Chimie Théorique » Opt'n Path

MODULE Path_module

! This module contains most of the variables needed for the path

!----------------------------------------------------------------------

!  Copyright 2003-2014 Ecole Normale Supérieure de Lyon,

!  Centre National de la Recherche Scientifique,

!  Université Claude Bernard Lyon 1. All rights reserved.

!

!  This work is registered with the Agency for the Protection of Programs

!  as IDDN.FR.001.100009.000.S.P.2014.000.30625

!

!  Authors: P. Fleurat-Lessard, P. Dayal

!  Contact: optnpath@gmail.com

!

! This file is part of "Opt'n Path".

!

!  "Opt'n Path" is free software: you can redistribute it and/or modify

!  it under the terms of the GNU Affero General Public License as

!  published by the Free Software Foundation, either version 3 of the License,

!  or (at your option) any later version.

!

!  "Opt'n Path" is distributed in the hope that it will be useful,

!  but WITHOUT ANY WARRANTY; without even the implied warranty of

!

!  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the

!  GNU Affero General Public License for more details.

!

!  You should have received a copy of the GNU Affero General Public License

!  along with "Opt'n Path". If not, see <http://www.gnu.org/licenses/>.

!

! Contact The Office of Technology Licensing, valorisation@ens-lyon.fr,

! for commercial licensing opportunities.

!----------------------------------------------------------------------

  use VarTypes

  IMPLICIT NONE

  SAVE

  INTEGER(KINT), PARAMETER :: NMaxL=21

  INTEGER(KINT), PARAMETER :: Max_Z=86

  INTEGER(KINT), PARAMETER :: MaxFroz=100

  REAL(KREAL), PARAMETER :: a0=0.529177249d0

  REAL(KREAL), PARAMETER :: Unit=1.d0/a0

  REAL(KREAL), PARAMETER :: Ang2au=a0, Au2Ang=Unit

  REAL(KREAL) :: Pi

 ! Frozen contains the indices of frozen atoms

  INTEGER(KINT),ALLOCATABLE :: Frozen(:) !Nat

 ! Cart contains the indices of atoms described in cartesian coords

  INTEGER(KINT),ALLOCATABLE :: Cart(:) !Nat

! intFroz is the number of internal coord frozen

! NFroz the number of frozen atoms

! Ncart the number of  atoms described in cartesian coords

  INTEGER(KINT) :: IntFroz, NFroz, NCart

! FrozAtoms is true for a frozen atom, false else.

  LOGICAL, ALLOCATABLE :: FrozAtoms(:)  !! Nat

! Number of Primitives (mainly for Baker coordinates)

  INTEGER(KINT) :: NPrim

! Nat number of atoms

  INTEGER(KINT) :: Nat

! NGeomI number of initial geometries

! NgeomF number of final geometries

  INTEGER(KINT) :: NGeomI, NGeomF

! NCoord=3*Nat or NFree depending on the coordinate choice

  INTEGER(KINT) :: NCoord

  INTEGER(KINT) :: NMaxPtPath=1000

! IReparam is the period of reparameterization of the Path

  INTEGER(KINT) :: IReparam=1

! IReparamT is the period of reparameterization of the tangents along the path

! Be default IReparamT=IReparam

  INTEGER(KINT) :: IReparamT

! ISpline is the iteration number where spline interpolation starts to be used

! instead of linear interpolation

  INTEGER(KINT) :: ISpline=1

! Linear: if TRUE, then we perform linear interpolation and not spline

  LOGICAL :: Linear

! FrozTol is the criterion to decide wether a frozen atom has moved between

! two initial geometries

  REAL(KREAL) :: FrozTol=1e-4

! BoxTol is the criterion to decide wether an atom has crossed the box between

! two initial geometries

  REAL(KREAL) :: BoxTol=0.5

  LOGICAL :: Freq, MW, Bohr, Renum, Hinv

! OptReac: if TRUE the reactants will be optimized. Default is FALSE

  LOGICAL :: OptReac

! OptProd: if TRUE the products will be optimized. Default is FALSE

  LOGICAL :: OptProd

! PathOnly: if TRUE, only the initial path will be constructed.

