From 4342987043b046c88a5bc2f5f2d8cf7619d48885 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 29 Jun 2021 11:23:47 -0400 Subject: [PATCH] rename example folders --- .../USER-MISC}/addtorque/in.addtorque | 0 .../USER-MISC}/addtorque/log.9Nov16.addtorque.g++.1 | 0 .../USER-MISC}/addtorque/log.9Nov16.addtorque.g++.4 | 0 .../misc => PACKAGES/USER-MISC}/agni/Al_jpc.agni | 0 .../misc => PACKAGES/USER-MISC}/agni/adatom.data | 0 .../misc => PACKAGES/USER-MISC}/agni/in.adatom | 0 .../misc => 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 .../misc => PACKAGES/USER-MISC}/agni/vacancy.data | 0 .../misc => PACKAGES/USER-MISC}/basal/almg.liu | 0 .../misc => PACKAGES/USER-MISC}/basal/in.basal | 0 .../USER-MISC}/cauchy/NiAlH_jea.eam.alloy | 0 .../{USER/misc => PACKAGES/USER-MISC}/cauchy/README | 0 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.../uef/npt_biaxial/log.27Nov18.npt_biaxial.g++.1 | 0 .../uef/npt_biaxial/log.27Nov18.npt_biaxial.g++.4 | 0 .../{USER => PACKAGES}/uef/nvt_uniaxial/data.wca | 0 .../uef/nvt_uniaxial/in.nvt_uniaxial | 0 .../uef/nvt_uniaxial/log.27Nov18.nvt_uniaxial.g++.1 | 0 .../uef/nvt_uniaxial/log.27Nov18.nvt_uniaxial.g++.4 | 0 examples/{USER => PACKAGES}/vtk/.gitignore | 0 examples/{USER => PACKAGES}/vtk/in.vtk | 0 examples/{USER => PACKAGES}/vtk/in.vtp | 0 examples/{USER => PACKAGES}/yaff/README | 0 .../{USER => PACKAGES}/yaff/mil53al/lammps.data | 0 examples/{USER => PACKAGES}/yaff/mil53al/lammps.in | 0 examples/{USER => PACKAGES}/yaff/mof5/lammps.data | 0 examples/{USER => PACKAGES}/yaff/mof5/lammps.in | 0 examples/README | 7 ++++--- 1351 files changed, 4 insertions(+), 3 deletions(-) rename examples/{USER/misc => PACKAGES/USER-MISC}/addtorque/in.addtorque (100%) rename examples/{USER/misc => PACKAGES/USER-MISC}/addtorque/log.9Nov16.addtorque.g++.1 (100%) rename examples/{USER/misc => 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examples/USER/misc/dpd_ext/dpdext_tstat/in.cg_spce rename to examples/PACKAGES/USER-MISC/dpd_ext/dpdext_tstat/in.cg_spce diff --git a/examples/USER/misc/dpd_ext/dpdext_tstat/log.10Mar21.dpdext.g++.1 b/examples/PACKAGES/USER-MISC/dpd_ext/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/USER-MISC/dpd_ext/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/USER-MISC/dpd_ext/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/USER-MISC/dpd_ext/dpdext_tstat/log.10Mar21.dpdext.g++.4 diff --git a/examples/USER/misc/drip/C.drip b/examples/PACKAGES/USER-MISC/drip/C.drip similarity index 100% rename from examples/USER/misc/drip/C.drip rename to examples/PACKAGES/USER-MISC/drip/C.drip diff --git a/examples/USER/misc/drip/CH.rebo b/examples/PACKAGES/USER-MISC/drip/CH.rebo similarity index 100% rename from examples/USER/misc/drip/CH.rebo rename to examples/PACKAGES/USER-MISC/drip/CH.rebo diff --git a/examples/USER/misc/drip/README.txt b/examples/PACKAGES/USER-MISC/drip/README.txt similarity index 100% rename from examples/USER/misc/drip/README.txt rename to examples/PACKAGES/USER-MISC/drip/README.txt diff --git a/examples/USER/misc/drip/data.C b/examples/PACKAGES/USER-MISC/drip/data.C similarity index 100% rename from examples/USER/misc/drip/data.C rename to examples/PACKAGES/USER-MISC/drip/data.C diff --git a/examples/USER/misc/drip/data.CH b/examples/PACKAGES/USER-MISC/drip/data.CH similarity index 100% rename from examples/USER/misc/drip/data.CH rename to examples/PACKAGES/USER-MISC/drip/data.CH diff --git a/examples/USER/misc/drip/in.CH_drip b/examples/PACKAGES/USER-MISC/drip/in.CH_drip similarity index 100% rename from examples/USER/misc/drip/in.CH_drip rename to examples/PACKAGES/USER-MISC/drip/in.CH_drip diff --git a/examples/USER/misc/drip/in.C_drip b/examples/PACKAGES/USER-MISC/drip/in.C_drip similarity index 100% rename from examples/USER/misc/drip/in.C_drip rename to examples/PACKAGES/USER-MISC/drip/in.C_drip diff --git a/examples/USER/misc/drip/log.30Apr19.CH_drip.g++.1 b/examples/PACKAGES/USER-MISC/drip/log.30Apr19.CH_drip.g++.1 similarity index 100% rename from examples/USER/misc/drip/log.30Apr19.CH_drip.g++.1 rename to examples/PACKAGES/USER-MISC/drip/log.30Apr19.CH_drip.g++.1 diff --git a/examples/USER/misc/drip/log.30Apr19.CH_drip.g++.4 b/examples/PACKAGES/USER-MISC/drip/log.30Apr19.CH_drip.g++.4 similarity index 100% rename from examples/USER/misc/drip/log.30Apr19.CH_drip.g++.4 rename to examples/PACKAGES/USER-MISC/drip/log.30Apr19.CH_drip.g++.4 diff --git a/examples/USER/misc/drip/log.30Apr19.C_drip.g++.1 b/examples/PACKAGES/USER-MISC/drip/log.30Apr19.C_drip.g++.1 similarity index 100% rename from examples/USER/misc/drip/log.30Apr19.C_drip.g++.1 rename to examples/PACKAGES/USER-MISC/drip/log.30Apr19.C_drip.g++.1 diff --git a/examples/USER/misc/drip/log.30Apr19.C_drip.g++.4 b/examples/PACKAGES/USER-MISC/drip/log.30Apr19.C_drip.g++.4 similarity index 100% rename from examples/USER/misc/drip/log.30Apr19.C_drip.g++.4 rename to examples/PACKAGES/USER-MISC/drip/log.30Apr19.C_drip.g++.4 diff --git a/examples/USER/misc/e3b/README b/examples/PACKAGES/USER-MISC/e3b/README similarity index 100% rename from examples/USER/misc/e3b/README rename to examples/PACKAGES/USER-MISC/e3b/README diff --git a/examples/USER/misc/e3b/e3b_box.data b/examples/PACKAGES/USER-MISC/e3b/e3b_box.data similarity index 100% rename from examples/USER/misc/e3b/e3b_box.data rename to examples/PACKAGES/USER-MISC/e3b/e3b_box.data diff --git a/examples/USER/misc/e3b/in.e3b-tip4p2005 b/examples/PACKAGES/USER-MISC/e3b/in.e3b-tip4p2005 similarity index 100% rename from examples/USER/misc/e3b/in.e3b-tip4p2005 rename to examples/PACKAGES/USER-MISC/e3b/in.e3b-tip4p2005 diff --git a/examples/USER/misc/e3b/log.29Mar2019.e3b-tip4p2005.g++.1 b/examples/PACKAGES/USER-MISC/e3b/log.29Mar2019.e3b-tip4p2005.g++.1 similarity index 100% rename from examples/USER/misc/e3b/log.29Mar2019.e3b-tip4p2005.g++.1 rename to examples/PACKAGES/USER-MISC/e3b/log.29Mar2019.e3b-tip4p2005.g++.1 diff --git a/examples/USER/misc/e3b/log.29Mar2019.e3b-tip4p2005.g++.4 b/examples/PACKAGES/USER-MISC/e3b/log.29Mar2019.e3b-tip4p2005.g++.4 similarity index 100% rename from examples/USER/misc/e3b/log.29Mar2019.e3b-tip4p2005.g++.4 rename to examples/PACKAGES/USER-MISC/e3b/log.29Mar2019.e3b-tip4p2005.g++.4 diff --git a/examples/USER/misc/edip/Si.edip b/examples/PACKAGES/USER-MISC/edip/Si.edip similarity index 100% rename from examples/USER/misc/edip/Si.edip rename to examples/PACKAGES/USER-MISC/edip/Si.edip diff --git a/examples/USER/misc/edip/SiC.edip b/examples/PACKAGES/USER-MISC/edip/SiC.edip similarity index 100% rename from examples/USER/misc/edip/SiC.edip rename to examples/PACKAGES/USER-MISC/edip/SiC.edip diff --git a/examples/USER/misc/edip/data.SiC b/examples/PACKAGES/USER-MISC/edip/data.SiC similarity index 100% rename from examples/USER/misc/edip/data.SiC rename to examples/PACKAGES/USER-MISC/edip/data.SiC diff --git a/examples/USER/misc/edip/in.edip-Si b/examples/PACKAGES/USER-MISC/edip/in.edip-Si similarity index 100% rename from examples/USER/misc/edip/in.edip-Si rename to examples/PACKAGES/USER-MISC/edip/in.edip-Si diff --git a/examples/USER/misc/edip/in.edip-Si-multi b/examples/PACKAGES/USER-MISC/edip/in.edip-Si-multi similarity index 100% rename from examples/USER/misc/edip/in.edip-Si-multi rename to examples/PACKAGES/USER-MISC/edip/in.edip-Si-multi diff --git a/examples/USER/misc/edip/in.edip-SiC b/examples/PACKAGES/USER-MISC/edip/in.edip-SiC similarity index 100% rename from examples/USER/misc/edip/in.edip-SiC rename to examples/PACKAGES/USER-MISC/edip/in.edip-SiC diff --git a/examples/USER/misc/edip/log.4May2017.g++.edip-Si-multi.1 b/examples/PACKAGES/USER-MISC/edip/log.4May2017.g++.edip-Si-multi.1 similarity index 100% rename from examples/USER/misc/edip/log.4May2017.g++.edip-Si-multi.1 rename to examples/PACKAGES/USER-MISC/edip/log.4May2017.g++.edip-Si-multi.1 diff --git a/examples/USER/misc/edip/log.4May2017.g++.edip-Si-multi.4 b/examples/PACKAGES/USER-MISC/edip/log.4May2017.g++.edip-Si-multi.4 similarity index 100% rename from examples/USER/misc/edip/log.4May2017.g++.edip-Si-multi.4 rename to examples/PACKAGES/USER-MISC/edip/log.4May2017.g++.edip-Si-multi.4 diff --git a/examples/USER/misc/edip/log.4May2017.g++.edip-Si.1 b/examples/PACKAGES/USER-MISC/edip/log.4May2017.g++.edip-Si.1 similarity index 100% rename from examples/USER/misc/edip/log.4May2017.g++.edip-Si.1 rename to examples/PACKAGES/USER-MISC/edip/log.4May2017.g++.edip-Si.1 diff --git a/examples/USER/misc/edip/log.4May2017.g++.edip-Si.4 b/examples/PACKAGES/USER-MISC/edip/log.4May2017.g++.edip-Si.4 similarity index 100% rename from examples/USER/misc/edip/log.4May2017.g++.edip-Si.4 rename to examples/PACKAGES/USER-MISC/edip/log.4May2017.g++.edip-Si.4 diff --git a/examples/USER/misc/edip/log.4May2017.g++.edip-SiC.1 b/examples/PACKAGES/USER-MISC/edip/log.4May2017.g++.edip-SiC.1 similarity index 100% rename from examples/USER/misc/edip/log.4May2017.g++.edip-SiC.1 rename to examples/PACKAGES/USER-MISC/edip/log.4May2017.g++.edip-SiC.1 diff --git a/examples/USER/misc/edip/log.4May2017.g++.edip-SiC.4 b/examples/PACKAGES/USER-MISC/edip/log.4May2017.g++.edip-SiC.4 similarity index 100% rename from examples/USER/misc/edip/log.4May2017.g++.edip-SiC.4 rename to examples/PACKAGES/USER-MISC/edip/log.4May2017.g++.edip-SiC.4 diff --git a/examples/USER/misc/ees/Data_region b/examples/PACKAGES/USER-MISC/ees/Data_region similarity index 100% rename from examples/USER/misc/ees/Data_region