From 9d208c9ebd37b4a62e8de77143f5bed2a8540dc3 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 29 Jun 2021 20:21:53 -0400 Subject: [PATCH] rename some examples folders --- doc/src/Examples.rst | 5 +++++ doc/src/Packages_details.rst | 6 +++--- doc/src/compute_basal_atom.rst | 2 +- doc/src/fix_dpd_energy.rst | 2 +- doc/src/fix_electron_stopping.rst | 2 +- doc/src/fix_grem.rst | 2 +- doc/src/fix_pafi.rst | 2 +- doc/src/fix_rhok.rst | 2 +- doc/src/fix_shardlow.rst | 2 +- doc/src/fix_wall_ees.rst | 2 +- doc/src/pair_agni.rst | 2 +- doc/src/pair_e3b.rst | 2 +- doc/src/pair_meam_sw_spline.rst | 2 +- examples/PACKAGES/{dpd => dpd-react}/README | 0 .../{dpd => dpd-react}/dpd-shardlow/data.dpd | 0 .../dpd-shardlow/in.dpd-shardlow | 0 .../dpd-shardlow/log.dpd-shardlow.reference | 0 .../PACKAGES/{dpd => dpd-react}/dpd-vv/data.dpd | 0 .../{dpd => dpd-react}/dpd-vv/in.dpd-vv | 0 .../dpd-vv/log.dpd-vv.reference | 0 .../{dpd => dpd-react}/dpde-shardlow/data.dpde | 0 .../dpde-shardlow/in.dpde-shardlow | 0 .../dpde-shardlow/log.dpde-shardlow.reference | 0 .../{dpd => dpd-react}/dpde-vv/data.dpd | 0 .../{dpd => dpd-react}/dpde-vv/in.dpde-vv | 0 .../dpde-vv/log.dpde-vv.reference | 0 .../{dpd => dpd-react}/dpdh-shardlow/data.dpdh | 0 .../dpdh-shardlow/in.dpdh-shardlow | 0 .../dpdh-shardlow/log.dpdh-shardlow.reference | 0 .../{dpd => dpd-react}/dpdp-shardlow/data.dpd | 0 .../dpdp-shardlow/in.dpdp-shardlow | 0 .../dpdp-shardlow/log.dpdp-shardlow.reference | 0 .../dpdrx-shardlow/in.dpdrx-shardlow | 0 .../dpdrx-shardlow/kinetics.dpdrx | 0 .../dpdrx-shardlow/log.dpdrx-shardlow.reference | 0 .../dpdrx-shardlow/params.exp6 | 0 .../{dpd => dpd-react}/dpdrx-shardlow/table.eos | 0 .../dpdrx-shardlow/thermo.dpdrx | 0 .../{dpd => dpd-react}/multi-lucy/in.multi-lucy | 0 .../multi-lucy/log.multi-lucy.reference | 0 .../multi-lucy/table.multibody | 0 .../2d-diffusion-in-shear-flow/in.lammps | 0 ...log.24Oct18.2d-diffusion-in-shear-flow.g++.1 | 0 ...log.24Oct18.2d-diffusion-in-shear-flow.g++.4 | 0 .../{sdpd => dpd-smooth}/2d-diffusion/in.lammps | 0 .../2d-diffusion/log.24Oct18.2d-diffusion.g++.1 | 0 .../2d-diffusion/log.24Oct18.2d-diffusion.g++.4 | 0 examples/PACKAGES/{sdpd => dpd-smooth}/README | 0 .../equipartition-verification/in.lammps | 0 .../log.24Oct18.equipartition.g++.1 | 0 .../log.24Oct18.equipartition.g++.4 | 0 examples/README | 17 ++++++++++++----- .../USER-MISC/addtorque/in.addtorque | 0 .../addtorque/log.9Nov16.addtorque.g++.1 | 0 .../addtorque/log.9Nov16.addtorque.g++.4 | 0 .../{PACKAGES => }/USER-MISC/agni/Al_jpc.agni | 0 .../{PACKAGES => }/USER-MISC/agni/adatom.data | 0 .../{PACKAGES => }/USER-MISC/agni/in.adatom | 0 .../{PACKAGES => }/USER-MISC/agni/in.vacancy | 0 .../USER-MISC/agni/log.20Jan21.adatom.g++.1 | 0 .../USER-MISC/agni/log.20Jan21.adatom.g++.4 | 0 .../USER-MISC/agni/log.20Jan21.vacancy.g++.1 | 0 .../USER-MISC/agni/log.20Jan21.vacancy.g++.4 | 0 .../{PACKAGES => }/USER-MISC/agni/vacancy.data | 0 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=> }/USER-MISC/dpd_ext/README | 0 .../USER-MISC/dpd_ext/dpdext/dpdext.data | 0 .../USER-MISC/dpd_ext/dpdext/in.dpdext | 0 .../dpd_ext/dpdext/log.10Mar21.dpdext.g++.1 | 0 .../dpd_ext/dpdext/log.10Mar21.dpdext.g++.4 | 0 .../USER-MISC/dpd_ext/dpdext_tstat/cg_spce.data | 0 .../dpd_ext/dpdext_tstat/cg_spce_table.pot | 0 .../USER-MISC/dpd_ext/dpdext_tstat/in.cg_spce | 0 .../dpdext_tstat/log.10Mar21.dpdext.g++.1 | 0 .../dpdext_tstat/log.10Mar21.dpdext.g++.4 | 0 examples/{PACKAGES => }/USER-MISC/drip/C.drip | 0 examples/{PACKAGES => }/USER-MISC/drip/CH.rebo | 0 .../{PACKAGES => }/USER-MISC/drip/README.txt | 0 examples/{PACKAGES => }/USER-MISC/drip/data.C | 0 examples/{PACKAGES => }/USER-MISC/drip/data.CH | 0 .../{PACKAGES => }/USER-MISC/drip/in.CH_drip | 0 .../{PACKAGES => }/USER-MISC/drip/in.C_drip | 0 .../USER-MISC/drip/log.30Apr19.CH_drip.g++.1 | 0 .../USER-MISC/drip/log.30Apr19.CH_drip.g++.4 | 0 .../USER-MISC/drip/log.30Apr19.C_drip.g++.1 | 0 .../USER-MISC/drip/log.30Apr19.C_drip.g++.4 | 0 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}/USER-MISC/ti/in.ti_spring (100%) diff --git a/doc/src/Examples.rst b/doc/src/Examples.rst index 18121ba338..0f1ab2626d 100644 --- a/doc/src/Examples.rst +++ b/doc/src/Examples.rst @@ -211,6 +211,8 @@ Uppercase directories +------------+--------------------------------------------------------------------------------------------------+ | UNITS | examples that run the same simulation in lj, real, metal units | +------------+--------------------------------------------------------------------------------------------------+ +| USER-MISC | examples for commands in the USER-MISC packages | ++------------+--------------------------------------------------------------------------------------------------+ | VISCOSITY | compute viscosity via several methods | +------------+--------------------------------------------------------------------------------------------------+ @@ -224,4 +226,7 @@ of the sub-directories have their own README files which give further instructions. See the :doc:`Packages_details ` doc page for more info on specific packages. +Similarly the USER-MISC directory has sub-directories for examples +corresponding to individual commands or styles in the USER-MISC package. + .. _openkim: https://openkim.org diff --git a/doc/src/Packages_details.rst b/doc/src/Packages_details.rst index ea4a6a172b..80730dfc59 100644 --- a/doc/src/Packages_details.rst +++ b/doc/src/Packages_details.rst @@ -1461,7 +1461,7 @@ Brennan (ARL). * :doc:`pair_style exp6/rx ` * :doc:`pair_style multi/lucy ` * :doc:`pair_style multi/lucy/rx ` -* examples/PACKAGES/dpd +* examples/PACKAGES/dpd-react ---------- @@ -1746,7 +1746,7 @@ src/USER-MISC/README file. * src/USER-MISC: filenames -> commands * src/USER-MISC/README * one page per individual command listed in src/USER-MISC/README -* examples/PACKAGES/USER-MISC +* examples/USER-MISC ---------- @@ -2442,7 +2442,7 @@ Sciences, Iran). * :doc:`pair_style sdpd/taitwater/isothermal ` * :doc:`fix meso/move ` * :doc:`fix rigid/meso ` -* examples/PACKAGES/sdpd +* examples/PACKAGES/dpd-smooth ---------- diff --git a/doc/src/compute_basal_atom.rst b/doc/src/compute_basal_atom.rst index cf1d6376bc..8d8037e54e 100644 --- a/doc/src/compute_basal_atom.rst +++ b/doc/src/compute_basal_atom.rst @@ -42,7 +42,7 @@ too frequently or to have multiple compute/dump commands, each of which computes this quantity. An example input script that uses this compute is provided -in examples/PACKAGES/USER-MISC/basal. +in examples/USER-MISC/basal. Output info """"""""""" diff --git a/doc/src/fix_dpd_energy.rst b/doc/src/fix_dpd_energy.rst index 53ce796ecc..a1e8ef2faf 100644 --- a/doc/src/fix_dpd_energy.rst +++ b/doc/src/fix_dpd_energy.rst @@ -45,7 +45,7 @@ can be specified by using fix *dpd/energy*\ , fix *nve* and pair_style *dpd/fdt/energy*\ . DPD under isoenthalpic conditions can be specified by using fix *dpd/energy*\ , fix *nph* and pair_style *dpd/fdt/energy*\ . Examples of each DPD variant are provided in the -examples/PACKAGES/dpd directory. +examples/PACKAGES/dpd-react directory. ---------- diff --git a/doc/src/fix_electron_stopping.rst b/doc/src/fix_electron_stopping.rst index 521f5a7e6e..62037e66c7 100644 --- a/doc/src/fix_electron_stopping.rst +++ b/doc/src/fix_electron_stopping.rst @@ -153,7 +153,7 @@ atoms moving above some minimum cutoff velocity (i.e., kinetic energy). These coefficients can be determined by fitting a quadratic polynomial to electronic stopping data predicted by, for example, SRIM or TD-DFT. Multiple 'Ecut c1 c2' values can be provided for multi-species simulations in the order -of the atom types. There is an examples/PACKAGES/USER-MISC/electron_stopping/ directory, +of the atom types. There is an examples/USER-MISC/electron_stopping/ directory, which illustrates uses of this command. Details of this implementation are further described in :ref:`Stewart2018 ` and :ref:`Lee2020 `. diff --git a/doc/src/fix_grem.rst b/doc/src/fix_grem.rst index ff7dc90973..0dedda1e2e 100644 --- a/doc/src/fix_grem.rst +++ b/doc/src/fix_grem.rst @@ -66,7 +66,7 @@ processors be on the order of the number of desired replicas. A 100-replica simulation would require at least 100 processors (1 per world at minimum). If many replicas are needed on a small number of processors, multi-replica runs can be run outside of LAMMPS. An -example of this can be found in examples/PACKAGES/USER-MISC/grem and has no +example of this can be found in examples/USER-MISC/grem and has no limit on the number of replicas per processor. However, this is very inefficient and error prone and should be avoided if possible. diff --git a/doc/src/fix_pafi.rst b/doc/src/fix_pafi.rst index 39e7ba71ce..f50dc1dc0e 100644 --- a/doc/src/fix_pafi.rst +++ b/doc/src/fix_pafi.rst @@ -45,7 +45,7 @@ projection is also calculated, whose time integral can be shown to be equal to the true free energy gradient along the minimum free energy path local to the reference pathway. A detailed discussion of the projection technique can be found in :ref:`(Swinburne) `. -This fix can be used with LAMMPS as demonstrated in examples/PACKAGES/USER-MISC/pafi, +This fix can be used with LAMMPS as demonstrated in examples/USER-MISC/pafi, though it is primarily intended to be coupled with the PAFI C++ code, developed at `https://github.com/tomswinburne/pafi `_, which distributes multiple LAMMPS workers in parallel to compute and collate diff --git a/doc/src/fix_rhok.rst b/doc/src/fix_rhok.rst index 46c171ae4f..71a575810c 100644 --- a/doc/src/fix_rhok.rst +++ b/doc/src/fix_rhok.rst @@ -43,7 +43,7 @@ used to study crystal-liquid interfaces and determine melting temperatures :ref:`(Pedersen) `. An