------------------------------------------------------- */ + +double PairDRIP::calc_repulsive(int const i, int const j, Param& p, + double const rsq, double const *rvec, double const *ni, + V3 const *dni_dri, V3 const *dni_drnb1, V3 const *dni_drnb2, + V3 const *dni_drnb3, double *const fi, double *const fj) +{ + double **f = atom->f; + double **x = atom->x; + + double C0 = p.C0; + double C2 = p.C2; + double C4 = p.C4; + double C = p.C; + double delta = p.delta; + double lambda = p.lambda; + double z0 = p.z0; + double cutoff = p.rcut; + + // nearest 3 neighbors of atoms i and j + int nbi1 = nearest3neigh[i][0]; + int nbi2 = nearest3neigh[i][1]; + int nbi3 = nearest3neigh[i][2]; + int nbj1 = nearest3neigh[j][0]; + int nbj2 = nearest3neigh[j][1]; + int nbj3 = nearest3neigh[j][2]; + + double fnbi1[DIM]; + double fnbi2[DIM]; + double fnbi3[DIM]; + double fnbj1[DIM]; + double fnbj2[DIM]; + double fnbj3[DIM]; + V3 dgij_dri; + V3 dgij_drj; + V3 dgij_drk1; + V3 dgij_drk2; + V3 dgij_drk3; + V3 dgij_drl1; + V3 dgij_drl2; + V3 dgij_drl3; + V3 drhosqij_dri; + V3 drhosqij_drj; + V3 drhosqij_drnb1; + V3 drhosqij_drnb2; + V3 drhosqij_drnb3; + + double r = sqrt(rsq); + + // derivative of rhosq w.r.t. atoms i j and the nearests 3 neighs of i + get_drhosqij(rvec, ni, dni_dri, dni_drnb1, dni_drnb2, dni_drnb3, drhosqij_dri, + drhosqij_drj, drhosqij_drnb1, drhosqij_drnb2, drhosqij_drnb3); + + // transverse decay function f(rho) and its derivative w.r.t. rhosq + double rhosqij; + double dtdij; + double tdij = td(C0, C2, C4, delta, rvec, r, ni, rhosqij, dtdij); + + // dihedral angle function and its derivateives + double dgij_drhosq; + double gij = dihedral(i, j, p, rhosqij, dgij_drhosq, dgij_dri, dgij_drj, + dgij_drk1, dgij_drk2, dgij_drk3, dgij_drl1, dgij_drl2, dgij_drl3); + + double V2 = C + tdij + gij; + + // tap part + double dtp; + double tp = tap(r, cutoff, dtp); + + // exponential part + double V1 = exp(-lambda * (r - z0)); + double dV1 = -V1 * lambda; + + // total energy + double phi = tp * V1 * V2; + + for (int k = 0; k < DIM; k++) { + // forces due to derivatives of tap and V1 + double tmp = HALF * (dtp * V1 + tp * dV1) * V2 * rvec[k] / r; + fi[k] += tmp; + fj[k] -= tmp; + + // contributions from transverse decay part tdij and the dihedral part gij + + // derivative of V2 contribute to atoms i, j + fi[k] -= HALF*tp*V1*((dtdij+dgij_drhosq)*drhosqij_dri[k]+dgij_dri[k]); + fj[k] -= HALF*tp*V1*((dtdij+dgij_drhosq)*drhosqij_drj[k]+dgij_drj[k]); + // derivative of V2 contribute to nearest 3 neighs of atom i + fnbi1[k] = -HALF*tp*V1*((dtdij+dgij_drhosq)*drhosqij_drnb1[k]+dgij_drk1[k]); + fnbi2[k] = -HALF*tp*V1*((dtdij+dgij_drhosq)*drhosqij_drnb2[k]+dgij_drk2[k]); + fnbi3[k] = -HALF*tp*V1*((dtdij+dgij_drhosq)*drhosqij_drnb3[k]+dgij_drk3[k]); + // derivative of V2 contribute to nearest 3 neighs of atom j + fnbj1[k] = -HALF * tp * V1 * dgij_drl1[k]; + fnbj2[k] = -HALF * tp * V1 * dgij_drl2[k]; + fnbj3[k] = -HALF * tp * V1 * dgij_drl3[k]; + } + + for (int k = 0; k < DIM; k++) { + f[nbi1][k] += fnbi1[k]; + f[nbi2][k] += fnbi2[k]; + f[nbi3][k] += fnbi3[k]; + f[nbj1][k] += fnbj1[k]; + f[nbj2][k] += fnbj2[k]; + f[nbj3][k] += fnbj3[k]; + } + + if (vflag_atom) { + // multiply since v_tally has a 0.5 coeff + for (int k = 0; k < DIM; k++) { + fnbi1[k] *= 2; + fnbi2[k] *= 2; + fnbi3[k] *= 2; + fnbj1[k] *= 2; + fnbj2[k] *= 2; + fnbj3[k] *= 2; + } + v_tally(nbi1, fnbi1, x[nbi1]); + v_tally(nbi2, fnbi2, x[nbi2]); + v_tally(nbi3, fnbi3, x[nbi3]); + v_tally(nbj1, fnbj1, x[nbj1]); + v_tally(nbj2, fnbj2, x[nbj2]); + v_tally(nbj3, fnbj3, x[nbj3]); + } + + return phi; +} + +/* ---------------------------------------------------------------------- */ + +void PairDRIP::find_nearest3neigh() +{ + int i, j, ii, jj, allnum, inum, jnum, itype, jtype, size; + double xtmp, ytmp, ztmp, delx, dely, delz, rsq; + int *ilist, *jlist, *numneigh, **firstneigh; + + double **x = atom->x; + int *type = atom->type; + + + allnum = list->inum + list->gnum; + inum = list->inum; + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + size = allnum; + memory->destroy(nearest3neigh); + memory->create(nearest3neigh, size, 3, "pair:nearest3neigh"); + + for (ii = 0; ii < allnum; ii++) { + i = ilist[ii]; + + // If "NULL" used in pair_coeff, i could be larger than allnum + if (i >= size) { + size = i+1; + memory->grow(nearest3neigh, size, 3, "pair:nearest3neigh"); + } + + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + itype = map[type[i]]; + jlist = firstneigh[i]; + jnum = numneigh[i]; + + // init nb1 to be the 1st nearest neigh, nb3 the 3rd nearest + int nb1 = -1; + int nb2 = -1; + int nb3 = -1; + double nb1_rsq = 1.0e10 + 1; + double nb2_rsq = 2.0e10; + double nb3_rsq = 3.0e10; + + for (jj = 0; jj < jnum; jj++) { + + j = jlist[jj]; + j &= NEIGHMASK; + jtype = map[type[j]]; + delx = x[j][0] - xtmp; + dely = x[j][1] - ytmp; + delz = x[j][2] - ztmp; + rsq = delx * delx + dely * dely + delz * delz; + + int iparam_ij = elem2param[itype][jtype]; + double ncutsq = params[iparam_ij].ncutsq; + + if (rsq < ncutsq && atom->molecule[i] == atom->molecule[j]) { + // find the 3 nearest neigh + if (rsq < nb1_rsq) { + nb3 = nb2; + nb2 = nb1; + nb1 = j; + nb3_rsq = nb2_rsq; + nb2_rsq = nb1_rsq; + nb1_rsq = rsq; + } + else if (rsq < nb2_rsq) { + nb3 = nb2; + nb2 = j; + nb3_rsq = nb2_rsq; + nb2_rsq = rsq; + } + else if (rsq < nb3_rsq) { + nb3 = j; + nb3_rsq = rsq; + } + + } + } // loop over jj + + // store neighbors to be used later to compute normal + if (nb3_rsq >= 1.0e10) { + if (ione(FLERR, "No enough neighbors to construct normal. Check the " + "configuration to see whether atoms fly away."); + } else { + // This only happens for ghost atoms that are near the boundary of the + // domain (i.e. r > r_cut + n_cut). These ghost atoms will not be + // the i j atoms in the compute function, but only neighbors of j atoms. + // It is allowed not to have three neighbors for these atoms, since + // their normals are not needed. + nearest3neigh[i][0] = -1; + nearest3neigh[i][1] = -1; + nearest3neigh[i][2] = -1; + } + } + else{ + nearest3neigh[i][0] = nb1; + nearest3neigh[i][1] = nb2; + nearest3neigh[i][2] = nb3; + } + } // loop over ii + +} + +/* ---------------------------------------------------------------------- */ + +void PairDRIP::calc_normal(int const i, double *const normal, + V3 *const dn_dri, V3 *const dn_drk1, V3 *const dn_drk2, V3 *const dn_drk3) +{ + int k1 = nearest3neigh[i][0]; + int k2 = nearest3neigh[i][1]; + int k3 = nearest3neigh[i][2]; + + // normal does not depend on i, setting to zero + for (int j = 0; j < DIM; j++) { + for (int k = 0; k < DIM; k++) { + dn_dri[j][k] = 0.0; + } + } + + // get normal and derives of normal w.r.t to its 3 nearest neighbors + double **x = atom->x; + deriv_cross(x[k1], x[k2], x[k3], normal, dn_drk1, dn_drk2, dn_drk3); +} + +/* ---------------------------------------------------------------------- */ + +void PairDRIP::get_drhosqij(double const *rij, double const *ni, + V3 const *dni_dri, V3 const *dni_drn1, V3 const *dni_drn2, + V3 const *dni_drn3, double *const drhosq_dri, double *const drhosq_drj, + double *const drhosq_drn1, double *const drhosq_drn2, + double *const drhosq_drn3) +{ + int k; + double ni_dot_rij = 0; + double dni_dri_dot_rij[DIM]; + double dni_drn1_dot_rij[DIM]; + double dni_drn2_dot_rij[DIM]; + double dni_drn3_dot_rij[DIM]; + + ni_dot_rij = dot(ni, rij); + mat_dot_vec(dni_dri, rij, dni_dri_dot_rij); + mat_dot_vec(dni_drn1, rij, dni_drn1_dot_rij); + mat_dot_vec(dni_drn2, rij, dni_drn2_dot_rij); + mat_dot_vec(dni_drn3, rij, dni_drn3_dot_rij); + + for (k = 0; k < DIM; k++) { + drhosq_dri[k] = -2*rij[k] - 2 * ni_dot_rij * (-ni[k] + dni_dri_dot_rij[k]); + drhosq_drj[k] = 2 * rij[k] - 2 * ni_dot_rij * ni[k]; + drhosq_drn1[k] = -2 * ni_dot_rij * dni_drn1_dot_rij[k]; + drhosq_drn2[k] = -2 * ni_dot_rij * dni_drn2_dot_rij[k]; + drhosq_drn3[k] = -2 * ni_dot_rij * dni_drn3_dot_rij[k]; + } +} + +/* ---------------------------------------------------------------------- + derivartive of transverse decay function f(rho) w.r.t. rho +------------------------------------------------------------------------- */ + +double PairDRIP::td(double C0, double C2, double C4, double delta, + double const *const rvec, double r, const double *const n, + double& rho_sq, double& dtd) +{ + double n_dot_r = dot(n, rvec); + + rho_sq = r * r - n_dot_r * n_dot_r; + + // in case n is [0, 0, 1] and rho_sq is negative due to numerical error + if (rho_sq < 0) { + rho_sq = 0; + } + + double del_sq = delta * delta; + double rod_sq = rho_sq / del_sq; + double td = exp(-rod_sq) * (C0 + rod_sq * (C2 + rod_sq * C4)); + dtd = -td / del_sq + exp(-rod_sq) * (C2 + 2 * C4 * rod_sq) / del_sq; + + return td; +} + +/* ---------------------------------------------------------------------- + derivartive of dihedral angle func gij w.r.t rho, and atom positions +------------------------------------------------------------------------- */ + +double PairDRIP::dihedral(const int i, const int j, Param& p, + double const rhosq, double& d_drhosq, + double *const d_dri, double *const d_drj, + double *const d_drk1, double *const d_drk2, double *const d_drk3, + double *const d_drl1, double *const d_drl2, double *const d_drl3) +{ + double **x = atom->x; + + // get parameter + double B = p.B; + double eta = p.eta; + double cut_rhosq = p.rhocutsq; + + // local vars + double cos_kl[3][3]; // cos_omega_k1ijl1, cos_omega_k1ijl2 ... + double d_dcos_kl[3][3]; // deriv of dihedral w.r.t to cos_omega_kijl + double dcos_kl[3][3][4][DIM]; // 4 indicates k, i, j, l. e.g. dcoskl[0][1][0] + // means dcos_omega_k1ijl2 / drk + + + // if larger than cutoff of rho, return 0 + if (rhosq >= cut_rhosq) { + d_drhosq = 0; + for (int dim = 0; dim < DIM; dim++) { + d_dri[dim] = 0; + d_drj[dim] = 0; + d_drk1[dim] = 0; + d_drk2[dim] = 0; + d_drk3[dim] = 0; + d_drl1[dim] = 0; + d_drl2[dim] = 0; + d_drl3[dim] = 0; + } + double dihe = 0.0; + return dihe; + } + // 3 neighs of atoms i and j + int k[3]; + int l[3]; + for (int m = 0; m < 3; m++) { + k[m] = nearest3neigh[i][m]; + l[m] = nearest3neigh[j][m]; + } + + // cos_omega_kijl and the derivatives w.r.t coordinates + for (int m = 0; m < 3; m++) { + for (int n = 0; n < 3; n++) { + cos_kl[m][n] = deriv_cos_omega(x[k[m]], x[i], x[j], x[l[n]], + dcos_kl[m][n][0], dcos_kl[m][n][1], + dcos_kl[m][n][2], dcos_kl[m][n][3]); + } + } + + double epart1 = exp(-eta * cos_kl[0][0] * cos_kl[0][1] * cos_kl[0][2]); + double epart2 = exp(-eta * cos_kl[1][0] * cos_kl[1][1] * cos_kl[1][2]); + double epart3 = exp(-eta * cos_kl[2][0] * cos_kl[2][1] * cos_kl[2][2]); + double D2 = epart1 + epart2 + epart3; + + // cutoff function + double d_drhosq_tap; + double D0 = B * tap_rho(rhosq, cut_rhosq, d_drhosq_tap); + + // dihedral energy + double dihe = D0 * D2; + + // deriv of dihedral w.r.t rhosq + d_drhosq = B * d_drhosq_tap * D2; + + // deriv of dihedral w.r.t cos_omega_kijl + d_dcos_kl[0][0] = -D0 * epart1 * eta * cos_kl[0][1] * cos_kl[0][2]; + d_dcos_kl[0][1] = -D0 * epart1 * eta * cos_kl[0][0] * cos_kl[0][2]; + d_dcos_kl[0][2] = -D0 * epart1 * eta * cos_kl[0][0] * cos_kl[0][1]; + d_dcos_kl[1][0] = -D0 * epart2 * eta * cos_kl[1][1] * cos_kl[1][2]; + d_dcos_kl[1][1] = -D0 * epart2 * eta * cos_kl[1][0] * cos_kl[1][2]; + d_dcos_kl[1][2] = -D0 * epart2 * eta * cos_kl[1][0] * cos_kl[1][1]; + d_dcos_kl[2][0] = -D0 * epart3 * eta * cos_kl[2][1] * cos_kl[2][2]; + d_dcos_kl[2][1] = -D0 * epart3 * eta * cos_kl[2][0] * cos_kl[2][2]; + d_dcos_kl[2][2] = -D0 * epart3 * eta * cos_kl[2][0] * cos_kl[2][1]; + + // initialization to be zero and later add values + for (int dim = 0; dim < DIM; dim++) { + d_drk1[dim] = 0.; + d_drk2[dim] = 0.; + d_drk3[dim] = 0.; + d_dri[dim] = 0.; + d_drj[dim] = 0.; + d_drl1[dim] = 0.; + d_drl2[dim] = 0.; + d_drl3[dim] = 0.; + } + + for (int m = 0; m < 3; m++) { + for (int dim = 0; dim < 3; dim++) { + d_drk1[dim] += d_dcos_kl[0][m] * dcos_kl[0][m][0][dim]; + d_drk2[dim] += d_dcos_kl[1][m] * dcos_kl[1][m][0][dim]; + d_drk3[dim] += d_dcos_kl[2][m] * dcos_kl[2][m][0][dim]; + d_drl1[dim] += d_dcos_kl[m][0] * dcos_kl[m][0][3][dim]; + d_drl2[dim] += d_dcos_kl[m][1] * dcos_kl[m][1][3][dim]; + d_drl3[dim] += d_dcos_kl[m][2] * dcos_kl[m][2][3][dim]; + } + for (int n = 0; n < 3; n++) { + for (int dim = 0; dim < 3; dim++) { + d_dri[dim] += d_dcos_kl[m][n] * dcos_kl[m][n][1][dim]; + d_drj[dim] += d_dcos_kl[m][n] * dcos_kl[m][n][2][dim]; + } + } + } + + return dihe; +} + +/* ---------------------------------------------------------------------- + compute cos(omega_kijl) and the derivateives +------------------------------------------------------------------------- */ + +double PairDRIP::deriv_cos_omega(double const *rk, double const *ri, + double const *rj, double const *rl, double *const dcos_drk, + double *const dcos_dri, double *const dcos_drj, double *const dcos_drl) +{ + double ejik[DIM]; + double eijl[DIM]; + double tmp1[DIM]; + double tmp2[DIM]; + double dejik_dri[DIM][DIM]; + double dejik_drj[DIM][DIM]; + double dejik_drk[DIM][DIM]; + double deijl_dri[DIM][DIM]; + double deijl_drj[DIM][DIM]; + double deijl_drl[DIM][DIM]; + + + // ejik and derivatives + // Note the returned dejik_dri ... are actually the transpose + deriv_cross(ri, rj, rk, ejik, dejik_dri, dejik_drj, dejik_drk); + + // flip sign + // deriv_cross computes rij cross rik, here we need rji cross rik + for (int m = 0; m < DIM; m++) { + ejik[m] = -ejik[m]; + for (int n = 0; n < DIM; n++) { + dejik_dri[m][n] = -dejik_dri[m][n]; + dejik_drj[m][n] = -dejik_drj[m][n]; + dejik_drk[m][n] = -dejik_drk[m][n]; + } + } + + // eijl and derivatives + deriv_cross(rj, ri, rl, eijl, deijl_drj, deijl_dri, deijl_drl); + // flip sign + for (int m = 0; m < DIM; m++) { + eijl[m] = -eijl[m]; + for (int n = 0; n < DIM; n++) { + deijl_drj[m][n] = -deijl_drj[m][n]; + deijl_dri[m][n] = -deijl_dri[m][n]; + deijl_drl[m][n] = -deijl_drl[m][n]; + } + } + + // dcos_drk + mat_dot_vec(dejik_drk, eijl, dcos_drk); + // dcos_dri + mat_dot_vec(dejik_dri, eijl, tmp1); + mat_dot_vec(deijl_dri, ejik, tmp2); + for (int m = 0; m < DIM; m++) { + dcos_dri[m] = tmp1[m] + tmp2[m]; + } + // dcos_drj + mat_dot_vec(dejik_drj, eijl, tmp1); + mat_dot_vec(deijl_drj, ejik, tmp2); + for (int m = 0; m < DIM; m++) { + dcos_drj[m] = tmp1[m] + tmp2[m]; + } + // dcos drl + mat_dot_vec(deijl_drl, ejik, dcos_drl); + + // cos_oemga_kijl + double cos_omega = dot(ejik, eijl); + + return cos_omega; +} + +/* ---------------------------------------------------------------------- */ + +double PairDRIP::tap(double r, double cutoff, double& dtap) +{ + double t; + double r_min = 0; + + if (r <= r_min) { + t = 1; + dtap = 0; + } + else { + double roc = (r - r_min) / (cutoff - r_min); + double roc_sq = roc * roc; + t = roc_sq*roc_sq*(-35.0 + 84.0 * roc + roc_sq * (-70.0 + 20.0 * roc)) + 1; + dtap = roc_sq * roc / (cutoff - r_min) + * (-140.0 + 420.0 * roc + roc_sq * (-420.0 + 140.0 * roc)); + } + + return t; +} + +/* ---------------------------------------------------------------------- */ + +double PairDRIP::tap_rho(double rhosq, double cut_rhosq, double& drhosq) +{ + double roc_sq; + double roc; + double t; + + roc_sq = rhosq / cut_rhosq; + roc = sqrt(roc_sq); + t = roc_sq*roc_sq*(-35.0 + 84.0 * roc + roc_sq * (-70.0 + 20.0 * roc)) + 1; + + // Note this dtap/drho_sq not dtap/drho + drhosq = roc_sq/cut_rhosq*(-70.0 + 210.0*roc + roc_sq*(-210.0 + 70.0*roc)); + + return t; +} + +/* ---------------------------------------------------------------------- + Compute the normalized cross product of two vector rkl, rkm, and the + derivates w.r.t rk, rl, rm. + Note, the returned dcross_drk, dcross_drl, and dcross_drm are actually the + transpose. +------------------------------------------------------------------------- */ + +void PairDRIP::deriv_cross(double const *rk, double const *rl, + double const *rm, double *const cross, + V3 *const dcross_drk, V3 *const dcross_drl, V3 *const dcross_drm) +{ + double x[DIM]; + double y[DIM]; + double p[DIM]; + double q; + double q_cubic; + double d_invq_d_x0; + double d_invq_d_x1; + double d_invq_d_x2; + double d_invq_d_y0; + double d_invq_d_y1; + double d_invq_d_y2; + + int i, j; + + + // get x = rkl and y = rkm + for (i = 0; i < DIM; i++) { + x[i] = rl[i] - rk[i]; + y[i] = rm[i] - rk[i]; + } + + // cross product + p[0] = x[1] * y[2] - x[2] * y[1]; + p[1] = x[2] * y[0] - x[0] * y[2]; + p[2] = x[0] * y[1] - x[1] * y[0]; + + q = sqrt(p[0] * p[0] + p[1] * p[1] + p[2] * p[2]); + + // normalized cross + cross[0] = p[0] / q; + cross[1] = p[1] / q; + cross[2] = p[2] / q; + + // compute derivatives + // derivative of inverse q (i.e. 1/q) w.r.t x and y + q_cubic = q * q * q; + d_invq_d_x0 = (+p[1] * y[2] - p[2] * y[1]) / q_cubic; + d_invq_d_x1 = (-p[0] * y[2] + p[2] * y[0]) / q_cubic; + d_invq_d_x2 = (p[0] * y[1] - p[1] * y[0]) / q_cubic; + d_invq_d_y0 = (-p[1] * x[2] + p[2] * x[1]) / q_cubic; + d_invq_d_y1 = (p[0] * x[2] - p[2] * x[0]) / q_cubic; + d_invq_d_y2 = (-p[0] * x[1] + p[1] * x[0]) / q_cubic; + + // dcross/drl transposed + dcross_drl[0][0] = p[0] * d_invq_d_x0; + dcross_drl[0][1] = -y[2] / q + p[1] * d_invq_d_x0; + dcross_drl[0][2] = y[1] / q + p[2] * d_invq_d_x0; + + dcross_drl[1][0] = y[2] / q + p[0] * d_invq_d_x1; + dcross_drl[1][1] = p[1] * d_invq_d_x1; + dcross_drl[1][2] = -y[0] / q + p[2] * d_invq_d_x1; + + dcross_drl[2][0] = -y[1] / q + p[0] * d_invq_d_x2; + dcross_drl[2][1] = y[0] / q + p[1] * d_invq_d_x2; + dcross_drl[2][2] = p[2] * d_invq_d_x2; + + // dcross/drm transposed + dcross_drm[0][0] = p[0] * d_invq_d_y0; + dcross_drm[0][1] = x[2] / q + p[1] * d_invq_d_y0; + dcross_drm[0][2] = -x[1] / q + p[2] * d_invq_d_y0; + + dcross_drm[1][0] = -x[2] / q + p[0] * d_invq_d_y1; + dcross_drm[1][1] = p[1] * d_invq_d_y1; + dcross_drm[1][2] = x[0] / q + p[2] * d_invq_d_y1; + + dcross_drm[2][0] = x[1] / q + p[0] * d_invq_d_y2; + dcross_drm[2][1] = -x[0] / q + p[1] * d_invq_d_y2; + dcross_drm[2][2] = p[2] * d_invq_d_y2; + + // dcross/drk transposed + for (i = 0; i < DIM; i++) { + for (j = 0; j < DIM; j++) { + dcross_drk[i][j] = -(dcross_drl[i][j] + dcross_drm[i][j]); + } + } +} diff --git a/src/USER-MISC/pair_drip.h b/src/USER-MISC/pair_drip.h new file mode 100644 index 0000000000..0a8f90dfc2 --- /dev/null +++ b/src/USER-MISC/pair_drip.h @@ -0,0 +1,148 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + 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 author: Mingjian Wen (University of Minnesota) + e-mail: wenxx151@umn.edu + + This implements the DRIP model as described in + M. Wen, S. Carr, S. Fang, E. Kaxiras, and E. B. Tadmor, + Phys. Rev. B, 98, 235404 (2018). +------------------------------------------------------------------------- */ + + +#ifdef PAIR_CLASS + +PairStyle(drip, PairDRIP) + +#else + +#ifndef LMP_PAIR_DRIP_H +#define LMP_PAIR_DRIP_H + +#include "pair.h" +#include "my_page.h" +#include + +namespace LAMMPS_NS { + +#define DIM 3 +typedef double V3[3]; + + +class PairDRIP : public Pair { +public: + PairDRIP(class LAMMPS *); + virtual ~PairDRIP(); + + virtual void compute(int, int); + void settings(int, char **); + void coeff(int, char **); + double init_one(int, int); + void init_style(); + +protected: + struct Param + { + int ielement, jelement; + double C0, C2, C4, C, delta, lambda, A, z0, B, eta, rhocut, rcut, ncut; + double rhocutsq, rcutsq, ncutsq; + }; + Param *params; // parameter set for I-J interactions + int **nearest3neigh; // nearest 3 neighbors of atoms + char **elements; // names of unique elements + int **elem2param; // mapping from element pairs to parameters + int *map; // mapping from atom types to elements + int nelements; // # of unique elements + double cutmax; // max cutoff for all species + + void read_file(char *); + void allocate(); + + // DRIP specific functions + double calc_attractive(Param&, double const, double const *, + double *const, double *const); + + double calc_repulsive(int const, int const, Param&, double const, + double const *, double const *, V3 const *, V3 const *, V3 const *, + V3 const *, double *const, double *const); + + void find_nearest3neigh(); + + void calc_normal(int const, double *const, V3 *const, V3 *const, V3 *const, + V3 *const); + + void get_drhosqij(double const *, double const *, V3 const *, V3 const *, + V3 const *, V3 const *, double *const, double *const, double *const, + double *const, double *const); + + double td(double, double, double, double, double const *const, double, + const double *const, double&, double&); + + double dihedral(const int, const int, Param&, double const, double&, + double *const, double *const, double *const, double *const, double *const, + double *const, double *const, double *const); + + double deriv_cos_omega(double const *, double const *, double const *, + double const *, double *const, double *const, double *const, + double *const); + + double tap(double, double, double&); + + double tap_rho(double, double, double&); + + void deriv_cross(double const *, double const *, double const *, + double *const, V3 *const, V3 *const, V3 *const); + + // inline functions + inline double dot(double const *x, double const *y) const + { + return x[0]*y[0]+x[1]*y[1]+x[2]*y[2]; + } + + inline void mat_dot_vec(V3 const *X, double const *y, double *const z) const + { + for (int k = 0; k < 3; k++) { + z[k] = X[k][0]*y[0]+X[k][1]*y[1]+X[k][2]*y[2]; + } + } + +}; +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +E: Incorrect args for pair coefficients + +Self-explanatory. Check the input script or data file. + +E: All pair coeffs are not set + +All pair coefficients must be set in the data file or by the +pair_coeff command before running a simulation. + +E: No enough neighbors to construct normal + +Cannot find three neighbors within cutoff of the target atom. +Check the configuration. + +*/ diff --git a/src/USER-MISC/pair_e3b.cpp b/src/USER-MISC/pair_e3b.cpp new file mode 100644 index 0000000000..43b472594a --- /dev/null +++ b/src/USER-MISC/pair_e3b.cpp @@ -0,0 +1,696 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + 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: Steven E Strong and Nicholas J Hestand + contact: stevene.strong at gmail dot com +------------------------------------------------------------------------- */ + +#include +#include +#include +#include + +#include "pair_e3b.h" + +#include "atom.h" +#include "neighbor.h" +#include "neigh_request.h" +#include "neigh_list.h" +#include "force.h" +#include "comm.h" +#include "memory.h" +#include "error.h" +#include "update.h" +#include "domain.h" +#include "citeme.h" + +//these are defined here to avoid confusing hardcoded indicies, but +//they do not allow flexibility. If they are changed the code will break +#define DIM 3 +#define NUMH 2 //number of hydrogen atoms per water molecule +#define NUMO 2 //number of oxygen atoms per pair of water molecules +#define BOND_DELTA 1.01 //buffer for OH bonds that aren't perfectly rigid + +using namespace LAMMPS_NS; +/* ---------------------------------------------------------------------- */ + +PairE3B::PairE3B(LAMMPS *lmp) : Pair(lmp),pairPerAtom(10) +{ + single_enable = 0; + restartinfo = 0; + one_coeff = 1; + nextra=4; //store and tally pot energy terms eA, eB, eC, and e2 + pvector = new double[nextra]; + + allocatedE3B = false; + pairO = NULL; + pairH = NULL; + exps = NULL; + del3 = NULL; + fpair3 = NULL; + sumExp = NULL; +} + +/* ---------------------------------------------------------------------- + check if allocated, since class can be destructed when incomplete +------------------------------------------------------------------------- */ + +PairE3B::~PairE3B() +{ + if (copymode) return; + + if (allocated) { + memory->destroy(setflag); + memory->destroy(cutsq); + } + if (allocatedE3B) { + memory->destroy(pairO); + memory->destroy(pairH); + memory->destroy(exps); + memory->destroy(del3); + memory->destroy(fpair3); + memory->destroy(sumExp); + } + + delete[] pvector; +} + +/* ---------------------------------------------------------------------- */ + +void PairE3B::compute(int eflag, int vflag) +{ + int i,j,k,h,ii,jj,hh,kk,inum,jnum,otherO; + double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair,rsq,tmpexp; + double fxtmp,fytmp,fztmp,fix,fiy,fiz; + double delxh,delyh,delzh,rsqh,tmpr; + double scFact1,scFact2,scEng,scDer; + int *ilist,*jlist,*numneigh,**firstneigh; + bool addedH; + + if (natoms != atom->natoms) + error->all(FLERR,"pair E3B requires a fixed number of atoms"); + + //clear sumExp array + memset(sumExp,0.0,nbytes); + + evdwl = 0.0; + pvector[0]=pvector[1]=pvector[2]=pvector[3]=0.0; + if (eflag || vflag) ev_setup(eflag,vflag); + else evflag = vflag_fdotr = 0; + + double **x = atom->x; + double **f = atom->f; + tagint *tag = atom->tag; + int *type = atom->type; + int nlocal = atom->nlocal; + int newton_pair = force->newton_pair; + + inum = list->inum; + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + int npair = 0; + // loop over half neighbor list of my atoms + for (ii = 0; ii < inum; ii++) { + i = ilist[ii]; + if (type[i]!=typeO) + continue; + + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + fix = fiy = fiz = 0.0; + + // two-body interactions + jlist = firstneigh[i]; + jnum = numneigh[i]; + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + j &= NEIGHMASK; + + //skip unless O-O interaction + if (type[j]!