rename to examples/PACKAGES/USER-MISC/ees/Data_region diff --git a/examples/USER/misc/ees/Data_wall b/examples/PACKAGES/USER-MISC/ees/Data_wall similarity index 100% rename from examples/USER/misc/ees/Data_wall rename to examples/PACKAGES/USER-MISC/ees/Data_wall diff --git a/examples/USER/misc/ees/README b/examples/PACKAGES/USER-MISC/ees/README similarity index 100% rename from examples/USER/misc/ees/README rename to examples/PACKAGES/USER-MISC/ees/README diff --git a/examples/USER/misc/ees/in.fix_wall b/examples/PACKAGES/USER-MISC/ees/in.fix_wall similarity index 100% rename from examples/USER/misc/ees/in.fix_wall rename to examples/PACKAGES/USER-MISC/ees/in.fix_wall diff --git a/examples/USER/misc/ees/in.fix_wall_region b/examples/PACKAGES/USER-MISC/ees/in.fix_wall_region similarity index 100% rename from examples/USER/misc/ees/in.fix_wall_region rename to examples/PACKAGES/USER-MISC/ees/in.fix_wall_region diff --git a/examples/USER/misc/ees/log.23Jun17.fix_wall.g++.1 b/examples/PACKAGES/USER-MISC/ees/log.23Jun17.fix_wall.g++.1 similarity index 100% rename from examples/USER/misc/ees/log.23Jun17.fix_wall.g++.1 rename to examples/PACKAGES/USER-MISC/ees/log.23Jun17.fix_wall.g++.1 diff --git a/examples/USER/misc/ees/log.23Jun17.fix_wall.g++.4 b/examples/PACKAGES/USER-MISC/ees/log.23Jun17.fix_wall.g++.4 similarity index 100% rename from examples/USER/misc/ees/log.23Jun17.fix_wall.g++.4 rename to examples/PACKAGES/USER-MISC/ees/log.23Jun17.fix_wall.g++.4 diff --git a/examples/USER/misc/ees/log.23Jun17.fix_wall_region.g++.1 b/examples/PACKAGES/USER-MISC/ees/log.23Jun17.fix_wall_region.g++.1 similarity index 100% rename from examples/USER/misc/ees/log.23Jun17.fix_wall_region.g++.1 rename to examples/PACKAGES/USER-MISC/ees/log.23Jun17.fix_wall_region.g++.1 diff --git a/examples/USER/misc/ees/log.23Jun17.fix_wall_region.g++.4 b/examples/PACKAGES/USER-MISC/ees/log.23Jun17.fix_wall_region.g++.4 similarity index 100% rename from examples/USER/misc/ees/log.23Jun17.fix_wall_region.g++.4 rename to examples/PACKAGES/USER-MISC/ees/log.23Jun17.fix_wall_region.g++.4 diff --git a/examples/USER/misc/electron_stopping/Si.Si.elstop b/examples/PACKAGES/USER-MISC/electron_stopping/Si.Si.elstop similarity index 100% rename from examples/USER/misc/electron_stopping/Si.Si.elstop rename to examples/PACKAGES/USER-MISC/electron_stopping/Si.Si.elstop diff --git a/examples/USER/misc/electron_stopping/Si.sw b/examples/PACKAGES/USER-MISC/electron_stopping/Si.sw similarity index 100% rename from examples/USER/misc/electron_stopping/Si.sw rename to examples/PACKAGES/USER-MISC/electron_stopping/Si.sw diff --git a/examples/USER/misc/electron_stopping/in.cascade_AlCu b/examples/PACKAGES/USER-MISC/electron_stopping/in.cascade_AlCu similarity index 100% rename from examples/USER/misc/electron_stopping/in.cascade_AlCu rename to examples/PACKAGES/USER-MISC/electron_stopping/in.cascade_AlCu diff --git a/examples/USER/misc/electron_stopping/in.cascade_SiSi b/examples/PACKAGES/USER-MISC/electron_stopping/in.cascade_SiSi similarity index 100% rename from examples/USER/misc/electron_stopping/in.cascade_SiSi rename to examples/PACKAGES/USER-MISC/electron_stopping/in.cascade_SiSi diff --git a/examples/USER/misc/electron_stopping/in.elstop b/examples/PACKAGES/USER-MISC/electron_stopping/in.elstop similarity index 100% rename from examples/USER/misc/electron_stopping/in.elstop rename to examples/PACKAGES/USER-MISC/electron_stopping/in.elstop diff --git a/examples/USER/misc/electron_stopping/in.elstop.only b/examples/PACKAGES/USER-MISC/electron_stopping/in.elstop.only similarity index 100% rename from examples/USER/misc/electron_stopping/in.elstop.only rename to examples/PACKAGES/USER-MISC/electron_stopping/in.elstop.only diff --git a/examples/USER/misc/electron_stopping/log.18Sep2020.cascade_AlCu.intel.1 b/examples/PACKAGES/USER-MISC/electron_stopping/log.18Sep2020.cascade_AlCu.intel.1 similarity index 100% rename from examples/USER/misc/electron_stopping/log.18Sep2020.cascade_AlCu.intel.1 rename to examples/PACKAGES/USER-MISC/electron_stopping/log.18Sep2020.cascade_AlCu.intel.1 diff --git a/examples/USER/misc/electron_stopping/log.18Sep2020.cascade_AlCu.intel.4 b/examples/PACKAGES/USER-MISC/electron_stopping/log.18Sep2020.cascade_AlCu.intel.4 similarity index 100% rename from examples/USER/misc/electron_stopping/log.18Sep2020.cascade_AlCu.intel.4 rename to examples/PACKAGES/USER-MISC/electron_stopping/log.18Sep2020.cascade_AlCu.intel.4 diff --git a/examples/USER/misc/electron_stopping/log.18Sep2020.cascade_SiSi.intel.1 b/examples/PACKAGES/USER-MISC/electron_stopping/log.18Sep2020.cascade_SiSi.intel.1 similarity index 100% rename from examples/USER/misc/electron_stopping/log.18Sep2020.cascade_SiSi.intel.1 rename to examples/PACKAGES/USER-MISC/electron_stopping/log.18Sep2020.cascade_SiSi.intel.1 diff --git a/examples/USER/misc/electron_stopping/log.18Sep2020.cascade_SiSi.intel.4 b/examples/PACKAGES/USER-MISC/electron_stopping/log.18Sep2020.cascade_SiSi.intel.4 similarity index 100% rename from examples/USER/misc/electron_stopping/log.18Sep2020.cascade_SiSi.intel.4 rename to examples/PACKAGES/USER-MISC/electron_stopping/log.18Sep2020.cascade_SiSi.intel.4 diff --git a/examples/USER/misc/electron_stopping/log.20Mar19.elstop.g++.1 b/examples/PACKAGES/USER-MISC/electron_stopping/log.20Mar19.elstop.g++.1 similarity index 100% rename from examples/USER/misc/electron_stopping/log.20Mar19.elstop.g++.1 rename to examples/PACKAGES/USER-MISC/electron_stopping/log.20Mar19.elstop.g++.1 diff --git a/examples/USER/misc/electron_stopping/log.20Mar19.elstop.g++.4 b/examples/PACKAGES/USER-MISC/electron_stopping/log.20Mar19.elstop.g++.4 similarity index 100% rename from examples/USER/misc/electron_stopping/log.20Mar19.elstop.g++.4 rename to examples/PACKAGES/USER-MISC/electron_stopping/log.20Mar19.elstop.g++.4 diff --git a/examples/USER/misc/electron_stopping/log.20Mar19.elstop.only.g++.1 b/examples/PACKAGES/USER-MISC/electron_stopping/log.20Mar19.elstop.only.g++.1 similarity index 100% rename from examples/USER/misc/electron_stopping/log.20Mar19.elstop.only.g++.1 rename to examples/PACKAGES/USER-MISC/electron_stopping/log.20Mar19.elstop.only.g++.1 diff --git a/examples/USER/misc/electron_stopping/log.20Mar19.elstop.only.g++.4 b/examples/PACKAGES/USER-MISC/electron_stopping/log.20Mar19.elstop.only.g++.4 similarity index 100% rename from examples/USER/misc/electron_stopping/log.20Mar19.elstop.only.g++.4 rename to examples/PACKAGES/USER-MISC/electron_stopping/log.20Mar19.elstop.only.g++.4 diff --git a/examples/USER/misc/entropy/Na_MendelevM_2014.eam.fs b/examples/PACKAGES/USER-MISC/entropy/Na_MendelevM_2014.eam.fs similarity index 100% rename from examples/USER/misc/entropy/Na_MendelevM_2014.eam.fs rename to examples/PACKAGES/USER-MISC/entropy/Na_MendelevM_2014.eam.fs diff --git a/examples/USER/misc/entropy/data.interface b/examples/PACKAGES/USER-MISC/entropy/data.interface similarity index 100% rename from examples/USER/misc/entropy/data.interface rename to examples/PACKAGES/USER-MISC/entropy/data.interface diff --git a/examples/USER/misc/entropy/in.entropy b/examples/PACKAGES/USER-MISC/entropy/in.entropy similarity index 100% rename from examples/USER/misc/entropy/in.entropy rename to examples/PACKAGES/USER-MISC/entropy/in.entropy diff --git a/examples/USER/misc/entropy/log.entropy b/examples/PACKAGES/USER-MISC/entropy/log.entropy similarity index 100% rename from examples/USER/misc/entropy/log.entropy rename to examples/PACKAGES/USER-MISC/entropy/log.entropy diff --git a/examples/USER/misc/extep/BN.data b/examples/PACKAGES/USER-MISC/extep/BN.data similarity index 100% rename from examples/USER/misc/extep/BN.data rename to examples/PACKAGES/USER-MISC/extep/BN.data diff --git a/examples/USER/misc/extep/in.extep-bn b/examples/PACKAGES/USER-MISC/extep/in.extep-bn similarity index 100% rename from examples/USER/misc/extep/in.extep-bn rename to examples/PACKAGES/USER-MISC/extep/in.extep-bn diff --git a/examples/USER/misc/extep/log.23Oct17.extep-bn.g++.1 b/examples/PACKAGES/USER-MISC/extep/log.23Oct17.extep-bn.g++.1 similarity index 100% rename from examples/USER/misc/extep/log.23Oct17.extep-bn.g++.1 rename to examples/PACKAGES/USER-MISC/extep/log.23Oct17.extep-bn.g++.1 diff --git a/examples/USER/misc/extep/log.23Oct17.extep-bn.g++.4 b/examples/PACKAGES/USER-MISC/extep/log.23Oct17.extep-bn.g++.4 similarity index 100% rename from examples/USER/misc/extep/log.23Oct17.extep-bn.g++.4 rename to examples/PACKAGES/USER-MISC/extep/log.23Oct17.extep-bn.g++.4 diff --git a/examples/USER/misc/filter_corotate/data.bpti b/examples/PACKAGES/USER-MISC/filter_corotate/data.bpti similarity index 100% rename from examples/USER/misc/filter_corotate/data.bpti rename to 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a/examples/USER/atc/drift_diffusion/in.schrodinger-poisson2d_convective b/examples/PACKAGES/atc/drift_diffusion/in.schrodinger-poisson2d_convective similarity index 100% rename from examples/USER/atc/drift_diffusion/in.schrodinger-poisson2d_convective rename to examples/PACKAGES/atc/drift_diffusion/in.schrodinger-poisson2d_convective diff --git a/examples/USER/atc/drift_diffusion/in.schrodinger-poisson2d_noatoms b/examples/PACKAGES/atc/drift_diffusion/in.schrodinger-poisson2d_noatoms similarity index 100% rename from examples/USER/atc/drift_diffusion/in.schrodinger-poisson2d_noatoms rename to