example of using the interface pinning method is located in the -*examples/PACKAGES/USER-MISC/rhok* directory. +*examples/USER-MISC/rhok* directory. Restart, fix_modify, output, run start/stop, minimize info """"""""""""""""""""""""""""""""""""""""""""""""""""""""""" diff --git a/doc/src/fix_shardlow.rst b/doc/src/fix_shardlow.rst index ce4fa0ac27..9f60df7e75 100644 --- a/doc/src/fix_shardlow.rst +++ b/doc/src/fix_shardlow.rst @@ -49,7 +49,7 @@ under isobaric conditions can be specified by using fix shardlow, fix *nph* and pair_style *dpd/fdt*\ . DPD under isoenthalpic conditions can be specified by using fix shardlow, fix *nph* and pair_style *dpd/fdt/energy*\ . Examples of each DPD variant are provided in the -examples/PACKAGES/dpd directory. +examples/PACKAGES/dpd-react directory. ---------- diff --git a/doc/src/fix_wall_ees.rst b/doc/src/fix_wall_ees.rst index fb88a24db9..1b1e904126 100644 --- a/doc/src/fix_wall_ees.rst +++ b/doc/src/fix_wall_ees.rst @@ -117,7 +117,7 @@ ellipsoidal particles according to the EES potential introduced above. Other details of this command are the same as for the :doc:`fix wall/region ` command. One may also find an example -of using this fix in the examples/PACKAGES/USER-MISC/ees/ directory. +of using this fix in the examples/USER-MISC/ees/ directory. ---------- diff --git a/doc/src/pair_agni.rst b/doc/src/pair_agni.rst index 7de3c76383..cfbcfb0c05 100644 --- a/doc/src/pair_agni.rst +++ b/doc/src/pair_agni.rst @@ -63,7 +63,7 @@ to specify the path for the force field file. An AGNI force field is fully specified by the filename which contains the parameters of the force field, i.e., the reference training environments used to construct the machine learning force field. Example force field -and input files are provided in the examples/PACKAGES/USER-MISC/agni directory. +and input files are provided in the examples/USER-MISC/agni directory. ---------- diff --git a/doc/src/pair_e3b.rst b/doc/src/pair_e3b.rst index 72c272a567..2083e61119 100644 --- a/doc/src/pair_e3b.rst +++ b/doc/src/pair_e3b.rst @@ -111,7 +111,7 @@ If the neigh setting is too large, the pair style will use more memory than nece This pair style tallies a breakdown of the total E3B potential energy into sub-categories, which can be accessed via the :doc:`compute pair ` 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/PACKAGES/USER-MISC/e3b directory for a complete example script. +See the examples/USER-MISC/e3b directory for a complete example script. ---------- diff --git a/doc/src/pair_meam_sw_spline.rst b/doc/src/pair_meam_sw_spline.rst index f1bc9df582..b57d122774 100644 --- a/doc/src/pair_meam_sw_spline.rst +++ b/doc/src/pair_meam_sw_spline.rst @@ -94,7 +94,7 @@ potentials. systems in the future. Example input scripts that use this pair style are provided -in the examples/PACKAGES/USER-MISC/meam_sw_spline directory. +in the examples/USER-MISC/meam_sw_spline directory. ---------- diff --git a/examples/PACKAGES/dpd/README b/examples/PACKAGES/dpd-react/README similarity index 100% rename from examples/PACKAGES/dpd/README rename to examples/PACKAGES/dpd-react/README diff --git a/examples/PACKAGES/dpd/dpd-shardlow/data.dpd b/examples/PACKAGES/dpd-react/dpd-shardlow/data.dpd similarity index 100% rename from examples/PACKAGES/dpd/dpd-shardlow/data.dpd rename to examples/PACKAGES/dpd-react/dpd-shardlow/data.dpd diff --git a/examples/PACKAGES/dpd/dpd-shardlow/in.dpd-shardlow b/examples/PACKAGES/dpd-react/dpd-shardlow/in.dpd-shardlow similarity index 100% rename from examples/PACKAGES/dpd/dpd-shardlow/in.dpd-shardlow rename to examples/PACKAGES/dpd-react/dpd-shardlow/in.dpd-shardlow diff --git a/examples/PACKAGES/dpd/dpd-shardlow/log.dpd-shardlow.reference b/examples/PACKAGES/dpd-react/dpd-shardlow/log.dpd-shardlow.reference similarity index 100% rename from examples/PACKAGES/dpd/dpd-shardlow/log.dpd-shardlow.reference rename to examples/PACKAGES/dpd-react/dpd-shardlow/log.dpd-shardlow.reference diff --git a/examples/PACKAGES/dpd/dpd-vv/data.dpd b/examples/PACKAGES/dpd-react/dpd-vv/data.dpd similarity index 100% rename from examples/PACKAGES/dpd/dpd-vv/data.dpd rename to examples/PACKAGES/dpd-react/dpd-vv/data.dpd diff --git a/examples/PACKAGES/dpd/dpd-vv/in.dpd-vv b/examples/PACKAGES/dpd-react/dpd-vv/in.dpd-vv similarity index 100% rename from examples/PACKAGES/dpd/dpd-vv/in.dpd-vv rename to examples/PACKAGES/dpd-react/dpd-vv/in.dpd-vv diff --git a/examples/PACKAGES/dpd/dpd-vv/log.dpd-vv.reference b/examples/PACKAGES/dpd-react/dpd-vv/log.dpd-vv.reference similarity index 100% rename from examples/PACKAGES/dpd/dpd-vv/log.dpd-vv.reference rename to examples/PACKAGES/dpd-react/dpd-vv/log.dpd-vv.reference diff --git a/examples/PACKAGES/dpd/dpde-shardlow/data.dpde b/examples/PACKAGES/dpd-react/dpde-shardlow/data.dpde similarity index 100% rename from