diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index a049ab8c28..a64d18a6da 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -138,15 +138,84 @@ install(TARGETS lmp EXPORT LAMMPS_Targets DESTINATION ${CMAKE_INSTALL_BINDIR}) option(CMAKE_VERBOSE_MAKEFILE "Generate verbose Makefiles" OFF) -set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE - GRANULAR KSPACE LATTE MANYBODY MC MESSAGE MISC ML-IAP MOLECULE PERI POEMS - PLUGIN QEQ REPLICA RIGID SHOCK SPIN ML-SNAP SRD KIM PYTHON MSCG MPIIO VORONOI - ADIOS ATC AWPMD BOCS CG-DNA DPD-MESO CG-SDK - COLVARS DIELECTRIC DIFFRACTION DPD-REACT DRUDE EFF FEP - H5MD ML-HDNNP LATBOLTZ MANIFOLD MDI MEAM MESONT MGPT - USER-MISC MOFFF MOLFILE NETCDF PHONON PLUMED PTM QTB - ML-RANN REACTION REAXFF SCAFACOS DPD-SMOOTH MACHDYN SMTBQ SPH - TALLY UEF VTK ML-QUIP QMMM YAFF ML-PACE BROWNIAN) +set(STANDARD_PACKAGES + ADIOS + ASPHERE + ATC + AWPMD + BOCS + BODY + BROWNIAN + CG-DNA + CG-SDK + CLASS2 + COLLOID + COLVARS + COMPRESS + DIELECTRIC + DIFFRACTION + DIPOLE + DPD-BASIC + DPD-MESO + DPD-REACT + DPD-SMOOTH + DRUDE + EFF + FEP + GRANULAR + H5MD + KIM + KSPACE + LATBOLTZ + LATTE + MACHDYN + MANIFOLD + MANYBODY + MC + MDI + MEAM + MESONT + MESSAGE + MGPT + MISC + ML-HDNNP + ML-IAP + ML-PACE + ML-QUIP + ML-RANN + ML-SNAP + MOFFF + MOLECULE + MOLFILE + MPIIO + MSCG + NETCDF + PERI + PHONON + PLUGIN + PLUMED + POEMS + PTM + PYTHON + QEQ + QMMM + QTB + REACTION + REAXFF + REPLICA + RIGID + SCAFACOS + SHOCK + SMTBQ + SPH + SPIN + SRD + TALLY + UEF + USER-MISC + VORONOI + VTK + YAFF) set(SUFFIX_PACKAGES CORESHELL GPU KOKKOS OPT INTEL OPENMP) diff --git a/cmake/presets/all_off.cmake b/cmake/presets/all_off.cmake index e77e4aae1a..c95d3e8463 100644 --- a/cmake/presets/all_off.cmake +++ b/cmake/presets/all_off.cmake @@ -19,6 +19,7 @@ set(ALL_PACKAGES DIELECTRIC DIFFRACTION DIPOLE + DPD-BASIC DPD-MESO DPD-REACT DPD-SMOOTH diff --git a/cmake/presets/all_on.cmake b/cmake/presets/all_on.cmake index 7df3512223..bc7ae553db 100644 --- a/cmake/presets/all_on.cmake +++ b/cmake/presets/all_on.cmake @@ -21,6 +21,7 @@ set(ALL_PACKAGES DIELECTRIC DIFFRACTION DIPOLE + DPD-BASIC DPD-MESO DPD-REACT DPD-SMOOTH diff --git a/cmake/presets/mingw-cross.cmake b/cmake/presets/mingw-cross.cmake index 0b24bfbc28..b07d1a707b 100644 --- a/cmake/presets/mingw-cross.cmake +++ b/cmake/presets/mingw-cross.cmake @@ -15,6 +15,7 @@ set(WIN_PACKAGES DIELECTRIC DIFFRACTION DIPOLE + DPD-BASIC DPD-MESO DPD-REACT DPD-SMOOTH diff --git a/cmake/presets/most.cmake b/cmake/presets/most.cmake index 3e8fc11f05..ae65cc75bb 100644 --- a/cmake/presets/most.cmake +++ b/cmake/presets/most.cmake @@ -17,6 +17,7 @@ set(ALL_PACKAGES DIELECTRIC DIFFRACTION DIPOLE + DPD-BASIC DPD-MESO DPD-REACT DPD-SMOOTH diff --git a/doc/src/Packages_details.rst b/doc/src/Packages_details.rst index fd43465f4a..cb3bb904b1 100644 --- a/doc/src/Packages_details.rst +++ b/doc/src/Packages_details.rst @@ -43,6 +43,7 @@ page gives those details. * :ref:`DIELECTRIC ` * :ref:`DIFFRACTION ` * :ref:`DIPOLE ` + * :ref:`DPD-BASIC ` * :ref:`DPD-MESO ` * :ref:`DPD-REACT ` * :ref:`DPD-SMOOTH ` @@ -560,6 +561,29 @@ short-range or long-range interactions. ---------- +.. _PKG-DPD-BASIC: + +DPD-BASIC package +-------------------- + +**Contents:** + +Pair styles for the basic dissipative particle dynamics (DPD) method +and DPD