examples/PACKAGES/atc/drift_diffusion/in.schrodinger-poisson2d_noatoms diff --git a/examples/USER/atc/drift_diffusion/no_atoms_ddm.screen b/examples/PACKAGES/atc/drift_diffusion/no_atoms_ddm.screen similarity index 100% rename from examples/USER/atc/drift_diffusion/no_atoms_ddm.screen rename to examples/PACKAGES/atc/drift_diffusion/no_atoms_ddm.screen diff --git 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--git a/examples/USER/atc/elastic/Ar_CauchyBorn.mat b/examples/PACKAGES/atc/elastic/Ar_CauchyBorn.mat similarity index 100% rename from examples/USER/atc/elastic/Ar_CauchyBorn.mat rename to examples/PACKAGES/atc/elastic/Ar_CauchyBorn.mat diff --git a/examples/USER/atc/elastic/Ar_CauchyBornLinear.mat b/examples/PACKAGES/atc/elastic/Ar_CauchyBornLinear.mat similarity index 100% rename from examples/USER/atc/elastic/Ar_CauchyBornLinear.mat rename to examples/PACKAGES/atc/elastic/Ar_CauchyBornLinear.mat diff --git a/examples/USER/atc/elastic/Ar_damped.mat b/examples/PACKAGES/atc/elastic/Ar_damped.mat similarity index 100% rename from examples/USER/atc/elastic/Ar_damped.mat rename to examples/PACKAGES/atc/elastic/Ar_damped.mat diff --git a/examples/USER/atc/elastic/Ar_elastic.mat b/examples/PACKAGES/atc/elastic/Ar_elastic.mat similarity index 100% rename from examples/USER/atc/elastic/Ar_elastic.mat rename to examples/PACKAGES/atc/elastic/Ar_elastic.mat diff --git a/examples/USER/atc/elastic/Ar_thermo_elastic.mat b/examples/PACKAGES/atc/elastic/Ar_thermo_elastic.mat similarity index 100% rename from examples/USER/atc/elastic/Ar_thermo_elastic.mat rename to examples/PACKAGES/atc/elastic/Ar_thermo_elastic.mat diff --git a/examples/USER/atc/elastic/Au_elastic.mat b/examples/PACKAGES/atc/elastic/Au_elastic.mat similarity index 100% rename from examples/USER/atc/elastic/Au_elastic.mat rename to examples/PACKAGES/atc/elastic/Au_elastic.mat diff --git a/examples/USER/atc/elastic/CNT.mat b/examples/PACKAGES/atc/elastic/CNT.mat similarity index 100% rename from examples/USER/atc/elastic/CNT.mat rename to examples/PACKAGES/atc/elastic/CNT.mat diff --git a/examples/USER/atc/elastic/CNT_electrostatic.mat b/examples/PACKAGES/atc/elastic/CNT_electrostatic.mat similarity index 100% rename from examples/USER/atc/elastic/CNT_electrostatic.mat rename to examples/PACKAGES/atc/elastic/CNT_electrostatic.mat diff --git a/examples/USER/atc/elastic/CNT_electrostatic2.mat b/examples/PACKAGES/atc/elastic/CNT_electrostatic2.mat similarity index 100% rename from examples/USER/atc/elastic/CNT_electrostatic2.mat rename to examples/PACKAGES/atc/elastic/CNT_electrostatic2.mat diff --git a/examples/USER/atc/elastic/CNT_id.mat b/examples/PACKAGES/atc/elastic/CNT_id.mat similarity index 100% rename from examples/USER/atc/elastic/CNT_id.mat rename to examples/PACKAGES/atc/elastic/CNT_id.mat diff --git a/examples/USER/atc/elastic/bar1d.screen b/examples/PACKAGES/atc/elastic/bar1d.screen similarity index 100% rename from examples/USER/atc/elastic/bar1d.screen rename to examples/PACKAGES/atc/elastic/bar1d.screen diff --git a/examples/USER/atc/elastic/bar1d_damped.screen b/examples/PACKAGES/atc/elastic/bar1d_damped.screen similarity index 100% rename from examples/USER/atc/elastic/bar1d_damped.screen rename to examples/PACKAGES/atc/elastic/bar1d_damped.screen diff --git a/examples/USER/atc/elastic/bar1d_flux.screen 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diff --git a/examples/USER/atc/elastic/cnt_electrostatic.screen b/examples/PACKAGES/atc/elastic/cnt_electrostatic.screen similarity index 100% rename from examples/USER/atc/elastic/cnt_electrostatic.screen rename to examples/PACKAGES/atc/elastic/cnt_electrostatic.screen diff --git a/examples/USER/atc/elastic/cnt_electrostatic2.screen b/examples/PACKAGES/atc/elastic/cnt_electrostatic2.screen similarity index 100% rename from examples/USER/atc/elastic/cnt_electrostatic2.screen rename to examples/PACKAGES/atc/elastic/cnt_electrostatic2.screen diff --git a/examples/USER/atc/elastic/cnt_fixed_charge.screen b/examples/PACKAGES/atc/elastic/cnt_fixed_charge.screen similarity index 100% rename from examples/USER/atc/elastic/cnt_fixed_charge.screen rename to examples/PACKAGES/atc/elastic/cnt_fixed_charge.screen diff --git a/examples/USER/atc/elastic/eam_energy.screen b/examples/PACKAGES/atc/elastic/eam_energy.screen similarity index 100% rename from examples/USER/atc/elastic/eam_energy.screen 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examples/PACKAGES/atc/fluids/Ar_thermal.mat diff --git a/examples/USER/atc/fluids/Ar_visc_no_atoms.mat b/examples/PACKAGES/atc/fluids/Ar_visc_no_atoms.mat similarity index 100% rename from examples/USER/atc/fluids/Ar_visc_no_atoms.mat rename to examples/PACKAGES/atc/fluids/Ar_visc_no_atoms.mat diff --git a/examples/USER/atc/fluids/Ar_viscosity.mat b/examples/PACKAGES/atc/fluids/Ar_viscosity.mat similarity index 100% rename from examples/USER/atc/fluids/Ar_viscosity.mat rename to examples/PACKAGES/atc/fluids/Ar_viscosity.mat diff --git a/examples/USER/atc/fluids/bar1d_fluids.screen b/examples/PACKAGES/atc/fluids/bar1d_fluids.screen similarity index 100% rename from examples/USER/atc/fluids/bar1d_fluids.screen rename to examples/PACKAGES/atc/fluids/bar1d_fluids.screen diff --git a/examples/USER/atc/fluids/concentration.screen b/examples/PACKAGES/atc/fluids/concentration.screen similarity index 100% rename from examples/USER/atc/fluids/concentration.screen rename to 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examples/USER/atc/fluids/in.conducting_interface rename to examples/PACKAGES/atc/fluids/in.conducting_interface diff --git a/examples/USER/atc/fluids/in.dielectric_interface b/examples/PACKAGES/atc/fluids/in.dielectric_interface similarity index 100% rename from examples/USER/atc/fluids/in.dielectric_interface rename to examples/PACKAGES/atc/fluids/in.dielectric_interface diff --git a/examples/USER/atc/fluids/in.double_layer b/examples/PACKAGES/atc/fluids/in.double_layer similarity index 100% rename from examples/USER/atc/fluids/in.double_layer rename to examples/PACKAGES/atc/fluids/in.double_layer diff --git a/examples/USER/atc/fluids/in.liquid_electrostatic b/examples/PACKAGES/atc/fluids/in.liquid_electrostatic similarity index 100% rename from examples/USER/atc/fluids/in.liquid_electrostatic rename to examples/PACKAGES/atc/fluids/in.liquid_electrostatic diff --git a/examples/USER/atc/fluids/in.opp_force b/examples/PACKAGES/atc/fluids/in.opp_force similarity index 100% rename from examples/USER/atc/fluids/in.opp_force rename to examples/PACKAGES/atc/fluids/in.opp_force diff --git a/examples/USER/atc/fluids/in.poisson b/examples/PACKAGES/atc/fluids/in.poisson similarity index 100% rename from examples/USER/atc/fluids/in.poisson rename to examples/PACKAGES/atc/fluids/in.poisson diff --git a/examples/USER/atc/fluids/in.shear_flow b/examples/PACKAGES/atc/fluids/in.shear_flow similarity index 100% rename from examples/USER/atc/fluids/in.shear_flow rename to examples/PACKAGES/atc/fluids/in.shear_flow diff --git a/examples/USER/atc/fluids/in.shear_no_atoms b/examples/PACKAGES/atc/fluids/in.shear_no_atoms similarity index 100% rename from examples/USER/atc/fluids/in.shear_no_atoms rename to examples/PACKAGES/atc/fluids/in.shear_no_atoms diff --git a/examples/USER/atc/fluids/interface_init.data b/examples/PACKAGES/atc/fluids/interface_init.data similarity index 100% rename from examples/USER/atc/fluids/interface_init.data rename to 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a/examples/USER/atc/fluids/waternve.atm b/examples/PACKAGES/atc/fluids/waternve.atm similarity index 100% rename from examples/USER/atc/fluids/waternve.atm rename to examples/PACKAGES/atc/fluids/waternve.atm diff --git a/examples/USER/atc/hardy/consistency.screen b/examples/PACKAGES/atc/hardy/consistency.screen similarity index 100% rename from examples/USER/atc/hardy/consistency.screen rename to examples/PACKAGES/atc/hardy/consistency.screen diff --git a/examples/USER/atc/hardy/eam_kernel_convergence.screen b/examples/PACKAGES/atc/hardy/eam_kernel_convergence.screen similarity index 100% rename from examples/USER/atc/hardy/eam_kernel_convergence.screen rename to examples/PACKAGES/atc/hardy/eam_kernel_convergence.screen diff --git a/examples/USER/atc/hardy/eam_unistrain_cell.screen b/examples/PACKAGES/atc/hardy/eam_unistrain_cell.screen similarity index 100% rename from examples/USER/atc/hardy/eam_unistrain_cell.screen rename to examples/PACKAGES/atc/hardy/eam_unistrain_cell.screen 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examples/USER/atc/hardy/eam_unistrain_step.screen rename to examples/PACKAGES/atc/hardy/eam_unistrain_step.screen diff --git a/examples/USER/atc/hardy/eam_volume_stretch.screen b/examples/PACKAGES/atc/hardy/eam_volume_stretch.screen similarity index 100% rename from examples/USER/atc/hardy/eam_volume_stretch.screen rename to examples/PACKAGES/atc/hardy/eam_volume_stretch.screen diff --git a/examples/USER/atc/hardy/eshelby_static.screen b/examples/PACKAGES/atc/hardy/eshelby_static.screen similarity index 100% rename from examples/USER/atc/hardy/eshelby_static.screen rename to examples/PACKAGES/atc/hardy/eshelby_static.screen diff --git a/examples/USER/atc/hardy/in.consistency b/examples/PACKAGES/atc/hardy/in.consistency similarity index 100% rename from examples/USER/atc/hardy/in.consistency rename to examples/PACKAGES/atc/hardy/in.consistency diff --git