Skip to content

Commit

Permalink
Implemented the possibility to use Orca instead of TM. (#23)
Browse files Browse the repository at this point in the history 
* Implemented the possibility to use Orca instead of TM.

   - Implemented a Orca Driver
   - Implemented a custom cosmo file writer to be able to read .cpcm
   files
   - Small Bugfixes

Note: Currently there is no dedicated ORCA Parametrisation.

Signed-off-by: MtoLStoN <[email protected]>

* Changed help routines to reflect the implementation of orca.

Rebranding

Signed-off-by: MtoLStoN <[email protected]>
  • Loading branch information
@MtoLStoN
MtoLStoN authored Jan 28, 2022
1 parent b7f6a5f commit b15d36e
Show file tree
Hide file tree
Showing 21 changed files with 444 additions and 147 deletions.
166 changes: 117 additions & 49 deletions app/main.f90
View file
Original file line number Diff line number Diff line change
@@ -1,20 +1,20 @@
! This file is part of COSMO-X.
! This file is part of CPCM-X.
! SPDX-Identifier: LGPL-3.0-or-later
!
! COSMO-X is free software: you can redistribute it and/or modify it under
! CPCM-X is free software: you can redistribute it and/or modify it under
! the terms of the GNU Lesser General Public License as published by
! the Free Software Foundation, either version 3 of the License, or
! (at your option) any later version.
!
! COSMO-X is distributed in the hope that it will be useful,
! CPCM-X 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 Lesser General Public License for more details.
!
! You should have received a copy of the GNU Lesser General Public License
! along with COSMO-X. If not, see <https://www.gnu.org/licenses/>.
! along with CPCM-X. If not, see <https://www.gnu.org/licenses/>.

program COSMOX
program CPCMX
use element_dict
use globals
use sort
Expand Down Expand Up @@ -64,7 +64,9 @@ program COSMOX
character(len=:), allocatable :: sac_param_path
character(len=:), allocatable :: smd_param_path
character(len=:), allocatable :: database
logical :: ML, sig_in, prof, smd_default, TM, time
character(len=:), allocatable :: qc_calc
character(len=:), allocatable :: xyz_input
logical :: ML, sig_in, prof, smd_default, time
character(len=:), allocatable :: model
end type configuration

Expand All @@ -79,7 +81,6 @@ program COSMOX
!! ------------------------------------------------------------
!! Read Command Line Arguments and set Parameters accordingly
!! ------------------------------------------------------------

Call timer%push("total")
Call get_arguments(config,error)
if (allocated(error)) then
Expand All @@ -88,7 +89,6 @@ program COSMOX
end if
Call echo_init(config)
Call initialize_param(config%sac_param_path,config%model,r_cav,disp_con,config%csm_solvent)

if (config%ML) then
Call init_pr
write(*,*) "Machine Learning Mode selected. Will Only Write an ML.data file." !! ML Mode deprecated
Expand All @@ -111,9 +111,18 @@ program COSMOX
!! ----------------------------------------------------------------------------------
!! Creating COSMO Files with QC packages
!! ----------------------------------------------------------------------------------
if (config%TM) then
if (allocated(config%qc_calc)) then
Call timer%push("qc_calc")
Call qc_cal(config%qc_eps,config%csm_solute,config%smd_solvent)
select case(config%qc_calc)
case('TM')
Call qc_cal(config%qc_eps,config%csm_solute,config%smd_solvent)
case('ORCA')
Call qc_cal(config%xyz_input,error)
case default
write(error_unit,'(a,a,a)') "Chosen program "//config%qc_calc//" not supported"
error stop
end select
Call check_error(error)
Call timer%pop()
end if
!! ----------------------------------------------------------------------------------
Expand Down Expand Up @@ -184,7 +193,7 @@ program COSMOX


!! ------------------------------------------------------------------------------------
!! Choice of the different post COSMO Models (sac,sac2010,sac2013,COSMO-RS)
!! Choice of the different post COSMO Models (sac,sac2010,sac2013,CPCM-RS)
!! ------------------------------------------------------------------------------------

select case (trim(config%model))
Expand Down Expand Up @@ -229,9 +238,9 @@ program COSMOX
! Call pr2018(solute_area,solute_elements,solute_ident,oh_sol,nh_sol,near_sol)
case ("crs")

!! COSMO-RS calculation starts here !!
!! CPCM-RS calculation starts here !!

