From f192102da98b47e60421a4b2cf20410f15e079d1 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 24 Jul 2021 20:53:23 -0400 Subject: [PATCH] move examples away from USER-MISC now that the package folder is gone --- .../{USER-MISC => PACKAGES}/agni/Al_jpc.agni | 0 .../{USER-MISC => PACKAGES}/agni/adatom.data | 0 .../{USER-MISC => PACKAGES}/agni/in.adatom | 0 .../{USER-MISC => PACKAGES}/agni/in.vacancy | 0 .../agni/log.20Jan21.adatom.g++.1 | 0 .../agni/log.20Jan21.adatom.g++.4 | 0 .../agni/log.20Jan21.vacancy.g++.1 | 0 .../agni/log.20Jan21.vacancy.g++.4 | 0 .../{USER-MISC => PACKAGES}/agni/vacancy.data | 0 .../{USER-MISC => PACKAGES}/basal/almg.liu | 0 .../{USER-MISC => PACKAGES}/basal/in.basal | 0 .../cauchy/NiAlH_jea.eam.alloy | 0 .../{USER-MISC => PACKAGES}/cauchy/README | 0 .../cauchy/in.cauchystat | 0 .../cauchy/log.2Jun2020.cauchystat.g++.1 | 0 .../charge_regulation/README | 0 .../charge_regulation/data.chreg-acid | 0 .../charge_regulation/data.chreg-acid-real | 0 .../charge_regulation/data.chreg-polymer | 0 .../charge_regulation/in.chreg-acid | 0 .../charge_regulation/in.chreg-acid-real | 0 .../charge_regulation/in.chreg-polymer | 0 .../log.10Feb21.chreg-acid.g++.1 | 0 .../log.10Feb21.chreg-acid.g++.4 | 0 .../log.10Feb21.chreg-polymer.g++.1 | 0 .../log.10Feb21.chreg-polymer.g++.4 | 0 .../log.11Apr21.chreg-acid-real.g++.1 | 0 .../log.11Apr21.chreg-acid-real.g++.4 | 0 .../cnp/Cu_Mishin1.eam | 0 examples/{USER-MISC => PACKAGES}/cnp/in.cnp | 0 .../cnp/log.31May17.cnp.g++.4 | 0 examples/{USER-MISC => PACKAGES}/e3b/README | 0 .../{USER-MISC => PACKAGES}/e3b/e3b_box.data | 0 .../e3b/in.e3b-tip4p2005 | 0 .../e3b/log.29Mar2019.e3b-tip4p2005.g++.1 | 0 .../e3b/log.29Mar2019.e3b-tip4p2005.g++.4 | 0 examples/{USER-MISC => PACKAGES}/edip/Si.edip | 0 .../{USER-MISC => PACKAGES}/edip/SiC.edip | 0 .../{USER-MISC => PACKAGES}/edip/data.SiC | 0 .../{USER-MISC => PACKAGES}/edip/in.edip-Si | 0 .../edip/in.edip-Si-multi | 0 .../{USER-MISC => PACKAGES}/edip/in.edip-SiC | 0 .../edip/log.4May2017.g++.edip-Si-multi.1 | 0 .../edip/log.4May2017.g++.edip-Si-multi.4 | 0 .../edip/log.4May2017.g++.edip-Si.1 | 0 .../edip/log.4May2017.g++.edip-Si.4 | 0 .../edip/log.4May2017.g++.edip-SiC.1 | 0 .../edip/log.4May2017.g++.edip-SiC.4 | 0 .../{USER-MISC => PACKAGES}/ees/Data_region | 0 .../{USER-MISC => PACKAGES}/ees/Data_wall | 0 examples/{USER-MISC => PACKAGES}/ees/README | 0 .../{USER-MISC => PACKAGES}/ees/in.fix_wall | 0 .../ees/in.fix_wall_region | 0 .../ees/log.23Jun17.fix_wall.g++.1 | 0 .../ees/log.23Jun17.fix_wall.g++.4 | 0 .../ees/log.23Jun17.fix_wall_region.g++.1 | 0 .../ees/log.23Jun17.fix_wall_region.g++.4 | 0 .../electron_stopping/Si.Si.elstop | 0 .../electron_stopping/Si.sw | 0 .../electron_stopping/in.cascade_AlCu | 0 .../electron_stopping/in.cascade_SiSi | 0 .../electron_stopping/in.elstop | 0 .../electron_stopping/in.elstop.only | 0 .../log.18Sep2020.cascade_AlCu.intel.1 | 0 .../log.18Sep2020.cascade_AlCu.intel.4 | 0 .../log.18Sep2020.cascade_SiSi.intel.1 | 0 .../log.18Sep2020.cascade_SiSi.intel.4 | 0 .../log.20Mar19.elstop.g++.1 | 0 .../log.20Mar19.elstop.g++.4 | 0 .../log.20Mar19.elstop.only.g++.1 | 0 .../log.20Mar19.elstop.only.g++.4 | 0 .../entropy/Na_MendelevM_2014.eam.fs | 0 .../entropy/data.interface | 0 .../entropy/in.entropy | 0 .../entropy/log.entropy | 0 .../{USER-MISC => PACKAGES}/extep/BN.data | 0 .../{USER-MISC => PACKAGES}/extep/in.extep-bn | 0 .../extep/log.23Oct17.extep-bn.g++.1 | 0 .../extep/log.23Oct17.extep-bn.g++.4 | 0 .../filter_corotate/data.bpti | 0 .../filter_corotate/data.peptide | 0 .../filter_corotate/in.bpti | 0 .../filter_corotate/in.peptide | 0 .../filter_corotate/log.22Jun2017.bpti.g++.1 | 0 .../filter_corotate/log.22Jun2017.bpti.g++.4 | 0 .../log.22Jun2017.peptide.g++.1 | 0 .../log.22Jun2017.peptide.g++.4 | 0 .../{USER-MISC => PACKAGES}/flow_gauss/README | 0 .../{USER-MISC => PACKAGES}/flow_gauss/in.GD | 0 .../flow_gauss/log.6Jul17.GD.g++.1 | 0 .../flow_gauss/log.6Jul17.GD.g++.4 | 0 .../flow_gauss/output-files/GD.out | 0 .../flow_gauss/output-files/Vy_profile | 0 .../flow_gauss/output-files/x_profiles | 0 .../gauss_diel/data.gauss-diel | 0 .../gauss_diel/in.gauss-diel | 0 .../gauss_diel/in.gauss-diel-cg | 0 .../gauss_diel/in.gauss-diel-split | 0 .../gauss_diel/log.gauss-diel | 0 .../gauss_diel/log.gauss-diel-cg | 0 .../gauss_diel/log.gauss-diel-split | 0 examples/{USER-MISC => PACKAGES}/hma/README | 0 examples/{USER-MISC => PACKAGES}/hma/hma.in | 0 .../hma/log.6Nov18.hma.g++.1 | 0 .../hma/log.6Nov18.hma.g++.4 | 0 .../{USER-MISC => PACKAGES}/ipi/C.opt.tersoff | 0 examples/{USER-MISC => PACKAGES}/ipi/README | 0 .../{USER-MISC => PACKAGES}/ipi/data.graphene | 0 .../ipi/i-pi_input.xml | 0 .../ipi/i-pi_positions.xyz | 0 .../{USER-MISC => PACKAGES}/ipi/in.graphene | 0 .../benzene_water/benzene_water.data | 0 .../benzene_water/benzene_water.in | 0 .../benzene_water.localdensity.table | 0 .../benzene_water/benzene_water.pair.table | 0 .../benzene_water/log.04Sep19.g++.1 | 0 .../methanol_implicit_water/log.04Sep19.g++.1 | 0 .../methanol_implicit_water.data | 0 .../methanol_implicit_water.in | 0 ...methanol_implicit_water.localdensity.table | 0 .../methanol_implicit_water.pair.table | 0 .../meam_spline/Si_1.meam.spline | 0 .../meam_spline/TiO.meam.spline | 0 .../meam_spline/in.meam-spline.Si | 0 .../meam_spline/in.meam-spline.TiO2 | 0 .../log.4May2017.meam-spline.Si.g++.1 | 0 .../log.4May2017.meam-spline.Si.g++.4 | 0 .../log.4May2017.meam-spline.TiO2.g++.1 | 0 .../log.4May2017.meam-spline.TiO2.g++.4 | 0 .../meam_sw_spline/Si/bcc.in | 0 .../meam_sw_spline/Si/bcc_relax.in | 0 .../meam_sw_spline/Si/dc.in | 0 .../meam_sw_spline/Si/dc_relax.in | 0 .../Si/energy_conservation.meam.sw.in | 0 .../meam_sw_spline/Si/fcc.in | 0 .../meam_sw_spline/Si/fcc_relax.in | 0 .../meam_sw_spline/Si/hcp_relax.in | 0 .../meam_sw_spline/Si/sc.in | 0 .../meam_sw_spline/Si/sc_relax.in | 0 .../meam_sw_spline/Si/single_atom.in | 0 .../meam_sw_spline/Ti/alpha.in | 0 .../meam_sw_spline/Ti/alpha_relaxation.in | 0 .../meam_sw_spline/Ti/beta.in | 0 .../Ti/energy_conservation.meam.sw.in | 0 .../meam_sw_spline/Ti/fcc.in | 0 .../meam_sw_spline/Ti/hexagonal.in | 0 .../meam_sw_spline/Ti/omega.in | 0 .../meam_sw_spline/Ti/single_atom.in | 0 .../momb/Ag_O1X5.5_O2X0.55.eam.fs | 0 examples/{USER-MISC => PACKAGES}/momb/README | 0 .../{USER-MISC => PACKAGES}/momb/in.system | 0 .../momb/log.17Mar2017.system.g++.1 | 0 .../momb/log.17Mar2017.system.g++.4 | 0 .../{USER-MISC => PACKAGES}/momb/system.data | 0 .../momentum/in.momentum | 0 examples/{USER-MISC => PACKAGES}/mop/data.mop | 0 .../mop/in.compute_stress_mop | 0 .../mop/log.5Sep18.compute_stress_mop.g++.1 | 0 .../mop/log.5Sep18.compute_stress_mop.g++.4 | 0 .../mop/moppz.time.reference | 0 .../mop/mopz0.time.reference | 0 .../orient_eco/Ni_u3.eam | 0 .../orient_eco/data.sigma5 | 0 .../orient_eco/in.orient_eco | 0 .../orient_eco/log.2Jun2020.orent_eco.g++.1 | 0 .../orient_eco/log.2Jun2020.orent_eco.g++.4 | 0 .../orient_eco/sigma5.ori | 0 .../{USER-MISC => PACKAGES}/pafi/.gitignore | 0 examples/{USER-MISC => PACKAGES}/pafi/README | 0 examples/{USER-MISC => PACKAGES}/pafi/in.pafi | 0 .../pafi/log.15Apr20.pafi.g++.1 | 0 .../pafi/log.15Apr20.pafi.g++.4 | 0 .../pafi/pafipath.4.data | 0 .../pimd/para-h2/H2.data | 0 .../pimd/para-h2/H2.xyz | 0 .../pimd/para-h2/NM.info | 0 .../pimd/para-h2/in.scp | 0 .../pimd/para-h2/pair.table | 0 .../pimd/para-h2/run.sh | 0 .../pimd/para-h2/vmd.src | 0 .../pimd/prot-hairpin/in.scp | 0 .../pimd/prot-hairpin/run.sh | 0 .../pimd/prot-hairpin/system.data | 0 .../{USER-MISC => PACKAGES}/rhok/README.md | 0 .../{USER-MISC => PACKAGES}/rhok/in.crystal | 0 .../{USER-MISC => PACKAGES}/rhok/in.pinning | 0 .../{USER-MISC => PACKAGES}/rhok/in.setup | 0 .../rhok/log.22Sep2017.crystal.g++.1 | 0 .../rhok/log.22Sep2017.crystal.g++.4 | 0 .../rhok/log.22Sep2017.pinning.g++.1 | 0 .../rhok/log.22Sep2017.pinning.g++.4 | 0 .../rhok/log.22Sep2017.setup.g++.1 | 0 .../rhok/log.22Sep2017.setup.g++.4 | 0 .../slater/data.after_equilibration | 0 .../slater/data.after_production_run | 0 .../{USER-MISC => PACKAGES}/slater/in.slater | 0 .../{USER-MISC => PACKAGES}/slater/log.lammps | 0 .../slater/tmp_1_1.rdf | 0 .../slater/tmp_1_2.rdf | 0 .../slater/tmp_1_3.rdf | 0 .../slater/tmp_2_2.rdf | 0 .../slater/tmp_2_3.rdf | 0 .../slater/tmp_3_3.rdf | 0 .../temper_npt/data.peptide | 0 .../temper_npt/in.temper_npt | 0 .../temper_npt/log.temper_npt-17Aug17.g++.8 | 0 .../temper_npt/log.temper_npt-17Aug17.g++.8.0 | 0 .../temper_npt/log.temper_npt-17Aug17.g++.8.1 | 0 .../temper_npt/log.temper_npt-17Aug17.g++.8.2 | 0 .../temper_npt/log.temper_npt-17Aug17.g++.8.3 | 0 .../temper_npt/log.temper_npt-17Aug17.g++.8.4 | 0 .../temper_npt/log.temper_npt-17Aug17.g++.8.5 | 0 .../temper_npt/log.temper_npt-17Aug17.g++.8.6 | 0 .../temper_npt/log.temper_npt-17Aug17.g++.8.7 | 0 .../{USER-MISC => PACKAGES}/ti/in.ti_spring | 0 examples/README | 19 +++++++------------ 216 files changed, 7 insertions(+), 12 deletions(-) rename examples/{USER-MISC => PACKAGES}/agni/Al_jpc.agni (100%) rename examples/{USER-MISC => PACKAGES}/agni/adatom.data (100%) rename examples/{USER-MISC => PACKAGES}/agni/in.adatom (100%) rename examples/{USER-MISC => PACKAGES}/agni/in.vacancy (100%) rename examples/{USER-MISC => PACKAGES}/agni/log.20Jan21.adatom.g++.1 (100%) rename examples/{USER-MISC => PACKAGES}/agni/log.20Jan21.adatom.g++.4 (100%) rename examples/{USER-MISC => PACKAGES}/agni/log.20Jan21.vacancy.g++.1 (100%) rename examples/{USER-MISC => PACKAGES}/agni/log.20Jan21.vacancy.g++.4 (100%) rename examples/{USER-MISC => PACKAGES}/agni/vacancy.data (100%) rename examples/{USER-MISC => PACKAGES}/basal/almg.liu (100%) rename examples/{USER-MISC => PACKAGES}/basal/in.basal (100%) rename examples/{USER-MISC => PACKAGES}/cauchy/NiAlH_jea.eam.alloy (100%) rename examples/{USER-MISC => PACKAGES}/cauchy/README (100%) rename examples/{USER-MISC => PACKAGES}/cauchy/in.cauchystat (100%) rename examples/{USER-MISC => PACKAGES}/cauchy/log.2Jun2020.cauchystat.g++.1 (100%) rename examples/{USER-MISC => PACKAGES}/charge_regulation/README (100%) rename examples/{USER-MISC => PACKAGES}/charge_regulation/data.chreg-acid (100%) rename examples/{USER-MISC => PACKAGES}/charge_regulation/data.chreg-acid-real (100%) rename examples/{USER-MISC => PACKAGES}/charge_regulation/data.chreg-polymer (100%) rename examples/{USER-MISC => PACKAGES}/charge_regulation/in.chreg-acid (100%) rename examples/{USER-MISC => PACKAGES}/charge_regulation/in.chreg-acid-real (100%) rename examples/{USER-MISC => PACKAGES}/charge_regulation/in.chreg-polymer (100%) rename examples/{USER-MISC => PACKAGES}/charge_regulation/log.10Feb21.chreg-acid.g++.1 (100%) rename examples/{USER-MISC => PACKAGES}/charge_regulation/log.10Feb21.chreg-acid.g++.4 (100%) rename examples/{USER-MISC => PACKAGES}/charge_regulation/log.10Feb21.chreg-polymer.g++.1 (100%) rename examples/{USER-MISC => PACKAGES}/charge_regulation/log.10Feb21.chreg-polymer.g++.4 (100%) rename examples/{USER-MISC => PACKAGES}/charge_regulation/log.11Apr21.chreg-acid-real.g++.1 (100%) rename examples/{USER-MISC => PACKAGES}/charge_regulation/log.11Apr21.chreg-acid-real.g++.4 (100%) rename examples/{USER-MISC => PACKAGES}/cnp/Cu_Mishin1.eam (100%) rename examples/{USER-MISC => PACKAGES}/cnp/in.cnp (100%) rename examples/{USER-MISC => PACKAGES}/cnp/log.31May17.cnp.g++.4 (100%) rename examples/{USER-MISC => PACKAGES}/e3b/README (100%) rename examples/{USER-MISC => PACKAGES}/e3b/e3b_box.data (100%) rename examples/{USER-MISC => PACKAGES}/e3b/in.e3b-tip4p2005 (100%) rename examples/{USER-MISC => PACKAGES}/e3b/log.29Mar2019.e3b-tip4p2005.g++.1 (100%) rename examples/{USER-MISC => PACKAGES}/e3b/log.29Mar2019.e3b-tip4p2005.g++.4 (100%) rename examples/{USER-MISC => PACKAGES}/edip/Si.edip (100%) rename examples/{USER-MISC => PACKAGES}/edip/SiC.edip (100%) rename examples/{USER-MISC => PACKAGES}/edip/data.SiC (100%) rename examples/{USER-MISC => PACKAGES}/edip/in.edip-Si (100%) rename examples/{USER-MISC => PACKAGES}/edip/in.edip-Si-multi (100%) rename examples/{USER-MISC => PACKAGES}/edip/in.edip-SiC (100%) rename examples/{USER-MISC => PACKAGES}/edip/log.4May2017.g++.edip-Si-multi.1 (100%) rename examples/{USER-MISC => PACKAGES}/edip/log.4May2017.g++.edip-Si-multi.4 (100%) rename examples/{USER-MISC => PACKAGES}/edip/log.4May2017.g++.edip-Si.1 (100%) rename examples/{USER-MISC => PACKAGES}/edip/log.4May2017.g++.edip-Si.4 (100%) rename examples/{USER-MISC => PACKAGES}/edip/log.4May2017.g++.edip-SiC.1 (100%) rename examples/{USER-MISC => PACKAGES}/edip/log.4May2017.g++.edip-SiC.4 (100%) rename examples/{USER-MISC => PACKAGES}/ees/Data_region (100%) rename examples/{USER-MISC => PACKAGES}/ees/Data_wall (100%) rename examples/{USER-MISC => PACKAGES}/ees/README (100%) rename examples/{USER-MISC => PACKAGES}/ees/in.fix_wall (100%) rename examples/{USER-MISC => PACKAGES}/ees/in.fix_wall_region (100%) rename examples/{USER-MISC => PACKAGES}/ees/log.23Jun17.fix_wall.g++.1 (100%) rename examples/{USER-MISC => PACKAGES}/ees/log.23Jun17.fix_wall.g++.4 (100%) rename examples/{USER-MISC => PACKAGES}/ees/log.23Jun17.fix_wall_region.g++.1 (100%) rename examples/{USER-MISC => PACKAGES}/ees/log.23Jun17.fix_wall_region.g++.4 (100%) rename examples/{USER-MISC => PACKAGES}/electron_stopping/Si.Si.elstop (100%) rename examples/{USER-MISC => PACKAGES}/electron_stopping/Si.sw (100%) rename examples/{USER-MISC => PACKAGES}/electron_stopping/in.cascade_AlCu (100%) rename examples/{USER-MISC => PACKAGES}/electron_stopping/in.cascade_SiSi (100%) rename examples/{USER-MISC => PACKAGES}/electron_stopping/in.elstop (100%) rename examples/{USER-MISC => PACKAGES}/electron_stopping/in.elstop.only (100%) rename examples/{USER-MISC => PACKAGES}/electron_stopping/log.18Sep2020.cascade_AlCu.intel.1 (100%) rename examples/{USER-MISC => PACKAGES}/electron_stopping/log.18Sep2020.cascade_AlCu.intel.4 (100%) rename examples/{USER-MISC => PACKAGES}/electron_stopping/log.18Sep2020.cascade_SiSi.intel.1 (100%) rename examples/{USER-MISC => PACKAGES}/electron_stopping/log.18Sep2020.cascade_SiSi.intel.4 (100%) rename examples/{USER-MISC => PACKAGES}/electron_stopping/log.20Mar19.elstop.g++.1 (100%) rename examples/{USER-MISC => PACKAGES}/electron_stopping/log.20Mar19.elstop.g++.4 (100%) rename examples/{USER-MISC => PACKAGES}/electron_stopping/log.20Mar19.elstop.only.g++.1 (100%) rename examples/{USER-MISC => PACKAGES}/electron_stopping/log.20Mar19.elstop.only.g++.4 (100%) rename examples/{USER-MISC => PACKAGES}/entropy/Na_MendelevM_2014.eam.fs (100%) rename examples/{USER-MISC => PACKAGES}/entropy/data.interface (100%) rename examples/{USER-MISC => PACKAGES}/entropy/in.entropy (100%) rename examples/{USER-MISC => PACKAGES}/entropy/log.entropy (100%) rename examples/{USER-MISC => PACKAGES}/extep/BN.data (100%) rename examples/{USER-MISC => PACKAGES}/extep/in.extep-bn (100%) rename examples/{USER-MISC => PACKAGES}/extep/log.23Oct17.extep-bn.g++.1 (100%) rename examples/{USER-MISC => PACKAGES}/extep/log.23Oct17.extep-bn.g++.4 (100%) rename examples/{USER-MISC => PACKAGES}/filter_corotate/data.bpti (100%) rename examples/{USER-MISC => PACKAGES}/filter_corotate/data.peptide (100%) rename examples/{USER-MISC => PACKAGES}/filter_corotate/in.bpti (100%) rename examples/{USER-MISC => PACKAGES}/filter_corotate/in.peptide (100%) rename examples/{USER-MISC => PACKAGES}/filter_corotate/log.22Jun2017.bpti.g++.1 (100%) rename examples/{USER-MISC => PACKAGES}/filter_corotate/log.22Jun2017.bpti.g++.4 (100%) rename examples/{USER-MISC => PACKAGES}/filter_corotate/log.22Jun2017.peptide.g++.1 (100%) rename examples/{USER-MISC => PACKAGES}/filter_corotate/log.22Jun2017.peptide.g++.4 (100%) rename examples/{USER-MISC => PACKAGES}/flow_gauss/README (100%) rename examples/{USER-MISC => PACKAGES}/flow_gauss/in.GD (100%) rename examples/{USER-MISC => PACKAGES}/flow_gauss/log.6Jul17.GD.g++.1 (100%) rename examples/{USER-MISC => PACKAGES}/flow_gauss/log.6Jul17.GD.g++.4 (100%) rename examples/{USER-MISC => PACKAGES}/flow_gauss/output-files/GD.out (100%) rename examples/{USER-MISC => PACKAGES}/flow_gauss/output-files/Vy_profile (100%) rename examples/{USER-MISC => PACKAGES}/flow_gauss/output-files/x_profiles (100%) rename examples/{USER-MISC => PACKAGES}/gauss_diel/data.gauss-diel (100%) rename examples/{USER-MISC => PACKAGES}/gauss_diel/in.gauss-diel (100%) rename examples/{USER-MISC => PACKAGES}/gauss_diel/in.gauss-diel-cg (100%) rename examples/{USER-MISC => PACKAGES}/gauss_diel/in.gauss-diel-split (100%) rename examples/{USER-MISC => PACKAGES}/gauss_diel/log.gauss-diel (100%) rename examples/{USER-MISC => PACKAGES}/gauss_diel/log.gauss-diel-cg (100%) rename examples/{USER-MISC => PACKAGES}/gauss_diel/log.gauss-diel-split (100%) rename examples/{USER-MISC => PACKAGES}/hma/README (100%) rename examples/{USER-MISC => PACKAGES}/hma/hma.in (100%) rename examples/{USER-MISC => PACKAGES}/hma/log.6Nov18.hma.g++.1 (100%) rename examples/{USER-MISC => PACKAGES}/hma/log.6Nov18.hma.g++.4 (100%) rename examples/{USER-MISC => PACKAGES}/ipi/C.opt.tersoff (100%) rename examples/{USER-MISC => PACKAGES}/ipi/README (100%) rename examples/{USER-MISC => PACKAGES}/ipi/data.graphene (100%) rename examples/{USER-MISC => PACKAGES}/ipi/i-pi_input.xml (100%) rename examples/{USER-MISC => PACKAGES}/ipi/i-pi_positions.xyz (100%) rename examples/{USER-MISC => PACKAGES}/ipi/in.graphene (100%) rename examples/{USER-MISC => PACKAGES}/local_density/benzene_water/benzene_water.data (100%) rename examples/{USER-MISC => PACKAGES}/local_density/benzene_water/benzene_water.in (100%) rename examples/{USER-MISC => PACKAGES}/local_density/benzene_water/benzene_water.localdensity.table (100%) rename examples/{USER-MISC => PACKAGES}/local_density/benzene_water/benzene_water.pair.table (100%) rename 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to examples/PACKAGES/ees/Data_region diff --git a/examples/USER-MISC/ees/Data_wall b/examples/PACKAGES/ees/Data_wall similarity index 100% rename from examples/USER-MISC/ees/Data_wall rename to examples/PACKAGES/ees/Data_wall diff --git a/examples/USER-MISC/ees/README b/examples/PACKAGES/ees/README similarity index 100% rename from examples/USER-MISC/ees/README rename to examples/PACKAGES/ees/README diff --git a/examples/USER-MISC/ees/in.fix_wall b/examples/PACKAGES/ees/in.fix_wall similarity index 100% rename from examples/USER-MISC/ees/in.fix_wall rename to examples/PACKAGES/ees/in.fix_wall diff --git a/examples/USER-MISC/ees/in.fix_wall_region b/examples/PACKAGES/ees/in.fix_wall_region similarity index 100% rename from examples/USER-MISC/ees/in.fix_wall_region rename to examples/PACKAGES/ees/in.fix_wall_region diff --git a/examples/USER-MISC/ees/log.23Jun17.fix_wall.g++.1 b/examples/PACKAGES/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/ees/log.23Jun17.fix_wall.g++.1 diff --git a/examples/USER-MISC/ees/log.23Jun17.fix_wall.g++.4 b/examples/PACKAGES/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/ees/log.23Jun17.fix_wall.g++.4 diff --git a/examples/USER-MISC/ees/log.23Jun17.fix_wall_region.g++.1 b/examples/PACKAGES/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/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/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/ees/log.23Jun17.fix_wall_region.g++.4 diff --git a/examples/USER-MISC/electron_stopping/Si.Si.elstop b/examples/PACKAGES/electron_stopping/Si.Si.elstop similarity index 100% rename from examples/USER-MISC/electron_stopping/Si.Si.elstop rename to examples/PACKAGES/electron_stopping/Si.Si.elstop diff --git a/examples/USER-MISC/electron_stopping/Si.sw b/examples/PACKAGES/electron_stopping/Si.sw similarity index 100% rename from examples/USER-MISC/electron_stopping/Si.sw rename to examples/PACKAGES/electron_stopping/Si.sw diff --git a/examples/USER-MISC/electron_stopping/in.cascade_AlCu b/examples/PACKAGES/electron_stopping/in.cascade_AlCu similarity index 100% rename from examples/USER-MISC/electron_stopping/in.cascade_AlCu rename to examples/PACKAGES/electron_stopping/in.cascade_AlCu diff --git a/examples/USER-MISC/electron_stopping/in.cascade_SiSi b/examples/PACKAGES/electron_stopping/in.cascade_SiSi similarity index 100% rename from examples/USER-MISC/electron_stopping/in.cascade_SiSi rename to examples/PACKAGES/electron_stopping/in.cascade_SiSi diff --git a/examples/USER-MISC/electron_stopping/in.elstop b/examples/PACKAGES/electron_stopping/in.elstop similarity index 100% rename from examples/USER-MISC/electron_stopping/in.elstop rename to examples/PACKAGES/electron_stopping/in.elstop diff --git a/examples/USER-MISC/electron_stopping/in.elstop.only b/examples/PACKAGES/electron_stopping/in.elstop.only similarity index 100% rename from examples/USER-MISC/electron_stopping/in.elstop.only rename to examples/PACKAGES/electron_stopping/in.elstop.only diff --git a/examples/USER-MISC/electron_stopping/log.18Sep2020.cascade_AlCu.intel.1 