a/examples/USER/atc/hardy/in.eam_kernel_convergence b/examples/PACKAGES/atc/hardy/in.eam_kernel_convergence similarity index 100% rename from examples/USER/atc/hardy/in.eam_kernel_convergence rename to examples/PACKAGES/atc/hardy/in.eam_kernel_convergence diff --git a/examples/USER/atc/hardy/in.eam_unistrain_cell b/examples/PACKAGES/atc/hardy/in.eam_unistrain_cell similarity index 100% rename from examples/USER/atc/hardy/in.eam_unistrain_cell rename to examples/PACKAGES/atc/hardy/in.eam_unistrain_cell diff --git a/examples/USER/atc/hardy/in.eam_unistrain_mesh b/examples/PACKAGES/atc/hardy/in.eam_unistrain_mesh similarity index 100% rename from examples/USER/atc/hardy/in.eam_unistrain_mesh rename to examples/PACKAGES/atc/hardy/in.eam_unistrain_mesh diff --git a/examples/USER/atc/hardy/in.eam_unistrain_qcylinder b/examples/PACKAGES/atc/hardy/in.eam_unistrain_qcylinder similarity index 100% rename from examples/USER/atc/hardy/in.eam_unistrain_qcylinder rename to examples/PACKAGES/atc/hardy/in.eam_unistrain_qcylinder diff --git a/examples/USER/atc/hardy/in.eam_unistrain_qsphere b/examples/PACKAGES/atc/hardy/in.eam_unistrain_qsphere similarity index 100% rename from examples/USER/atc/hardy/in.eam_unistrain_qsphere rename to examples/PACKAGES/atc/hardy/in.eam_unistrain_qsphere diff --git a/examples/USER/atc/hardy/in.eam_unistrain_step b/examples/PACKAGES/atc/hardy/in.eam_unistrain_step similarity index 100% rename from examples/USER/atc/hardy/in.eam_unistrain_step rename to examples/PACKAGES/atc/hardy/in.eam_unistrain_step diff --git a/examples/USER/atc/hardy/in.eam_volume_stretch b/examples/PACKAGES/atc/hardy/in.eam_volume_stretch similarity index 100% rename from examples/USER/atc/hardy/in.eam_volume_stretch rename to examples/PACKAGES/atc/hardy/in.eam_volume_stretch diff --git a/examples/USER/atc/hardy/in.eshelby_static b/examples/PACKAGES/atc/hardy/in.eshelby_static similarity index 100% rename from examples/USER/atc/hardy/in.eshelby_static rename to examples/PACKAGES/atc/hardy/in.eshelby_static diff --git a/examples/USER/atc/hardy/in.nvt b/examples/PACKAGES/atc/hardy/in.nvt similarity index 100% rename from examples/USER/atc/hardy/in.nvt rename to examples/PACKAGES/atc/hardy/in.nvt diff --git a/examples/USER/atc/hardy/nvt.data b/examples/PACKAGES/atc/hardy/nvt.data similarity index 100% rename from examples/USER/atc/hardy/nvt.data rename to examples/PACKAGES/atc/hardy/nvt.data diff --git a/examples/USER/atc/hardy/nvt.init b/examples/PACKAGES/atc/hardy/nvt.init similarity index 100% rename from examples/USER/atc/hardy/nvt.init rename to examples/PACKAGES/atc/hardy/nvt.init diff --git a/examples/USER/atc/hardy/nvt.screen b/examples/PACKAGES/atc/hardy/nvt.screen similarity index 100% rename from examples/USER/atc/hardy/nvt.screen rename to examples/PACKAGES/atc/hardy/nvt.screen diff --git a/examples/USER/atc/mesh/Ar_ttm.mat b/examples/PACKAGES/atc/mesh/Ar_ttm.mat similarity index 100% rename from examples/USER/atc/mesh/Ar_ttm.mat rename to examples/PACKAGES/atc/mesh/Ar_ttm.mat diff --git a/examples/USER/atc/mesh/Si.mat b/examples/PACKAGES/atc/mesh/Si.mat similarity index 100% rename from examples/USER/atc/mesh/Si.mat rename to examples/PACKAGES/atc/mesh/Si.mat diff --git a/examples/USER/atc/mesh/circle_temp.init b/examples/PACKAGES/atc/mesh/circle_temp.init similarity index 100% rename from examples/USER/atc/mesh/circle_temp.init rename to examples/PACKAGES/atc/mesh/circle_temp.init diff --git a/examples/USER/atc/mesh/gaussianIC1d_hex.screen b/examples/PACKAGES/atc/mesh/gaussianIC1d_hex.screen similarity index 100% rename from examples/USER/atc/mesh/gaussianIC1d_hex.screen rename to examples/PACKAGES/atc/mesh/gaussianIC1d_hex.screen diff --git a/examples/USER/atc/mesh/gaussianIC2d_hex.screen b/examples/PACKAGES/atc/mesh/gaussianIC2d_hex.screen similarity index 100% rename from examples/USER/atc/mesh/gaussianIC2d_hex.screen rename to examples/PACKAGES/atc/mesh/gaussianIC2d_hex.screen diff --git a/examples/USER/atc/mesh/gaussianIC2d_hex20_uniform.screen b/examples/PACKAGES/atc/mesh/gaussianIC2d_hex20_uniform.screen similarity index 100% rename from examples/USER/atc/mesh/gaussianIC2d_hex20_uniform.screen rename to examples/PACKAGES/atc/mesh/gaussianIC2d_hex20_uniform.screen diff --git a/examples/USER/atc/mesh/gaussianIC2d_hex27_uniform.screen b/examples/PACKAGES/atc/mesh/gaussianIC2d_hex27_uniform.screen similarity index 100% rename from examples/USER/atc/mesh/gaussianIC2d_hex27_uniform.screen rename to examples/PACKAGES/atc/mesh/gaussianIC2d_hex27_uniform.screen diff --git a/examples/USER/atc/mesh/gaussianIC2d_hex_uniform.screen b/examples/PACKAGES/atc/mesh/gaussianIC2d_hex_uniform.screen similarity index 100% rename from examples/USER/atc/mesh/gaussianIC2d_hex_uniform.screen rename to examples/PACKAGES/atc/mesh/gaussianIC2d_hex_uniform.screen diff --git a/examples/USER/atc/mesh/gaussianIC2d_tet.screen b/examples/PACKAGES/atc/mesh/gaussianIC2d_tet.screen similarity index 100% rename from examples/USER/atc/mesh/gaussianIC2d_tet.screen rename to examples/PACKAGES/atc/mesh/gaussianIC2d_tet.screen diff --git a/examples/USER/atc/mesh/in.gaussianIC1d_hex b/examples/PACKAGES/atc/mesh/in.gaussianIC1d_hex similarity index 100% rename from examples/USER/atc/mesh/in.gaussianIC1d_hex rename to examples/PACKAGES/atc/mesh/in.gaussianIC1d_hex diff --git a/examples/USER/atc/mesh/in.gaussianIC2d_hex b/examples/PACKAGES/atc/mesh/in.gaussianIC2d_hex similarity index 100% rename from examples/USER/atc/mesh/in.gaussianIC2d_hex rename to examples/PACKAGES/atc/mesh/in.gaussianIC2d_hex diff --git a/examples/USER/atc/mesh/in.gaussianIC2d_hex20_uniform b/examples/PACKAGES/atc/mesh/in.gaussianIC2d_hex20_uniform similarity index 100% rename from examples/USER/atc/mesh/in.gaussianIC2d_hex20_uniform rename to examples/PACKAGES/atc/mesh/in.gaussianIC2d_hex20_uniform diff --git a/examples/USER/atc/mesh/in.gaussianIC2d_hex27_uniform b/examples/PACKAGES/atc/mesh/in.gaussianIC2d_hex27_uniform similarity index 100% rename from examples/USER/atc/mesh/in.gaussianIC2d_hex27_uniform rename to examples/PACKAGES/atc/mesh/in.gaussianIC2d_hex27_uniform diff --git a/examples/USER/atc/mesh/in.gaussianIC2d_tet b/examples/PACKAGES/atc/mesh/in.gaussianIC2d_tet similarity index 100% rename from examples/USER/atc/mesh/in.gaussianIC2d_tet rename to examples/PACKAGES/atc/mesh/in.gaussianIC2d_tet diff --git a/examples/USER/atc/mesh/in.kernel2d_hex b/examples/PACKAGES/atc/mesh/in.kernel2d_hex similarity index 100% rename from examples/USER/atc/mesh/in.kernel2d_hex rename to examples/PACKAGES/atc/mesh/in.kernel2d_hex diff --git a/examples/USER/atc/mesh/in.kernel2d_tet b/examples/PACKAGES/atc/mesh/in.kernel2d_tet similarity index 100% rename from examples/USER/atc/mesh/in.kernel2d_tet rename to examples/PACKAGES/atc/mesh/in.kernel2d_tet diff --git a/examples/USER/atc/mesh/in.mesh2d_tet b/examples/PACKAGES/atc/mesh/in.mesh2d_tet similarity index 100% rename from examples/USER/atc/mesh/in.mesh2d_tet rename to examples/PACKAGES/atc/mesh/in.mesh2d_tet diff --git a/examples/USER/atc/mesh/in.semicircle b/examples/PACKAGES/atc/mesh/in.semicircle similarity index 100% rename from examples/USER/atc/mesh/in.semicircle rename to examples/PACKAGES/atc/mesh/in.semicircle diff --git a/examples/USER/atc/mesh/kernel2d_hex.screen b/examples/PACKAGES/atc/mesh/kernel2d_hex.screen similarity index 100% rename from examples/USER/atc/mesh/kernel2d_hex.screen rename to examples/PACKAGES/atc/mesh/kernel2d_hex.screen diff --git a/examples/USER/atc/mesh/kernel2d_tet.screen b/examples/PACKAGES/atc/mesh/kernel2d_tet.screen similarity index 100% rename from examples/USER/atc/mesh/kernel2d_tet.screen rename to examples/PACKAGES/atc/mesh/kernel2d_tet.screen diff --git a/examples/USER/atc/mesh/mesh2d_tet.screen b/examples/PACKAGES/atc/mesh/mesh2d_tet.screen similarity index 100% rename from examples/USER/atc/mesh/mesh2d_tet.screen rename to examples/PACKAGES/atc/mesh/mesh2d_tet.screen diff --git a/examples/USER/atc/mesh/semicircle.init b/examples/PACKAGES/atc/mesh/semicircle.init similarity index 100% rename from examples/USER/atc/mesh/semicircle.init rename to examples/PACKAGES/atc/mesh/semicircle.init diff --git a/examples/USER/atc/mesh/semicircle.screen b/examples/PACKAGES/atc/mesh/semicircle.screen similarity index 100% rename from examples/USER/atc/mesh/semicircle.screen rename to examples/PACKAGES/atc/mesh/semicircle.screen diff --git a/examples/USER/atc/mesh/si_semicircle.init b/examples/PACKAGES/atc/mesh/si_semicircle.init similarity index 100% rename from examples/USER/atc/mesh/si_semicircle.init rename to examples/PACKAGES/atc/mesh/si_semicircle.init diff --git a/examples/USER/atc/mesh/temp.init b/examples/PACKAGES/atc/mesh/temp.init similarity index 100% rename from examples/USER/atc/mesh/temp.init rename to examples/PACKAGES/atc/mesh/temp.init diff --git a/examples/USER/atc/molecule/harmonic_bonds.init b/examples/PACKAGES/atc/molecule/harmonic_bonds.init similarity index 100% rename from examples/USER/atc/molecule/harmonic_bonds.init rename to examples/PACKAGES/atc/molecule/harmonic_bonds.init diff --git a/examples/USER/atc/molecule/harmonic_bonds.screen b/examples/PACKAGES/atc/molecule/harmonic_bonds.screen similarity index 100% rename from examples/USER/atc/molecule/harmonic_bonds.screen rename to examples/PACKAGES/atc/molecule/harmonic_bonds.screen diff --git a/examples/USER/atc/molecule/in.harmonic_bonds