thermostatting. + +**Author:** Kurt Smith (U Pittsburgh), Martin Svoboda, Martin Lisal (ICPF and UJEP) + +**Supporting info:** + +* src/DPD-BASIC: filenames -> commands +* :doc:`pair_style dpd ` +* :doc:`pair_style dpd/tstat ` +* :doc:`pair_style dpd/ext ` +* :doc:`pair_style dpd/ext/tstat ` +* examples/PACKAGES/dpd-basic + +---------- + .. _PKG-DPD-MESO: DPD-MESO package diff --git a/doc/src/Packages_list.rst b/doc/src/Packages_list.rst index b643cc542d..44c05f8a39 100644 --- a/doc/src/Packages_list.rst +++ b/doc/src/Packages_list.rst @@ -113,6 +113,11 @@ whether an extra library is needed to build and use the package: - :doc:`pair_style lj/.../dipole ` - dipole - no + * - :ref:`DPD-BASIC ` + - basic DPD models + - :doc:`pair_styles dpd dpd/tstat ` :doc:`dpd/ext dpd/ext/tstat ` + - PACKAGES/dpd-basic + - no * - :ref:`DPD-MESO ` - mesoscale DPD models - :doc:`pair_style edpd ` diff --git a/doc/src/pair_dpd.rst b/doc/src/pair_dpd.rst index 62cf94786d..aa8323379a 100644 --- a/doc/src/pair_dpd.rst +++ b/doc/src/pair_dpd.rst @@ -154,14 +154,14 @@ These pair styles do not support the :doc:`pair_modify ` tail option for adding long-range tail corrections to energy and pressure. -These pair styles writes their information to :doc:`binary restart files `, so pair_style and pair_coeff commands do not need -to be specified in an input script that reads a restart file. Note -that the user-specified random number seed is stored in the restart -file, so when a simulation is restarted, each processor will -re-initialize its random number generator the same way it did -initially. This means the random forces will be random, but will not -be the same as they would have been if the original simulation had -continued past the restart time. +These pair styles write their information to :doc:`binary restart files +`, so pair_style and pair_coeff commands do not need to be +specified in an input script that reads a restart file. Note that the +user-specified random number seed is stored in the restart file, so when +a simulation is restarted, each processor will re-initialize its random +number generator the same way it did initially. This means the random +forces will be random, but will not be the same as they would have been +if the original simulation had continued past the restart time. These pair styles can only be used via the *pair* keyword of the :doc:`run_style respa ` command. They do not support the @@ -177,22 +177,26 @@ this. Restrictions """""""""""" +These styles are part of the DPD-BASIC package. They are only enabled if +LAMMPS was built with that package. See the :doc:`Build package +` doc page for more info. + The default frequency for rebuilding neighbor lists is every 10 steps (see the :doc:`neigh_modify ` command). This may be too -infrequent for style *dpd* simulations since particles move rapidly -and can overlap by large amounts. If this setting yields a non-zero -number of "dangerous" reneighborings (printed at the end of a -simulation), you should experiment with forcing reneighboring more -often and see if system energies/trajectories change. +infrequent for style *dpd* simulations since particles move rapidly and +can overlap by large amounts. If this setting yields a non-zero number +of "dangerous" reneighborings (printed at the end of a simulation), you +should