b/examples/PACKAGES/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/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/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/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/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/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/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/electron_stopping/log.18Sep2020.cascade_SiSi.intel.4 diff --git a/examples/USER-MISC/electron_stopping/log.20Mar19.elstop.g++.1 b/examples/PACKAGES/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/electron_stopping/log.20Mar19.elstop.g++.1 diff --git a/examples/USER-MISC/electron_stopping/log.20Mar19.elstop.g++.4 b/examples/PACKAGES/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/electron_stopping/log.20Mar19.elstop.g++.4 diff --git a/examples/USER-MISC/electron_stopping/log.20Mar19.elstop.only.g++.1 b/examples/PACKAGES/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/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/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/electron_stopping/log.20Mar19.elstop.only.g++.4 diff --git a/examples/USER-MISC/entropy/Na_MendelevM_2014.eam.fs b/examples/PACKAGES/entropy/Na_MendelevM_2014.eam.fs similarity index 100% rename from examples/USER-MISC/entropy/Na_MendelevM_2014.eam.fs rename to examples/PACKAGES/entropy/Na_MendelevM_2014.eam.fs diff --git a/examples/USER-MISC/entropy/data.interface b/examples/PACKAGES/entropy/data.interface similarity index 100% rename from examples/USER-MISC/entropy/data.interface rename to examples/PACKAGES/entropy/data.interface diff --git a/examples/USER-MISC/entropy/in.entropy b/examples/PACKAGES/entropy/in.entropy similarity index 100% rename from examples/USER-MISC/entropy/in.entropy rename to examples/PACKAGES/entropy/in.entropy diff --git a/examples/USER-MISC/entropy/log.entropy b/examples/PACKAGES/entropy/log.entropy similarity index 100% rename from examples/USER-MISC/entropy/log.entropy rename to examples/PACKAGES/entropy/log.entropy diff --git a/examples/USER-MISC/extep/BN.data b/examples/PACKAGES/extep/BN.data similarity index 100% rename from examples/USER-MISC/extep/BN.data rename to examples/PACKAGES/extep/BN.data diff --git a/examples/USER-MISC/extep/in.extep-bn b/examples/PACKAGES/extep/in.extep-bn similarity index 100% rename from examples/USER-MISC/extep/in.extep-bn rename to examples/PACKAGES/extep/in.extep-bn diff --git a/examples/USER-MISC/extep/log.23Oct17.extep-bn.g++.1 b/examples/PACKAGES/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/extep/log.23Oct17.extep-bn.g++.1 diff --git a/examples/USER-MISC/extep/log.23Oct17.extep-bn.g++.4 b/examples/PACKAGES/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/extep/log.23Oct17.extep-bn.g++.4 diff --git a/examples/USER-MISC/filter_corotate/data.bpti b/examples/PACKAGES/filter_corotate/data.bpti similarity index 100% rename from examples/USER-MISC/filter_corotate/data.bpti rename to examples/PACKAGES/filter_corotate/data.bpti diff --git a/examples/USER-MISC/filter_corotate/data.peptide b/examples/PACKAGES/filter_corotate/data.peptide similarity index 100% rename from examples/USER-MISC/filter_corotate/data.peptide rename to examples/PACKAGES/filter_corotate/data.peptide diff --git a/examples/USER-MISC/filter_corotate/in.bpti b/examples/PACKAGES/filter_corotate/in.bpti similarity index 100% rename from examples/USER-MISC/filter_corotate/in.bpti rename to examples/PACKAGES/filter_corotate/in.bpti diff --git a/examples/USER-MISC/filter_corotate/in.peptide b/examples/PACKAGES/filter_corotate/in.peptide similarity index 100% rename from examples/USER-MISC/filter_corotate/in.peptide rename to examples/PACKAGES/filter_corotate/in.peptide diff --git a/examples/USER-MISC/filter_corotate/log.22Jun2017.bpti.g++.1 b/examples/PACKAGES/filter_corotate/log.22Jun2017.bpti.g++.1 similarity index 100% rename from examples/USER-MISC/filter_corotate/log.22Jun2017.bpti.g++.1 rename to examples/PACKAGES/filter_corotate/log.22Jun2017.bpti.g++.1 diff --git a/examples/USER-MISC/filter_corotate/log.22Jun2017.bpti.g++.4 b/examples/PACKAGES/filter_corotate/log.22Jun2017.bpti.g++.4 similarity index 100% rename from examples/USER-MISC/filter_corotate/log.22Jun2017.bpti.g++.4 rename to examples/PACKAGES/filter_corotate/log.22Jun2017.bpti.g++.4 diff --git a/examples/USER-MISC/filter_corotate/log.22Jun2017.peptide.g++.1 b/examples/PACKAGES/filter_corotate/log.22Jun2017.peptide.g++.1 similarity index 100% rename from examples/USER-MISC/filter_corotate/log.22Jun2017.peptide.g++.1 rename to examples/PACKAGES/filter_corotate/log.22Jun2017.peptide.g++.1 diff --git a/examples/USER-MISC/filter_corotate/log.22Jun2017.peptide.g++.4 b/examples/PACKAGES/filter_corotate/log.22Jun2017.peptide.g++.4 similarity index 100% rename from examples/USER-MISC/filter_corotate/log.22Jun2017.peptide.g++.4 rename to examples/PACKAGES/filter_corotate/log.22Jun2017.peptide.g++.4 diff --git a/examples/USER-MISC/flow_gauss/README b/examples/PACKAGES/flow_gauss/README similarity index 100% rename from examples/USER-MISC/flow_gauss/README rename to examples/PACKAGES/flow_gauss/README diff --git a/examples/USER-MISC/flow_gauss/in.GD