! Default is FALSE, that is OpenPath construct the path and optimize it

  LOGICAL :: PathOnly

! CalcEReac: if TRUE the reactants energy will be computed. Default is FALSE

! Not compatible with RunMode=Para

  LOGICAL :: CalcEReac

! CalEProd: if TRUE the products energy will be computed. Default is FALSE

! Not compatible with RunMode=Para

  LOGICAL :: CalcEProd

! AnaGeom: if TRUE the geometries are analyzed

  LOGICAL :: AnaGeom

! Name of the file to analyse geometries

  CHARACTER(LCHARS) :: AnaFile

! Name of the Gplot file to see the path evolution

  CHARACTER(LCHARS) :: GplotFile

! Nb: number of variables to monitor, including Centers of Mass

  INTEGER(KINT) :: Nb

! NbVar: number of geometrical variables to monitor

  INTEGER(KINT) :: NbVar

! NbCom: number of center of mass to create

  INTEGER(KINT) :: NbCom

  TYPE(ListCoord), POINTER :: GeomList,CurVar

  TYPE(Barycenter), POINTER :: Bary,CurBary

! Format to print the values

  CHARACTER(VLCHARS) :: FormAna

! Factor to use to print the values

  REAL(KREAL), ALLOCATABLE :: PrintGeomFactor(:) ! NbVar

! How to update the Hessian

  LOGICAL :: IniHup,HupNeighbour

  REAL(KREAL) :: Fact,FTan

! IGeomRef is the index of the reference geometry, used to calculate the Zmat

! or the Baker coordinates.

  INTEGER(KINT) :: IGeomRef=-1

! For geometry optimization , OptGeom is the index of the starting geometry

  INTEGER(KINT) :: OptGeom=-1

! Optimization parameter

  INTEGER(KINT) :: MaxCyc

  REAL(KREAL) :: SThresh, Smax, SthreshRms

  REAL(KREAL) :: GThresh, GThreshRMS

! Name of the file to print geometries and their energies

  CHARACTER(LCHARS) :: GeomFile

! Flag to decide if we print something in GeomFile

  LOGICAL :: FPrintGeom

! Number of steps in memory for Step_RFO_all

  INTEGER(KINT) :: NGintMax = 10

  CHARACTER(SCHARS) :: Coord='HYBRID'

  CHARACTER(SCHARS) :: Step_method='RFO'

  CHARACTER(SCHARS) :: Prog="GAUSSIAN"

  CHARACTER(VLCHARS) :: ProgExe="g03"

! Input: format of the geometry input

! PFL 2013/02: This name is dumb ! I should have used GeomFormat ! => To DO!!

  CHARACTER(SCHARS) :: Input

! Poscar: is the name to use for POSCAR files for VASP

  CHARACTER(SCHARS) :: Poscar

! PFL 06/2011: HesUpd is deprecated

! I replace it by HUpdate that is more intuitive to me

  CHARACTER(SCHARS) :: hesupd="BFGS"

! HUpdate indicates which method to use for updating the Hessian or its inverse

  CHARACTER(SCHARS) :: HUpdate="BFGS"

  REAL(KREAL), ALLOCATABLE, TARGET :: XyzGeomI(:,:,:) ! (NGeomI,3,Nat)

  REAL(KREAL), ALLOCATABLE :: XyzGeomF(:,:,:) ! (NGeomF,3,Nat)

  REAL(KREAL), ALLOCATABLE :: XyzTangent(:,:)   ! (NGeomF,3*Nat)

  REAL(KREAL), ALLOCATABLE :: IntTangent(:,:)   ! (NGeomF,Nfree=3Nat-6)

  REAL(KREAL), ALLOCATABLE :: IntCoordI(:,:) ! (NGeomI,3*Nat-6)

  ! IntCoordF: Final Internal coordinates for number of final geometries.

  ! 3*Nat-6 is the number of coordinates (NCoord) of each geometry.

  REAL(KREAL), ALLOCATABLE :: IntCoordF(:,:) ! (NGeomF,3*Nat-6)

  REAL(KREAL), ALLOCATABLE :: Vfree(:,:) ! (Ncoord,Ncoord)

  REAL(KREAL), ALLOCATABLE :: SGeom(:) ! (NGeomF)

  REAL(KREAL), ALLOCATABLE :: Energies(:) ! NGeomF

! NCoord=3*Nat or NFree depending on the coordinate choice

  REAL(KREAL), ALLOCATABLE :: Grad(:,:) ! (NGeomF,NCoord)

  REAL(KREAL), ALLOCATABLE :: Hess(:,:,:)  !(NgeomF, N,N)

  REAL(KREAL), ALLOCATABLE :: DzDc(:,:,:,:) ! (3,Nat,3,Nat)

  REAL(KREAL), ALLOCATABLE :: BMat_BakerT(:,:) ! (3*Nat,NCoord)

  INTEGER(KINT), ALLOCATABLE :: IndZmat(:,:)   ! (Nat,5)

  INTEGER(KINT), ALLOCATABLE :: Order(:),OrderInv(:) ! Nat

  CHARACTER(10), ALLOCATABLE :: AtName(:) ! Nat

  INTEGER(KINT), ALLOCATABLE :: Atome(:) ! Nat

  REAL(KREAL), ALLOCATABLE :: MassAt(:)   ! Nat

  REAL(KREAL), ALLOCATABLE :: BTransInv(:,:) ! BTransInv (3*Nat-6,3*Nat), used for Baker case.