examples/PACKAGES/dpd/dpde-shardlow/data.dpde rename to examples/PACKAGES/dpd-react/dpde-shardlow/data.dpde diff --git a/examples/PACKAGES/dpd/dpde-shardlow/in.dpde-shardlow b/examples/PACKAGES/dpd-react/dpde-shardlow/in.dpde-shardlow similarity index 100% rename from examples/PACKAGES/dpd/dpde-shardlow/in.dpde-shardlow rename to examples/PACKAGES/dpd-react/dpde-shardlow/in.dpde-shardlow diff --git a/examples/PACKAGES/dpd/dpde-shardlow/log.dpde-shardlow.reference b/examples/PACKAGES/dpd-react/dpde-shardlow/log.dpde-shardlow.reference similarity index 100% rename from examples/PACKAGES/dpd/dpde-shardlow/log.dpde-shardlow.reference rename to examples/PACKAGES/dpd-react/dpde-shardlow/log.dpde-shardlow.reference diff --git a/examples/PACKAGES/dpd/dpde-vv/data.dpd b/examples/PACKAGES/dpd-react/dpde-vv/data.dpd similarity index 100% rename from examples/PACKAGES/dpd/dpde-vv/data.dpd rename to examples/PACKAGES/dpd-react/dpde-vv/data.dpd diff --git a/examples/PACKAGES/dpd/dpde-vv/in.dpde-vv b/examples/PACKAGES/dpd-react/dpde-vv/in.dpde-vv similarity index 100% rename from examples/PACKAGES/dpd/dpde-vv/in.dpde-vv rename to examples/PACKAGES/dpd-react/dpde-vv/in.dpde-vv diff --git a/examples/PACKAGES/dpd/dpde-vv/log.dpde-vv.reference b/examples/PACKAGES/dpd-react/dpde-vv/log.dpde-vv.reference similarity index 100% rename from examples/PACKAGES/dpd/dpde-vv/log.dpde-vv.reference rename to examples/PACKAGES/dpd-react/dpde-vv/log.dpde-vv.reference diff --git a/examples/PACKAGES/dpd/dpdh-shardlow/data.dpdh b/examples/PACKAGES/dpd-react/dpdh-shardlow/data.dpdh similarity index 100% rename from examples/PACKAGES/dpd/dpdh-shardlow/data.dpdh rename to examples/PACKAGES/dpd-react/dpdh-shardlow/data.dpdh diff --git a/examples/PACKAGES/dpd/dpdh-shardlow/in.dpdh-shardlow b/examples/PACKAGES/dpd-react/dpdh-shardlow/in.dpdh-shardlow similarity index 100% rename from examples/PACKAGES/dpd/dpdh-shardlow/in.dpdh-shardlow rename to examples/PACKAGES/dpd-react/dpdh-shardlow/in.dpdh-shardlow diff --git a/examples/PACKAGES/dpd/dpdh-shardlow/log.dpdh-shardlow.reference b/examples/PACKAGES/dpd-react/dpdh-shardlow/log.dpdh-shardlow.reference similarity index 100% rename from examples/PACKAGES/dpd/dpdh-shardlow/log.dpdh-shardlow.reference rename to examples/PACKAGES/dpd-react/dpdh-shardlow/log.dpdh-shardlow.reference diff --git a/examples/PACKAGES/dpd/dpdp-shardlow/data.dpd b/examples/PACKAGES/dpd-react/dpdp-shardlow/data.dpd similarity index 100% rename from examples/PACKAGES/dpd/dpdp-shardlow/data.dpd rename to examples/PACKAGES/dpd-react/dpdp-shardlow/data.dpd diff --git a/examples/PACKAGES/dpd/dpdp-shardlow/in.dpdp-shardlow b/examples/PACKAGES/dpd-react/dpdp-shardlow/in.dpdp-shardlow similarity index 100% rename from examples/PACKAGES/dpd/dpdp-shardlow/in.dpdp-shardlow rename to examples/PACKAGES/dpd-react/dpdp-shardlow/in.dpdp-shardlow diff --git a/examples/PACKAGES/dpd/dpdp-shardlow/log.dpdp-shardlow.reference b/examples/PACKAGES/dpd-react/dpdp-shardlow/log.dpdp-shardlow.reference similarity index 100% rename from examples/PACKAGES/dpd/dpdp-shardlow/log.dpdp-shardlow.reference rename to examples/PACKAGES/dpd-react/dpdp-shardlow/log.dpdp-shardlow.reference diff --git a/examples/PACKAGES/dpd/dpdrx-shardlow/in.dpdrx-shardlow b/examples/PACKAGES/dpd-react/dpdrx-shardlow/in.dpdrx-shardlow similarity index 100% rename from examples/PACKAGES/dpd/dpdrx-shardlow/in.dpdrx-shardlow rename to examples/PACKAGES/dpd-react/dpdrx-shardlow/in.dpdrx-shardlow diff --git a/examples/PACKAGES/dpd/dpdrx-shardlow/kinetics.dpdrx b/examples/PACKAGES/dpd-react/dpdrx-shardlow/kinetics.dpdrx similarity index 100% rename from examples/PACKAGES/dpd/dpdrx-shardlow/kinetics.dpdrx rename to examples/PACKAGES/dpd-react/dpdrx-shardlow/kinetics.dpdrx diff --git a/examples/PACKAGES/dpd/dpdrx-shardlow/log.dpdrx-shardlow.reference b/examples/PACKAGES/dpd-react/dpdrx-shardlow/log.dpdrx-shardlow.reference similarity index 100% rename from examples/PACKAGES/dpd/dpdrx-shardlow/log.dpdrx-shardlow.reference rename to examples/PACKAGES/dpd-react/dpdrx-shardlow/log.dpdrx-shardlow.reference diff --git a/examples/PACKAGES/dpd/dpdrx-shardlow/params.exp6 b/examples/PACKAGES/dpd-react/dpdrx-shardlow/params.exp6 similarity index 100% rename from examples/PACKAGES/dpd/dpdrx-shardlow/params.exp6 rename to examples/PACKAGES/dpd-react/dpdrx-shardlow/params.exp6 diff --git a/examples/PACKAGES/dpd/dpdrx-shardlow/table.eos b/examples/PACKAGES/dpd-react/dpdrx-shardlow/table.eos similarity index 100% rename from examples/PACKAGES/dpd/dpdrx-shardlow/table.eos rename to examples/PACKAGES/dpd-react/dpdrx-shardlow/table.eos diff --git a/examples/PACKAGES/dpd/dpdrx-shardlow/thermo.dpdrx b/examples/PACKAGES/dpd-react/dpdrx-shardlow/thermo.dpdrx similarity index 100% rename from examples/PACKAGES/dpd/dpdrx-shardlow/thermo.dpdrx rename to