b/examples/PACKAGES/flow_gauss/in.GD similarity index 100% rename from examples/USER-MISC/flow_gauss/in.GD rename to examples/PACKAGES/flow_gauss/in.GD diff --git a/examples/USER-MISC/flow_gauss/log.6Jul17.GD.g++.1 b/examples/PACKAGES/flow_gauss/log.6Jul17.GD.g++.1 similarity index 100% rename from examples/USER-MISC/flow_gauss/log.6Jul17.GD.g++.1 rename to examples/PACKAGES/flow_gauss/log.6Jul17.GD.g++.1 diff --git a/examples/USER-MISC/flow_gauss/log.6Jul17.GD.g++.4 b/examples/PACKAGES/flow_gauss/log.6Jul17.GD.g++.4 similarity index 100% rename from examples/USER-MISC/flow_gauss/log.6Jul17.GD.g++.4 rename to examples/PACKAGES/flow_gauss/log.6Jul17.GD.g++.4 diff --git a/examples/USER-MISC/flow_gauss/output-files/GD.out b/examples/PACKAGES/flow_gauss/output-files/GD.out similarity index 100% rename from examples/USER-MISC/flow_gauss/output-files/GD.out rename to examples/PACKAGES/flow_gauss/output-files/GD.out diff --git a/examples/USER-MISC/flow_gauss/output-files/Vy_profile b/examples/PACKAGES/flow_gauss/output-files/Vy_profile similarity index 100% rename from examples/USER-MISC/flow_gauss/output-files/Vy_profile rename to examples/PACKAGES/flow_gauss/output-files/Vy_profile diff --git a/examples/USER-MISC/flow_gauss/output-files/x_profiles b/examples/PACKAGES/flow_gauss/output-files/x_profiles similarity index 100% rename from examples/USER-MISC/flow_gauss/output-files/x_profiles rename to examples/PACKAGES/flow_gauss/output-files/x_profiles diff --git a/examples/USER-MISC/gauss_diel/data.gauss-diel b/examples/PACKAGES/gauss_diel/data.gauss-diel similarity index 100% rename from examples/USER-MISC/gauss_diel/data.gauss-diel rename to examples/PACKAGES/gauss_diel/data.gauss-diel diff --git a/examples/USER-MISC/gauss_diel/in.gauss-diel b/examples/PACKAGES/gauss_diel/in.gauss-diel similarity index 100% rename from examples/USER-MISC/gauss_diel/in.gauss-diel rename to examples/PACKAGES/gauss_diel/in.gauss-diel diff --git a/examples/USER-MISC/gauss_diel/in.gauss-diel-cg b/examples/PACKAGES/gauss_diel/in.gauss-diel-cg similarity index 100% rename from examples/USER-MISC/gauss_diel/in.gauss-diel-cg rename to examples/PACKAGES/gauss_diel/in.gauss-diel-cg diff --git a/examples/USER-MISC/gauss_diel/in.gauss-diel-split b/examples/PACKAGES/gauss_diel/in.gauss-diel-split similarity index 100% rename from examples/USER-MISC/gauss_diel/in.gauss-diel-split rename to examples/PACKAGES/gauss_diel/in.gauss-diel-split diff --git a/examples/USER-MISC/gauss_diel/log.gauss-diel b/examples/PACKAGES/gauss_diel/log.gauss-diel similarity index 100% rename from examples/USER-MISC/gauss_diel/log.gauss-diel rename to examples/PACKAGES/gauss_diel/log.gauss-diel diff --git a/examples/USER-MISC/gauss_diel/log.gauss-diel-cg b/examples/PACKAGES/gauss_diel/log.gauss-diel-cg similarity index 100% rename from examples/USER-MISC/gauss_diel/log.gauss-diel-cg rename to examples/PACKAGES/gauss_diel/log.gauss-diel-cg diff --git a/examples/USER-MISC/gauss_diel/log.gauss-diel-split b/examples/PACKAGES/gauss_diel/log.gauss-diel-split similarity index 100% rename from examples/USER-MISC/gauss_diel/log.gauss-diel-split rename to examples/PACKAGES/gauss_diel/log.gauss-diel-split diff --git a/examples/USER-MISC/hma/README b/examples/PACKAGES/hma/README similarity index 100% rename from examples/USER-MISC/hma/README rename to examples/PACKAGES/hma/README diff --git a/examples/USER-MISC/hma/hma.in b/examples/PACKAGES/hma/hma.in similarity index 100% rename from examples/USER-MISC/hma/hma.in rename to examples/PACKAGES/hma/hma.in diff --git a/examples/USER-MISC/hma/log.6Nov18.hma.g++.1 b/examples/PACKAGES/hma/log.6Nov18.hma.g++.1 similarity index 100% rename from examples/USER-MISC/hma/log.6Nov18.hma.g++.1 rename to examples/PACKAGES/hma/log.6Nov18.hma.g++.1 diff --git a/examples/USER-MISC/hma/log.6Nov18.hma.g++.4 b/examples/PACKAGES/hma/log.6Nov18.hma.g++.4 similarity index 100% rename from examples/USER-MISC/hma/log.6Nov18.hma.g++.4 rename to examples/PACKAGES/hma/log.6Nov18.hma.g++.4 diff --git a/examples/USER-MISC/ipi/C.opt.tersoff b/examples/PACKAGES/ipi/C.opt.tersoff similarity index 100% rename from examples/USER-MISC/ipi/C.opt.tersoff rename to examples/PACKAGES/ipi/C.opt.tersoff diff --git a/examples/USER-MISC/ipi/README b/examples/PACKAGES/ipi/README similarity index 100% rename from examples/USER-MISC/ipi/README rename to examples/PACKAGES/ipi/README diff --git a/examples/USER-MISC/ipi/data.graphene b/examples/PACKAGES/ipi/data.graphene similarity index 100% rename from examples/USER-MISC/ipi/data.graphene rename to examples/PACKAGES/ipi/data.graphene diff --git a/examples/USER-MISC/ipi/i-pi_input.xml b/examples/PACKAGES/ipi/i-pi_input.xml similarity index 100% rename from examples/USER-MISC/ipi/i-pi_input.xml rename to examples/PACKAGES/ipi/i-pi_input.xml diff --git a/examples/USER-MISC/ipi/i-pi_positions.xyz b/examples/PACKAGES/ipi/i-pi_positions.xyz similarity index 100% rename from examples/USER-MISC/ipi/i-pi_positions.xyz rename to examples/PACKAGES/ipi/i-pi_positions.xyz diff --git a/examples/USER-MISC/ipi/in.graphene b/examples/PACKAGES/ipi/in.graphene similarity index 100% rename from examples/USER-MISC/ipi/in.graphene rename to examples/PACKAGES/ipi/in.graphene