root / src / Path_module.f90
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MODULE Path_module |
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! This module contains most of the variables needed for the path |
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|
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!---------------------------------------------------------------------- |
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! Copyright 2003-2014 Ecole Normale Supérieure de Lyon, |
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! Centre National de la Recherche Scientifique, |
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! Université Claude Bernard Lyon 1. All rights reserved. |
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! |
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! This work is registered with the Agency for the Protection of Programs |
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! as IDDN.FR.001.100009.000.S.P.2014.000.30625 |
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! |
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! Authors: P. Fleurat-Lessard, P. Dayal |
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! Contact: optnpath@gmail.com |
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! |
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! This file is part of "Opt'n Path". |
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! |
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! "Opt'n Path" is free software: you can redistribute it and/or modify |
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! it under the terms of the GNU Affero General Public License as |
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! published by the Free Software Foundation, either version 3 of the License, |
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! or (at your option) any later version. |
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! |
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! "Opt'n Path" is distributed in the hope that it will be useful, |
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! but WITHOUT ANY WARRANTY; without even the implied warranty of |
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! |
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! MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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! GNU Affero General Public License for more details. |
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! |
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! You should have received a copy of the GNU Affero General Public License |
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! along with "Opt'n Path". If not, see <http://www.gnu.org/licenses/>. |
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! |
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! Contact The Office of Technology Licensing, valorisation@ens-lyon.fr, |
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! for commercial licensing opportunities. |
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!---------------------------------------------------------------------- |
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|
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use VarTypes |
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|
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IMPLICIT NONE |
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|
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SAVE |
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|
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INTEGER(KINT), PARAMETER :: NMaxL=21 |
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INTEGER(KINT), PARAMETER :: Max_Z=86 |
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INTEGER(KINT), PARAMETER :: MaxFroz=100 |
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REAL(KREAL), PARAMETER :: a0=0.529177249d0 |
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REAL(KREAL), PARAMETER :: Unit=1.d0/a0 |
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REAL(KREAL), PARAMETER :: Ang2au=a0, Au2Ang=Unit |
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REAL(KREAL) :: Pi |
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|
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! Frozen contains the indices of frozen atoms |
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INTEGER(KINT),ALLOCATABLE :: Frozen(:) !Nat |
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! Cart contains the indices of atoms described in cartesian coords |
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INTEGER(KINT),ALLOCATABLE :: Cart(:) !Nat |
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! intFroz is the number of internal coord frozen |
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! NFroz the number of frozen atoms |
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! Ncart the number of atoms described in cartesian coords |
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INTEGER(KINT) :: IntFroz, NFroz, NCart |
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! FrozAtoms is true for a frozen atom, false else. |
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LOGICAL, ALLOCATABLE :: FrozAtoms(:) !! Nat |
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! Number of Primitives (mainly for Baker coordinates) |
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INTEGER(KINT) :: NPrim |
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! Nat number of atoms |
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INTEGER(KINT) :: Nat |
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! NGeomI number of initial geometries |
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! NgeomF number of final geometries |
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INTEGER(KINT) :: NGeomI, NGeomF |
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! NCoord=3*Nat or NFree depending on the coordinate choice |
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INTEGER(KINT) :: NCoord |
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INTEGER(KINT) :: NMaxPtPath=1000 |
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! IReparam is the period of reparameterization of the Path |