examples/PACKAGES/dpd-react/dpdrx-shardlow/thermo.dpdrx diff --git a/examples/PACKAGES/dpd/multi-lucy/in.multi-lucy b/examples/PACKAGES/dpd-react/multi-lucy/in.multi-lucy similarity index 100% rename from examples/PACKAGES/dpd/multi-lucy/in.multi-lucy rename to examples/PACKAGES/dpd-react/multi-lucy/in.multi-lucy diff --git a/examples/PACKAGES/dpd/multi-lucy/log.multi-lucy.reference b/examples/PACKAGES/dpd-react/multi-lucy/log.multi-lucy.reference similarity index 100% rename from examples/PACKAGES/dpd/multi-lucy/log.multi-lucy.reference rename to examples/PACKAGES/dpd-react/multi-lucy/log.multi-lucy.reference diff --git a/examples/PACKAGES/dpd/multi-lucy/table.multibody b/examples/PACKAGES/dpd-react/multi-lucy/table.multibody similarity index 100% rename from examples/PACKAGES/dpd/multi-lucy/table.multibody rename to examples/PACKAGES/dpd-react/multi-lucy/table.multibody diff --git a/examples/PACKAGES/sdpd/2d-diffusion-in-shear-flow/in.lammps b/examples/PACKAGES/dpd-smooth/2d-diffusion-in-shear-flow/in.lammps similarity index 100% rename from examples/PACKAGES/sdpd/2d-diffusion-in-shear-flow/in.lammps rename to examples/PACKAGES/dpd-smooth/2d-diffusion-in-shear-flow/in.lammps diff --git a/examples/PACKAGES/sdpd/2d-diffusion-in-shear-flow/log.24Oct18.2d-diffusion-in-shear-flow.g++.1 b/examples/PACKAGES/dpd-smooth/2d-diffusion-in-shear-flow/log.24Oct18.2d-diffusion-in-shear-flow.g++.1 similarity index 100% rename from examples/PACKAGES/sdpd/2d-diffusion-in-shear-flow/log.24Oct18.2d-diffusion-in-shear-flow.g++.1 rename to examples/PACKAGES/dpd-smooth/2d-diffusion-in-shear-flow/log.24Oct18.2d-diffusion-in-shear-flow.g++.1 diff --git a/examples/PACKAGES/sdpd/2d-diffusion-in-shear-flow/log.24Oct18.2d-diffusion-in-shear-flow.g++.4 b/examples/PACKAGES/dpd-smooth/2d-diffusion-in-shear-flow/log.24Oct18.2d-diffusion-in-shear-flow.g++.4 similarity index 100% rename from examples/PACKAGES/sdpd/2d-diffusion-in-shear-flow/log.24Oct18.2d-diffusion-in-shear-flow.g++.4 rename to examples/PACKAGES/dpd-smooth/2d-diffusion-in-shear-flow/log.24Oct18.2d-diffusion-in-shear-flow.g++.4 diff --git a/examples/PACKAGES/sdpd/2d-diffusion/in.lammps b/examples/PACKAGES/dpd-smooth/2d-diffusion/in.lammps similarity index 100% rename from examples/PACKAGES/sdpd/2d-diffusion/in.lammps rename to examples/PACKAGES/dpd-smooth/2d-diffusion/in.lammps diff --git a/examples/PACKAGES/sdpd/2d-diffusion/log.24Oct18.2d-diffusion.g++.1 b/examples/PACKAGES/dpd-smooth/2d-diffusion/log.24Oct18.2d-diffusion.g++.1 similarity index 100% rename from examples/PACKAGES/sdpd/2d-diffusion/log.24Oct18.2d-diffusion.g++.1 rename to examples/PACKAGES/dpd-smooth/2d-diffusion/log.24Oct18.2d-diffusion.g++.1 diff --git a/examples/PACKAGES/sdpd/2d-diffusion/log.24Oct18.2d-diffusion.g++.4 b/examples/PACKAGES/dpd-smooth/2d-diffusion/log.24Oct18.2d-diffusion.g++.4 similarity index 100% rename from examples/PACKAGES/sdpd/2d-diffusion/log.24Oct18.2d-diffusion.g++.4 rename to examples/PACKAGES/dpd-smooth/2d-diffusion/log.24Oct18.2d-diffusion.g++.4 diff --git a/examples/PACKAGES/sdpd/README b/examples/PACKAGES/dpd-smooth/README similarity index 100% rename from examples/PACKAGES/sdpd/README rename to examples/PACKAGES/dpd-smooth/README diff --git a/examples/PACKAGES/sdpd/equipartition-verification/in.lammps b/examples/PACKAGES/dpd-smooth/equipartition-verification/in.lammps similarity index 100% rename from examples/PACKAGES/sdpd/equipartition-verification/in.lammps rename to examples/PACKAGES/dpd-smooth/equipartition-verification/in.lammps diff --git a/examples/PACKAGES/sdpd/equipartition-verification/log.24Oct18.equipartition.g++.1 b/examples/PACKAGES/dpd-smooth/equipartition-verification/log.24Oct18.equipartition.g++.1 similarity index 100% rename from examples/PACKAGES/sdpd/equipartition-verification/log.24Oct18.equipartition.g++.1 rename to examples/PACKAGES/dpd-smooth/equipartition-verification/log.24Oct18.equipartition.g++.1 diff --git a/examples/PACKAGES/sdpd/equipartition-verification/log.24Oct18.equipartition.g++.4 b/examples/PACKAGES/dpd-smooth/equipartition-verification/log.24Oct18.equipartition.g++.4 similarity index 100% rename from examples/PACKAGES/sdpd/equipartition-verification/log.24Oct18.equipartition.g++.4 rename to examples/PACKAGES/dpd-smooth/equipartition-verification/log.24Oct18.equipartition.g++.4 diff --git a/examples/README b/examples/README index f0e84f18c1..4f4f671a29 100644 --- a/examples/README +++ b/examples/README @@ -5,7 +5,8 @@ problems you can run with LAMMPS. lower-case directories = simple test problems for LAMMPS and its packages upper-case directories = more complex problems -PACKAGE directory with its own sub-directories = tests for specific packages +PACKAGES directory with its own sub-directories = tests for specific packages +USER-MISC directory with its own sub-directories = tests for commands in