experiment with forcing reneighboring more often and see if +system energies/trajectories change. -These pair styles requires you to use the :doc:`comm_modify vel yes ` command so that velocities are stored by ghost -atoms. +These pair styles requires you to use the :doc:`comm_modify vel yes +` command so that velocities are stored by ghost atoms. These pair styles will not restart exactly when using the :doc:`read_restart ` command, though they should provide -statistically similar results. This is because the forces they -compute depend on atom velocities. See the -:doc:`read_restart ` command for more details. +statistically similar results. This is because the forces they compute +depend on atom velocities. See the :doc:`read_restart ` +command for more details. Related commands """""""""""""""" diff --git a/doc/src/pair_dpd_ext.rst b/doc/src/pair_dpd_ext.rst index cfc72fe84c..0523a19e0b 100644 --- a/doc/src/pair_dpd_ext.rst +++ b/doc/src/pair_dpd_ext.rst @@ -38,12 +38,19 @@ Examples Description """"""""""" -The style *dpd/ext* computes an extended force field for dissipative particle dynamics (DPD) following the exposition in :ref:`(Groot) `, :ref:`(Junghans) `. +The style *dpd/ext* computes an extended force field for dissipative +particle dynamics (DPD) following the exposition in :ref:`(Groot) +`, :ref:`(Junghans) `. -Style *dpd/ext/tstat* invokes an extended DPD thermostat on pairwise interactions, equivalent to the non-conservative portion of the extended DPD force field. To use *dpd/ext/tstat* as a thermostat for another pair style, use the :doc:`pair_style hybrid/overlay ` command to compute both the desired pair interaction and the thermostat for each pair of particles. +Style *dpd/ext/tstat* invokes an extended DPD thermostat on pairwise +interactions, equivalent to the non-conservative portion of the extended +DPD force field. To use *dpd/ext/tstat* as a thermostat for another pair +style, use the :doc:`pair_style hybrid/overlay ` command to +compute both the desired pair interaction and the thermostat for each +pair of particles. -For the style *dpd/ext*\ , the force on atom I due to atom J is given as a sum -of 3 terms +For the style *dpd/ext*\ , the force on atom I due to atom J is given as +a sum of 3 terms .. math:: @@ -53,17 +60,51 @@ of 3 terms f^R = & \sigma_{\parallel} w_{\parallel}(r) \frac{\alpha}{\sqrt{\Delta t}} \hat{\mathbf{r}}_{ij} + \sigma_{\perp} w_{\perp} (r) ( \mathbf{I} - \hat{\mathbf{r}}_{ij} \hat{\mathbf{r}}_{ij}^{\rm T} ) \frac{\mathbf{\xi}_{ij}}{\sqrt{\Delta t}}\\ w(r) = & 1 - r/r_c \\ -where :math:`\mathbf{f}^C` is a conservative force, :math:`\mathbf{f}^D` is a dissipative force, and :math:`\mathbf{f}^R` is a random force. :math:`A_{ij}` is the maximum repulsion between the two atoms, :math:`\hat{\mathbf{r}}_{ij}` is a unit vector in the direction :math:`\mathbf{r}_i - \mathbf{r}_j`, :math:`\mathbf{v}_{ij} = \mathbf{v}_i - \mathbf{v}_j` is the vector difference in velocities of the two atoms, :math:`\alpha` and :math:`\mathbf{\xi}_{ij}` are Gaussian random numbers with zero mean and unit variance, :math:`\Delta t` is the timestep, :math:`w (r) = 1 - r / r_c` is a weight function for the conservative interactions that varies between 0 and 1, :math:`r_c` is the corresponding cutoff, :math:`w_{\alpha} ( r ) = ( 1 - r / \bar{r}_c )^{s_{\alpha}}`, :math:`\alpha \equiv ( \parallel, \perp )`, are weight functions with coefficients :math:`s_\alpha` that vary between 0 and 1, :math:`\bar{r}_c` is the corresponding cutoff, :math:`\mathbf{I}` is the unit matrix, :math:`\sigma_{\alpha} = \sqrt{2 k T \gamma_{\alpha}}`, where :math:`k` is the Boltzmann constant and :math:`T` is the temperature in the pair\_style command. +where :math:`\mathbf{f}^C` is a conservative force, :math:`\mathbf{f}^D` +is a dissipative force, and :math:`\mathbf{f}^R` is a random +force. :math:`A_{ij}` is the maximum repulsion between the two atoms, +:math:`\hat{\mathbf{r}}_{ij}` is a unit vector in the direction +:math:`\mathbf{r}_i - \mathbf{r}_j`, :math:`\mathbf{v}_{ij} = +\mathbf{v}_i - \mathbf{v}_j` is the vector difference in velocities of +the two atoms, :math:`\alpha` and :math:`\mathbf{\xi}_{ij}` are Gaussian +random numbers with zero mean and unit variance, :math:`\Delta t` is the +timestep, :math:`w (r) = 1 - r / r_c` is a weight function for the +conservative interactions that varies between 0 and 1, :math:`r_c` is +the corresponding cutoff, :math:`w_{\alpha} ( r ) = ( 1 - r / \bar{r}_c +)^{s_{\alpha}}`, :math:`\alpha \equiv ( \parallel, \perp )`, are weight +functions with coefficients :math:`s_\alpha` that vary between 0 and 1, +:math:`\bar{r}_c` is the corresponding cutoff, :math:`\mathbf{I}` is the +unit matrix, :math:`\sigma_{\alpha} = \sqrt{2 k T \gamma_{\alpha}}`, +where :math:`k` is the Boltzmann constant and :math:`T` is the +temperature in the pair\_style command. -For the style *dpd/ext/tstat*\ , the force on atom I due to atom J is the same as the above equation, except that the conservative :math:`\mathbf{f}^C` term is dropped. Also, during the run, T is set each timestep to a ramped value from Tstart to Tstop. +For the style *dpd/ext/tstat*\ , the force on atom I due to atom J is +the same as the above equation, except that the conservative +:math:`\mathbf{f}^C` term is dropped. Also, during the run, T is set +each timestep to a ramped value from Tstart to Tstop. -For the style *dpd/ext*\ , the pairwise energy associated with style *dpd/ext* is only due to the conservative force term :math:`\mathbf{f}^C`, and is shifted to be zero at the cutoff distance :math:`r_c`. The pairwise virial is calculated using all three terms. There is no pairwise energy for style *dpd/ext/tstat*, but the last two terms of the formula contribute the virial. +For the style *dpd/ext*\ , the pairwise energy associated with style +*dpd/ext* is only due to the conservative force term +:math:`\mathbf{f}^C`, and is shifted to be zero at the cutoff distance +:math:`r_c`. The pairwise virial is calculated using all three +terms. There is no pairwise energy for style *dpd/ext/tstat*, but the +last two terms of the formula contribute the virial. -For the style *dpd/ext/tstat*, the force on atom I due to atom J is the same as the above equation, except that the conservative :math:`\mathbf{f}^C` term is dropped. Also, during the run, T is set each timestep to a ramped value from Tstart to Tstop. +For the style *dpd/ext/tstat*, the force on atom I due to atom J is the +same as the above equation, except that the conservative +:math:`\mathbf{f}^C` term is dropped. Also, during the run, T is set +each timestep to a ramped value from Tstart