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INTEGER(KINT) :: IReparam=1 |
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! IReparamT is the period of reparameterization of the tangents along the path |
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! Be default IReparamT=IReparam |
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INTEGER(KINT) :: IReparamT |
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! ISpline is the iteration number where spline interpolation starts to be used |
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! instead of linear interpolation |
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INTEGER(KINT) :: ISpline=1 |
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! Linear: if TRUE, then we perform linear interpolation and not spline |
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LOGICAL :: Linear |
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|
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! FrozTol is the criterion to decide wether a frozen atom has moved between |
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! two initial geometries |
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REAL(KREAL) :: FrozTol=1e-4 |
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|
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! BoxTol is the criterion to decide wether an atom has crossed the box between |
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! two initial geometries |
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REAL(KREAL) :: BoxTol=0.5 |
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|
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LOGICAL :: Freq, MW, Bohr, Renum, Hinv |
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! OptReac: if TRUE the reactants will be optimized. Default is FALSE |
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LOGICAL :: OptReac |
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! OptProd: if TRUE the products will be optimized. Default is FALSE |
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LOGICAL :: OptProd |
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! PathOnly: if TRUE, only the initial path will be constructed. |
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! Default is FALSE, that is OpenPath construct the path and optimize it |
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LOGICAL :: PathOnly |
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! CalcEReac: if TRUE the reactants energy will be computed. Default is FALSE |
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! Not compatible with RunMode=Para |
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LOGICAL :: CalcEReac |
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! CalEProd: if TRUE the products energy will be computed. Default is FALSE |
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! Not compatible with RunMode=Para |
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LOGICAL :: CalcEProd |
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! AnaGeom: if TRUE the geometries are analyzed |
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LOGICAL :: AnaGeom |
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! Name of the file to analyse geometries |
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CHARACTER(LCHARS) :: AnaFile |
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! Name of the Gplot file to see the path evolution |
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CHARACTER(LCHARS) :: GplotFile |
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! Nb: number of variables to monitor, including Centers of Mass |
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INTEGER(KINT) :: Nb |
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! NbVar: number of geometrical variables to monitor |
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INTEGER(KINT) :: NbVar |
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! NbCom: number of center of mass to create |
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INTEGER(KINT) :: NbCom |
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TYPE(ListCoord), POINTER :: GeomList,CurVar |
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TYPE(Barycenter), POINTER :: Bary,CurBary |
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! Format to print the values |
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CHARACTER(VLCHARS) :: FormAna |
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! Factor to use to print the values |
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REAL(KREAL), ALLOCATABLE :: PrintGeomFactor(:) ! NbVar |
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! How to update the Hessian |
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LOGICAL :: IniHup,HupNeighbour |
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|
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REAL(KREAL) :: Fact,FTan |
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! IGeomRef is the index of the reference geometry, used to calculate the Zmat |
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! or the Baker coordinates. |
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INTEGER(KINT) :: IGeomRef=-1 |
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! For geometry optimization , OptGeom is the index of the starting geometry |
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INTEGER(KINT) :: OptGeom=-1 |
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|
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! Optimization parameter |
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INTEGER(KINT) :: MaxCyc |
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REAL(KREAL) :: SThresh, Smax, SthreshRms |
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REAL(KREAL) :: GThresh, GThreshRMS |
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! Name of the file to print geometries and their energies |
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CHARACTER(LCHARS) :: GeomFile |
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! Flag to decide if we print something in GeomFile |
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LOGICAL :: FPrintGeom |