diff --git a/examples/USER-MISC/local_density/benzene_water/benzene_water.data b/examples/PACKAGES/local_density/benzene_water/benzene_water.data similarity index 100% rename from examples/USER-MISC/local_density/benzene_water/benzene_water.data rename to examples/PACKAGES/local_density/benzene_water/benzene_water.data diff --git a/examples/USER-MISC/local_density/benzene_water/benzene_water.in b/examples/PACKAGES/local_density/benzene_water/benzene_water.in similarity index 100% rename from examples/USER-MISC/local_density/benzene_water/benzene_water.in rename to examples/PACKAGES/local_density/benzene_water/benzene_water.in diff --git a/examples/USER-MISC/local_density/benzene_water/benzene_water.localdensity.table b/examples/PACKAGES/local_density/benzene_water/benzene_water.localdensity.table similarity index 100% rename from examples/USER-MISC/local_density/benzene_water/benzene_water.localdensity.table rename to examples/PACKAGES/local_density/benzene_water/benzene_water.localdensity.table diff --git a/examples/USER-MISC/local_density/benzene_water/benzene_water.pair.table b/examples/PACKAGES/local_density/benzene_water/benzene_water.pair.table similarity index 100% rename from examples/USER-MISC/local_density/benzene_water/benzene_water.pair.table rename to examples/PACKAGES/local_density/benzene_water/benzene_water.pair.table diff --git a/examples/USER-MISC/local_density/benzene_water/log.04Sep19.g++.1 b/examples/PACKAGES/local_density/benzene_water/log.04Sep19.g++.1 similarity index 100% rename from examples/USER-MISC/local_density/benzene_water/log.04Sep19.g++.1 rename to examples/PACKAGES/local_density/benzene_water/log.04Sep19.g++.1 diff --git a/examples/USER-MISC/local_density/methanol_implicit_water/log.04Sep19.g++.1 b/examples/PACKAGES/local_density/methanol_implicit_water/log.04Sep19.g++.1 similarity index 100% rename from examples/USER-MISC/local_density/methanol_implicit_water/log.04Sep19.g++.1 rename to examples/PACKAGES/local_density/methanol_implicit_water/log.04Sep19.g++.1 diff --git a/examples/USER-MISC/local_density/methanol_implicit_water/methanol_implicit_water.data b/examples/PACKAGES/local_density/methanol_implicit_water/methanol_implicit_water.data similarity index 100% rename from examples/USER-MISC/local_density/methanol_implicit_water/methanol_implicit_water.data rename to examples/PACKAGES/local_density/methanol_implicit_water/methanol_implicit_water.data diff --git a/examples/USER-MISC/local_density/methanol_implicit_water/methanol_implicit_water.in b/examples/PACKAGES/local_density/methanol_implicit_water/methanol_implicit_water.in similarity index 100% rename from examples/USER-MISC/local_density/methanol_implicit_water/methanol_implicit_water.in rename to examples/PACKAGES/local_density/methanol_implicit_water/methanol_implicit_water.in diff --git a/examples/USER-MISC/local_density/methanol_implicit_water/methanol_implicit_water.localdensity.table b/examples/PACKAGES/local_density/methanol_implicit_water/methanol_implicit_water.localdensity.table similarity index 100% rename from examples/USER-MISC/local_density/methanol_implicit_water/methanol_implicit_water.localdensity.table rename to examples/PACKAGES/local_density/methanol_implicit_water/methanol_implicit_water.localdensity.table diff --git a/examples/USER-MISC/local_density/methanol_implicit_water/methanol_implicit_water.pair.table b/examples/PACKAGES/local_density/methanol_implicit_water/methanol_implicit_water.pair.table similarity index 100% rename from examples/USER-MISC/local_density/methanol_implicit_water/methanol_implicit_water.pair.table rename to examples/PACKAGES/local_density/methanol_implicit_water/methanol_implicit_water.pair.table diff --git a/examples/USER-MISC/meam_spline/Si_1.meam.spline b/examples/PACKAGES/meam_spline/Si_1.meam.spline similarity index 100% rename from examples/USER-MISC/meam_spline/Si_1.meam.spline rename to examples/PACKAGES/meam_spline/Si_1.meam.spline diff --git a/examples/USER-MISC/meam_spline/TiO.meam.spline b/examples/PACKAGES/meam_spline/TiO.meam.spline similarity index 100% rename from examples/USER-MISC/meam_spline/TiO.meam.spline rename to examples/PACKAGES/meam_spline/TiO.meam.spline diff --git a/examples/USER-MISC/meam_spline/in.meam-spline.Si b/examples/PACKAGES/meam_spline/in.meam-spline.Si similarity index 100% rename from examples/USER-MISC/meam_spline/in.meam-spline.Si rename to examples/PACKAGES/meam_spline/in.meam-spline.Si diff --git a/examples/USER-MISC/meam_spline/in.meam-spline.TiO2 b/examples/PACKAGES/meam_spline/in.meam-spline.TiO2 similarity index 100% rename from examples/USER-MISC/meam_spline/in.meam-spline.TiO2 rename to examples/PACKAGES/meam_spline/in.meam-spline.TiO2 diff --git a/examples/USER-MISC/meam_spline/log.4May2017.meam-spline.Si.g++.1 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b/examples/PACKAGES/meam_spline/log.4May2017.meam-spline.TiO2.g++.4 similarity index 100% rename from examples/USER-MISC/meam_spline/log.4May2017.meam-spline.TiO2.g++.4 rename to examples/PACKAGES/meam_spline/log.4May2017.meam-spline.TiO2.g++.4 diff --git a/examples/USER-MISC/meam_sw_spline/Si/bcc.in b/examples/PACKAGES/meam_sw_spline/Si/bcc.in similarity index 100% rename from