to Tstop. -For the style *dpd/ext*\ , the pairwise energy associated with style *dpd/ext* is only due to the conservative force term :math:`\mathbf{f}^C`, and is shifted to be zero at the cutoff distance :math:`r_c`. The pairwise virial is calculated using all three terms. There is no pairwise energy for style *dpd/ext/tstat*, but the last two terms of the formula contribute the virial. +For the style *dpd/ext*\ , the pairwise energy associated with style +*dpd/ext* is only due to the conservative force term +:math:`\mathbf{f}^C`, and is shifted to be zero at the cutoff distance +:math:`r_c`. The pairwise virial is calculated using all three +terms. There is no pairwise energy for style *dpd/ext/tstat*, but the +last two terms of the formula contribute the virial. -For the style *dpd/ext*, the following coefficients must be defined for each pair of atoms types via the :doc:`pair_coeff ` command as in the examples above: +For the style *dpd/ext*, the following coefficients must be defined for +each pair of atoms types via the :doc:`pair_coeff ` command +as in the examples above: * A (force units) * :math:`\gamma_{\perp}` (force/velocity units) @@ -72,35 +113,55 @@ For the style *dpd/ext*, the following coefficients must be defined for each pai * :math:`s_{\parallel}` (unitless) * :math:`r_c` (distance units) -The last coefficient is optional. If not specified, the global DPD cutoff is used. Note that :math:`\sigma`'s are set equal to :math:`\sqrt{2 k T \gamma}`, where :math:`T` is the temperature set by the :doc:`pair_style ` command so it does not need to be specified. +The last coefficient is optional. If not specified, the global DPD +cutoff is used. Note that :math:`\sigma`'s are set equal to +:math:`\sqrt{2 k T \gamma}`, where :math:`T` is the temperature set by +the :doc:`pair_style ` command so it does not need to be +specified. - -For the style *dpd/ext/tstat*, the coefficients defined for each pair of atoms types via the :doc:`pair_coeff ` command is the same, except that A is not included. +For the style *dpd/ext/tstat*, the coefficients defined for each pair of +atoms types via the :doc:`pair_coeff ` command is the same, +except that A is not included. .. note:: - If you are modeling DPD polymer chains, you may want to use the :doc:`pair_style srp ` command in conjunction with these pair styles. It is a soft segmental repulsive potential (SRP) that can prevent DPD polymer chains from crossing each other. + If you are modeling DPD polymer chains, you may want to use the + :doc:`pair_style srp ` command in conjunction with these pair + styles. It is a soft segmental repulsive potential (SRP) that can + prevent DPD polymer chains from crossing each other. .. note:: - The virial calculation for pressure when using this pair style includes all the components of force listed above, including the random force. + The virial calculation for pressure when using this pair style includes + all the components of force listed above, including the random force. ---------- **Mixing, shift, table, tail correction, restart, rRESPA info**\ : -The style *dpd/ext* does not support mixing. Thus, coefficients for all I,J pairs must be specified explicitly. +The style *dpd/ext* does not support mixing. Thus, coefficients for all +I,J pairs must be specified explicitly. -The pair styles