b/examples/PACKAGES/atc/molecule/in.harmonic_bonds similarity index 100% rename from examples/USER/atc/molecule/in.harmonic_bonds rename to examples/PACKAGES/atc/molecule/in.harmonic_bonds diff --git a/examples/USER/atc/molecule/in.polarize b/examples/PACKAGES/atc/molecule/in.polarize similarity index 100% rename from examples/USER/atc/molecule/in.polarize rename to examples/PACKAGES/atc/molecule/in.polarize diff --git a/examples/USER/atc/molecule/in.quartic_bonds b/examples/PACKAGES/atc/molecule/in.quartic_bonds similarity index 100% rename from examples/USER/atc/molecule/in.quartic_bonds rename to examples/PACKAGES/atc/molecule/in.quartic_bonds diff --git a/examples/USER/atc/molecule/in.water b/examples/PACKAGES/atc/molecule/in.water similarity index 100% rename from examples/USER/atc/molecule/in.water rename to examples/PACKAGES/atc/molecule/in.water diff --git a/examples/USER/atc/molecule/polarize.screen b/examples/PACKAGES/atc/molecule/polarize.screen similarity index 100% rename from examples/USER/atc/molecule/polarize.screen rename to examples/PACKAGES/atc/molecule/polarize.screen diff --git a/examples/USER/atc/molecule/quartic_bonds.data b/examples/PACKAGES/atc/molecule/quartic_bonds.data similarity index 100% rename from examples/USER/atc/molecule/quartic_bonds.data rename to examples/PACKAGES/atc/molecule/quartic_bonds.data diff --git a/examples/USER/atc/molecule/quartic_bonds.screen b/examples/PACKAGES/atc/molecule/quartic_bonds.screen similarity index 100% rename from examples/USER/atc/molecule/quartic_bonds.screen rename to examples/PACKAGES/atc/molecule/quartic_bonds.screen diff --git a/examples/USER/atc/molecule/water.init b/examples/PACKAGES/atc/molecule/water.init similarity index 100% rename from examples/USER/atc/molecule/water.init rename to examples/PACKAGES/atc/molecule/water.init diff --git a/examples/USER/atc/molecule/water.mat b/examples/PACKAGES/atc/molecule/water.mat similarity index 100% rename from examples/USER/atc/molecule/water.mat rename to examples/PACKAGES/atc/molecule/water.mat diff --git a/examples/USER/atc/molecule/water.screen b/examples/PACKAGES/atc/molecule/water.screen similarity index 100% rename from examples/USER/atc/molecule/water.screen rename to examples/PACKAGES/atc/molecule/water.screen diff --git a/examples/USER/atc/molecule/waterequil.init b/examples/PACKAGES/atc/molecule/waterequil.init similarity index 100% rename from examples/USER/atc/molecule/waterequil.init rename to examples/PACKAGES/atc/molecule/waterequil.init diff --git a/examples/USER/atc/thermal/Ar_thermal.mat b/examples/PACKAGES/atc/thermal/Ar_thermal.mat similarity index 100% rename from examples/USER/atc/thermal/Ar_thermal.mat rename to examples/PACKAGES/atc/thermal/Ar_thermal.mat diff --git a/examples/USER/atc/thermal/all_atoms.init b/examples/PACKAGES/atc/thermal/all_atoms.init similarity index 100% rename from examples/USER/atc/thermal/all_atoms.init rename to examples/PACKAGES/atc/thermal/all_atoms.init diff --git a/examples/USER/atc/thermal/bar1d.screen b/examples/PACKAGES/atc/thermal/bar1d.screen similarity index 100% rename from examples/USER/atc/thermal/bar1d.screen rename to examples/PACKAGES/atc/thermal/bar1d.screen diff --git a/examples/USER/atc/thermal/bar1d_all_atoms.screen b/examples/PACKAGES/atc/thermal/bar1d_all_atoms.screen similarity index 100% rename from examples/USER/atc/thermal/bar1d_all_atoms.screen rename to examples/PACKAGES/atc/thermal/bar1d_all_atoms.screen diff 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a/examples/USER/atc/two_temperature/uniform_heating.init b/examples/PACKAGES/atc/two_temperature/uniform_heating.init similarity index 100% rename from examples/USER/atc/two_temperature/uniform_heating.init rename to examples/PACKAGES/atc/two_temperature/uniform_heating.init diff --git a/examples/USER/atc/two_temperature/uniform_heating.screen b/examples/PACKAGES/atc/two_temperature/uniform_heating.screen similarity index 100% rename from examples/USER/atc/two_temperature/uniform_heating.screen rename to examples/PACKAGES/atc/two_temperature/uniform_heating.screen diff --git a/examples/USER/awpmd/README b/examples/PACKAGES/awpmd/README similarity index 100% rename from examples/USER/awpmd/README rename to examples/PACKAGES/awpmd/README diff --git a/examples/USER/awpmd/data.h_atom b/examples/PACKAGES/awpmd/data.h_atom similarity index 100% rename from examples/USER/awpmd/data.h_atom rename to examples/PACKAGES/awpmd/data.h_atom diff --git a/examples/USER/awpmd/data.h_molecule 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to examples/PACKAGES/fep/C7inEthanol/fep01/in.insertion diff --git a/examples/USER/fep/C7inEthanol/fep01/log.insertion b/examples/PACKAGES/fep/C7inEthanol/fep01/log.insertion similarity index 100% rename from examples/USER/fep/C7inEthanol/fep01/log.insertion rename to examples/PACKAGES/fep/C7inEthanol/fep01/log.insertion diff --git a/examples/USER/fep/C7inEthanol/fep10/data.init_conf_with_heptane b/examples/PACKAGES/fep/C7inEthanol/fep10/data.init_conf_with_heptane similarity index 100% rename from examples/USER/fep/C7inEthanol/fep10/data.init_conf_with_heptane rename to examples/PACKAGES/fep/C7inEthanol/fep10/data.init_conf_with_heptane diff --git a/examples/USER/fep/C7inEthanol/fep10/in.deletion b/examples/PACKAGES/fep/C7inEthanol/fep10/in.deletion similarity index 100% rename from examples/USER/fep/C7inEthanol/fep10/in.deletion rename to examples/PACKAGES/fep/C7inEthanol/fep10/in.deletion diff --git a/examples/USER/fep/C7inEthanol/fep10/log.deletion 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from examples/USER/fep/CC-CO/fep01/log.fep01 rename to examples/PACKAGES/fep/CC-CO/fep01/log.fep01 diff --git a/examples/USER/fep/CC-CO/fep10/fep10.fep b/examples/PACKAGES/fep/CC-CO/fep10/fep10.fep similarity index 100% rename from examples/USER/fep/CC-CO/fep10/fep10.fep rename to examples/PACKAGES/fep/CC-CO/fep10/fep10.fep diff --git a/examples/USER/fep/CC-CO/fep10/in.fep10.lmp b/examples/PACKAGES/fep/CC-CO/fep10/in.fep10.lmp similarity index 100% rename from examples/USER/fep/CC-CO/fep10/in.fep10.lmp rename to examples/PACKAGES/fep/CC-CO/fep10/in.fep10.lmp diff --git a/examples/USER/fep/CC-CO/fep10/log.fep10 b/examples/PACKAGES/fep/CC-CO/fep10/log.fep10 similarity index 100% rename from examples/USER/fep/CC-CO/fep10/log.fep10 rename to examples/PACKAGES/fep/CC-CO/fep10/log.fep10 diff --git a/examples/USER/fep/CC-CO/mols/CC-CO.ff b/examples/PACKAGES/fep/CC-CO/mols/CC-CO.ff similarity index 100% rename from examples/USER/fep/CC-CO/mols/CC-CO.ff rename to 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b/examples/PACKAGES/fep/CC-CO/mols/data.1.lmp similarity index 100% rename from examples/USER/fep/CC-CO/mols/data.1.lmp rename to examples/PACKAGES/fep/CC-CO/mols/data.1.lmp diff --git a/examples/USER/fep/CC-CO/mols/spce.ff b/examples/PACKAGES/fep/CC-CO/mols/spce.ff similarity index 100% rename from examples/USER/fep/CC-CO/mols/spce.ff rename to examples/PACKAGES/fep/CC-CO/mols/spce.ff diff --git a/examples/USER/fep/CC-CO/mols/spce.zmat b/examples/PACKAGES/fep/CC-CO/mols/spce.zmat similarity index 100% rename from examples/USER/fep/CC-CO/mols/spce.zmat rename to examples/PACKAGES/fep/CC-CO/mols/spce.zmat diff --git a/examples/USER/fep/CH4-CF4/README.md b/examples/PACKAGES/fep/CH4-CF4/README.md similarity index 100% rename from examples/USER/fep/CH4-CF4/README.md rename to examples/PACKAGES/fep/CH4-CF4/README.md diff --git a/examples/USER/fep/CH4-CF4/bar01/bar01.fep b/examples/PACKAGES/fep/CH4-CF4/bar01/bar01.fep similarity index 100% rename from examples/USER/fep/CH4-CF4/bar01/bar01.fep rename to examples/PACKAGES/fep/CH4-CF4/bar01/bar01.fep diff --git a/examples/USER/fep/CH4-CF4/bar01/in.bar01.lmp b/examples/PACKAGES/fep/CH4-CF4/bar01/in.bar01.lmp similarity index 100% rename from examples/USER/fep/CH4-CF4/bar01/in.bar01.lmp rename to examples/PACKAGES/fep/CH4-CF4/bar01/in.bar01.lmp diff --git a/examples/USER/fep/CH4-CF4/bar01/log.bar01 b/examples/PACKAGES/fep/CH4-CF4/bar01/log.bar01 similarity index 100% rename from examples/USER/fep/CH4-CF4/bar01/log.bar01 rename to examples/PACKAGES/fep/CH4-CF4/bar01/log.bar01 diff --git a/examples/USER/fep/CH4-CF4/bar10/bar10.fep b/examples/PACKAGES/fep/CH4-CF4/bar10/bar10.fep similarity index 100% rename from examples/USER/fep/CH4-CF4/bar10/bar10.fep rename to examples/PACKAGES/fep/CH4-CF4/bar10/bar10.fep diff --git a/examples/USER/fep/CH4-CF4/bar10/in.bar10.lmp b/examples/PACKAGES/fep/CH4-CF4/bar10/in.bar10.lmp similarity index 100% rename from examples/USER/fep/CH4-CF4/bar10/in.bar10.lmp rename to examples/PACKAGES/fep/CH4-CF4/bar10/in.bar10.lmp diff --git a/examples/USER/fep/CH4-CF4/bar10/log.ber10 b/examples/PACKAGES/fep/CH4-CF4/bar10/log.ber10 similarity index 100% rename from examples/USER/fep/CH4-CF4/bar10/log.ber10 rename to examples/PACKAGES/fep/CH4-CF4/bar10/log.ber10 diff --git a/examples/USER/fep/CH4-CF4/fep01/fep01.fep b/examples/PACKAGES/fep/CH4-CF4/fep01/fep01.fep similarity index 100% rename from examples/USER/fep/CH4-CF4/fep01/fep01.fep rename to examples/PACKAGES/fep/CH4-CF4/fep01/fep01.fep diff --git a/examples/USER/fep/CH4-CF4/fep01/in.fep01.lmp b/examples/PACKAGES/fep/CH4-CF4/fep01/in.fep01.lmp similarity index 100% rename from examples/USER/fep/CH4-CF4/fep01/in.fep01.lmp rename to examples/PACKAGES/fep/CH4-CF4/fep01/in.fep01.lmp diff --git a/examples/USER/fep/CH4-CF4/fep01/log.fep01 b/examples/PACKAGES/fep/CH4-CF4/fep01/log.fep01 