=typeO) + continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; //OO distance + + //two body interaction + //not shifted b/c k2=4.87/A, so at cutoff (5.2A) e^(-kr) = 1e-11 + if (rsq < rc2sq) { + tmpr = sqrt(rsq); + tmpexp = e2 * exp(-k2*tmpr); + fpair = k2 * tmpexp / tmpr; + + fxtmp = delx*fpair; + fytmp = dely*fpair; + fztmp = delz*fpair; + fix += fxtmp; + fiy += fytmp; + fiz += fztmp; + f[j][0] -= fxtmp; + f[j][1] -= fytmp; + f[j][2] -= fztmp; + + if (evflag) { + ev_tally(i,j,nlocal,newton_pair,tmpexp,0.0,fpair,delx,dely,delz); + pvector[0] += tmpexp; + } + } //end if rsqmap(tag[otherO]+hh+1); + //if hydrogen atom is missing, bond potential or shake will + //catch this, so don't need to check here + //if (h<0) + // error->one(FLERR,"hydrogen atom missing"); + h = domain->closest_image(otherO,h); + pairH[npair][kk][hh] = h; + + delxh = x[k][0] - x[h][0]; + delyh = x[k][1] - x[h][1]; + delzh = x[k][2] - x[h][2]; + rsqh = delxh*delxh + delyh*delyh + delzh*delzh; + + if (rsqh < rc3sq) { + + tmpr = sqrt(rsqh); + tmpexp = exp(-k3*tmpr); + if (tmpr > rs) { + scFact1 = rc3-tmpr; + scFact2 = sc_num + 2*tmpr; + scEng = scFact1*scFact1*scFact2*sc_denom; + scDer = k3*scEng - 6*scFact1*(rs-tmpr)*sc_denom; + } else { + scDer = k3; + scEng = 1.0; + } + + //need to keep fpair3 separate from del3 for virial + fpair3[npair][kk][hh] = scDer*tmpexp/tmpr; + tmpexp *= scEng; + exps[npair][kk][hh] = tmpexp; + del3[npair][kk][hh][0] = delxh; + del3[npair][kk][hh][1] = delyh; + del3[npair][kk][hh][2] = delzh; + + //accumulate global vector of sum(e^kr) + //tags start at 1, so subtract one to index sumExp + sumExp[tag[k]-1] += tmpexp; + sumExp[tag[h]-1] += tmpexp; + + addedH = true; + } else { + exps [npair][kk][hh] = 0.0; + fpair3[npair][kk][hh] = 0.0; + } //if < rc3sq + } //end loop through 2 Hs + } //end for kk in NUMO + //if added a pair, check if array is too small and grow + if (addedH) { + npair++; + if (npair >= pairmax) + error->one(FLERR,"neigh is too small"); + } + } //end if < rc3deltaSq + } //end for jj neigh + + //add 2-body forces on i + f[i][0] += fix; + f[i][1] += fiy; + f[i][2] += fiz; + } //end for ii + + //communicate sumExp array + //tested that no change in speed with MPI_IN_PLACE + MPI_Allreduce(MPI_IN_PLACE,sumExp,maxID,MPI_DOUBLE,MPI_SUM,world); + + //now loop through list of pairs, calculating 3body forces + int j2,otherH; + double partA,partB,partC; + for (ii = 0; ii < npair; ii++) { + + for (kk=0; kkntypes; + + memory->create(setflag,n+1,n+1,"pair:setflag"); + memory->create(cutsq,n+1,n+1,"pair:cutsq"); +} + +void PairE3B::allocateE3B() +{ + allocatedE3B = true; + + //TODO: get memory->grow working for 4d arrays + pairmax = atom->nlocal*pairPerAtom; //initial guess for size of pair lists + memory->create(pairO ,pairmax,NUMO ,"pair:pairO"); + memory->create(pairH ,pairmax,NUMO,NUMH ,"pair:pairH"); + memory->create(exps ,pairmax,NUMO,NUMH ,"pair:exps"); + memory->create(fpair3,pairmax,NUMO,NUMH ,"pair:fpair3"); + memory->create(del3 ,pairmax,NUMO,NUMH,DIM,"pair:del3"); + + //set del3 to zero to silence valgrind memcheck errors + //don't need to do this in every call to compute() because we set + //exps and fpair3 to zero, and all uses of del3 are multiplied by one of those + int ii,jj,kk,ll; + for (ii=0; iinatoms; + maxID=find_maxID(); + if (!natoms) + error->all(FLERR,"No atoms found"); + memory->create(sumExp,maxID,"pair:sumExp"); + nbytes = sizeof(double) * maxID; +} + +/* ---------------------------------------------------------------------- + global settings +------------------------------------------------------------------------- */ + +void PairE3B::settings(int narg, char **arg) +{ + if (narg != 1) error->all(FLERR,"Illegal pair_style command"); + typeO=force->inumeric(FLERR,arg[0]); + if (typeO<1 || typeO>atom->ntypes) + error->all(FLERR,"Invalid Otype: out of bounds"); +} + +/* ---------------------------------------------------------------------- + coeffs must be * * keyword/value + keyword/values set the potential parameters +------------------------------------------------------------------------- */ +void PairE3B::coeff(int narg, char **arg) +{ + if (!allocated) allocate(); + + //1=* 2=* 3/4=1st keyword/value + if (narg < 4) + error->all(FLERR,"There must be at least one keyword given to pair_coeff"); + + // ensure I,J args are * * + if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0) + error->all(FLERR,"Incorrect args for pair coefficients"); + + // clear setflag since coeff() called once with I,J = * * + int n = atom->ntypes; + for (int i = 1; i <= n; i++) + for (int j = i; j <= n; j++) + setflag[i][j] = 0; + + setflag[typeO][typeO]=1; + + //parse keyword/value pairs + double bondL=0.0; //OH bond length + bool repeatFlag=false; + int presetFlag; + + //clear parameters + e2=ea=eb=ec=k3=k2=NAN; + rs=rc3=rc2=0.0; + + int iarg = 2; //beginning of keyword/value pairs + while(iarg < narg) { + char *keyword = arg[iarg++]; + if (checkKeyword(keyword,"Ea",1,narg-iarg)) + ea=force->numeric(FLERR,arg[iarg++]); + else if (checkKeyword(keyword,"Eb",1,narg-iarg)) + eb=force->numeric(FLERR,arg[iarg++]); + else if (checkKeyword(keyword,"Ec",1,narg-iarg)) + ec=force->numeric(FLERR,arg[iarg++]); + else if (checkKeyword(keyword,"K3",1,narg-iarg)) + k3=force->numeric(FLERR,arg[iarg++]); + else if (checkKeyword(keyword,"Rs",1,narg-iarg)) + rs=force->numeric(FLERR,arg[iarg++]); + else if (checkKeyword(keyword,"Rc3",1,narg-iarg)) + rc3=force->numeric(FLERR,arg[iarg++]); + else if (checkKeyword(keyword,"Rc2",1,narg-iarg)) + rc2=force->numeric(FLERR,arg[iarg++]); + else if (checkKeyword(keyword,"bondL",1,narg-iarg)) + bondL=force->numeric(FLERR,arg[iarg++]); + else if (checkKeyword(keyword,"E2",1,narg-iarg)) + e2=force->numeric(FLERR,arg[iarg++]); + else if (checkKeyword(keyword,"K2",1,narg-iarg)) + k2=force->numeric(FLERR,arg[iarg++]); + else if (checkKeyword(keyword,"neigh",1,narg-iarg)) + pairPerAtom=force->inumeric(FLERR,arg[iarg++]); + else if (checkKeyword(keyword,"preset",1,narg-iarg)) { + presetFlag=force->inumeric(FLERR,arg[iarg++]); + presetParam(presetFlag,repeatFlag,bondL); + } else { + char str[256]; + snprintf(str,256,"Keyword %s is unknown",keyword); + error->all(FLERR,str); + } + } + + checkInputs(bondL); + + //cutmax for neighbor listing + cutmax = std::max(rc2,rc3); + rc2sq = rc2*rc2; + rc3sq = rc3*rc3; + rc3deltaSq = (rc3+bondL)*(rc3+bondL); + + double tmpfact=1.0/(rc3-rs); + sc_denom=tmpfact*tmpfact*tmpfact; + sc_num=rc3-3*rs; +} + +/* ---------------------------------------------------------------------- + init specific to this pair styles +------------------------------------------------------------------------- */ + +void PairE3B::init_style() +{ + if (atom->tag_enable == 0) + error->all(FLERR,"Pair style E3B requires atom IDs"); + if (force->newton_pair == 0) + error->all(FLERR,"Pair style E3B requires newton pair on"); + + // need a half neighbor list + neighbor->request(this,instance_me); + + if (!force->pair_match("tip4p",false,0)) + if (comm->me==0) error->warning(FLERR,"E3B pair_style is designed for use with hybrid/overlay tip4p style"); + + if (!allocatedE3B) allocateE3B(); +} + + +static const char cite_E3B1[] = + "Explicit Three-Body (E3B) potential for water:\n\n" + "@article{kumar_water_2008,\n" + "title = {Water Simulation Model with Explicit Three-Molecule Interactions},\n" + "volume = {112},\n" + "doi = {10.1021/jp8009468},\n" + "number = {28},\n" + "journal = {J Phys. Chem. B},\n" + "author = {Kumar, R. and Skinner, J. L.},\n" + "year = {2008},\n" + "pages = {8311--8318}\n" + "}\n\n"; + +static const char cite_E3B2[] = + "Explicit Three-Body (E3B) potential for water:\n\n" + "@article{tainter_robust_2011,\n" + "title = {Robust three-body water simulation model},\n" + "volume = {134},\n" + "doi = {10.1063/1.3587053},\n" + "number = {18},\n" + "journal = {J. Chem. Phys},\n" + "author = {Tainter, C. J. and Pieniazek, P. A. and Lin, Y.-S. and Skinner, J. L.},\n" + "year = {2011},\n" + "pages = {184501}\n" + "}\n\n"; + +static const char cite_E3B3[] = + "Explicit Three-Body (E3B) potential for water:\n\n" + "@article{tainter_reparametrized_2015,\n" + "title = {Reparametrized {E3B} (Explicit Three-Body) Water Model Using the {TIP4P/2005} Model as a Reference},\n" + "volume = {11},\n" + "doi = {10.1021/acs.jctc.5b00117},\n" + "number = {5},\n" + "journal = {J. Chem. Theory Comput.},\n" + "author = {Tainter, Craig J. and Shi, Liang and Skinner, James L.},\n" + "year = {2015},\n" + "pages = {2268--2277}\n" + "}\n\n"; + +void PairE3B::presetParam(const int flag,bool &repeatFlag,double &bondL) { + if (repeatFlag) { + error->all(FLERR, + "Cannot request two different sets of preset parameters"); + } + repeatFlag=true; + + if (!std::isnan(ea) || !std::isnan(eb) || !std::isnan(ec) || + !std::isnan(e2) || !std::isnan(k3) || !std::isnan(k2) || + bondL!=0.0 || rs!