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|
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! Number of steps in memory for Step_RFO_all |
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INTEGER(KINT) :: NGintMax = 10 |
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|
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CHARACTER(SCHARS) :: Coord='HYBRID' |
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CHARACTER(SCHARS) :: Step_method='RFO' |
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CHARACTER(SCHARS) :: Prog="GAUSSIAN" |
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CHARACTER(VLCHARS) :: ProgExe="g03" |
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! Input: format of the geometry input |
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! PFL 2013/02: This name is dumb ! I should have used GeomFormat ! => To DO!! |
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CHARACTER(SCHARS) :: Input |
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! Poscar: is the name to use for POSCAR files for VASP |
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CHARACTER(SCHARS) :: Poscar |
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|
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! PFL 06/2011: HesUpd is deprecated |
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! I replace it by HUpdate that is more intuitive to me |
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CHARACTER(SCHARS) :: hesupd="BFGS" |
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! HUpdate indicates which method to use for updating the Hessian or its inverse |
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CHARACTER(SCHARS) :: HUpdate="BFGS" |
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|
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REAL(KREAL), ALLOCATABLE, TARGET :: XyzGeomI(:,:,:) ! (NGeomI,3,Nat) |
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REAL(KREAL), ALLOCATABLE :: XyzGeomF(:,:,:) ! (NGeomF,3,Nat) |
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REAL(KREAL), ALLOCATABLE :: XyzTangent(:,:) ! (NGeomF,3*Nat) |
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REAL(KREAL), ALLOCATABLE :: IntTangent(:,:) ! (NGeomF,Nfree=3Nat-6) |
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REAL(KREAL), ALLOCATABLE :: IntCoordI(:,:) ! (NGeomI,3*Nat-6) |
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! IntCoordF: Final Internal coordinates for number of final geometries. |
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! 3*Nat-6 is the number of coordinates (NCoord) of each geometry. |
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REAL(KREAL), ALLOCATABLE :: IntCoordF(:,:) ! (NGeomF,3*Nat-6) |
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REAL(KREAL), ALLOCATABLE :: Vfree(:,:) ! (Ncoord,Ncoord) |
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REAL(KREAL), ALLOCATABLE :: SGeom(:) ! (NGeomF) |
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REAL(KREAL), ALLOCATABLE :: Energies(:) ! NGeomF |
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! NCoord=3*Nat or NFree depending on the coordinate choice |
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REAL(KREAL), ALLOCATABLE :: Grad(:,:) ! (NGeomF,NCoord) |
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REAL(KREAL), ALLOCATABLE :: Hess(:,:,:) !(NgeomF, N,N) |
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REAL(KREAL), ALLOCATABLE :: DzDc(:,:,:,:) ! (3,Nat,3,Nat) |
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REAL(KREAL), ALLOCATABLE :: BMat_BakerT(:,:) ! (3*Nat,NCoord) |
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INTEGER(KINT), ALLOCATABLE :: IndZmat(:,:) ! (Nat,5) |
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INTEGER(KINT), ALLOCATABLE :: Order(:),OrderInv(:) ! Nat |
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CHARACTER(10), ALLOCATABLE :: AtName(:) ! Nat |
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INTEGER(KINT), ALLOCATABLE :: Atome(:) ! Nat |
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REAL(KREAL), ALLOCATABLE :: MassAt(:) ! Nat |
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REAL(KREAL), ALLOCATABLE :: BTransInv(:,:) ! BTransInv (3*Nat-6,3*Nat), used for Baker case. |
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REAL(KREAL), ALLOCATABLE :: BTransInvF(:,:,:) ! BTransInvF (NGeomF,3*Nat-6,3*Nat) |
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! BTransInv_local (3*Nat-6,3*Nat), used for Baker case in Opt_Geom.f90 |
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REAL(KREAL), ALLOCATABLE :: BTransInv_local(:,:) |
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REAL(KREAL), ALLOCATABLE :: UMat(:,:) !(NPrim,3*Nat-6) |
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REAL(KREAL), ALLOCATABLE :: UMat_local(:,:) !(NPrim,3*Nat-6) |
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REAL(KREAL), ALLOCATABLE :: UMatF(:,:,:) !(NGeomF,NPrim,3*Nat-6) |
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!REAL(KREAL), ALLOCATABLE :: IntCoordIBaker(:,:) ! (NGeomI,NCoord=3*Nat-6) |
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! IntCoordIBaker allocated in PathCreate.f90 |
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REAL(KREAL), ALLOCATABLE :: Xprimitive(:,:) ! Xprimitive(NgeomI,NPrim) |
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REAL(KREAL), ALLOCATABLE :: Xprimitive_t(:) ! used in ConvertBakerInternal_cart.f as a temporary variable. |
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REAL(KREAL), ALLOCATABLE :: XprimitiveF(:,:) ! Xprimitive(NgeomF,NPrim) |
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REAL(KREAL), ALLOCATABLE :: GeomOld_all(:,:) |
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REAL(KREAL), ALLOCATABLE :: GeomOld(:) ! Used in DIIS step method. |
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|
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LOGICAL, PARAMETER :: FRot=.TRUE., FAlign=.TRUE. |
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REAL(KREAL), ALLOCATABLE :: BprimT(:,:) !(3*Nat,NPrim). This is B^prim. |
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REAL(KREAL), ALLOCATABLE :: BBT(:,:) ! BBT (3*Nat-6,3*Nat-6), used for Baker case |
