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checklist.f
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checklist.f
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MODULE setup_checklist
use type_m
use MM_input
use parameters_m
use util_m , only: to_upper_case
use Structure_Builder , only: Unit_Cell
use OMP_lib
use MPI_definitions_m , only : np
public :: checklist , dump_driver_parameters_and_tuning , Checking_Topology , need_MM_stuff
private
! module variables ...
logical :: need_MM_stuff
logical :: done = .false.
contains
!
!
!
!====================
subroutine checklist
!====================
implicit none
! local parameters ...
logical , parameter :: T_ = .true. , F_ = .false.
! local variables ...
! feel free to add your own dynemol-for-dummies checklist ...
select case( DRIVER )
case( "q_dynamics" , "slice_Cheb" , "slice_AO" , "slice_FSSH" , "slice_CSDM" )
If( ad_hoc == F_ .OR. Survival == F_ ) then
CALL warning("halting: the DRIVER you chose must go with Survival = T_ AND ad_hoc = T")
stop
end If
case( "avrg_confgs" )
If( file_type /= "trajectory" ) stop ">>> Mind: if DRIVER=^avrg_confgs^: file_type must be ^trajectory^; check parameters.f"
If( nuclear_matter /= "extended_sys" ) stop ">>> Mind: if DRIVER=^avrg_confgs^: nuclear_matter must be ^extended_sys^; check parameters.f"
case( "Genetic_Alg" )
If( nuclear_matter /= "extended_sys" ) stop ">>> Mind: if DRIVER=^Genetic_Alg^: nuclear_matter must be ^extended_sys^; check parameters.f"
If( EnvField_ == .true. ) stop ">>> Mind: if DRIVER=^Genetic_Alg^: flag ^EnvField_ = F_^; check parameters.f"
end select
If ( DP_moment .neqv. any(Unit_Cell%DPF(:)) ) then
stop ">>> halting: variables DP_moment and %DPF (via ad_hoc tuning) do not agree, check consistency of input parameters"
End If
If ( (frame_step /= 1) .AND. (file_type /= "trajectory") ) then
CALL warning("halting: frame_step /= 1, only for avrg_confgs or time-slice dynamics")
stop
End If
need_MM_stuff = EnvField_ .OR. (driver == "MM_Dynamics") .OR. (nuclear_matter == "MDynamics") .OR. (Environ_Type == "DP_MM")
end subroutine checklist
!
!
!
!
!============================================
subroutine dump_driver_parameters_and_tuning
!============================================
implicit none
! local parameters ...
character(len=3) :: month(12)=["Jan","Feb","Mar","Apr","May","Jun","Jul","Aug","Sep","Oct","Nov","Dec"]
! local variables ...
integer :: ioerr , date_time(8)
character(len=3) :: tag , EH_MM
character(len=12) :: number_string , keyword
character(len=80) :: line
open (10, file='log.trunk/driver_parms_and_tuning.log', status='unknown')
call date_and_time(values=date_time)
write(10,29) month(date_time(2)),date_time(3),date_time(1),date_time(5),date_time(6)
write(10,27) np
write(10,28) OMP_GET_MAX_threads()
write(10,'(''<====== ############### ==>'')')
write(10,'(''<==== PARAMETERS ====>'')')
write(10,'(''<== ############### ======>'')')
write(10,*)
write(10,'(" DRIVER :" , A12 )') DRIVER
if( .not. static ) then
if( DRIVER /= "MM_Dynamics" ) then
tag = merge("no ","yes", (DRIVER == "slice_CSDM") .OR. (DRIVER == "slice_FSSH") )