do not support the :doc:`pair_modify ` shift option for the energy of the pair interaction. Note that as discussed above, the energy due to the conservative :math:`\mathbf{f}^C` term is already shifted to be zero at the cutoff distance :math:`r_c`. +The pair styles do not support the :doc:`pair_modify ` +shift option for the energy of the pair interaction. Note that as +discussed above, the energy due to the conservative :math:`\mathbf{f}^C` +term is already shifted to be zero at the cutoff distance :math:`r_c`. -The :doc:`pair_modify ` table option is not relevant for the style *dpd/ext*. +The :doc:`pair_modify ` table option is not relevant for +the style *dpd/ext*. -The style *dpd/ext* does not support the :doc:`pair_modify ` tail option for adding long-range tail corrections to energy and pressure. +The style *dpd/ext* does not support the :doc:`pair_modify +` tail option for adding long-range tail corrections to +energy and pressure. -The pair styles can only be used via the pair keyword of the :doc:`run_style respa ` command. They do not support the *inner*\ , *middle*\ , and *outer*\ keywords. +The pair styles can only be used via the pair keyword of the +:doc:`run_style respa ` command. They do not support the +*inner*\ , *middle*\ , and *outer*\ keywords. -The style *dpd/ext/tstat* can ramp its target temperature over multiple runs, using the start and stop keywords of the :doc:`run ` command. See the :doc:`run ` command for details of how to do this. +The style *dpd/ext/tstat* can ramp its target temperature over multiple +runs, using the start and stop keywords of the :doc:`run ` +command. See the :doc:`run ` command for details of how to do this. ---------- @@ -108,31 +169,42 @@ The style *dpd/ext/tstat* can ramp its target temperature over multiple runs, us Restrictions """""""""""" -The default frequency for rebuilding neighbor lists is every 10 steps (see the :doc:`neigh_modify ` command). This may be too infrequent for style *dpd/ext* simulations since particles move rapidly and can overlap by large amounts. If this setting yields a non-zero number of \say{dangerous} reneighborings (printed at the end of a simulation), you should experiment with forcing reneighboring more often and see if system energies/trajectories change. +These styles are part of the DPD-BASIC package. They are only enabled if +LAMMPS was built with that package. See the :doc:`Build package +` doc page for more info. -The pair styles require to use the :doc:`comm_modify vel yes ` command so that velocities are stored by ghost atoms. +The default frequency for rebuilding neighbor lists is every 10 steps +(see the :doc:`neigh_modify ` command). This may be too +infrequent for style *dpd/ext* simulations since particles move rapidly +and can overlap by large amounts. If this setting yields a non-zero +number of \say{dangerous} reneighborings (printed at the end of a +simulation), you should experiment with forcing reneighboring more often +and see if system energies/trajectories change. -The pair styles will not restart exactly when using the :doc:`read_restart ` command, though they should provide statistically similar results. This is because the forces they compute depend on atom velocities. See the :doc:`read_restart ` command for more details. +The pair styles require to use the :doc:`comm_modify vel yes +` command so that velocities are stored by ghost atoms. + +The pair styles will not restart exactly when using the +:doc:`read_restart ` command, though they should provide +statistically similar results. This is because the forces they compute +depend on atom velocities. See the :doc:`read_restart ` +command for more details. Related commands """""""""""""""" -:doc:`pair_style dpd `, :doc:`pair_coeff `, :doc:`fix nvt `, :doc:`fix langevin `, :doc:`pair_style srp ` +:doc:`pair_style dpd `, :doc:`pair_coeff `, +:doc:`fix nvt `, :doc:`fix langevin `, +:doc:`pair_style srp ` **Default:** none - ---------- - .. _Groot: - - **(Groot)** Groot and Warren, J Chem Phys, 107, 4423-35 (1997). .. _Junghans: - - **(Junghans)** Junghans, Praprotnik and Kremer, Soft Matter 4, 156, 1119-1128 (2008). diff --git a/examples/USER-MISC/dpd_ext/README b/examples/PACKAGES/dpd-basic/README similarity index 100% rename from examples/USER-MISC/dpd_ext/README rename to examples/PACKAGES/dpd-basic/README diff --git a/examples/USER-MISC/dpd_ext/dpdext/dpdext.data b/examples/PACKAGES/dpd-basic/dpdext/dpdext.data similarity index 100% rename from examples/USER-MISC/dpd_ext/dpdext/dpdext.data rename to examples/PACKAGES/dpd-basic/dpdext/dpdext.data diff --git a/examples/USER-MISC/dpd_ext/dpdext/in.dpdext b/examples/PACKAGES/dpd-basic/dpdext/in.dpdext similarity index 100% rename from examples/USER-MISC/dpd_ext/dpdext/in.dpdext rename to examples/PACKAGES/dpd-basic/dpdext/in.dpdext diff --git a/examples/USER-MISC/dpd_ext/dpdext/log.10Mar21.dpdext.g++.1 b/examples/PACKAGES/dpd-basic/dpdext/log.10Mar21.dpdext.g++.1 similarity index 100% rename from examples/USER-MISC/dpd_ext/dpdext/log.10Mar21.dpdext.g++.1 rename to examples/PACKAGES/dpd-basic/dpdext/log.10Mar21.dpdext.g++.1 diff --git a/examples/USER-MISC/dpd_ext/dpdext/log.10Mar21.dpdext.g++.4 b/examples/PACKAGES/dpd-basic/dpdext/log.10Mar21.dpdext.g++.4 similarity index 100% rename from examples/USER-MISC/dpd_ext/dpdext/log.10Mar21.dpdext.g++.4 rename to examples/PACKAGES/dpd-basic/dpdext/log.10Mar21.dpdext.g++.4 diff --git a/examples/USER-MISC/dpd_ext/dpdext_tstat/cg_spce.data b/examples/PACKAGES/dpd-basic/dpdext_tstat/cg_spce.data similarity index 100% rename from examples/USER-MISC/dpd_ext/dpdext_tstat/cg_spce.data rename to examples/PACKAGES/dpd-basic/dpdext_tstat/cg_spce.data diff --git a/examples/USER-MISC/dpd_ext/dpdext_tstat/cg_spce_table.pot b/examples/PACKAGES/dpd-basic/dpdext_tstat/cg_spce_table.pot similarity index 100% rename from examples/USER-MISC/dpd_ext/dpdext_tstat/cg_spce_table.pot rename to examples/PACKAGES/dpd-basic/dpdext_tstat/cg_spce_table.pot diff --git a/examples/USER-MISC/dpd_ext/dpdext_tstat/in.cg_spce b/examples/PACKAGES/dpd-basic/dpdext_tstat/in.cg_spce similarity index 100% rename from examples/USER-MISC/dpd_ext/dpdext_tstat/in.cg_spce rename to examples/PACKAGES/dpd-basic/dpdext_tstat/in.cg_spce diff --git a/examples/USER-MISC/dpd_ext/dpdext_tstat/log.10Mar21.dpdext.g++.1 b/examples/PACKAGES/dpd-basic/dpdext_tstat/log.10Mar21.dpdext.g++.1 similarity index 100% rename from examples/USER-MISC/dpd_ext/dpdext_tstat/log.10Mar21.dpdext.g++.1 rename to examples/PACKAGES/dpd-basic/dpdext_tstat/log.10Mar21.dpdext.g++.1 diff --git a/examples/USER-MISC/dpd_ext/dpdext_tstat/log.10Mar21.dpdext.g++.4 