USER-MISC package Each is discussed below. @@ -170,6 +171,12 @@ The MC directory has an example script for using LAMMPS as an energy-evaluation engine in a iterative Monte Carlo energy-relaxation loop. +The PACKAGES directory contains subdirectories of example scripts for +individual packages. Most of those are contributed by the corresponding +package developers. See the README files in those directories +for more info. See the doc/html/Build_package.html file for more info +about installing and building packages. + The TIP4P directory has an example for testing forces computed on a GPU. @@ -179,11 +186,11 @@ lj, real, and metal. So that you can see how to scale/unscale input and output values read/written by LAMMPS to verify you are performing the same simulation in different unit systems. -The PACKAGES directory contains subdirectories of example scripts for -individual packages. Most of those are contributed by the corresponding -package developers. See the README files in those directories +The USER-MISC directory contains subdirectories of example scripts for +individual commands in the USER-MISC package. Most of those are contributed +by the corresponding developers. See the README files in those directories for more info. See the doc/html/Build_package.html file for more info -about installing and building user packages. +about installing and building packages. The VISCOSITY directory has example scripts for computing the viscosity of a LJ liquid using 4 different methods. See the diff --git a/examples/PACKAGES/USER-MISC/addtorque/in.addtorque b/examples/USER-MISC/addtorque/in.addtorque similarity index 100% rename from examples/PACKAGES/USER-MISC/addtorque/in.addtorque rename to examples/USER-MISC/addtorque/in.addtorque diff --git a/examples/PACKAGES/USER-MISC/addtorque/log.9Nov16.addtorque.g++.1 b/examples/USER-MISC/addtorque/log.9Nov16.addtorque.g++.1 similarity index 100% rename from examples/PACKAGES/USER-MISC/addtorque/log.9Nov16.addtorque.g++.1 rename to examples/USER-MISC/addtorque/log.9Nov16.addtorque.g++.1 diff --git a/examples/PACKAGES/USER-MISC/addtorque/log.9Nov16.addtorque.g++.4 b/examples/USER-MISC/addtorque/log.9Nov16.addtorque.g++.4 similarity index 100% rename from examples/PACKAGES/USER-MISC/addtorque/log.9Nov16.addtorque.g++.4 rename to examples/USER-MISC/addtorque/log.9Nov16.addtorque.g++.4 diff --git a/examples/PACKAGES/USER-MISC/agni/Al_jpc.agni b/examples/USER-MISC/agni/Al_jpc.agni similarity index 100% rename from examples/PACKAGES/USER-MISC/agni/Al_jpc.agni rename to examples/USER-MISC/agni/Al_jpc.agni diff --git a/examples/PACKAGES/USER-MISC/agni/adatom.data b/examples/USER-MISC/agni/adatom.data similarity index 100% rename from examples/PACKAGES/USER-MISC/agni/adatom.data rename to examples/USER-MISC/agni/adatom.data diff --git a/examples/PACKAGES/USER-MISC/agni/in.adatom b/examples/USER-MISC/agni/in.adatom similarity index 100% rename from examples/PACKAGES/USER-MISC/agni/in.adatom rename to examples/USER-MISC/agni/in.adatom diff --git a/examples/PACKAGES/USER-MISC/agni/in.vacancy b/examples/USER-MISC/agni/in.vacancy similarity index 100% rename from examples/PACKAGES/USER-MISC/agni/in.vacancy rename to examples/USER-MISC/agni/in.vacancy diff --git a/examples/PACKAGES/USER-MISC/agni/log.20Jan21.adatom.g++.1 b/examples/USER-MISC/agni/log.20Jan21.adatom.g++.1 similarity index 100% rename from examples/PACKAGES/USER-MISC/agni/log.20Jan21.adatom.g++.1 rename to examples/USER-MISC/agni/log.20Jan21.adatom.g++.1 diff --git a/examples/PACKAGES/USER-MISC/agni/log.20Jan21.adatom.g++.4 b/examples/USER-MISC/agni/log.20Jan21.adatom.g++.4 similarity index 100% rename from examples/PACKAGES/USER-MISC/agni/log.20Jan21.adatom.g++.4 rename to examples/USER-MISC/agni/log.20Jan21.adatom.g++.4 diff --git a/examples/PACKAGES/USER-MISC/agni/log.20Jan21.vacancy.g++.1 b/examples/USER-MISC/agni/log.20Jan21.vacancy.g++.1 similarity index 100% rename from examples/PACKAGES/USER-MISC/agni/log.20Jan21.vacancy.g++.1 rename to examples/USER-MISC/agni/log.20Jan21.vacancy.g++.1 diff --git a/examples/PACKAGES/USER-MISC/agni/log.20Jan21.vacancy.g++.4 b/examples/USER-MISC/agni/log.20Jan21.vacancy.g++.4 similarity index 100% rename from examples/PACKAGES/USER-MISC/agni/log.20Jan21.vacancy.g++.4 rename to examples/USER-MISC/agni/log.20Jan21.vacancy.g++.4 diff --git a/examples/PACKAGES/USER-MISC/agni/vacancy.data b/examples/USER-MISC/agni/vacancy.data similarity index 100% rename from examples/PACKAGES/USER-MISC/agni/vacancy.data rename to examples/USER-MISC/agni/vacancy.data diff --git a/examples/PACKAGES/USER-MISC/basal/almg.liu b/examples/USER-MISC/basal/almg.liu similarity index 100% rename from examples/PACKAGES/USER-MISC/basal/almg.liu rename to examples/USER-MISC/basal/almg.liu diff --git a/examples/PACKAGES/USER-MISC/basal/in.basal