! Calculate sv0,svt for COSMO-RS
! Calculate sv0,svt for CPCM-RS

Call average_charge(param(1)*2.0_wp, solvent_xyz,solvent_su,solvent_area,solvent_sv0)
Call ortho_charge(solvent_sv,solvent_sv0,solvent_svt)
Expand All @@ -247,7 +256,7 @@ program COSMOX
! &solute_pot,solute_elements,solute_ident,disp_con, T,r_cav)
!end if

! Computation of COSMO-RS equations (here may be something wrong atm)
! Computation of CPCM-RS equations (here may be something wrong atm)
Call timer%push("solv")
Call compute_solvent(solv_pot,solvent_sv,solvent_svt,solvent_area,T,500,0.0001,solvent_ident,solvent_hb)
Call timer%pop()
Expand Down Expand Up @@ -337,6 +346,7 @@ subroutine help(unit)

write(unit, '(2x, a, t25, a)') &
" --solvent", "Specify a solvent and uses configuration given in config.toml.", &
"","For Orca this needs an .xyz file as input (e.g. csx inp.xyz --solvent water)",&
" --newrc", "Creates a sample configuration file (config.toml).", &
" --newinput", "Creates a sample input file csx.input in the currect working directory.", &
" --keyword", "Shows a list of possible Keywords for the csx.input file.", &
Expand All @@ -357,12 +367,15 @@ subroutine sample(filename,rc)
open(newunit=unit,file=filename)
if (rc) then
write(unit,'(a)') &
'# This is a Sample CSX Configuration File', &
'# To work with this file, an environmental variable CSXHOME has to be set.', &
'# This File has to be placed in the CSXHOME path.', &
'# All Parameters and the Database need to be placed in CSXHOME.', &
'# This is a Sample CPX Configuration File', &
'# To work with this file, an environmental variable CPXHOME has to be set.', &
'# This File has to be placed in the CPXHOME path.', &
'# All Parameters and the Database need to be placed in CPXHOME.', &
'', &
'# Path or Filename for the parameters for Water. (Path in respective to CSXHOME)', &
'# Default QC Program for the Single Point Calculations', &
'prog="TM"', &
'', &
'# Path or Filename for the parameters for Water. (Path in respective to CPXHOME)', &
'smd_h2o="smd_h2o"', &
'crs_h2o="crs.param_h2o"', &
'', &
Expand Down Expand Up @@ -405,9 +418,10 @@ subroutine print_keywords(unit)
""

write(unit, '(2x, a, t25, a)') &
" crs", "Invokes the standard COSMO-X model.", &
" crs", "Invokes the standard CPCM-X model.", &
" sac, sac2010", "Invokes an SAC based model with or without HB splitting (needs different parameters).", &
" TM/TM=epsilon", "Starts with single point calculation for the solute. Needs control file. (default: epsilon=infinity)", &
" ORCA", "Starts with single point calculation for the solute with epsilon=infinity. Needs .xyz file.", &
" time", "Shows additional Information about the time needed for various steps of the algorithm.", &
" onlyprof", "Only calculates a Sigma Profile and prints it in a .sigma file.", &
" sigma_in", "Expects Sigma Profiles instead of .cosmo files (only for SAC based models).", &
Expand Down Expand Up @@ -469,6 +483,13 @@ subroutine get_arguments(config, error)
end if
call fatal_error(error, "Too many positional arguments present")
exit
case default
if ((.not.allocated(config%xyz_input))) then
call move_alloc(arg, config%xyz_input)
cycle
end if
call fatal_error(error, "Too many positional arguments present")
exit
end select
end do