  REAL(KREAL), ALLOCATABLE :: BTransInvF(:,:,:) ! BTransInvF (NGeomF,3*Nat-6,3*Nat)

  ! BTransInv_local (3*Nat-6,3*Nat), used for Baker case in Opt_Geom.f90

  REAL(KREAL), ALLOCATABLE :: BTransInv_local(:,:)

  REAL(KREAL), ALLOCATABLE :: UMat(:,:) !(NPrim,3*Nat-6)

  REAL(KREAL), ALLOCATABLE :: UMat_local(:,:) !(NPrim,3*Nat-6)

  REAL(KREAL), ALLOCATABLE :: UMatF(:,:,:) !(NGeomF,NPrim,3*Nat-6)

  !REAL(KREAL), ALLOCATABLE :: IntCoordIBaker(:,:) ! (NGeomI,NCoord=3*Nat-6)

  ! IntCoordIBaker allocated in PathCreate.f90

  REAL(KREAL), ALLOCATABLE :: Xprimitive(:,:) ! Xprimitive(NgeomI,NPrim)

  REAL(KREAL), ALLOCATABLE :: Xprimitive_t(:) ! used in ConvertBakerInternal_cart.f as a temporary variable.

  REAL(KREAL), ALLOCATABLE :: XprimitiveF(:,:) ! Xprimitive(NgeomF,NPrim)

  REAL(KREAL), ALLOCATABLE :: GeomOld_all(:,:)

  REAL(KREAL), ALLOCATABLE :: GeomOld(:) ! Used in DIIS step method.

  LOGICAL, PARAMETER :: FRot=.TRUE., FAlign=.TRUE.

  REAL(KREAL), ALLOCATABLE :: BprimT(:,:) !(3*Nat,NPrim). This is B^prim.

  REAL(KREAL), ALLOCATABLE :: BBT(:,:) ! BBT (3*Nat-6,3*Nat-6), used for Baker case

  REAL(KREAL), ALLOCATABLE :: BBT_inv(:,:) ! BBT_inv (3*Nat-6,3*Nat-6), used for Baker case

  INTEGER(KINT) :: Symmetry_elimination

  LOGICAL :: FirstTimePathCreate

  Type (ListCoord), POINTER :: Coordinate, CurrentCoord

  Type (ListCoord), POINTER :: ScanCoord

! Triggers the dynamical update of the maximum step

  LOGICAL :: DynMaxStep

! Triggers the alignment of not

  LOGICAL :: Align

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

!

! Flags for printing

!

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

! Vmd is set to TRUE if user wants to use VMD to look

! at the Path.

! For now, used only for VASP

  LOGICAL :: Vmd

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

!

! Variables for periodic calculations

!

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

! Lattice constants

  REAL(KREAL) :: lat_a(3), lat_b(3), lat_c(3)

! Inverse lattice constants

  REAL(KREAL) :: Latr(3,3)

! FPBC : True if this is a periodic calculations

  LOGICAL :: FPBC

! Possible values for ka, kb, kc in VectorPer (and other periodic operations)

  INTEGER(KINT) :: kaBeg,kaEnd,kbBeg,kbEnd,kcBeg,kcEnd

! Number of periodic directions

  INTEGER(KINT) :: IPer

! Reference cartesian coordinates

  REAL(KREAL), ALLOCATABLE :: XGeomRefPBC(:),YGeomRefPBC(:),ZGeomRefPBC(:) ! Nat

! How shall we print the cartesian coordinates ?

! if V_Direct='DIRECT' then we use fractional coord (ie divided by unit cell

! vectors).

  CHARACTER(LCHARS) :: V_direct, V_direct_write

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

!

! Variables for VASP input/output

!

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

  REAL(KREAL), ALLOCATABLE :: X0_vasp(:),Y0_vasp(:), Z0_vasp(:) ! nat

! AutoCart : true if user let PATH determines which atoms should be

! described in cartesian when COORD=MIXED

  LOGICAL :: AutoCart

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

!

! General

!