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REAL(KREAL), ALLOCATABLE :: BBT_inv(:,:) ! BBT_inv (3*Nat-6,3*Nat-6), used for Baker case |
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INTEGER(KINT) :: Symmetry_elimination |
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LOGICAL :: FirstTimePathCreate |
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|
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Type (ListCoord), POINTER :: Coordinate, CurrentCoord |
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Type (ListCoord), POINTER :: ScanCoord |
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|
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! Triggers the dynamical update of the maximum step |
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LOGICAL :: DynMaxStep |
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|
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! Triggers the alignment of not |
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LOGICAL :: Align |
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|
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|
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|
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!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! |
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! |
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! Flags for printing |
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! |
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!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! |
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|
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! Vmd is set to TRUE if user wants to use VMD to look |
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! at the Path. |
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! For now, used only for VASP |
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|
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LOGICAL :: Vmd |
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|
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|
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!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! |
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! |
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! Variables for periodic calculations |
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! |
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!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! |
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|
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! Lattice constants |
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REAL(KREAL) :: lat_a(3), lat_b(3), lat_c(3) |
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! Inverse lattice constants |
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REAL(KREAL) :: Latr(3,3) |
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! FPBC : True if this is a periodic calculations |
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LOGICAL :: FPBC |
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! Possible values for ka, kb, kc in VectorPer (and other periodic operations) |
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INTEGER(KINT) :: kaBeg,kaEnd,kbBeg,kbEnd,kcBeg,kcEnd |
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! Number of periodic directions |
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INTEGER(KINT) :: IPer |
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! Reference cartesian coordinates |
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REAL(KREAL), ALLOCATABLE :: XGeomRefPBC(:),YGeomRefPBC(:),ZGeomRefPBC(:) ! Nat |
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! How shall we print the cartesian coordinates ? |
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! if V_Direct='DIRECT' then we use fractional coord (ie divided by unit cell |
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! vectors). |
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CHARACTER(LCHARS) :: V_direct, V_direct_write |
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|
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|
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!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! |
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! |
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! Variables for VASP input/output |
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! |
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!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! |
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|
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REAL(KREAL), ALLOCATABLE :: X0_vasp(:),Y0_vasp(:), Z0_vasp(:) ! nat |
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! AutoCart : true if user let PATH determines which atoms should be |
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! described in cartesian when COORD=MIXED |
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LOGICAL :: AutoCart |
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|
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|
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!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! |
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! |
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! General |
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! |
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!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! |
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|
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CHARACTER(2) :: Nom(0:max_Z)=(/ ' X',' H', 'HE', & |
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'LI','BE', ' B',' C',' N',' O',' F','NE', & |
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'NA','MG', 'AL','SI',' P',' S','CL','AR', & |
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' K','CA', & |
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'SC','TI',' V','CR','MN','FE','CO','NI','CU','ZN', & |
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'GA','GE','AS','SE','BR','KR', & |
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'RB','SR', & |