b/examples/PACKAGES/dpd-basic/dpdext_tstat/log.10Mar21.dpdext.g++.4 similarity index 100% rename from examples/USER-MISC/dpd_ext/dpdext_tstat/log.10Mar21.dpdext.g++.4 rename to examples/PACKAGES/dpd-basic/dpdext_tstat/log.10Mar21.dpdext.g++.4 diff --git a/src/.gitignore b/src/.gitignore index 8d73a5b295..67072d5137 100644 --- a/src/.gitignore +++ b/src/.gitignore @@ -1429,6 +1429,10 @@ /pair_thole.h /pair_buck_mdf.cpp /pair_buck_mdf.h +/pair_dpd.cpp +/pair_dpd.h +/pair_dpd_tstat.cpp +/pair_dpd_tstat.h /pair_dpd_ext.cpp /pair_dpd_ext.h /pair_dpd_ext_tstat.cpp diff --git a/src/pair_dpd.cpp b/src/DPD-BASIC/pair_dpd.cpp similarity index 100% rename from src/pair_dpd.cpp rename to src/DPD-BASIC/pair_dpd.cpp diff --git a/src/pair_dpd.h b/src/DPD-BASIC/pair_dpd.h similarity index 100% rename from src/pair_dpd.h rename to src/DPD-BASIC/pair_dpd.h diff --git a/src/USER-MISC/pair_dpd_ext.cpp b/src/DPD-BASIC/pair_dpd_ext.cpp similarity index 100% rename from src/USER-MISC/pair_dpd_ext.cpp rename to src/DPD-BASIC/pair_dpd_ext.cpp diff --git a/src/USER-MISC/pair_dpd_ext.h b/src/DPD-BASIC/pair_dpd_ext.h similarity index 100% rename from src/USER-MISC/pair_dpd_ext.h rename to src/DPD-BASIC/pair_dpd_ext.h diff --git a/src/USER-MISC/pair_dpd_ext_tstat.cpp b/src/DPD-BASIC/pair_dpd_ext_tstat.cpp similarity index 100% rename from src/USER-MISC/pair_dpd_ext_tstat.cpp rename to src/DPD-BASIC/pair_dpd_ext_tstat.cpp diff --git a/src/USER-MISC/pair_dpd_ext_tstat.h b/src/DPD-BASIC/pair_dpd_ext_tstat.h similarity index 100% rename from src/USER-MISC/pair_dpd_ext_tstat.h rename to src/DPD-BASIC/pair_dpd_ext_tstat.h diff --git a/src/pair_dpd_tstat.cpp b/src/DPD-BASIC/pair_dpd_tstat.cpp similarity index 100% rename from src/pair_dpd_tstat.cpp rename to src/DPD-BASIC/pair_dpd_tstat.cpp diff --git a/src/pair_dpd_tstat.h b/src/DPD-BASIC/pair_dpd_tstat.h similarity index 100% rename from src/pair_dpd_tstat.h rename to src/DPD-BASIC/pair_dpd_tstat.h diff --git a/src/Makefile b/src/Makefile index 9beba726cc..52dff05148 100644 --- a/src/Makefile +++ b/src/Makefile @@ -63,6 +63,7 @@ PACKAGE = \ coreshell \ diffraction \ dipole \ + dpd-basic \ dpd-meso \ dpd-react \ dpd-smooth \ @@ -148,6 +149,7 @@ PACKMOST = \ coreshell \ diffraction \ dipole \ + dpd-basic \ dpd-meso \ dpd-react \ dpd-smooth \ diff --git a/src/Purge.list b/src/Purge.list index 88d9e22e59..3debc2ef6d 100644 --- a/src/Purge.list +++ b/src/Purge.list @@ -51,6 +51,11 @@ lmpinstalledpkgs.h lmpgitversion.h mliap_model_python_couple.cpp mliap_model_python_couple.h +# moved to DPD-BASIC package on 1 July 2021 +pair_dpd.cpp +pair_dpd.h +pair_dpd_tstat.cpp +pair_dpd_tstat.h # removed on 14 May 2021 nstencil_half_bin_2d_newton_ssa.cpp nstencil_half_bin_2d_newton_ssa.h diff --git a/src/USER-MISC/README b/src/USER-MISC/README index d6f859b359..fd60ecf586 100644 --- a/src/USER-MISC/README +++ b/src/USER-MISC/README @@ -89,8 +89,6 @@ pair_style coul/slater/long, Evangelos Voyiatzis, evoyiatzis at gmail.com, 26 Fe 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 dpd/ext, Martin Svoboda, Karel Sindelka, Martin Lisal, ICPF and UJEP, svobod.martin at gmail dot com, 23 Apr 21 -pair_style dpd/ext/tstat, Martin Svoboda, Karel Sindelka, Martin Lisal, ICPF and UJEP , svobod.martin at gmail dot com, 23 Apr 21 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