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

  CHARACTER(2) :: Nom(0:max_Z)=(/ ' X',' H',                   'HE',  &

                'LI','BE',            ' B',' C',' N',' O',' F','NE',  &

                'NA','MG',            'AL','SI',' P',' S','CL','AR',  &

                ' K','CA',                                            &

            'SC','TI',' V','CR','MN','FE','CO','NI','CU','ZN',        &

                                      'GA','GE','AS','SE','BR','KR',  &

                'RB','SR',                                            &

            ' Y','ZR','NB','MO','TC','RU','RH','PD','AG','CD',        &

                                      'IN','SN','SB','TE',' I','XE',  &

                'CS','BA',                                            &

            'LA',                                                     &

              'CE','PR','ND','PM','SM','EU','GD','TB','DY','HO',      &

              'ER','TM','YB','LU',                                    &

                     'HF','TA',' W','RE','OS','IR','PT','AU','HG',    &

                                      'TL','PB','BI','PO','AT','RN'/)

! This is the new table, more complete, taken from a periodic table

! some value have been changed to be consistent

  REAL(KREAL) ::  r_cov(0:max_Z)=(/ 1e-13, 37.,                93.,     &

!     2           'LI','BE',          ' B',' C',' N',' O',' F','NE',

                  123.,90.,            82., 77., 75., 73., 71., 69.,     &

!     3           'NA','MG',          'AL','SI',' P',' S','CL','AR',

                  154.,136.,          118.,111.,106.,102., 99., 97.,     &

!     4           ' K','CA',

                  203.,  174.,                                           &

!     4       'SC','TI',' V','CR','MN','FE','CO','NI','CU','ZN',

             144.,132.,122.,118.,117.,117.,116.,115.,117.,125.,          &

!     4                               'GA','GE','AS','SE','BR','KR',

                                     120.,122.,122.,117.,114.,110.,      &

!     5           'RB','SR',

                 216.,191.,                                              &

!     5       ' Y','ZR','NB','MO','TC','RU','RH','PD','AG','CD',

              162.,145.,134.,130.,127.,125.,125.,128.,134.,148.,         &

!     5                               'IN','SN','SB','TE',' I','XE',

                                     144.,140.,143.,135.,133.,130.,      &

!     6           'CS','BA',

                 235., 198.,                                             &

!     6       'LA',

!               'CE','PR','ND','PM','SM','EU','GD','TB','DY','HO',      &

!               'ER','TM','YB','LU',                                    &

             169.,                                                       &

             165., 165., 164., 163., 162., 185., 161., 159., 159., 158., &

             157., 156., 184.,156.,                                      &

!     6                'HF','TA',' W','RE','OS','IR','PT','AU','HG',

!     6                                 'TL','PB','BI','PO','AT','RN'/

             144., 134., 130., 126., 126., 127., 120., 134., 149.,       &

                        148., 147., 146., 146., 148., 151. /)

  REAL(KREAL) :: Mass(0:Max_Z)=(/0.0D0,1.0078D0,          4.0026D0,      &

                  7.0160D0, 9.0122D0,11.0093D0,                          &

                 12.0000D0,14.0031D0,15.9949D0,18.9984D0,19.9924D0,      &

                 22.9898D0,23.9850D0,26.9815D0,                          &

                 27.9769D0,30.9738D0,31.9721D0,34.9688D0,39.9624D0,      &

                 39.0983D0,40.08D0,                                      &

                   44.9559D0, 47.88D0, 50.9415D0, 51.996D0, 54.9380D0,   &

                   55.847D0, 58.9332D0, 58.69D0, 63.546D0, 65.39D0,      &

                 69.72D0,72.59D0,74.9216D0,78.96D0,79.904D0,83.80D0,     &

                 85.4678D0,87.62D0,88.9059D0,91.224D0,92.9064D0,         &

         95.94D0,98D0,101.07D0,102.906D0,106.42D0,107.868D0,112.41D0,    &

         114.82D0,118.71D0,121.75D0,127.60D0,126.905D0,131.29D0,         &

!     6           'CS','BA',

                 132.905D0,137.34D0,                                      &

!     6       'LA',

!               'CE','PR','ND','PM','SM','EU','GD',

!               'TB','DY','HO', 'ER','TM','YB','LU',

            138.91D0,                                                      &

            140.12D0, 130.91D0, 144.24D0,147.D0,150.35D0, 151.96D0,157.25D0,  &

          158.924D0, 162.50D0, 164.93D0, 167.26D0,168.93D0,173.04D0,174.97D0, &

!     6                'HF','TA',' W','RE','OS','IR','PT',

!                      'AU','HG',

!     6                                 'TL','PB','BI','PO','AT','RN'/

         178.49D0, 180.95D0, 183.85D0, 186.2D0, 190.2D0, 192.2D0, 195.09D0,  &

             196.97D0, 200.59D0,                                             &

             204.37D0, 207.19D0,208.98D0,210.D0,210.D0,222.D0 /)

      END MODULE Path_module