examples/USER-MISC/meam_sw_spline/Si/bcc.in rename to examples/PACKAGES/meam_sw_spline/Si/bcc.in diff --git a/examples/USER-MISC/meam_sw_spline/Si/bcc_relax.in b/examples/PACKAGES/meam_sw_spline/Si/bcc_relax.in similarity index 100% rename from examples/USER-MISC/meam_sw_spline/Si/bcc_relax.in rename to examples/PACKAGES/meam_sw_spline/Si/bcc_relax.in diff --git a/examples/USER-MISC/meam_sw_spline/Si/dc.in b/examples/PACKAGES/meam_sw_spline/Si/dc.in similarity index 100% rename from examples/USER-MISC/meam_sw_spline/Si/dc.in rename to examples/PACKAGES/meam_sw_spline/Si/dc.in diff --git 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to examples/PACKAGES/slater/tmp_3_3.rdf diff --git a/examples/USER-MISC/temper_npt/data.peptide b/examples/PACKAGES/temper_npt/data.peptide similarity index 100% rename from examples/USER-MISC/temper_npt/data.peptide rename to examples/PACKAGES/temper_npt/data.peptide diff --git a/examples/USER-MISC/temper_npt/in.temper_npt b/examples/PACKAGES/temper_npt/in.temper_npt similarity index 100% rename from examples/USER-MISC/temper_npt/in.temper_npt rename to examples/PACKAGES/temper_npt/in.temper_npt diff --git a/examples/USER-MISC/temper_npt/log.temper_npt-17Aug17.g++.8 b/examples/PACKAGES/temper_npt/log.temper_npt-17Aug17.g++.8 similarity index 100% rename from examples/USER-MISC/temper_npt/log.temper_npt-17Aug17.g++.8 rename to examples/PACKAGES/temper_npt/log.temper_npt-17Aug17.g++.8 diff --git a/examples/USER-MISC/temper_npt/log.temper_npt-17Aug17.g++.8.0 b/examples/PACKAGES/temper_npt/log.temper_npt-17Aug17.g++.8.0 similarity index 100% rename from examples/USER-MISC/temper_npt/log.temper_npt-17Aug17.g++.8.0 rename to examples/PACKAGES/temper_npt/log.temper_npt-17Aug17.g++.8.0 diff --git a/examples/USER-MISC/temper_npt/log.temper_npt-17Aug17.g++.8.1 b/examples/PACKAGES/temper_npt/log.temper_npt-17Aug17.g++.8.1 similarity index 100% rename from examples/USER-MISC/temper_npt/log.temper_npt-17Aug17.g++.8.1 rename to examples/PACKAGES/temper_npt/log.temper_npt-17Aug17.g++.8.1 diff --git a/examples/USER-MISC/temper_npt/log.temper_npt-17Aug17.g++.8.2 b/examples/PACKAGES/temper_npt/log.temper_npt-17Aug17.g++.8.2 similarity index 100% rename from examples/USER-MISC/temper_npt/log.temper_npt-17Aug17.g++.8.2 rename to examples/PACKAGES/temper_npt/log.temper_npt-17Aug17.g++.8.2 diff --git a/examples/USER-MISC/temper_npt/log.temper_npt-17Aug17.g++.8.3 b/examples/PACKAGES/temper_npt/log.temper_npt-17Aug17.g++.8.3 similarity index 100% rename from examples/USER-MISC/temper_npt/log.temper_npt-17Aug17.g++.8.3 rename to examples/PACKAGES/temper_npt/log.temper_npt-17Aug17.g++.8.3 diff --git a/examples/USER-MISC/temper_npt/log.temper_npt-17Aug17.g++.8.4 b/examples/PACKAGES/temper_npt/log.temper_npt-17Aug17.g++.8.4 similarity index 100% rename from examples/USER-MISC/temper_npt/log.temper_npt-17Aug17.g++.8.4 rename to examples/PACKAGES/temper_npt/log.temper_npt-17Aug17.g++.8.4 diff --git a/examples/USER-MISC/temper_npt/log.temper_npt-17Aug17.g++.8.5 b/examples/PACKAGES/temper_npt/log.temper_npt-17Aug17.g++.8.5 similarity index 100% rename from examples/USER-MISC/temper_npt/log.temper_npt-17Aug17.g++.8.5 rename to examples/PACKAGES/temper_npt/log.temper_npt-17Aug17.g++.8.5 diff --git a/examples/USER-MISC/temper_npt/log.temper_npt-17Aug17.g++.8.6 b/examples/PACKAGES/temper_npt/log.temper_npt-17Aug17.g++.8.6 similarity index 100% rename from examples/USER-MISC/temper_npt/log.temper_npt-17Aug17.g++.8.6 rename to examples/PACKAGES/temper_npt/log.temper_npt-17Aug17.g++.8.6 diff --git a/examples/USER-MISC/temper_npt/log.temper_npt-17Aug17.g++.8.7 b/examples/PACKAGES/temper_npt/log.temper_npt-17Aug17.g++.8.7 similarity index 100% rename from examples/USER-MISC/temper_npt/log.temper_npt-17Aug17.g++.8.7 rename to examples/PACKAGES/temper_npt/log.temper_npt-17Aug17.g++.8.7 diff --git a/examples/USER-MISC/ti/in.ti_spring b/examples/PACKAGES/ti/in.ti_spring similarity index 100% rename from examples/USER-MISC/ti/in.ti_spring rename to examples/PACKAGES/ti/in.ti_spring diff --git a/examples/README b/examples/README index 68825a7dbd..9e873b49b9 100644 --- a/examples/README +++ b/examples/README @@ -5,8 +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 -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 +PACKAGES directory with its own sub-directories = tests for styles from specific packages Each is discussed below. @@ -172,10 +171,12 @@ 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. +individual packages or additional individual styles. Most of those are +contributed by the corresponding package or style developers. +See the README files in those directories (if available) or the +corresponding doc page in the manual for more info. See the +https://docs.lammps.org/Build_package.html page for more info about +installing and building packages. The TIP4P directory has an example for testing forces computed on a GPU. @@ -186,12 +187,6 @@ 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-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 packages. - The VISCOSITY directory has example scripts for computing the viscosity of a LJ liquid using 4 different methods. See the VISCOSITY/README file for more info.