similarity index 100% rename from examples/USER/fep/CH4-CF4/fep01/log.fep01 rename to examples/PACKAGES/fep/CH4-CF4/fep01/log.fep01 diff --git a/examples/USER/fep/CH4-CF4/fep10/fep10.fep b/examples/PACKAGES/fep/CH4-CF4/fep10/fep10.fep similarity index 100% rename from examples/USER/fep/CH4-CF4/fep10/fep10.fep rename to examples/PACKAGES/fep/CH4-CF4/fep10/fep10.fep diff --git a/examples/USER/fep/CH4-CF4/fep10/in.fep10.lmp b/examples/PACKAGES/fep/CH4-CF4/fep10/in.fep10.lmp similarity index 100% rename from examples/USER/fep/CH4-CF4/fep10/in.fep10.lmp rename to examples/PACKAGES/fep/CH4-CF4/fep10/in.fep10.lmp diff --git a/examples/USER/fep/CH4-CF4/fep10/log.fep01 b/examples/PACKAGES/fep/CH4-CF4/fep10/log.fep01 similarity index 100% rename from examples/USER/fep/CH4-CF4/fep10/log.fep01 rename to examples/PACKAGES/fep/CH4-CF4/fep10/log.fep01 diff --git a/examples/USER/fep/CH4-CF4/mols/CF4-CH4.zmat b/examples/PACKAGES/fep/CH4-CF4/mols/CF4-CH4.zmat similarity index 100% rename from examples/USER/fep/CH4-CF4/mols/CF4-CH4.zmat rename to 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--git a/examples/USER/fep/CH4-CF4/mols/spce.ff b/examples/PACKAGES/fep/CH4-CF4/mols/spce.ff similarity index 100% rename from examples/USER/fep/CH4-CF4/mols/spce.ff rename to examples/PACKAGES/fep/CH4-CF4/mols/spce.ff diff --git a/examples/USER/fep/CH4-CF4/mols/spce.zmat b/examples/PACKAGES/fep/CH4-CF4/mols/spce.zmat similarity index 100% rename from examples/USER/fep/CH4-CF4/mols/spce.zmat rename to examples/PACKAGES/fep/CH4-CF4/mols/spce.zmat diff --git a/examples/USER/fep/CH4hyd/README.md b/examples/PACKAGES/fep/CH4hyd/README.md similarity index 100% rename from examples/USER/fep/CH4hyd/README.md rename to examples/PACKAGES/fep/CH4hyd/README.md diff --git a/examples/USER/fep/CH4hyd/fdti01/fdti01.fep b/examples/PACKAGES/fep/CH4hyd/fdti01/fdti01.fep similarity index 100% rename from examples/USER/fep/CH4hyd/fdti01/fdti01.fep rename to examples/PACKAGES/fep/CH4hyd/fdti01/fdti01.fep diff --git a/examples/USER/fep/CH4hyd/fdti01/in.fdti01.lmp b/examples/PACKAGES/fep/CH4hyd/fdti01/in.fdti01.lmp similarity index 100% rename from examples/USER/fep/CH4hyd/fdti01/in.fdti01.lmp rename to examples/PACKAGES/fep/CH4hyd/fdti01/in.fdti01.lmp diff --git a/examples/USER/fep/CH4hyd/fdti01/log.fdti01 b/examples/PACKAGES/fep/CH4hyd/fdti01/log.fdti01 similarity index 100% rename from examples/USER/fep/CH4hyd/fdti01/log.fdti01 rename to examples/PACKAGES/fep/CH4hyd/fdti01/log.fdti01 diff --git a/examples/USER/fep/CH4hyd/fdti10/fdti10.fep b/examples/PACKAGES/fep/CH4hyd/fdti10/fdti10.fep similarity index 100% rename from examples/USER/fep/CH4hyd/fdti10/fdti10.fep rename to examples/PACKAGES/fep/CH4hyd/fdti10/fdti10.fep diff --git a/examples/USER/fep/CH4hyd/fdti10/in.fdti10.lmp b/examples/PACKAGES/fep/CH4hyd/fdti10/in.fdti10.lmp similarity index 100% rename from examples/USER/fep/CH4hyd/fdti10/in.fdti10.lmp rename to examples/PACKAGES/fep/CH4hyd/fdti10/in.fdti10.lmp diff --git a/examples/USER/fep/CH4hyd/fdti10/log.fdti10 b/examples/PACKAGES/fep/CH4hyd/fdti10/log.fdti10 similarity index 100% rename from examples/USER/fep/CH4hyd/fdti10/log.fdti10 rename to examples/PACKAGES/fep/CH4hyd/fdti10/log.fdti10 diff --git a/examples/USER/fep/CH4hyd/fep01/fep01.fep b/examples/PACKAGES/fep/CH4hyd/fep01/fep01.fep similarity index 100% rename from examples/USER/fep/CH4hyd/fep01/fep01.fep rename to examples/PACKAGES/fep/CH4hyd/fep01/fep01.fep diff --git a/examples/USER/fep/CH4hyd/fep01/in.fep01.lmp b/examples/PACKAGES/fep/CH4hyd/fep01/in.fep01.lmp similarity index 100% rename from examples/USER/fep/CH4hyd/fep01/in.fep01.lmp rename to examples/PACKAGES/fep/CH4hyd/fep01/in.fep01.lmp diff --git a/examples/USER/fep/CH4hyd/fep01/log.fep01 b/examples/PACKAGES/fep/CH4hyd/fep01/log.fep01 similarity index 100% rename from examples/USER/fep/CH4hyd/fep01/log.fep01 rename to examples/PACKAGES/fep/CH4hyd/fep01/log.fep01 diff --git a/examples/USER/fep/CH4hyd/fep10/fep10.fep b/examples/PACKAGES/fep/CH4hyd/fep10/fep10.fep similarity 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a/examples/USER/phonon/dynamical_matrix_command/Silicon/ff-silicon.lmp b/examples/PACKAGES/phonon/dynamical_matrix_command/Silicon/ff-silicon.lmp similarity index 100% rename from examples/USER/phonon/dynamical_matrix_command/Silicon/ff-silicon.lmp rename to examples/PACKAGES/phonon/dynamical_matrix_command/Silicon/ff-silicon.lmp diff --git a/examples/USER/phonon/dynamical_matrix_command/Silicon/in.silicon b/examples/PACKAGES/phonon/dynamical_matrix_command/Silicon/in.silicon similarity index 100% rename from examples/USER/phonon/dynamical_matrix_command/Silicon/in.silicon rename to examples/PACKAGES/phonon/dynamical_matrix_command/Silicon/in.silicon diff --git a/examples/USER/phonon/dynamical_matrix_command/Silicon/lmp_bank/amorphous_silicon.lmp b/examples/PACKAGES/phonon/dynamical_matrix_command/Silicon/lmp_bank/amorphous_silicon.lmp similarity index 100% rename from examples/USER/phonon/dynamical_matrix_command/Silicon/lmp_bank/amorphous_silicon.lmp rename to 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b/examples/PACKAGES/phonon/dynamical_matrix_command/Silicon/lmp_bank/silicon_8.lmp similarity index 100% rename from examples/USER/phonon/dynamical_matrix_command/Silicon/lmp_bank/silicon_8.lmp rename to examples/PACKAGES/phonon/dynamical_matrix_command/Silicon/lmp_bank/silicon_8.lmp diff --git a/examples/USER/phonon/dynamical_matrix_command/Silicon/results/dynmat.dat b/examples/PACKAGES/phonon/dynamical_matrix_command/Silicon/results/dynmat.dat similarity index 100% rename from examples/USER/phonon/dynamical_matrix_command/Silicon/results/dynmat.dat rename to examples/PACKAGES/phonon/dynamical_matrix_command/Silicon/results/dynmat.dat diff --git a/examples/USER/phonon/dynamical_matrix_command/Silicon/results/out.silicon b/examples/PACKAGES/phonon/dynamical_matrix_command/Silicon/results/out.silicon similarity index 100% rename from examples/USER/phonon/dynamical_matrix_command/Silicon/results/out.silicon rename to 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a/examples/USER/qtb/alpha_quartz_qtb/in.alpha_quartz_qtb b/examples/PACKAGES/qtb/alpha_quartz_qtb/in.alpha_quartz_qtb similarity index 100% rename from examples/USER/qtb/alpha_quartz_qtb/in.alpha_quartz_qtb rename to examples/PACKAGES/qtb/alpha_quartz_qtb/in.alpha_quartz_qtb diff --git a/examples/USER/qtb/alpha_quartz_qtb/log.15Jun20.alpha_quartz_qtb.g++.1 b/examples/PACKAGES/qtb/alpha_quartz_qtb/log.15Jun20.alpha_quartz_qtb.g++.1 similarity index 100% rename from examples/USER/qtb/alpha_quartz_qtb/log.15Jun20.alpha_quartz_qtb.g++.1 rename to examples/PACKAGES/qtb/alpha_quartz_qtb/log.15Jun20.alpha_quartz_qtb.g++.1 diff --git a/examples/USER/qtb/alpha_quartz_qtb/log.15Jun20.alpha_quartz_qtb.g++.4 b/examples/PACKAGES/qtb/alpha_quartz_qtb/log.15Jun20.alpha_quartz_qtb.g++.4 similarity index 100% rename from examples/USER/qtb/alpha_quartz_qtb/log.15Jun20.alpha_quartz_qtb.g++.4 rename to examples/PACKAGES/qtb/alpha_quartz_qtb/log.15Jun20.alpha_quartz_qtb.g++.4 diff --git a/examples/USER/qtb/methane_qbmsst/ffield.reax b/examples/PACKAGES/qtb/methane_qbmsst/ffield.reax similarity index 100% rename from examples/USER/qtb/methane_qbmsst/ffield.reax rename to examples/PACKAGES/qtb/methane_qbmsst/ffield.reax diff --git a/examples/USER/qtb/methane_qbmsst/methane_qbmsst.in b/examples/PACKAGES/qtb/methane_qbmsst/methane_qbmsst.in similarity index 100% rename from examples/USER/qtb/methane_qbmsst/methane_qbmsst.in rename to examples/PACKAGES/qtb/methane_qbmsst/methane_qbmsst.in diff --git a/examples/USER/qtb/methane_qbmsst/methane_qtb.mod b/examples/PACKAGES/qtb/methane_qbmsst/methane_qtb.mod similarity index 100% rename from examples/USER/qtb/methane_qbmsst/methane_qtb.mod rename to examples/PACKAGES/qtb/methane_qbmsst/methane_qtb.mod diff --git a/examples/USER/qtb/methane_qtb/ffield.reax b/examples/PACKAGES/qtb/methane_qtb/ffield.reax similarity index 100% rename from examples/USER/qtb/methane_qtb/ffield.reax rename to 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a/examples/USER/reaction/tiny_epoxy/log.20Nov19.tiny_epoxy.stabilized.g++.4 b/examples/PACKAGES/reaction/tiny_epoxy/log.20Nov19.tiny_epoxy.stabilized.g++.4 similarity index 100% rename from examples/USER/reaction/tiny_epoxy/log.20Nov19.tiny_epoxy.stabilized.g++.4 rename to examples/PACKAGES/reaction/tiny_epoxy/log.20Nov19.tiny_epoxy.stabilized.g++.4 diff --git a/examples/USER/reaction/tiny_epoxy/rxn1_stp1.map b/examples/PACKAGES/reaction/tiny_epoxy/rxn1_stp1.map similarity index 100% rename from examples/USER/reaction/tiny_epoxy/rxn1_stp1.map rename to examples/PACKAGES/reaction/tiny_epoxy/rxn1_stp1.map diff --git a/examples/USER/reaction/tiny_epoxy/rxn1_stp1_post.data_template b/examples/PACKAGES/reaction/tiny_epoxy/rxn1_stp1_post.data_template similarity index 100% rename from examples/USER/reaction/tiny_epoxy/rxn1_stp1_post.data_template rename to examples/PACKAGES/reaction/tiny_epoxy/rxn1_stp1_post.data_template diff --git 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a/examples/USER/reaction/tiny_nylon/in.tiny_nylon.stabilized_variable_probability b/examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.stabilized_variable_probability similarity index 100% rename from examples/USER/reaction/tiny_nylon/in.tiny_nylon.stabilized_variable_probability rename to examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.stabilized_variable_probability diff --git a/examples/USER/reaction/tiny_nylon/in.tiny_nylon.unstabilized b/examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.unstabilized similarity index 100% rename from examples/USER/reaction/tiny_nylon/in.tiny_nylon.unstabilized rename to examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.unstabilized diff --git a/examples/USER/reaction/tiny_nylon/log.22Apr20.tiny_nylon.stabilized_variable_probability.g++.1 b/examples/PACKAGES/reaction/tiny_nylon/log.22Apr20.tiny_nylon.stabilized_variable_probability.g++.1 similarity index 100% rename from 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from examples/USER/reaction/tiny_nylon/log.5Jun19.tiny_nylon.unstabilized.g++.4 rename to examples/PACKAGES/reaction/tiny_nylon/log.5Jun19.tiny_nylon.unstabilized.g++.4 diff --git a/examples/USER/reaction/tiny_nylon/rxn1_stp1_map b/examples/PACKAGES/reaction/tiny_nylon/rxn1_stp1_map similarity index 100% rename from examples/USER/reaction/tiny_nylon/rxn1_stp1_map rename to examples/PACKAGES/reaction/tiny_nylon/rxn1_stp1_map diff --git a/examples/USER/reaction/tiny_nylon/rxn1_stp1_reacted.data_template b/examples/PACKAGES/reaction/tiny_nylon/rxn1_stp1_reacted.data_template similarity index 100% rename from examples/USER/reaction/tiny_nylon/rxn1_stp1_reacted.data_template rename to examples/PACKAGES/reaction/tiny_nylon/rxn1_stp1_reacted.data_template diff --git a/examples/USER/reaction/tiny_nylon/rxn1_stp1_unreacted.data_template b/examples/PACKAGES/reaction/tiny_nylon/rxn1_stp1_unreacted.data_template similarity index 100% rename from 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a/examples/USER/reaction/tiny_polystyrene/2styrene_unreacted.data_template b/examples/PACKAGES/reaction/tiny_polystyrene/2styrene_unreacted.data_template similarity index 100% rename from examples/USER/reaction/tiny_polystyrene/2styrene_unreacted.data_template rename to examples/PACKAGES/reaction/tiny_polystyrene/2styrene_unreacted.data_template diff --git a/examples/USER/reaction/tiny_polystyrene/chain_chain_map b/examples/PACKAGES/reaction/tiny_polystyrene/chain_chain_map similarity index 100% rename from examples/USER/reaction/tiny_polystyrene/chain_chain_map rename to examples/PACKAGES/reaction/tiny_polystyrene/chain_chain_map diff --git a/examples/USER/reaction/tiny_polystyrene/chain_chain_reacted.data_template b/examples/PACKAGES/reaction/tiny_polystyrene/chain_chain_reacted.data_template similarity index 100% rename from examples/USER/reaction/tiny_polystyrene/chain_chain_reacted.data_template rename to 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a/examples/USER/reaction/tiny_polystyrene/log.20Nov19.tiny_polystyrene.stabilized.g++.1 b/examples/PACKAGES/reaction/tiny_polystyrene/log.20Nov19.tiny_polystyrene.stabilized.g++.1 similarity index 100% rename from examples/USER/reaction/tiny_polystyrene/log.20Nov19.tiny_polystyrene.stabilized.g++.1 rename to examples/PACKAGES/reaction/tiny_polystyrene/log.20Nov19.tiny_polystyrene.stabilized.g++.1 diff --git a/examples/USER/reaction/tiny_polystyrene/log.20Nov19.tiny_polystyrene.stabilized.g++.4 b/examples/PACKAGES/reaction/tiny_polystyrene/log.20Nov19.tiny_polystyrene.stabilized.g++.4 similarity index 100% rename from examples/USER/reaction/tiny_polystyrene/log.20Nov19.tiny_polystyrene.stabilized.g++.4 rename to examples/PACKAGES/reaction/tiny_polystyrene/log.20Nov19.tiny_polystyrene.stabilized.g++.4 diff --git a/examples/USER/reaction/tiny_polystyrene/tiny_polystyrene.data b/examples/PACKAGES/reaction/tiny_polystyrene/tiny_polystyrene.data similarity index 100% rename from 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examples/PACKAGES/smd/funnel_flow/log.9Oct20.funnel_flow.g++.4 diff --git a/examples/USER/smd/rubber_rings_3d/in.rubber_rings_3d b/examples/PACKAGES/smd/rubber_rings_3d/in.rubber_rings_3d similarity index 100% rename from examples/USER/smd/rubber_rings_3d/in.rubber_rings_3d rename to examples/PACKAGES/smd/rubber_rings_3d/in.rubber_rings_3d diff --git a/examples/USER/smd/rubber_rings_3d/log.9Oct20.rubber_rings_3d.g++.1 b/examples/PACKAGES/smd/rubber_rings_3d/log.9Oct20.rubber_rings_3d.g++.1 similarity index 100% rename from examples/USER/smd/rubber_rings_3d/log.9Oct20.rubber_rings_3d.g++.1 rename to examples/PACKAGES/smd/rubber_rings_3d/log.9Oct20.rubber_rings_3d.g++.1 diff --git a/examples/USER/smd/rubber_rings_3d/log.9Oct20.rubber_rings_3d.g++.4 b/examples/PACKAGES/smd/rubber_rings_3d/log.9Oct20.rubber_rings_3d.g++.4 similarity index 100% rename from examples/USER/smd/rubber_rings_3d/log.9Oct20.rubber_rings_3d.g++.4 rename to examples/PACKAGES/smd/rubber_rings_3d/log.9Oct20.rubber_rings_3d.g++.4 diff --git a/examples/USER/smd/rubber_rings_3d/washer_hex_adjusted.data b/examples/PACKAGES/smd/rubber_rings_3d/washer_hex_adjusted.data similarity index 100% rename from examples/USER/smd/rubber_rings_3d/washer_hex_adjusted.data rename to examples/PACKAGES/smd/rubber_rings_3d/washer_hex_adjusted.data diff --git a/examples/USER/smd/rubber_strip_pull/in.rubber_strip_pull b/examples/PACKAGES/smd/rubber_strip_pull/in.rubber_strip_pull similarity index 100% rename from examples/USER/smd/rubber_strip_pull/in.rubber_strip_pull rename to examples/PACKAGES/smd/rubber_strip_pull/in.rubber_strip_pull diff --git a/examples/USER/smd/rubber_strip_pull/log.9Oct20.rubber_strip_pull.g++.1 b/examples/PACKAGES/smd/rubber_strip_pull/log.9Oct20.rubber_strip_pull.g++.1 similarity index 100% rename from examples/USER/smd/rubber_strip_pull/log.9Oct20.rubber_strip_pull.g++.1 rename to examples/PACKAGES/smd/rubber_strip_pull/log.9Oct20.rubber_strip_pull.g++.1 diff --git a/examples/USER/smd/rubber_strip_pull/log.9Oct20.rubber_strip_pull.g++.4 b/examples/PACKAGES/smd/rubber_strip_pull/log.9Oct20.rubber_strip_pull.g++.4 similarity index 100% rename from examples/USER/smd/rubber_strip_pull/log.9Oct20.rubber_strip_pull.g++.4 rename to examples/PACKAGES/smd/rubber_strip_pull/log.9Oct20.rubber_strip_pull.g++.4 diff --git a/examples/USER/smd/rubber_strip_pull/plot.gpl b/examples/PACKAGES/smd/rubber_strip_pull/plot.gpl similarity index 100% rename from examples/USER/smd/rubber_strip_pull/plot.gpl rename to examples/PACKAGES/smd/rubber_strip_pull/plot.gpl diff --git a/examples/USER/smtbq/data.Alpha b/examples/PACKAGES/smtbq/data.Alpha similarity index 100% rename from examples/USER/smtbq/data.Alpha rename to examples/PACKAGES/smtbq/data.Alpha diff --git a/examples/USER/smtbq/ffield.smtbq.Al b/examples/PACKAGES/smtbq/ffield.smtbq.Al similarity index 100% rename from examples/USER/smtbq/ffield.smtbq.Al rename to examples/PACKAGES/smtbq/ffield.smtbq.Al diff --git a/examples/USER/smtbq/ffield.smtbq.Al2O3 b/examples/PACKAGES/smtbq/ffield.smtbq.Al2O3 similarity index 100% rename from examples/USER/smtbq/ffield.smtbq.Al2O3 rename to examples/PACKAGES/smtbq/ffield.smtbq.Al2O3 diff --git a/examples/USER/smtbq/ffield.smtbq.TiO2 b/examples/PACKAGES/smtbq/ffield.smtbq.TiO2 similarity index 100% rename from examples/USER/smtbq/ffield.smtbq.TiO2 rename to examples/PACKAGES/smtbq/ffield.smtbq.TiO2 diff --git a/examples/USER/smtbq/in.smtbq.Al b/examples/PACKAGES/smtbq/in.smtbq.Al similarity index 100% rename from examples/USER/smtbq/in.smtbq.Al rename to examples/PACKAGES/smtbq/in.smtbq.Al diff --git a/examples/USER/smtbq/in.smtbq.Al2O3 b/examples/PACKAGES/smtbq/in.smtbq.Al2O3 similarity index 100% rename from examples/USER/smtbq/in.smtbq.Al2O3 rename to examples/PACKAGES/smtbq/in.smtbq.Al2O3 diff --git a/examples/USER/smtbq/in.smtbq.TiO2 b/examples/PACKAGES/smtbq/in.smtbq.TiO2 similarity index 100% rename from examples/USER/smtbq/in.smtbq.TiO2 rename to examples/PACKAGES/smtbq/in.smtbq.TiO2 diff --git a/examples/USER/smtbq/log.smtbq.Al.g++.1 b/examples/PACKAGES/smtbq/log.smtbq.Al.g++.1 similarity index 100% rename from examples/USER/smtbq/log.smtbq.Al.g++.1 rename to examples/PACKAGES/smtbq/log.smtbq.Al.g++.1 diff --git a/examples/USER/smtbq/log.smtbq.Al.g++.4 b/examples/PACKAGES/smtbq/log.smtbq.Al.g++.4 similarity index 100% rename from examples/USER/smtbq/log.smtbq.Al.g++.4 rename to examples/PACKAGES/smtbq/log.smtbq.Al.g++.4 diff --git a/examples/USER/smtbq/log.smtbq.Al2O3.g++.1 b/examples/PACKAGES/smtbq/log.smtbq.Al2O3.g++.1 similarity index 100% rename from examples/USER/smtbq/log.smtbq.Al2O3.g++.1 rename to examples/PACKAGES/smtbq/log.smtbq.Al2O3.g++.1 diff --git a/examples/USER/smtbq/log.smtbq.Al2O3.g++.4 b/examples/PACKAGES/smtbq/log.smtbq.Al2O3.g++.4 similarity index 100% rename from examples/USER/smtbq/log.smtbq.Al2O3.g++.4 rename to examples/PACKAGES/smtbq/log.smtbq.Al2O3.g++.4 diff --git a/examples/USER/smtbq/log.smtbq.TiO2.g++.1 b/examples/PACKAGES/smtbq/log.smtbq.TiO2.g++.1 similarity index 100% rename from examples/USER/smtbq/log.smtbq.TiO2.g++.1 rename to examples/PACKAGES/smtbq/log.smtbq.TiO2.g++.1 diff --git a/examples/USER/smtbq/log.smtbq.TiO2.g++.4 b/examples/PACKAGES/smtbq/log.smtbq.TiO2.g++.4 similarity index 100% rename from examples/USER/smtbq/log.smtbq.TiO2.g++.4 rename to examples/PACKAGES/smtbq/log.smtbq.TiO2.g++.4 diff --git a/examples/USER/sph/README b/examples/PACKAGES/sph/README similarity index 100% rename from examples/USER/sph/README rename to examples/PACKAGES/sph/README diff --git a/examples/USER/sph/cavity_flow/cavity_flow.lmp b/examples/PACKAGES/sph/cavity_flow/cavity_flow.lmp similarity index 100% rename