Expand All @@ -481,7 +502,7 @@ subroutine get_arguments(config, error)

end subroutine get_arguments

!> Subroutine to Read the COSMO-SACMD Input File
!> Subroutine to Read the CPCM-SACMD Input File
subroutine read_input(config,error)
type(configuration) :: config
type(error_type), allocatable :: error
Expand All @@ -499,11 +520,10 @@ subroutine read_input(config,error)
config%sig_in=.FALSE.
config%prof=.FALSE.
config%smd_default=.FALSE.
config%TM=.FALSE.
config%time=.FALSE.
config%qc_eps=0
config%probe=0.4
!> Check if the COSMO-SACMD Input File Exists.
!> Check if the CPCM-SACMD Input File Exists.
ex=.false.
INQUIRE(file=config%input,exist=ex)
IF (.NOT. ex) then
Expand Down Expand Up @@ -534,8 +554,28 @@ subroutine read_input(config,error)
end if

select case(keyword)
case ('TM')
config%TM=.true.
case ('TM','tm')
if (allocated(config%qc_calc)) then
Call fatal_error(error,"Too many Arguments for QC calculation.")
return
end if
Call move_line("TM",config%qc_calc)
if (equal .ne. 0) then
select case(substring)
case ('default','minnesota')
config%qc_eps=-1
case ('infinity')
config%qc_eps=0
case default
read(substring,*) config%qc_eps
end select
end if
case ('ORCA','Orca','orca')
if (allocated(config%qc_calc)) then
Call fatal_error(error,"Too many Arguments for QC calculation.")
return
end if
Call move_line("ORCA",config%qc_calc)
if (equal .ne. 0) then
select case(substring)
case ('default','minnesota')
Expand Down Expand Up @@ -588,7 +628,7 @@ subroutine use_default(config, solv, error)
!> Solvent used for default configuration
character(:), allocatable, intent(inout) :: solv
!> Configuration Type
type(configuration), intent(out) :: config
type(configuration), intent(inout) :: config
!> Error handling
type(error_type), allocatable, intent(out) :: error
!> Toml unit
Expand All @@ -611,7 +651,6 @@ subroutine use_default(config, solv, error)
config%sig_in=.FALSE.
config%prof=.FALSE.
config%smd_default=.FALSE.
config%TM=.FALSE.
config%time=.FALSE.
config%qc_eps=0
config%probe=0.4
Expand All @@ -620,32 +659,34 @@ subroutine use_default(config, solv, error)
call move_line(solv//".cosmo",config%csm_solvent)
call move_line("solute.cosmo",config%csm_solute)
call move_line("crs",config%model)
config%TM=.TRUE.
Call get_variable("CSXHOME",home)
Call get_variable("CPXHOME",home)

if (.not.allocated(home)) then
call fatal_error(error, "CSXHOME Variable ist not set.")
call fatal_error(error, "CPXHOME Variable ist not set.")
RETURN
end if

ex=.false.


if (home(len(home):len(home)) .ne. "/") call move_line(home//"/",home)

INQUIRE(file=home//"config.toml",exist=ex)

if (.not. ex) then
call fatal_error(error, "No config.toml found in "//home)
if (home(len(home):len(home)) .ne. "/") call fatal_error(error, "No config.toml found in "//home&
&//"."//NEW_LINE('a')//'Your path should probable end with an "/".')
return
end if

open(input_unit,file=home//"config.toml")
call toml_parse(config_table,input_unit,config_error)
close(input_unit)

if (allocated(config_table)) then
call config_table%get_keys(list)
do nconf=1,size(list)
select case(list(nconf)%key)
case("prog")
call get_value(config_table,list(nconf),line2)
call move_line(line2,config%qc_calc)
case("smd_h2o")
if (solv .eq. "water") then
call get_value(config_table,list(nconf),line2)
Expand Down Expand Up @@ -733,25 +774,42 @@ subroutine use_default(config, solv, error)

end subroutine use_default

subroutine move_line(line,aline)
subroutine move_line(line,aline,hignore)
!> Line to write into the allocatable unit
character(*), intent(in) :: line
!> Ignores everything after an hashtag (default=true)
logical, intent(in), optional :: hignore
!> Allocatable character array to be set to line
character(:), allocatable, intent(inout) :: aline

integer :: i
logical :: ignore

ignore=.true.