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' Y','ZR','NB','MO','TC','RU','RH','PD','AG','CD', & |
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'IN','SN','SB','TE',' I','XE', & |
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'CS','BA', & |
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'LA', & |
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'CE','PR','ND','PM','SM','EU','GD','TB','DY','HO', & |
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'ER','TM','YB','LU', & |
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'HF','TA',' W','RE','OS','IR','PT','AU','HG', & |
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'TL','PB','BI','PO','AT','RN'/) |
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|
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! This is the new table, more complete, taken from a periodic table |
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! some value have been changed to be consistent |
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REAL(KREAL) :: r_cov(0:max_Z)=(/ 1e-13, 37., 93., & |
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! 2 'LI','BE', ' B',' C',' N',' O',' F','NE', |
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123.,90., 82., 77., 75., 73., 71., 69., & |
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! 3 'NA','MG', 'AL','SI',' P',' S','CL','AR', |
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154.,136., 118.,111.,106.,102., 99., 97., & |
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! 4 ' K','CA', |
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203., 174., & |
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! 4 'SC','TI',' V','CR','MN','FE','CO','NI','CU','ZN', |
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144.,132.,122.,118.,117.,117.,116.,115.,117.,125., & |
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! 4 'GA','GE','AS','SE','BR','KR', |
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120.,122.,122.,117.,114.,110., & |
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! 5 'RB','SR', |
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216.,191., & |
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! 5 ' Y','ZR','NB','MO','TC','RU','RH','PD','AG','CD', |
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162.,145.,134.,130.,127.,125.,125.,128.,134.,148., & |
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! 5 'IN','SN','SB','TE',' I','XE', |
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144.,140.,143.,135.,133.,130., & |
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! 6 'CS','BA', |
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235., 198., & |
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! 6 'LA', |
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! 'CE','PR','ND','PM','SM','EU','GD','TB','DY','HO', & |
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! 'ER','TM','YB','LU', & |
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169., & |
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165., 165., 164., 163., 162., 185., 161., 159., 159., 158., & |
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157., 156., 184.,156., & |
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! 6 'HF','TA',' W','RE','OS','IR','PT','AU','HG', |
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! 6 'TL','PB','BI','PO','AT','RN'/ |
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144., 134., 130., 126., 126., 127., 120., 134., 149., & |
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148., 147., 146., 146., 148., 151. /) |
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|
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REAL(KREAL) :: Mass(0:Max_Z)=(/0.0D0,1.0078D0, 4.0026D0, & |
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7.0160D0, 9.0122D0,11.0093D0, & |
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12.0000D0,14.0031D0,15.9949D0,18.9984D0,19.9924D0, & |
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22.9898D0,23.9850D0,26.9815D0, & |
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27.9769D0,30.9738D0,31.9721D0,34.9688D0,39.9624D0, & |
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39.0983D0,40.08D0, & |
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44.9559D0, 47.88D0, 50.9415D0, 51.996D0, 54.9380D0, & |
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55.847D0, 58.9332D0, 58.69D0, 63.546D0, 65.39D0, & |
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69.72D0,72.59D0,74.9216D0,78.96D0,79.904D0,83.80D0, & |
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85.4678D0,87.62D0,88.9059D0,91.224D0,92.9064D0, & |
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95.94D0,98D0,101.07D0,102.906D0,106.42D0,107.868D0,112.41D0, & |
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114.82D0,118.71D0,121.75D0,127.60D0,126.905D0,131.29D0, & |
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! 6 'CS','BA', |
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132.905D0,137.34D0, & |
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! 6 'LA', |
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! 'CE','PR','ND','PM','SM','EU','GD', |
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! 'TB','DY','HO', 'ER','TM','YB','LU', |
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138.91D0, & |
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140.12D0, 130.91D0, 144.24D0,147.D0,150.35D0, 151.96D0,157.25D0, & |
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158.924D0, 162.50D0, 164.93D0, 167.26D0,168.93D0,173.04D0,174.97D0, & |
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! 6 'HF','TA',' W','RE','OS','IR','PT', |
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! 'AU','HG', |
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! 6 'TL','PB','BI','PO','AT','RN'/ |
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178.49D0, 180.95D0, 183.85D0, 186.2D0, 190.2D0, 192.2D0, 195.09D0, & |
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196.97D0, 200.59D0, & |
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204.37D0, 207.19D0,208.98D0,210.D0,210.D0,222.D0 /) |
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|
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END MODULE Path_module |