b/examples/USER-MISC/basal/in.basal similarity index 100% rename from examples/PACKAGES/USER-MISC/basal/in.basal rename to examples/USER-MISC/basal/in.basal diff --git a/examples/PACKAGES/USER-MISC/cauchy/NiAlH_jea.eam.alloy b/examples/USER-MISC/cauchy/NiAlH_jea.eam.alloy similarity index 100% rename from examples/PACKAGES/USER-MISC/cauchy/NiAlH_jea.eam.alloy rename to examples/USER-MISC/cauchy/NiAlH_jea.eam.alloy diff --git a/examples/PACKAGES/USER-MISC/cauchy/README b/examples/USER-MISC/cauchy/README similarity index 100% rename from examples/PACKAGES/USER-MISC/cauchy/README rename to examples/USER-MISC/cauchy/README diff --git a/examples/PACKAGES/USER-MISC/cauchy/in.cauchystat b/examples/USER-MISC/cauchy/in.cauchystat similarity index 100% rename from examples/PACKAGES/USER-MISC/cauchy/in.cauchystat rename to examples/USER-MISC/cauchy/in.cauchystat diff --git a/examples/PACKAGES/USER-MISC/cauchy/log.2Jun2020.cauchystat.g++.1 b/examples/USER-MISC/cauchy/log.2Jun2020.cauchystat.g++.1 similarity index 100% rename from examples/PACKAGES/USER-MISC/cauchy/log.2Jun2020.cauchystat.g++.1 rename to examples/USER-MISC/cauchy/log.2Jun2020.cauchystat.g++.1 diff --git a/examples/PACKAGES/USER-MISC/charge_regulation/README b/examples/USER-MISC/charge_regulation/README similarity index 100% rename from examples/PACKAGES/USER-MISC/charge_regulation/README rename to examples/USER-MISC/charge_regulation/README diff --git a/examples/PACKAGES/USER-MISC/charge_regulation/data.chreg-acid b/examples/USER-MISC/charge_regulation/data.chreg-acid similarity index 100% rename from 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a/examples/PACKAGES/USER-MISC/charge_regulation/log.10Feb21.chreg-acid.g++.4 b/examples/USER-MISC/charge_regulation/log.10Feb21.chreg-acid.g++.4 similarity index 100% rename from examples/PACKAGES/USER-MISC/charge_regulation/log.10Feb21.chreg-acid.g++.4 rename to examples/USER-MISC/charge_regulation/log.10Feb21.chreg-acid.g++.4 diff --git a/examples/PACKAGES/USER-MISC/charge_regulation/log.10Feb21.chreg-polymer.g++.1 b/examples/USER-MISC/charge_regulation/log.10Feb21.chreg-polymer.g++.1 similarity index 100% rename from examples/PACKAGES/USER-MISC/charge_regulation/log.10Feb21.chreg-polymer.g++.1 rename to examples/USER-MISC/charge_regulation/log.10Feb21.chreg-polymer.g++.1 diff --git a/examples/PACKAGES/USER-MISC/charge_regulation/log.10Feb21.chreg-polymer.g++.4 b/examples/USER-MISC/charge_regulation/log.10Feb21.chreg-polymer.g++.4 similarity index 100% rename from examples/PACKAGES/USER-MISC/charge_regulation/log.10Feb21.chreg-polymer.g++.4 rename to 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a/examples/PACKAGES/USER-MISC/dpd_ext/dpdext/in.dpdext b/examples/USER-MISC/dpd_ext/dpdext/in.dpdext similarity index 100% rename from examples/PACKAGES/USER-MISC/dpd_ext/dpdext/in.dpdext rename to examples/USER-MISC/dpd_ext/dpdext/in.dpdext diff --git a/examples/PACKAGES/USER-MISC/dpd_ext/dpdext/log.10Mar21.dpdext.g++.1 b/examples/USER-MISC/dpd_ext/dpdext/log.10Mar21.dpdext.g++.1 similarity index 100% rename from examples/PACKAGES/USER-MISC/dpd_ext/dpdext/log.10Mar21.dpdext.g++.1 rename to examples/USER-MISC/dpd_ext/dpdext/log.10Mar21.dpdext.g++.1 diff --git a/examples/PACKAGES/USER-MISC/dpd_ext/dpdext/log.10Mar21.dpdext.g++.4 b/examples/USER-MISC/dpd_ext/dpdext/log.10Mar21.dpdext.g++.4 similarity index 100% rename from examples/PACKAGES/USER-MISC/dpd_ext/dpdext/log.10Mar21.dpdext.g++.4 rename to examples/USER-MISC/dpd_ext/dpdext/log.10Mar21.dpdext.g++.4 diff --git a/examples/PACKAGES/USER-MISC/dpd_ext/dpdext_tstat/cg_spce.data b/examples/USER-MISC/dpd_ext/dpdext_tstat/cg_spce.data similarity index 100% rename from examples/PACKAGES/USER-MISC/dpd_ext/dpdext_tstat/cg_spce.data rename to examples/USER-MISC/dpd_ext/dpdext_tstat/cg_spce.data diff --git a/examples/PACKAGES/USER-MISC/dpd_ext/dpdext_tstat/cg_spce_table.pot b/examples/USER-MISC/dpd_ext/dpdext_tstat/cg_spce_table.pot similarity index 100% rename from examples/PACKAGES/USER-MISC/dpd_ext/dpdext_tstat/cg_spce_table.pot rename to examples/USER-MISC/dpd_ext/dpdext_tstat/cg_spce_table.pot diff --git a/examples/PACKAGES/USER-MISC/dpd_ext/dpdext_tstat/in.cg_spce b/examples/USER-MISC/dpd_ext/dpdext_tstat/in.cg_spce similarity index 100% rename from examples/PACKAGES/USER-MISC/dpd_ext/dpdext_tstat/in.cg_spce rename to examples/USER-MISC/dpd_ext/dpdext_tstat/in.cg_spce diff --git a/examples/PACKAGES/USER-MISC/dpd_ext/dpdext_tstat/log.10Mar21.dpdext.g++.1 b/examples/USER-MISC/dpd_ext/dpdext_tstat/log.10Mar21.dpdext.g++.1 similarity index 100% rename from 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a/examples/PACKAGES/USER-MISC/drip/log.30Apr19.CH_drip.g++.1 b/examples/USER-MISC/drip/log.30Apr19.CH_drip.g++.1 similarity index 100% rename from examples/PACKAGES/USER-MISC/drip/log.30Apr19.CH_drip.g++.1 rename to