if (present(hignore)) then
if (.not. hignore) ignore=.false.
end if

if (allocated(aline)) deallocate(aline)
do i= 1,len(trim(line))
if (line(i:i) .EQ. "#") then
allocate(character(len(trim(line(1:i-1)))) :: aline)
aline=trim(line(1:i-1))
exit
end if
if (i .EQ. len(trim(line))) then
allocate(character(len(trim(line(1:i)))) :: aline)
aline=trim(line(1:i))
exit
end if
end do

if (ignore) then
do i= 1,len(trim(line))
if (line(i:i) .EQ. "#") then
allocate(character(len(trim(line(1:i-1)))) :: aline)
aline=trim(line(1:i-1))
exit
end if
if (i .EQ. len(trim(line))) then
allocate(character(len(trim(line(1:i)))) :: aline)
aline=trim(line(1:i))
exit
end if
end do
else
allocate(character(len(trim(line))) :: aline)
aline=trim(line)
end if
end subroutine move_line

subroutine echo_init(config)
Expand All @@ -770,10 +828,20 @@ subroutine echo_init(config)
"Solvent:", config%smd_solvent, &
"Corresponding COSMO File:", config%csm_solvent

if (.NOT. config%TM) write(output_unit,'(5x,a,t35,a)') &
if (.NOT. allocated(config%qc_calc)) write(output_unit,'(5x,a,t35,a)') &
"Solute COSMO File:", config%csm_solute

end subroutine echo_init

end program COSMOX
subroutine check_error(error)
type(error_type), intent(in), allocatable :: error

if (allocated(error)) then
write(error_unit,'(a)') error%message
error stop
end if

end subroutine check_error

end program CPCMX

12 changes: 6 additions & 6 deletions app/meson.build
View file
Original file line number Diff line number Diff line change
@@ -1,22 +1,22 @@
# This file is part of COSMO-X.
# This file is part of CPCM-X.
# SPDX-Identifier: LGPL-3.0-or-later
#
# COSMO-X is free software: you can redistribute it and/or modify it under
# CPCM-X is free software: you can redistribute it and/or modify it under
# the terms of the GNU Lesser General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# COSMO-X is distributed in the hope that it will be useful,
# CPCM-X 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 Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public License
# along with COSMO-X. If not, see <https://www.gnu.org/licenses/>.
# along with CPCM-X. If not, see <https://www.gnu.org/licenses/>.

csx_exe = executable(
cpx_exe = executable(
meson.project_name(),
sources: files('main.f90'),
dependencies: csx_dep,
dependencies: cpx_dep,
install: true,
)
13 changes: 8 additions & 5 deletions config.toml
View file
Original file line number Diff line number Diff line change
@@ -1,9 +1,12 @@
# This is a Sample CSX Configuration File
# To work with this file, an environmental variable CSXHOME has to be set.
# This File has to be placed in the CSXHOME path.
# All Parameters and the Database need to be placed in CSXHOME.
# This is a Sample CPX Configuration File
# To work with this file, an environmental variable CPXHOME has to be set.
# This File has to be placed in the CPXHOME path.
# All Parameters and the Database need to be placed in CPXHOME.

# Path or Filename for the parameters for Water. (Path in respective to CSXHOME)
# Default QC Program for the Single Point Calculations
prog="TM"

# Path or Filename for the parameters for Water. (Path in respective to CPXHOME)
smd_h2o="smd_h2o"
crs_h2o="crs.param_h2o"

Expand Down
Loading

0 comments on commit b15d36e

Please sign in to comment.