From 7a9038502d2374008ccd436f17aa209b913d7a23 Mon Sep 17 00:00:00 2001 From: Alexander Zech Date: Fri, 4 Dec 2020 10:35:46 -0800 Subject: [PATCH 1/5] Add empirical dispersion to atomistic category --- schema/models_directory/pb/at.json | 18 +++++++ schema/models_directory/pb/at/disp.json | 18 +++++++ schema/models_directory/pb/at/disp/dft_d.json | 52 +++++++++++++++++++ 3 files changed, 88 insertions(+) create mode 100644 schema/models_directory/pb/at.json create mode 100644 schema/models_directory/pb/at/disp.json create mode 100644 schema/models_directory/pb/at/disp/dft_d.json diff --git a/schema/models_directory/pb/at.json b/schema/models_directory/pb/at.json new file mode 100644 index 000000000..a3a63eab8 --- /dev/null +++ b/schema/models_directory/pb/at.json @@ -0,0 +1,18 @@ +{ + "$schema": "http://json-schema.org/draft-04/schema#", + "allOf": [ + { + "$ref": "../pb.json" + } + ], + "properties": { + "tier2": { + "enum": [ + { + "name": "atomistic", + "slug": "at" + } + ] + } + } +} diff --git a/schema/models_directory/pb/at/disp.json b/schema/models_directory/pb/at/disp.json new file mode 100644 index 000000000..16c71d550 --- /dev/null +++ b/schema/models_directory/pb/at/disp.json @@ -0,0 +1,18 @@ +{ + "$schema": "http://json-schema.org/draft-04/schema#", + "allOf": [ + { + "$ref": "../at.json" + } + ], + "properties": { + "tier3": { + "enum": [ + { + "name": "atomistic dispersion model", + "slug": "disp" + } + ] + } + } +} diff --git a/schema/models_directory/pb/at/disp/dft_d.json b/schema/models_directory/pb/at/disp/dft_d.json new file mode 100644 index 000000000..9aef12702 --- /dev/null +++ b/schema/models_directory/pb/at/disp/dft_d.json @@ -0,0 +1,52 @@ +{ + "schemaId": "models-directory-at-disp-dft-d", + "$schema": "http://json-schema.org/draft-04/schema#", + "title": "Grimme-type empirical dispersion model for DFT (DFT-D)", + "allOf": [ + { + "$ref": "../disp.json" + } + ], + "properties": { + "type": { + "enum": [ + { + "name": "Empirical dispersion DFT-D", + "slug": "empirical-dft-d" + } + ] + }, + "subtype": { + "enum": [ + { + "name": "DFT-D2", + "slug": "dft-d2" + }, + { + "name": "DFT-CHG", + "slug": "dft-chg" + }, + { + "name": "DFT-D3(0)", + "slug": "dft-d3-0" + }, + { + "name": "DFT-D3(BJ)", + "slug": "dft-d3-bj" + }, + { + "name": "DFT-D3(CSO)", + "slug": "dft-d3-cso" + }, + { + "name": "DFT-D3M(BJ)", + "slug": "dft-d3-bj-m" + }, + { + "name": "DFT-D3(op)", + "slug": "dft-d3-op" + } + ] + } + } +} From c4f2591fd9e5512b646c1fa1d41885b833d8ef62 Mon Sep 17 00:00:00 2001 From: Alexander Zech Date: Sun, 6 Dec 2020 12:59:47 -0800 Subject: [PATCH 2/5] Add list of DFT dispersion models with literature references --- manifest/dft_dispersion.yaml | 87 ++++++++++++++++++++++++++++++++++++ 1 file changed, 87 insertions(+) create mode 100644 manifest/dft_dispersion.yaml diff --git a/manifest/dft_dispersion.yaml b/manifest/dft_dispersion.yaml new file mode 100644 index 000000000..0b29c2b5f --- /dev/null +++ b/manifest/dft_dispersion.yaml @@ -0,0 +1,87 @@ +# +# This file contains a collection of DFT dispersion corrections +# (also known as "DFT methods for van-der-Waals interactions") +# + +# --------------------------------------- +# Non-local correlation functionals +# (see also dft_unit_functionals section) +# --------------------------------------- +nlc_functionals: + usage: intra-SCF + - name: vdW-DF-04 by Langreth, Lundqvist, et al. + slug: vdw-df-04 + doi: + - 10.1103/PhysRevLett.92.246401 + - 10.1103/PhysRevLett.95.109902 + - name: vdW-DF-10 by Lee, et al. (reparametrization of vdW-DF-04) + slug: vdw-df-10 + doi: 10.1103/PhysRevB.82.081101 + - name: VV09 by Vydrov and Van Voorhis + slug: vv09 + doi: + - 10.1103/PhysRevLett.103.063004 + - 10.1063/1.3398840 + - name: VV10 by Vydrov and Van Voorhis + slug: vv10 + doi: 10.1063/1.3521275 + - name: rVV10 by Sabatini, et al. + slug: rvv10 + doi: 10.1103/PhysRevB.87.041108 +# --------------------------------------- +# Empirical dispersion models +# --------------------------------------- +empirical_dispersion: + usage: post-SCF + - name: DFT-D2 by Grimme + slug: dft-d2 + doi: 10.1002/jcc.20495 + - name: DFT-CHG by Chai and Head-Gordon + slug: dft-chg + doi: 10.1039/b810189b + - name: DFT-D3(0) by Grimme + slug: dft-d3-0 + doi: 10.1063/1.3382344 + - name: DFT-D3(BJ) by Becke and Johnson + slug: dft-d3-bj + doi: 10.1002/jcc.21759 + - name: DFT-D3(CSO) by Schröder et al. + slug: dft-d3-cso + doi: 10.1021/acs.jctc.5b00400 + - name: DFT-D3M(BJ) reparametrized DFT-D3(BJ) by Smith et al. + slug: dft-d3-bj-m + doi: 10.1021/acs.jpclett.6b00780 + - name: DFT-D3(op) optimized power approach by Witte et al. + slug: dft-d3-op + doi: 10.1021/acs.jctc.7b00176 +# ------------------------------------------- +# Exchange-Dipole Model (XDM) of Dispersion +# ------------------------------------------- +exchange_dipole: + usage: post-SCF + - name: XDM6 by Becke and Johnson + slug: xdm6 + doi: + - 10.1063/1.1884601 + - 10.1063/1.1949201 + - name: XDM10 + slug: xdm10 + doi: 10.1063/1.1949201 +# ---------------------------------------------------- +# Tkatchenko-Scheffler van der Waals Model (TS-vdW) +# ---------------------------------------------------- +tkatchenko_scheffler: + usage: post-SCF + - name: Tkatchenko-Scheffler vdW model + slug: ts_vdw + doi: 10.1103/PhysRevLett.102.073005 +# ----------------------------------------- +# Many-Body Dispersion (MBD) Method +# ----------------------------------------- +many_body_dispersion: + usage: post-SCF + - name: MBD with range-separated self-consistent screening (MBD@rsSCS) + slug: mbd-rsscs + doi: 10.1063/1.4865104 + + From de1c4551395cbccade814bf750229d2e55a0ad87 Mon Sep 17 00:00:00 2001 From: Alexander Zech Date: Sun, 6 Dec 2020 13:02:42 -0800 Subject: [PATCH 3/5] Add explanation for model name abbreviations --- schema/models_directory/pb/at/disp/dft_d.json | 1 + 1 file changed, 1 insertion(+) diff --git a/schema/models_directory/pb/at/disp/dft_d.json b/schema/models_directory/pb/at/disp/dft_d.json index 9aef12702..7d4fbc37f 100644 --- a/schema/models_directory/pb/at/disp/dft_d.json +++ b/schema/models_directory/pb/at/disp/dft_d.json @@ -2,6 +2,7 @@ "schemaId": "models-directory-at-disp-dft-d", "$schema": "http://json-schema.org/draft-04/schema#", "title": "Grimme-type empirical dispersion model for DFT (DFT-D)", + "description": "Abbreviations taken from manifest/dft_dispersion.yaml", "allOf": [ { "$ref": "../disp.json" From e2170182fcb7ba2b402dc2449f78b1eadf4561ea Mon Sep 17 00:00:00 2001 From: Alexander Zech Date: Wed, 16 Dec 2020 09:18:03 -0800 Subject: [PATCH 4/5] Add XDM dispersion model + tests --- .../models_directory/pb/at/disp/dft_d.json | 29 ++++++++++++++++ example/models_directory/pb/at/disp/xdm.json | 29 ++++++++++++++++ schema/models_directory/pb/at/disp/xdm.json | 34 +++++++++++++++++++ 3 files changed, 92 insertions(+) create mode 100644 example/models_directory/pb/at/disp/dft_d.json create mode 100644 example/models_directory/pb/at/disp/xdm.json create mode 100644 schema/models_directory/pb/at/disp/xdm.json diff --git a/example/models_directory/pb/at/disp/dft_d.json b/example/models_directory/pb/at/disp/dft_d.json new file mode 100644 index 000000000..1dc9ac4a6 --- /dev/null +++ b/example/models_directory/pb/at/disp/dft_d.json @@ -0,0 +1,29 @@ +{ + "tier1": { + "name": "physics-based", + "slug": "pb" + }, + "tier2": { + "name": "atomistic", + "slug": "at" + }, + "tier3": { + "name": "atomistic dispersion model", + "slug": "disp" + }, + "type": { + "name": "Empirical dispersion DFT-D", + "slug": "empirical-dft-d" + }, + "subtype": { + "name": "DFT-D3(0)", + "slug": "dft-d3-0" + }, + "modifier": [ + ], + "tags": [ + ], + "method": { + "...": "include(../../../../method.json)" + } +} diff --git a/example/models_directory/pb/at/disp/xdm.json b/example/models_directory/pb/at/disp/xdm.json new file mode 100644 index 000000000..166b59fc8 --- /dev/null +++ b/example/models_directory/pb/at/disp/xdm.json @@ -0,0 +1,29 @@ +{ + "tier1": { + "name": "physics-based", + "slug": "pb" + }, + "tier2": { + "name": "atomistic", + "slug": "at" + }, + "tier3": { + "name": "atomistic dispersion model", + "slug": "disp" + }, + "type": { + "name": "Exchange-Dipole Model", + "slug": "exchange-dipole-model" + }, + "subtype": { + "name": "XDM6", + "slug": "xdm6" + }, + "modifier": [ + ], + "tags": [ + ], + "method": { + "...": "include(../../../../method.json)" + } +} diff --git a/schema/models_directory/pb/at/disp/xdm.json b/schema/models_directory/pb/at/disp/xdm.json new file mode 100644 index 000000000..01c7fcc39 --- /dev/null +++ b/schema/models_directory/pb/at/disp/xdm.json @@ -0,0 +1,34 @@ +{ + "schemaId": "models-directory-at-disp-xdm", + "$schema": "http://json-schema.org/draft-04/schema#", + "title": "Exchange-Dipole Model (XDM)", + "description": "See work by Becke and Johnson (doi: 10.1063/1.1884601)", + "allOf": [ + { + "$ref": "../disp.json" + } + ], + "properties": { + "type": { + "enum": [ + { + "name": "Exchange-Dipole Model", + "slug": "exchange-dipole-model" + } + ] + }, + "subtype": { + "description": "Whether C6 dispersion coefficient (XDM6) or higher-order coefficients are used", + "enum": [ + { + "name": "XDM6", + "slug": "xdm6" + }, + { + "name": "XDM10", + "slug": "xdm10" + } + ] + } + } +} From 4f8702a1ad82e77ed7ff48261cea3a3306e83681 Mon Sep 17 00:00:00 2001 From: Alexander Zech Date: Mon, 21 Dec 2020 18:25:08 -0800 Subject: [PATCH 5/5] re-classify XDM into QM category --- .../pb/{at => qm}/disp/xdm.json | 6 +++--- schema/models_directory/pb/qm/disp.json | 18 ++++++++++++++++++ .../pb/{at => qm}/disp/xdm.json | 2 +- 3 files changed, 22 insertions(+), 4 deletions(-) rename example/models_directory/pb/{at => qm}/disp/xdm.json (79%) create mode 100644 schema/models_directory/pb/qm/disp.json rename schema/models_directory/pb/{at => qm}/disp/xdm.json (94%) diff --git a/example/models_directory/pb/at/disp/xdm.json b/example/models_directory/pb/qm/disp/xdm.json similarity index 79% rename from example/models_directory/pb/at/disp/xdm.json rename to example/models_directory/pb/qm/disp/xdm.json index 166b59fc8..49528695c 100644 --- a/example/models_directory/pb/at/disp/xdm.json +++ b/example/models_directory/pb/qm/disp/xdm.json @@ -4,11 +4,11 @@ "slug": "pb" }, "tier2": { - "name": "atomistic", - "slug": "at" + "name": "quantum-mechanical", + "slug": "qm" }, "tier3": { - "name": "atomistic dispersion model", + "name": "quantum-mechanical dispersion model", "slug": "disp" }, "type": { diff --git a/schema/models_directory/pb/qm/disp.json b/schema/models_directory/pb/qm/disp.json new file mode 100644 index 000000000..b1781356e --- /dev/null +++ b/schema/models_directory/pb/qm/disp.json @@ -0,0 +1,18 @@ +{ + "$schema": "http://json-schema.org/draft-04/schema#", + "allOf": [ + { + "$ref": "../qm.json" + } + ], + "properties": { + "tier3": { + "enum": [ + { + "name": "quantum-mechanical dispersion model", + "slug": "disp" + } + ] + } + } +} diff --git a/schema/models_directory/pb/at/disp/xdm.json b/schema/models_directory/pb/qm/disp/xdm.json similarity index 94% rename from schema/models_directory/pb/at/disp/xdm.json rename to schema/models_directory/pb/qm/disp/xdm.json index 01c7fcc39..a0049815a 100644 --- a/schema/models_directory/pb/at/disp/xdm.json +++ b/schema/models_directory/pb/qm/disp/xdm.json @@ -1,5 +1,5 @@ { - "schemaId": "models-directory-at-disp-xdm", + "schemaId": "models-directory-qm-disp-xdm", "$schema": "http://json-schema.org/draft-04/schema#", "title": "Exchange-Dipole Model (XDM)", "description": "See work by Becke and Johnson (doi: 10.1063/1.1884601)",