examples/USER-MISC/drip/log.30Apr19.CH_drip.g++.1 diff --git a/examples/PACKAGES/USER-MISC/drip/log.30Apr19.CH_drip.g++.4 b/examples/USER-MISC/drip/log.30Apr19.CH_drip.g++.4 similarity index 100% rename from examples/PACKAGES/USER-MISC/drip/log.30Apr19.CH_drip.g++.4 rename to examples/USER-MISC/drip/log.30Apr19.CH_drip.g++.4 diff --git a/examples/PACKAGES/USER-MISC/drip/log.30Apr19.C_drip.g++.1 b/examples/USER-MISC/drip/log.30Apr19.C_drip.g++.1 similarity index 100% rename from examples/PACKAGES/USER-MISC/drip/log.30Apr19.C_drip.g++.1 rename to examples/USER-MISC/drip/log.30Apr19.C_drip.g++.1 diff --git a/examples/PACKAGES/USER-MISC/drip/log.30Apr19.C_drip.g++.4 b/examples/USER-MISC/drip/log.30Apr19.C_drip.g++.4 similarity index 100% rename from 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a/examples/PACKAGES/USER-MISC/ilp_graphene_hbn/gr_hBN_Cstack_2L_noH.data b/examples/USER-MISC/ilp_graphene_hbn/gr_hBN_Cstack_2L_noH.data similarity index 100% rename from examples/PACKAGES/USER-MISC/ilp_graphene_hbn/gr_hBN_Cstack_2L_noH.data rename to examples/USER-MISC/ilp_graphene_hbn/gr_hBN_Cstack_2L_noH.data diff --git a/examples/PACKAGES/USER-MISC/ilp_graphene_hbn/hBN_AA_prime_stack_2L_noH.data b/examples/USER-MISC/ilp_graphene_hbn/hBN_AA_prime_stack_2L_noH.data similarity index 100% rename from examples/PACKAGES/USER-MISC/ilp_graphene_hbn/hBN_AA_prime_stack_2L_noH.data rename to examples/USER-MISC/ilp_graphene_hbn/hBN_AA_prime_stack_2L_noH.data diff --git a/examples/PACKAGES/USER-MISC/ilp_graphene_hbn/hBN_AB_stack_2L_noH_equi_300K.data b/examples/USER-MISC/ilp_graphene_hbn/hBN_AB_stack_2L_noH_equi_300K.data similarity index 100% rename from examples/PACKAGES/USER-MISC/ilp_graphene_hbn/hBN_AB_stack_2L_noH_equi_300K.data rename to 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diff --git a/examples/PACKAGES/USER-MISC/ipi/C.opt.tersoff b/examples/USER-MISC/ipi/C.opt.tersoff similarity index 100% rename from examples/PACKAGES/USER-MISC/ipi/C.opt.tersoff rename to examples/USER-MISC/ipi/C.opt.tersoff diff --git a/examples/PACKAGES/USER-MISC/ipi/README b/examples/USER-MISC/ipi/README similarity index 100% rename from examples/PACKAGES/USER-MISC/ipi/README rename to examples/USER-MISC/ipi/README diff --git a/examples/PACKAGES/USER-MISC/ipi/data.graphene b/examples/USER-MISC/ipi/data.graphene similarity index 100% rename from examples/PACKAGES/USER-MISC/ipi/data.graphene rename to examples/USER-MISC/ipi/data.graphene diff --git a/examples/PACKAGES/USER-MISC/ipi/i-pi_input.xml b/examples/USER-MISC/ipi/i-pi_input.xml similarity index 100% rename from examples/PACKAGES/USER-MISC/ipi/i-pi_input.xml rename to examples/USER-MISC/ipi/i-pi_input.xml diff --git a/examples/PACKAGES/USER-MISC/ipi/i-pi_positions.xyz b/examples/USER-MISC/ipi/i-pi_positions.xyz similarity index 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examples/PACKAGES/USER-MISC/temper_npt/log.temper_npt-17Aug17.g++.8.4 rename to examples/USER-MISC/temper_npt/log.temper_npt-17Aug17.g++.8.4 diff --git a/examples/PACKAGES/USER-MISC/temper_npt/log.temper_npt-17Aug17.g++.8.5 b/examples/USER-MISC/temper_npt/log.temper_npt-17Aug17.g++.8.5 similarity index 100% rename from examples/PACKAGES/USER-MISC/temper_npt/log.temper_npt-17Aug17.g++.8.5 rename to examples/USER-MISC/temper_npt/log.temper_npt-17Aug17.g++.8.5 diff --git a/examples/PACKAGES/USER-MISC/temper_npt/log.temper_npt-17Aug17.g++.8.6 b/examples/USER-MISC/temper_npt/log.temper_npt-17Aug17.g++.8.6 similarity index 100% rename from examples/PACKAGES/USER-MISC/temper_npt/log.temper_npt-17Aug17.g++.8.6 rename to examples/USER-MISC/temper_npt/log.temper_npt-17Aug17.g++.8.6 diff --git a/examples/PACKAGES/USER-MISC/temper_npt/log.temper_npt-17Aug17.g++.8.7 b/examples/USER-MISC/temper_npt/log.temper_npt-17Aug17.g++.8.7 similarity index 100% rename from examples/PACKAGES/USER-MISC/temper_npt/log.temper_npt-17Aug17.g++.8.7 rename to examples/USER-MISC/temper_npt/log.temper_npt-17Aug17.g++.8.7 diff --git a/examples/PACKAGES/USER-MISC/ti/in.ti_spring b/examples/USER-MISC/ti/in.ti_spring similarity index 100% rename from examples/PACKAGES/USER-MISC/ti/in.ti_spring rename to examples/USER-MISC/ti/in.ti_spring diff --git a/src/DPD-REACT/README b/src/DPD-REACT/README index 58c8d87334..c79a2455b0 100644 --- a/src/DPD-REACT/README +++ b/src/DPD-REACT/README @@ -27,7 +27,7 @@ dpd/conservative" and "pair dpd/fdt" and "pair dpd/fdt/energy" commands to get started. At the bottom of the doc page are many links to additional documentation contained in the doc/USER/dpd directory. -There are example scripts for using this package in examples/PACKAGES/dpd. +There are example scripts for using this package in examples/PACKAGES/dpd-react. The primary people who created this package are James Larentzos (james.p.larentzos.civ at mail.mil), Timothy Mattox (Timothy.Mattox at