=0.0 || rc3!=0.0 || rc2!=0.0 ) + error->all(FLERR,"Preset keyword will overwrite another keyword setting"); + + double econv,lconv; + if (strcmp(update->unit_style,"real") == 0) { + econv=1.0/4.184; + lconv=1.0; + } else if (strcmp(update->unit_style,"metal") == 0) { + econv=0.103653271; + lconv=1.0; + } else if (strcmp(update->unit_style,"si") == 0) { + econv=1.660578e-21; + lconv=1e-10; + } else if (strcmp(update->unit_style,"cgs") == 0) { + econv=1.660578e-14; + lconv=1e-8; + } else { + char str[256]; + snprintf(str,256, + "Pre-defined E3B parameters have not been set for %s units.", + update->unit_style); + error->all(FLERR,str); + } + + //here parameters are defined in kJ/mol and A + //they will be converted to the lammps units after + if (flag==2008) { + error->all(FLERR,"\"preset 2008\" is not yet supported, because this would require distinct k3 coefficients, use \"preset 2011\" or \"preset 2015\""); + if (lmp->citeme) lmp->citeme->add(cite_E3B1); + ea = 4699.6; + eb =-2152.9; + ec = 1312.7; + //ka = 1.0/1.88; + //kb = 1.0/1.71; + //kc = 1.0/1.56; + e2 = 1.925e6; + k2 = 4.67; + rs = 5.0; + rc3 = 5.2; + rc2 = 5.2; + bondL = 0.9572; + } else if (flag==2011) { + if (lmp->citeme) lmp->citeme->add(cite_E3B2); + ea = 1745.7; + eb =-4565.0; + ec = 7606.8; + k3 = 1.907; + e2 = 2.349e6; + k2 = 4.872; + rs = 5.0; + rc3 = 5.2; + rc2 = 5.2; + bondL = 0.9572; + } else if (flag==2015) { + if (lmp->citeme) lmp->citeme->add(cite_E3B3); + ea = 150.0; + eb =-1005.0; + ec = 1880.0; + k3 = 1.907; + e2 = 0.453e6; + k2 = 4.872; + rs = 5.0; + rc3 = 5.2; + rc2 = 5.2; + bondL = 0.9572; + } else + error->all(FLERR,"Unknown argument: preset only takes 2011 or 2015 as arguments"); + + //convert units + ea *= econv; + eb *= econv; + ec *= econv; + e2 *= econv; + k3 /= lconv; + k2 /= lconv; + rs *= lconv; + rc2 *= lconv; + rc3 *= lconv; + bondL *= lconv*BOND_DELTA; +} + +/* ---------------------------------------------------------------------- + init for one type pair i,j and corresponding j,i +------------------------------------------------------------------------- */ +//pair.cpp::init uses this to set cutsq array, used for neighboring, etc +double PairE3B::init_one(int i, int j) +{ + if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set"); + + return cutmax; +} + +bool PairE3B::checkKeyword(const char *thiskey,const char *test,const int nVal, const int nRem) { + if (strcmp(thiskey,test) == 0) { + if(nRemall(FLERR,str); + } + return true; + } + return false; +} + +//find max atom ID for all atoms +//from fix_deposit.cpp +tagint PairE3B::find_maxID() +{ + tagint *tag = atom->tag; + int nlocal = atom->nlocal; + + tagint max = 0; + tagint maxID; + for (int i = 0; i < nlocal; i++) max = MAX(max,tag[i]); + MPI_Allreduce(&max,&maxID,1,MPI_LMP_TAGINT,MPI_MAX,world); + + return maxID; +} + +void PairE3B::checkInputs(const double &bondL) { + //first check that all necessary values were set + if (rc2==0.0) + error->all(FLERR,"rc2 keyword missing"); + if (rs==0.0) + error->all(FLERR,"Rs keyword missing"); + if (rc3==0.0) + error->all(FLERR,"Rc3 keyword missing"); + if (bondL==0.0) + error->all(FLERR,"bondL keyword missing"); + if (std::isnan(ea)) + error->all(FLERR,"Ea keyword missing"); + if (std::isnan(eb)) + error->all(FLERR,"Eb keyword missing"); + if (std::isnan(ec)) + error->all(FLERR,"Ec keyword missing"); + if (std::isnan(k3)) + error->all(FLERR,"K3 keyword missing"); + if (std::isnan(e2)) + error->all(FLERR,"E2 keyword missing"); + if (std::isnan(k2)) + error->all(FLERR,"K2 keyword missing"); + + //now test that values are within acceptable ranges + if (k2 < 0.0 or k3 < 0.0) + error->all(FLERR,"exponential decay is negative"); + if (bondL<0.0) + error->all(FLERR,"OH bond length is negative"); + if (rc2 < 0.0 || rc3 < 0.0 || rs < 0.0) + error->all(FLERR,"potential cutoff is negative"); + if (rs > rc3) + error->all(FLERR,"potential switching distance is larger than cutoff"); + if (rs==rc3) + error->warning(FLERR,"potential switching distance is equal to cutoff: this is untested and not conserve energy"); + if (pairPerAtom<0) + error->all(FLERR,"neigh is negative"); +} diff --git a/src/USER-MISC/pair_e3b.h b/src/USER-MISC/pair_e3b.h new file mode 100644 index 0000000000..b37eee57f6 --- /dev/null +++ b/src/USER-MISC/pair_e3b.h @@ -0,0 +1,68 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + 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 + +PairStyle(e3b,PairE3B) + +#else + +#ifndef LMP_PAIR_E3B_H +#define LMP_PAIR_E3B_H + +#include "pair.h" + +namespace LAMMPS_NS { + +class PairE3B : public Pair { + public: + PairE3B(class LAMMPS *); + virtual ~PairE3B(); + virtual void compute(int, int); + void settings(int, char **); + virtual void coeff(int, char **); + virtual double init_one(int, int); + virtual void init_style(); + +protected: + //potential parameters + int typeO; + double ea,eb,ec; //three body energies + double k3; //three body exponential decay (units inverse length) + double rs,rc3,rc2; //rs: switching cutuff, rc3: cutoff for 3-body + double e2,k2; //2-body energy and exp decay + double cutmax; //max cutoff of all interactions + double rc2sq,rc3sq,rc3deltaSq; + double sc_denom,sc_num; + + //list of indexes of Os and Hs in each pair + int pairmax,pairPerAtom; // size of pair list + int **pairO,***pairH; // pair lists + double ***exps,****del3,***fpair3,*sumExp; + int maxID; //size of global sumExp array + size_t nbytes; //size of sumExp array in bytes + int natoms; //to make sure number of atoms is constant + + virtual void allocate(); + void allocateE3B(); + bool allocatedE3B; + //for reading settings from pair_style input + bool checkKeyword(const char *,const char *,const int, const int); + void checkInputs(const double &bondL); + void presetParam(const int flag,bool &repeatFlag,double &bondL); + tagint find_maxID(); +}; +} + +#endif +#endif diff --git a/src/USER-MISC/pair_ilp_graphene_hbn.cpp b/src/USER-MISC/pair_ilp_graphene_hbn.cpp index a8c9c686f1..a41c660b7b 100644 --- a/src/USER-MISC/pair_ilp_graphene_hbn.cpp +++ b/src/USER-MISC/pair_ilp_graphene_hbn.cpp @@ -47,6 +47,7 @@ using namespace LAMMPS_NS; PairILPGrapheneHBN::PairILPGrapheneHBN(LAMMPS *lmp) : Pair(lmp) { restartinfo = 0; + one_coeff = 1; // initialize element to parameter maps nelements = 0; @@ -71,7 +72,7 @@ PairILPGrapheneHBN::PairILPGrapheneHBN(LAMMPS *lmp) : Pair(lmp) // always compute energy offset offset_flag = 1; - // set comm size needed by this Pair + // set comm size needed by this pair style comm_forward = 39; tap_flag = 1; } @@ -801,9 +802,10 @@ void PairILPGrapheneHBN::coeff(int narg, char **arg) error->all(FLERR,"Incorrect args for pair coefficients"); if (!allocated) allocate(); - int ilo,ihi,jlo,jhi; - force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi); - force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi); + // insure I,J args are * * + + if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0) + error->all(FLERR,"Incorrect args for pair coefficients"); // read args that map atom types to elements in potential file // map[i] = which element the Ith atom type is, -1 if NULL @@ -837,16 +839,23 @@ void PairILPGrapheneHBN::coeff(int narg, char **arg) read_file(arg[2]); - double cut_one = cut_global; + // clear setflag since coeff() called once with I,J = * * + + n = atom->ntypes; + for (int i = 1; i <= n; i++) + for (int j = i; j <= n; j++) + setflag[i][j] = 0; + + // set setflag i,j for type pairs where both are mapped to elements int count = 0; - for (int i = ilo; i <= ihi; i++) { - for (int j = MAX(jlo,i); j <= jhi; j++) { - cut[i][j] = cut_one; - setflag[i][j] = 1; - count++; - } - } + for (int i = 1; i <= n; i++) + for (int j = i; j <= n; j++) + if (map[i] >= 0 && map[j] >= 0) { + setflag[i][j] = 1; + cut[i][j] = cut_global; + count++; + } if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); } @@ -859,6 +868,8 @@ void PairILPGrapheneHBN::coeff(int narg, char **arg) double PairILPGrapheneHBN::init_one(int i, int j) { if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set"); + if (!offset_flag) + error->all(FLERR,"Must use 'pair_modify shift yes' with this pair style"); if (offset_flag && (cut[i][j] > 0.0)) { int iparam_ij = elem2param[map[i]][map[j]]; diff --git a/src/USER-MISC/pair_kolmogorov_crespi_full.cpp b/src/USER-MISC/pair_kolmogorov_crespi_full.cpp index 39535109cd..e73278968d 100644 --- a/src/USER-MISC/pair_kolmogorov_crespi_full.cpp +++ b/src/USER-MISC/pair_kolmogorov_crespi_full.cpp @@ -46,6 +46,9 @@ using namespace LAMMPS_NS; PairKolmogorovCrespiFull::PairKolmogorovCrespiFull(LAMMPS *lmp) : Pair(lmp) { + restartinfo = 0; + one_coeff = 1; + // initialize element to parameter maps nelements = 0; elements = NULL; @@ -256,7 +259,7 @@ void PairKolmogorovCrespiFull::compute(int eflag, int vflag) // calculate the forces acted on the neighbors of atom i from atom j KC_neighs_i = KC_firstneigh[i]; - for (kk = 0; kk < KC_numneigh[i]; kk++) { + for (kk = 0; kk < KC_numneigh[i]; kk++) { k = KC_neighs_i[kk]; if (k == i) continue; // derivatives of the product of rij and ni respect to rk, k=0,1,2, where atom k is the neighbors of atom i @@ -277,7 +280,7 @@ void PairKolmogorovCrespiFull::compute(int eflag, int vflag) // calculate the forces acted on the neighbors of atom j from atom i KC_neighs_j = KC_firstneigh[j]; - for (ll = 0; ll < KC_numneigh[j]; ll++) { + for (ll = 0; ll < KC_numneigh[j]; ll++) { l = KC_neighs_j[ll]; if (l == j) continue; // derivatives of the product of rji and nj respect to rl, l=0,1,2, where atom l is the neighbors of atom j @@ -805,9 +808,10 @@ void PairKolmogorovCrespiFull::coeff(int narg, char **arg) error->all(FLERR,"Incorrect args for pair coefficients"); if (!allocated) allocate(); - int ilo,ihi,jlo,jhi; - force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi); - force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi); + // insure I,J args are * * + + if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0) + error->all(FLERR,"Incorrect args for pair coefficients"); // read args that map atom types to elements in potential file // map[i] = which element the Ith atom type is, -1 if NULL @@ -841,16 +845,23 @@ void PairKolmogorovCrespiFull::coeff(int narg, char **arg) read_file(arg[2]); - double cut_one = cut_global; + // clear setflag since coeff() called once with I,J = * * + + n = atom->ntypes; + for (int i = 1; i <= n; i++) + for (int j = i; j <= n; j++) + setflag[i][j] = 0; + + // set setflag i,j for type pairs where both are mapped to elements int count = 0; - for (int i = ilo; i <= ihi; i++) { - for (int j = MAX(jlo,i); j <= jhi; j++) { - cut[i][j] = cut_one; - setflag[i][j] = 1; - count++; - } - } + for (int i = 1; i <= n; i++) + for (int j = i; j <= n; j++) + if (map[i] >= 0 && map[j] >= 0) { + setflag[i][j] = 1; + cut[i][j] = cut_global; + count++; + } if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); } @@ -863,6 +874,8 @@ void PairKolmogorovCrespiFull::coeff(int narg, char **arg) double PairKolmogorovCrespiFull::init_one(int i, int j) { if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set"); + if (!offset_flag) + error->all(FLERR,"Must use 'pair_modify shift yes' with this pair style"); if (offset_flag && (cut[i][j] > 0.0)) { int iparam_ij = elem2param[map[i]][map[j]]; diff --git a/src/USER-MISC/pair_kolmogorov_crespi_z.cpp b/src/USER-MISC/pair_kolmogorov_crespi_z.cpp index dcea990a3b..79d6aa3daf 100644 --- a/src/USER-MISC/pair_kolmogorov_crespi_z.cpp +++ b/src/USER-MISC/pair_kolmogorov_crespi_z.cpp @@ -259,17 +259,18 @@ void PairKolmogorovCrespiZ::coeff(int narg, char **arg) } } - read_file(arg[2]); - double cut_one = cut_global; + // set setflag only for i,j pairs where both are mapped to elements int count = 0; for (int i = ilo; i <= ihi; i++) { for (int j = MAX(jlo,i); j <= jhi; j++) { - cut[i][j] = cut_one; - setflag[i][j] = 1; - count++; + if ((map[i] >=0) && (map[j] >= 0)) { + cut[i][j] = cut_global; + setflag[i][j] = 1; + count++; + } } } @@ -284,6 +285,8 @@ void PairKolmogorovCrespiZ::coeff(int narg, char **arg) double PairKolmogorovCrespiZ::init_one(int i, int j) { if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set"); + if (!offset_flag) + error->all(FLERR,"Must use 'pair_modify shift yes' with this pair style"); if (offset_flag && (cut[i][j] > 0.0)) { int iparam_ij = elem2param[map[i]][map[j]]; diff --git a/src/USER-MISC/pair_lebedeva_z.cpp b/src/USER-MISC/pair_lebedeva_z.cpp index 0ab22e04c1..c9d90e2850 100644 --- a/src/USER-MISC/pair_lebedeva_z.cpp +++ b/src/USER-MISC/pair_lebedeva_z.cpp @@ -44,6 +44,7 @@ using namespace LAMMPS_NS; PairLebedevaZ::PairLebedevaZ(LAMMPS *lmp) : Pair(lmp) { single_enable = 0; + restartinfo = 0; // initialize element to parameter maps nelements = 0; @@ -254,17 +255,18 @@ void PairLebedevaZ::coeff(int narg, char **arg) } } - read_file(arg[2]); - double cut_one = cut_global; + // set setflag only for i,j pairs where both are mapped to elements int count = 0; for (int i = ilo; i <= ihi; i++) { for (int j = MAX(jlo,i); j <= jhi; j++) { - cut[i][j] = cut_one; - setflag[i][j] = 1; - count++; + if ((map[i] >= 0) && (map[j] >= 0)) { + cut[i][j] = cut_global; + setflag[i][j] = 1; + count++; + } } } @@ -279,6 +281,8 @@ void PairLebedevaZ::coeff(int narg, char **arg) double PairLebedevaZ::init_one(int i, int j) { if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set"); + if (!offset_flag) + error->all(FLERR,"Must use 'pair_modify shift yes' with this pair style"); if (offset_flag && (cut[i][j] > 0.0)) { int iparam_ij = elem2param[map[i]][map[j]]; diff --git a/src/USER-MISC/pair_lennard_mdf.cpp b/src/USER-MISC/pair_lennard_mdf.cpp index b51639e80e..e2e81e4943 100644 --- a/src/USER-MISC/pair_lennard_mdf.cpp +++ b/src/USER-MISC/pair_lennard_mdf.cpp @@ -251,13 +251,7 @@ void PairLJ_AB_MDF::coeff(int narg, char **arg) double PairLJ_AB_MDF::init_one(int i, int j) { - if (setflag[i][j] == 0) { - aparm[i][j] = mix_energy(aparm[i][i],aparm[j][j], - bparm[i][i],bparm[j][j]); - bparm[i][j] = mix_distance(bparm[i][i],bparm[j][j]); - cut_inner[i][j] = mix_distance(cut_inner[i][i],cut_inner[j][j]); - cut[i][j] = mix_distance(cut[i][i],cut[j][j]); - } + if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set"); cut_inner_sq[i][j] = cut_inner[i][j]*cut_inner[i][j]; diff --git a/src/USER-MISC/pair_lj_mdf.cpp b/src/USER-MISC/pair_lj_mdf.cpp index ca0118ffb0..cfe125f21f 100644 --- a/src/USER-MISC/pair_lj_mdf.cpp +++ b/src/USER-MISC/pair_lj_mdf.cpp @@ -33,7 +33,9 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -PairLJMDF::PairLJMDF(LAMMPS *lmp) : Pair(lmp) {} +PairLJMDF::PairLJMDF(LAMMPS *lmp) : Pair(lmp) { + writedata = 1; +} /* ---------------------------------------------------------------------- */ @@ -349,6 +351,29 @@ void PairLJMDF::read_restart_settings(FILE *fp) MPI_Bcast(&mix_flag,1,MPI_INT,0,world); } +/* ---------------------------------------------------------------------- + proc 0 writes to data file +------------------------------------------------------------------------- */ + +void PairLJMDF::write_data(FILE *fp) +{ + for (int i = 1; i <= atom->ntypes; i++) + fprintf(fp,"%d %g %g\n",i,epsilon[i][i],sigma[i][i]); +} + +/* ---------------------------------------------------------------------- + proc 0 writes all pairs to data file +------------------------------------------------------------------------- */ + +void PairLJMDF::write_data_all(FILE *fp) +{ + for (int i = 1; i <= atom->ntypes; i++) + for (int j = i; j <= atom->ntypes; j++) + fprintf(fp,"%d %d %g %g %g %g\n", + i,j,epsilon[i][j],sigma[i][j], + cut_inner[i][j],cut[i][j]); +} + /* ---------------------------------------------------------------------- */ double PairLJMDF::single(int /*i*/, int /*j*/, int itype, int jtype, diff --git a/src/USER-MISC/pair_lj_mdf.h b/src/USER-MISC/pair_lj_mdf.h index c6236a923c..6ce6fdda2c 100644 --- a/src/USER-MISC/pair_lj_mdf.h +++ b/src/USER-MISC/pair_lj_mdf.h @@ -37,6 +37,8 @@ class PairLJMDF : public Pair { void read_restart(FILE *); void write_restart_settings(FILE *); void read_restart_settings(FILE *); + void write_data(FILE *); + void write_data_all(FILE *); double single(int, int, int, int, double, double, double, double &); void *extract(const char *, int &); diff --git a/src/USER-OMP/pair_airebo_morse_omp.cpp b/src/USER-OMP/pair_airebo_morse_omp.cpp index b923775a27..5d5ac0b885 100644 --- a/src/USER-OMP/pair_airebo_morse_omp.cpp +++ b/src/USER-OMP/pair_airebo_morse_omp.cpp @@ -19,7 +19,9 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -PairAIREBOMorseOMP::PairAIREBOMorseOMP(LAMMPS *lmp) : PairAIREBOOMP(lmp) {} +PairAIREBOMorseOMP::PairAIREBOMorseOMP(LAMMPS *lmp) : PairAIREBOOMP(lmp) { + variant = AIREBO_M; +} /* ---------------------------------------------------------------------- global settings diff --git a/src/USER-OMP/pair_reaxc_omp.cpp b/src/USER-OMP/pair_reaxc_omp.cpp index 927a63a90f..2f17515130 100644 --- a/src/USER-OMP/pair_reaxc_omp.cpp +++ b/src/USER-OMP/pair_reaxc_omp.cpp @@ -373,7 +373,7 @@ void PairReaxCOMP::init_style( ) if (fix_reax == NULL) { char **fixarg = new char*[3]; - fixarg[0] = (char *) "REAXC"; + fixarg[0] = (char *) fix_id; fixarg[1] = (char *) "all"; fixarg[2] = (char *) "REAXC"; modify->add_fix(3,fixarg); @@ -643,4 +643,3 @@ void PairReaxCOMP::FindBond() } } } - diff --git a/src/USER-OMP/pair_rebo_omp.cpp b/src/USER-OMP/pair_rebo_omp.cpp index 2b58b45b53..bd98c6426c 100644 --- a/src/USER-OMP/pair_rebo_omp.cpp +++ b/src/USER-OMP/pair_rebo_omp.cpp @@ -18,7 +18,9 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -PairREBOOMP::PairREBOOMP(LAMMPS *lmp) : PairAIREBOOMP(lmp) {} +PairREBOOMP::PairREBOOMP(LAMMPS *lmp) : PairAIREBOOMP(lmp) { + variant = REBO_2; +} /* ---------------------------------------------------------------------- global settings @@ -31,3 +33,36 @@ void PairREBOOMP::settings(int narg, char ** /* arg */) cutlj = 0.0; ljflag = torflag = 0; } + +/* ---------------------------------------------------------------------- + initialize spline knot values +------------------------------------------------------------------------- */ + +void PairREBOOMP::spline_init() { + PairAIREBO::spline_init(); + + int i,j,k; + + PCCf[0][2] = 0.007860700254745; + PCCf[0][3] = 0.016125364564267; + PCCf[1][1] = 0.003026697473481; + PCCf[1][2] = 0.006326248241119; + PCCf[2][0] = 0.; + PCCf[2][1] = 0.003179530830731; + + for (int nH = 0; nH < 4; nH++) { + for (int nC = 0; nC < 4; nC++) { + double y[4] = {0}, y1[4] = {0}, y2[4] = {0}; + y[0] = PCCf[nC][nH]; + y[1] = PCCf[nC][nH+1]; + y[2] = PCCf[nC+1][nH]; + y[3] = PCCf[nC+1][nH+1]; + Spbicubic_patch_coeffs(nC, nC+1, nH, nH+1, y, y1, y2, &pCC[nC][nH][0]); + y[0] = PCHf[nC][nH]; + y[1] = PCHf[nC][nH+1]; + y[2] = PCHf[nC+1][nH]; + y[3] = PCHf[nC+1][nH+1]; + Spbicubic_patch_coeffs(nC, nC+1, nH, nH+1, y, y1, y2, &pCH[nC][nH][0]); + } + } +} diff --git a/src/USER-OMP/pair_rebo_omp.h b/src/USER-OMP/pair_rebo_omp.h index 9ff28a260b..ef837f33df 100644 --- a/src/USER-OMP/pair_rebo_omp.h +++ b/src/USER-OMP/pair_rebo_omp.h @@ -28,6 +28,8 @@ class PairREBOOMP : public PairAIREBOOMP { public: PairREBOOMP(class LAMMPS *); virtual void settings(int, char **); + protected: + void spline_init(); }; } diff --git a/src/USER-OMP/reaxc_nonbonded_omp.cpp b/src/USER-OMP/reaxc_nonbonded_omp.cpp index a93cd54931..ea92e0c210 100644 --- a/src/USER-OMP/reaxc_nonbonded_omp.cpp +++ b/src/USER-OMP/reaxc_nonbonded_omp.cpp @@ -281,6 +281,7 @@ void Tabulated_vdW_Coulomb_Energy_OMP(reax_system *system,control_params *contro int tid = 0; #endif long froffset = (system->N * tid); + LR_lookup_table ** & LR = system->LR; class PairReaxCOMP *pair_reax_ptr; pair_reax_ptr = static_cast(system->pair_ptr); diff --git a/src/USER-REAXC/pair_reaxc.cpp b/src/USER-REAXC/pair_reaxc.cpp index 3f80f2101d..8f8dcfb8fc 100644 --- a/src/USER-REAXC/pair_reaxc.cpp +++ b/src/USER-REAXC/pair_reaxc.cpp @@ -74,6 +74,9 @@ PairReaxC::PairReaxC(LAMMPS *lmp) : Pair(lmp) manybody_flag = 1; ghostneigh = 1; + fix_id = new char[24]; + snprintf(fix_id,24,"REAXC_%d",instance_me); + system = (reax_system *) memory->smalloc(sizeof(reax_system),"reax:system"); memset(system,0,sizeof(reax_system)); @@ -135,7 +138,8 @@ PairReaxC::~PairReaxC() { if (copymode) return; - if (fix_reax) modify->delete_fix("REAXC"); + if (fix_reax) modify->delete_fix(fix_id); + delete[] fix_id; if (setup_flag) { Close_Output_Files( system, control, out_control, mpi_data ); @@ -412,7 +416,7 @@ void PairReaxC::init_style( ) if (fix_reax == NULL) { char **fixarg = new char*[3]; - fixarg[0] = (char *) "REAXC"; + fixarg[0] = (char *) fix_id; fixarg[1] = (char *) "all"; fixarg[2] = (char *) "REAXC"; modify->add_fix(3,fixarg); diff --git a/src/USER-REAXC/pair_reaxc.h b/src/USER-REAXC/pair_reaxc.h index 91b44be661..a833ddbcf0 100644 --- a/src/USER-REAXC/pair_reaxc.h +++ b/src/USER-REAXC/pair_reaxc.h @@ -60,6 +60,7 @@ class PairReaxC : public Pair { bigint ngroup; protected: + char *fix_id; double cutmax; int nelements; // # of unique elements char **elements; // names of unique elements diff --git a/src/USER-REAXC/reaxc_lookup.cpp b/src/USER-REAXC/reaxc_lookup.cpp index 74d8176522..8d33a33fba 100644 --- a/src/USER-REAXC/reaxc_lookup.cpp +++ b/src/USER-REAXC/reaxc_lookup.cpp @@ -29,7 +29,6 @@ #include "reaxc_nonbonded.h" #include "reaxc_tool_box.h" -LR_lookup_table **LR; void Tridiagonal_Solve( const double *a, const double *b, double *c, double *d, double *x, unsigned int n){ @@ -157,6 +156,7 @@ int Init_Lookup_Tables( reax_system *system, control_params *control, double dr; double *h, *fh, *fvdw, *fele, *fCEvd, *fCEclmb; double v0_vdw, v0_ele, vlast_vdw, vlast_ele; + LR_lookup_table ** & LR = system->LR; /* initializations */ v0_vdw = 0; @@ -273,6 +273,7 @@ void Deallocate_Lookup_Tables( reax_system *system ) { int i, j; int ntypes; + LR_lookup_table ** & LR = system->LR; ntypes = system->reax_param.num_atom_types; diff --git a/src/USER-REAXC/reaxc_nonbonded.cpp b/src/USER-REAXC/reaxc_nonbonded.cpp index c13bc0d89f..b0fea8c1b9 100644 --- a/src/USER-REAXC/reaxc_nonbonded.cpp +++ b/src/USER-REAXC/reaxc_nonbonded.cpp @@ -220,6 +220,7 @@ void Tabulated_vdW_Coulomb_Energy( reax_system *system,control_params *control, far_neighbor_data *nbr_pj; reax_list *far_nbrs; LR_lookup_table *t; + LR_lookup_table ** & LR = system->LR; natoms = system->n; far_nbrs = (*lists) + FAR_NBRS; diff --git a/src/USER-REAXC/reaxc_types.h b/src/USER-REAXC/reaxc_types.h index b05f655040..0821c065cc 100644 --- a/src/USER-REAXC/reaxc_types.h +++ b/src/USER-REAXC/reaxc_types.h @@ -395,6 +395,8 @@ typedef struct double ghost_cutoff; } boundary_cutoff; + +struct _LR_lookup_table; // forward declaration struct _reax_system { reax_interaction reax_param; @@ -418,6 +420,8 @@ struct _reax_system int mincap; double safezone, saferzone; + _LR_lookup_table **LR; + int omp_active; }; typedef _reax_system reax_system; @@ -883,7 +887,7 @@ struct cubic_spline_coef -typedef struct +typedef struct _LR_lookup_table { double xmin, xmax; int n; @@ -897,7 +901,6 @@ typedef struct cubic_spline_coef *vdW, *CEvd; cubic_spline_coef *ele, *CEclmb; } LR_lookup_table; -extern LR_lookup_table **LR; /* function pointer defs */ typedef void (*evolve_function)(reax_system*, control_params*, diff --git a/src/domain.cpp b/src/domain.cpp index 86c4eb2c02..4f23423ae8 100644 --- a/src/domain.cpp +++ b/src/domain.cpp @@ -57,6 +57,7 @@ Domain::Domain(LAMMPS *lmp) : Pointers(lmp) { box_exist = 0; box_change = 0; + deform_flag = deform_vremap = deform_groupbit = 0; dimension = 3; nonperiodic = 0; diff --git a/src/error.cpp b/src/error.cpp index 7c2d3c5409..cc80dcb4d8 100644 --- a/src/error.cpp +++ b/src/error.cpp @@ -212,6 +212,8 @@ void Error::one(const char *file, int line, const char *str) snprintf(msg, 100, "ERROR on proc %d: %s (%s:%d)\n", me, str, truncpath(file), line); throw LAMMPSAbortException(msg, world); #else + if (screen) fflush(screen); + if (logfile) fflush(logfile); MPI_Abort(world,1); #endif } diff --git a/src/fix_print.cpp b/src/fix_print.cpp index 969fcf8140..f6db88114a 100644 --- a/src/fix_print.cpp +++ b/src/fix_print.cpp @@ -29,11 +29,18 @@ using namespace FixConst; FixPrint::FixPrint(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg), - fp(NULL), string(NULL), copy(NULL), work(NULL) + fp(NULL), string(NULL), copy(NULL), work(NULL), var_print(NULL) { if (narg < 5) error->all(FLERR,"Illegal fix print command"); - nevery = force->inumeric(FLERR,arg[3]); - if (nevery <= 0) error->all(FLERR,"Illegal fix print command"); + if (strstr(arg[3],"v_") == arg[3]) { + int n = strlen(&arg[3][2]) + 1; + var_print = new char[n]; + strcpy(var_print,&arg[3][2]); + nevery = 1; + } else { + nevery = force->inumeric(FLERR,arg[3]); + if (nevery <= 0) error->all(FLERR,"Illegal fix print command"); + } MPI_Comm_rank(world,&me); @@ -89,13 +96,6 @@ FixPrint::FixPrint(LAMMPS *lmp, int narg, char **arg) : } delete [] title; - - // add nfirst to all computes that store invocation times - // since don't know a priori which are invoked via variables by this fix - // once in end_of_step() can set timestep for ones actually invoked - - const bigint nfirst = (update->ntimestep/nevery)*nevery + nevery; - modify->addstep_compute_all(nfirst); } /* ---------------------------------------------------------------------- */ @@ -103,6 +103,7 @@ FixPrint::FixPrint(LAMMPS *lmp, int narg, char **arg) : FixPrint::~FixPrint() { delete [] string; + delete [] var_print; memory->sfree(copy); memory->sfree(work); @@ -120,8 +121,35 @@ int FixPrint::setmask() /* ---------------------------------------------------------------------- */ +void FixPrint::init() +{ + if (var_print) { + ivar_print = input->variable->find(var_print); + if (ivar_print < 0) + error->all(FLERR,"Variable name for fix print timestep does not exist"); + if (!input->variable->equalstyle(ivar_print)) + error->all(FLERR,"Variable for fix print timestep is invalid style"); + next_print = static_cast + (input->variable->compute_equal(ivar_print)); + if (next_print <= update->ntimestep) + error->all(FLERR,"Fix print timestep variable returned a bad timestep"); + } else { + next_print = (update->ntimestep/nevery)*nevery + nevery; + } + + // add next_print to all computes that store invocation times + // since don't know a priori which are invoked via variables by this fix + // once in end_of_step() can set timestep for ones actually invoked + + modify->addstep_compute_all(next_print); +} + +/* ---------------------------------------------------------------------- */ + void FixPrint::end_of_step() { + if (update->ntimestep != next_print) return; + // make a copy of string to work on // substitute for $ variables (no printing) // append a newline and print final copy @@ -132,7 +160,15 @@ void FixPrint::end_of_step() strcpy(copy,string); input->substitute(copy,work,maxcopy,maxwork,0); - modify->addstep_compute(update->ntimestep + nevery); + if (var_print) { + next_print = static_cast + (input->variable->compute_equal(ivar_print)); + if (next_print <= update->ntimestep) + error->all(FLERR,"Fix print timestep variable returned a bad timestep"); + } else { + next_print = (update->ntimestep/nevery)*nevery + nevery; + } + modify->addstep_compute(next_print); if (me == 0) { if (screenflag && screen) fprintf(screen,"%s\n",copy); diff --git a/src/fix_print.h b/src/fix_print.h index 1f6efdf108..37b6680aee 100644 --- a/src/fix_print.h +++ b/src/fix_print.h @@ -29,6 +29,7 @@ class FixPrint : public Fix { public: FixPrint(class LAMMPS *, int, char **); ~FixPrint(); + void init(); int setmask(); void end_of_step(); @@ -37,6 +38,9 @@ class FixPrint : public Fix { FILE *fp; char *string,*copy,*work; int maxcopy,maxwork; + char *var_print; + int ivar_print; + bigint next_print; }; } diff --git a/src/output.cpp b/src/output.cpp index 884647f478..55eaeb0aaa 100644 --- a/src/output.cpp +++ b/src/output.cpp @@ -675,8 +675,13 @@ void Output::set_thermo(int narg, char **arg) { if (narg != 1) error->all(FLERR,"Illegal thermo command"); + // always reset var_thermo, so it is possible to switch back from + // variable spaced thermo outputs to constant spaced ones. + + delete [] var_thermo; + var_thermo = NULL; + if (strstr(arg[0],"v_") == arg[0]) { - delete [] var_thermo; int n = strlen(&arg[0][2]) + 1; var_thermo = new char[n]; strcpy(var_thermo,&arg[0][2]); diff --git a/src/version.h b/src/version.h index 94fee893cb..0377cb9b35 100644 --- a/src/version.h +++ b/src/version.h @@ -1 +1 @@ -#define LAMMPS_VERSION "29 Mar 2019" +#define LAMMPS_VERSION "15 May 2019" diff --git a/tools/README b/tools/README index 6bf7d6b878..54f8d86898 100644 --- a/tools/README +++ b/tools/README @@ -39,6 +39,7 @@ pymol_asphere convert LAMMPS output of ellipsoids to PyMol format python Python scripts for post-processing LAMMPS output reax Tools for analyzing output of ReaxFF simulations smd convert Smooth Mach Dynamics triangles to VTK +spin perform a cubic polynomial interpolation of a GNEB MEP vim add-ons to VIM editor for editing LAMMPS input scripts xmgrace a collection of scripts to generate xmgrace plots diff --git a/tools/spin/interpolate_gneb/README b/tools/spin/interpolate_gneb/README new file mode 100644 index 0000000000..ab30373249 --- /dev/null +++ b/tools/spin/interpolate_gneb/README @@ -0,0 +1,31 @@ +Interpolate.x tries to perform a cubic polynomial interpolation +of the MEP. + +Compile the program with: +gcc interpolate.c -o interpolate.x + +and then run it as: +./interpolate.x + +Enter N-1 (with N the number of replica). +The program reads the "neb_init.dat", in which you need to +replace the current values by your GNEB outputs. + +Each line corresponds to a replica, and has to respectively +contain: + +Reac. coords /tab/ pot. energy /tab/ fm dot tangent /tab/ +geodesic dist to next replica + +All those information can be provided by the verbose output of +a neb/spin calculation + +The progam outputs the interpolation result, and the +interpolated MEP in "interpolation_result.dat". + +This code is a courtesy of Aleksei Ivanov, University of +Iceland. +For more explanation about this calculation, see Appendix D +of the following reference: +Bessarab, P. F., Uzdin, V. M., & Jónsson, H. (2015). +Computer Physics Communications, 196, 335-347. diff --git a/tools/spin/interpolate_gneb/interpolate.c b/tools/spin/interpolate_gneb/interpolate.c new file mode 100644 index 0000000000..32734ee224 --- /dev/null +++ b/tools/spin/interpolate_gneb/interpolate.c @@ -0,0 +1,106 @@ +/* ------------------------------------------------------------------------ + Provide some explanation here +------------------------------------------------------------------------- */ + +/* ------------------------------------------------------------------------ + This program is a courtesy of Aleksei Ivanov (Univ. of Iceland) + Contributing authors: Aleksei Ivanov (Univ. of Iceland), + Julien Tranchida (SNL) +------------------------------------------------------------------------- */ + +#include +#include +#include + +// calculate cubic coefficients + +void count_coefficient(double *V, double *F, double *R, double *a, double *b, + double *c,double *d,int M){ + /* R = square of distance between images*/ + /* V = energy of images */ + /* F = projection of real real forces along the path? */ + int i; + for(i = 0; i < M ; i++) { + a[i] = ( -2.0*(V[i+1]-V[i])/R[i] - F[i] - F[i+1] ) / (R[i]*R[i]); + //a[i] = ( -2.0*(V[i+1]-V[i])/sqrt(R[i]) - F[i] - F[i+1] ) / R[i]; + b[i] = ( 3.0*(V[i+1]-V[i]) + (2.0*F[i]+F[i+1])*R[i] ) / (R[i]*R[i]); + //b[i] = ( 3.0*(V[i+1]-V[i]) + (2.0*F[i]+F[i+1])*sqrt(R[i]) ) / R[i]; + c[i] = -F[i]; + d[i] = V[i]; + } +} + +// cubic spline + +double spline(double a,double b,double c,double d,double x) { + return (a*x*x*x + b*x*x + c*x + d); +} + +int main() { + int M=0; // M+1 = number of images + double *fmdottan; // projection of real forces on tangent path + double *coords; // initial value of reaction coords + double *V; // energy of images + double *dist; // square of the distance between images + double *a, *b, *c, *d ; // coefficients of cubic functions + double x; // reaction coordinate + double A,B; // additional variables for rnd + double length = 0.0; + int i,j; + FILE *data; + + printf("Enter M = number of images - 1 \n"); + scanf("%d",&M); + + // allocating and initializing tables + + a = calloc(M,sizeof(double)); // cubic coefficients + b = calloc(M,sizeof(double)); + c = calloc(M,sizeof(double)); + d = calloc(M,sizeof(double)); + V = calloc((M+1),sizeof(double)); // energies + coords = calloc((M+1),sizeof(double)); // reaction coordinates + fmdottan = calloc((M+1),sizeof(double)); // fm dot tangent + dist = calloc(M+1,sizeof(double)); // distance between images + + // reading input file + + if((data=fopen("neb_init.dat","r")) == NULL) { + printf("Incorrect input file name."); + return 0; + } + + for(j=0; j < M+1; j++) { + fscanf(data,"%lf\t%lf\t%lf\t%lf\n",&coords[j],&V[j],&fmdottan[j],&dist[j]); + length += dist[j]; + printf("%lf %lf %lf %lf\n",coords[j],V[j],fmdottan[j],dist[j]); + } + + if( (fclose(data)) == 0) { + printf("Data stored, input file closed.\n "); + } + + // calculate value of coefficients + + count_coefficient(V,fmdottan,dist,a,b,c,d,M); + + // plot result of the interpolation + + if( ( data=fopen("interpolation_result.dat","w") )== NULL) { + printf("Interpolation file could not be open."); + return 0; + } + + A = B = 0.0; + for(i = 0; i < M ; i++) { + B += dist[i]; + printf("%13le\n",B); + for(j = 0; j <= 1000; j++) { + x = dist[i]*1.0e-3*j; + fprintf(data,"%13lf\t%13le\n",(x+A)/length,spline(a[i],b[i],c[i],d[i],x)); + } + A += dist[i]; + } + + return 0; +} diff --git a/tools/spin/interpolate_gneb/neb_init.dat b/tools/spin/interpolate_gneb/neb_init.dat new file mode 100644 index 0000000000..7a56274a31 --- /dev/null +++ b/tools/spin/interpolate_gneb/neb_init.dat @@ -0,0 +1,8 @@ +0.0000000 -3.915271 3.4995081e-17 2.4573077 +0.14285714 -3.9148148 -0.00059075739 2.4573077 +0.28571429 -3.9136926 -0.00072315767 2.4573077 +0.42857143 -3.9127883 -0.0003191228 2.4573265 +0.57142857 -3.9127883 0.0003191228 2.4403341 +0.71428571 -3.9136926 0.00072315767 2.4044093 +0.85714286 -3.9148148 0.00059075739 2.3766041 +1.0000000 -3.915271 -4.1231828e-17 0.0000000