from examples/USER/sph/cavity_flow/cavity_flow.lmp rename to examples/PACKAGES/sph/cavity_flow/cavity_flow.lmp diff --git a/examples/USER/sph/heatconduction/compare_analytic.gpl b/examples/PACKAGES/sph/heatconduction/compare_analytic.gpl similarity index 100% rename from examples/USER/sph/heatconduction/compare_analytic.gpl rename to examples/PACKAGES/sph/heatconduction/compare_analytic.gpl diff --git a/examples/USER/sph/heatconduction/sph_heat_conduction_2d.lmp b/examples/PACKAGES/sph/heatconduction/sph_heat_conduction_2d.lmp similarity index 100% rename from examples/USER/sph/heatconduction/sph_heat_conduction_2d.lmp rename to examples/PACKAGES/sph/heatconduction/sph_heat_conduction_2d.lmp diff --git a/examples/USER/sph/heatconduction/sph_heat_conduction_3d.lmp b/examples/PACKAGES/sph/heatconduction/sph_heat_conduction_3d.lmp similarity index 100% rename from examples/USER/sph/heatconduction/sph_heat_conduction_3d.lmp rename to examples/PACKAGES/sph/heatconduction/sph_heat_conduction_3d.lmp diff --git a/examples/USER/sph/shock_tube/compare_exact.gpl b/examples/PACKAGES/sph/shock_tube/compare_exact.gpl similarity index 100% rename from examples/USER/sph/shock_tube/compare_exact.gpl rename to examples/PACKAGES/sph/shock_tube/compare_exact.gpl diff --git a/examples/USER/sph/shock_tube/exact_solution.dat b/examples/PACKAGES/sph/shock_tube/exact_solution.dat similarity index 100% rename from examples/USER/sph/shock_tube/exact_solution.dat rename to examples/PACKAGES/sph/shock_tube/exact_solution.dat diff --git a/examples/USER/sph/shock_tube/shock2d.lmp b/examples/PACKAGES/sph/shock_tube/shock2d.lmp similarity index 100% rename from examples/USER/sph/shock_tube/shock2d.lmp rename to examples/PACKAGES/sph/shock_tube/shock2d.lmp diff --git a/examples/USER/sph/shock_tube/shock3d.lmp b/examples/PACKAGES/sph/shock_tube/shock3d.lmp similarity index 100% rename from examples/USER/sph/shock_tube/shock3d.lmp rename to examples/PACKAGES/sph/shock_tube/shock3d.lmp diff --git a/examples/USER/sph/water_collapse/data.initial b/examples/PACKAGES/sph/water_collapse/data.initial similarity index 100% rename from examples/USER/sph/water_collapse/data.initial rename to examples/PACKAGES/sph/water_collapse/data.initial diff --git a/examples/USER/sph/water_collapse/water_collapse.lmp b/examples/PACKAGES/sph/water_collapse/water_collapse.lmp similarity index 100% rename from examples/USER/sph/water_collapse/water_collapse.lmp rename to examples/PACKAGES/sph/water_collapse/water_collapse.lmp diff --git a/examples/USER/tally/README b/examples/PACKAGES/tally/README similarity index 100% rename from examples/USER/tally/README rename to examples/PACKAGES/tally/README diff --git a/examples/USER/tally/data.spce b/examples/PACKAGES/tally/data.spce similarity index 100% rename from examples/USER/tally/data.spce rename to examples/PACKAGES/tally/data.spce diff --git a/examples/USER/tally/in.force b/examples/PACKAGES/tally/in.force similarity index 100% rename from examples/USER/tally/in.force rename to examples/PACKAGES/tally/in.force diff --git a/examples/USER/tally/in.pe b/examples/PACKAGES/tally/in.pe similarity index 100% rename from examples/USER/tally/in.pe rename to examples/PACKAGES/tally/in.pe diff --git a/examples/USER/tally/in.stress b/examples/PACKAGES/tally/in.stress similarity index 100% rename from examples/USER/tally/in.stress rename to examples/PACKAGES/tally/in.stress diff --git a/examples/USER/tally/log.12Jun17.force.1 b/examples/PACKAGES/tally/log.12Jun17.force.1 similarity index 100% rename from examples/USER/tally/log.12Jun17.force.1 rename to examples/PACKAGES/tally/log.12Jun17.force.1 diff --git a/examples/USER/tally/log.12Jun17.force.4 b/examples/PACKAGES/tally/log.12Jun17.force.4 similarity index 100% rename from examples/USER/tally/log.12Jun17.force.4 rename to examples/PACKAGES/tally/log.12Jun17.force.4 diff --git a/examples/USER/tally/log.12Jun17.pe.1 b/examples/PACKAGES/tally/log.12Jun17.pe.1 similarity index 100% rename from examples/USER/tally/log.12Jun17.pe.1 rename to examples/PACKAGES/tally/log.12Jun17.pe.1 diff --git a/examples/USER/tally/log.12Jun17.pe.4 b/examples/PACKAGES/tally/log.12Jun17.pe.4 similarity index 100% rename from examples/USER/tally/log.12Jun17.pe.4 rename to examples/PACKAGES/tally/log.12Jun17.pe.4 diff --git a/examples/USER/tally/log.12Jun17.stress.1 b/examples/PACKAGES/tally/log.12Jun17.stress.1 similarity index 100% rename from examples/USER/tally/log.12Jun17.stress.1 rename to examples/PACKAGES/tally/log.12Jun17.stress.1 diff --git a/examples/USER/tally/log.12Jun17.stress.4 b/examples/PACKAGES/tally/log.12Jun17.stress.4 similarity index 100% rename from examples/USER/tally/log.12Jun17.stress.4 rename to examples/PACKAGES/tally/log.12Jun17.stress.4 diff --git a/examples/USER/uef/README b/examples/PACKAGES/uef/README similarity index 100% rename from examples/USER/uef/README rename to examples/PACKAGES/uef/README diff --git a/examples/USER/uef/npt_biaxial/data.wca b/examples/PACKAGES/uef/npt_biaxial/data.wca similarity index 100% rename from examples/USER/uef/npt_biaxial/data.wca rename to examples/PACKAGES/uef/npt_biaxial/data.wca diff --git a/examples/USER/uef/npt_biaxial/in.npt_biaxial b/examples/PACKAGES/uef/npt_biaxial/in.npt_biaxial similarity index 100% rename from examples/USER/uef/npt_biaxial/in.npt_biaxial rename to examples/PACKAGES/uef/npt_biaxial/in.npt_biaxial diff --git a/examples/USER/uef/npt_biaxial/log.27Nov18.npt_biaxial.g++.1 b/examples/PACKAGES/uef/npt_biaxial/log.27Nov18.npt_biaxial.g++.1 similarity index 100% rename from examples/USER/uef/npt_biaxial/log.27Nov18.npt_biaxial.g++.1 rename to examples/PACKAGES/uef/npt_biaxial/log.27Nov18.npt_biaxial.g++.1 diff --git a/examples/USER/uef/npt_biaxial/log.27Nov18.npt_biaxial.g++.4 b/examples/PACKAGES/uef/npt_biaxial/log.27Nov18.npt_biaxial.g++.4 similarity index 100% rename from examples/USER/uef/npt_biaxial/log.27Nov18.npt_biaxial.g++.4 rename to examples/PACKAGES/uef/npt_biaxial/log.27Nov18.npt_biaxial.g++.4 diff --git a/examples/USER/uef/nvt_uniaxial/data.wca b/examples/PACKAGES/uef/nvt_uniaxial/data.wca similarity index 100% rename from examples/USER/uef/nvt_uniaxial/data.wca rename to examples/PACKAGES/uef/nvt_uniaxial/data.wca diff --git a/examples/USER/uef/nvt_uniaxial/in.nvt_uniaxial b/examples/PACKAGES/uef/nvt_uniaxial/in.nvt_uniaxial similarity index 100% rename from examples/USER/uef/nvt_uniaxial/in.nvt_uniaxial rename to examples/PACKAGES/uef/nvt_uniaxial/in.nvt_uniaxial diff --git a/examples/USER/uef/nvt_uniaxial/log.27Nov18.nvt_uniaxial.g++.1 b/examples/PACKAGES/uef/nvt_uniaxial/log.27Nov18.nvt_uniaxial.g++.1 similarity index 100% rename from examples/USER/uef/nvt_uniaxial/log.27Nov18.nvt_uniaxial.g++.1 rename to examples/PACKAGES/uef/nvt_uniaxial/log.27Nov18.nvt_uniaxial.g++.1 diff --git a/examples/USER/uef/nvt_uniaxial/log.27Nov18.nvt_uniaxial.g++.4 b/examples/PACKAGES/uef/nvt_uniaxial/log.27Nov18.nvt_uniaxial.g++.4 similarity index 100% rename from examples/USER/uef/nvt_uniaxial/log.27Nov18.nvt_uniaxial.g++.4 rename to examples/PACKAGES/uef/nvt_uniaxial/log.27Nov18.nvt_uniaxial.g++.4 diff --git a/examples/USER/vtk/.gitignore b/examples/PACKAGES/vtk/.gitignore similarity index 100% rename from examples/USER/vtk/.gitignore rename to examples/PACKAGES/vtk/.gitignore diff --git a/examples/USER/vtk/in.vtk b/examples/PACKAGES/vtk/in.vtk similarity index 100% rename from examples/USER/vtk/in.vtk rename to examples/PACKAGES/vtk/in.vtk diff --git a/examples/USER/vtk/in.vtp b/examples/PACKAGES/vtk/in.vtp similarity index 100% rename from examples/USER/vtk/in.vtp rename to examples/PACKAGES/vtk/in.vtp diff --git a/examples/USER/yaff/README b/examples/PACKAGES/yaff/README similarity index 100% rename from examples/USER/yaff/README rename to examples/PACKAGES/yaff/README diff --git a/examples/USER/yaff/mil53al/lammps.data b/examples/PACKAGES/yaff/mil53al/lammps.data similarity index 100% rename from examples/USER/yaff/mil53al/lammps.data rename to examples/PACKAGES/yaff/mil53al/lammps.data diff --git a/examples/USER/yaff/mil53al/lammps.in b/examples/PACKAGES/yaff/mil53al/lammps.in similarity index 100% rename from examples/USER/yaff/mil53al/lammps.in rename to examples/PACKAGES/yaff/mil53al/lammps.in diff --git a/examples/USER/yaff/mof5/lammps.data b/examples/PACKAGES/yaff/mof5/lammps.data similarity index 100% rename from examples/USER/yaff/mof5/lammps.data rename to examples/PACKAGES/yaff/mof5/lammps.data diff --git a/examples/USER/yaff/mof5/lammps.in b/examples/PACKAGES/yaff/mof5/lammps.in similarity index 100% rename from examples/USER/yaff/mof5/lammps.in rename to examples/PACKAGES/yaff/mof5/lammps.in diff --git a/examples/README b/examples/README index 9efac36a47..f0e84f18c1 100644 --- a/examples/README +++ b/examples/README @@ -5,7 +5,7 @@ problems you can run with LAMMPS. lower-case directories = simple test problems for LAMMPS and its packages upper-case directories = more complex problems -USER directory with its own sub-directories = tests for USER packages +PACKAGE directory with its own sub-directories = tests for specific packages Each is discussed below. @@ -179,8 +179,9 @@ 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 USER directory contains subdirectories of user-provided example -scripts for ser packages. See the README files in those directories +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 user packages.