write(10,'(" QMMM :" , A10)' , advance=tag) merge(".true. <==",".false. ",QMMM)
If( tag == "no" ) then
write(10,'(" rnd_seed =" , A11)') merge(" .true. <=="," .false. ",rnd_seed)
write(10,'(t29," DK_of_mixing = " , A6)') DK_of_mixing
end IF
write(10,'(" OPT_parms :" , A10)') merge(".true. <==",".false. ",OPT_parms)
write(10,'(" SPECTRUM :" , A10)') merge(".true. <==",".false. ",SPECTRUM)
write(10,'(" Alpha_Tensor :" , A10)') merge(".true. <==",".false. ",Alpha_Tensor)
tag = merge("no ","yes",GaussianCube)
write(10 , '(" GaussianCube :" , A10)' , advance=tag) merge(".true. <==",".false. ",GaussianCube)
If( GaussianCube ) &
write(10,'(" GaussianCube_step = " , I0)') GaussianCube_step
tag = merge("no ","yes",NetCharge)
write(10 , '(" NetCharge :" , A10)') merge(".true. <==",".false. ",NetCharge)
write(10,'(" DensityMatrix :" , A10)') merge(".true. <==",".false. ",DensityMatrix)
write(10,'(" AutoCorrelation :" , A10)') merge(".true. <==",".false. ",AutoCorrelation)
write(10,'(" VDOS_ :" , A10)') merge(".true. <==",".false. ",VDOS_)
tag = merge("no ","yes",EnvField_)
write(10 , '(" EnvField_ :" , A10)' , advance=tag) merge(".true. <==",".false. ",EnvField_)
If( EnvField_) then
write(10,'(" Environ_Type =" , A6)' , advance=tag) Environ_Type
write(10,'(" / Environ_step = " , I0)') Environ_step
end IF
write(10,'(" Coulomb_ :" , A10)') merge(".true. <==",".false. ",Coulomb_)
write(10,'(" Induced_ :" , A10)') merge(".true. <==",".false. ",Induced_)
write(10,'(" frame_step : " , I0)') frame_step
end if
write(10,'(" ad_hoc :" , A10)') merge(".true. <==",".false. ",ad_hoc)
write(10,'(" restart :" , A10)') merge(".true. <==",".false. ",restart)
write( number_string , '(F12.4)' ) t_f
write(10,'(" t_f : " , A12)') adjustl(number_string)
write(10,'(" n_t : " , I0)') n_t
if( (DRIVER(1:5) == "slice") .or. DRIVER == "q_dynamics" .or. DRIVER == "avrg_confgs") then
write(10,'(" CT_dump_step : " , I0)') CT_dump_step
write(10,'(" n_part : " , I0)') n_part
write(10,'(" hole_state : " , I0)') hole_state
write(10,'(" electron_state : " , I0)') electron_state
end if
write(10,'(" nnx , nny : " , I0,I2)') nnx , nny
write(10,'(" PBC : " , I0,I2,I2)') PBC
write(10,*)
elseif( DRIVER == "Genetic_Alg" ) then
write(10,'(" OPT_parms :" , A10)') merge(".true. <==",".false. ",OPT_parms)
write(10,'(" DP_Moment :" , A10)') merge(".true. <==",".false. ",DP_Moment)
write(10,'(" Alpha_Tensor :" , A10)') merge(".true. <==",".false. ",Alpha_Tensor)
write(10,'(" ad_hoc :" , A10)') merge(".true. <==",".false. ",ad_hoc)
write(10,'(" GaussianCube :" , A10)') merge(".true. <==",".false. ",GaussianCube)
write(10,'(" Pop_Size :" , I0)') Pop_Size
write(10,'(" N_generations :" , I0)') N_generations
write( number_string , '(F8.5)' ) Pop_range
write(10,'(" Pop_range :" , A8)') adjustl(number_string)
write(10,'(" selection_by :" , A8)') adjustl(selection_by)
tag = merge("no ","yes",Mutate_Cross)
write(10 , '(" Mutate_Cross :" , A10)' , advance=tag) merge(".true. <==",".false. ",Mutate_Cross)
If( Mutate_Cross ) &
write(10,'(" Mutation_rate = " , F5.3)') Mutation_rate
write(10,'(" Adaptive_ :" , A10)') merge(".true. <==",".false. ",Adaptive_)
tag = merge("no ","yes",CG_)
write(10,'(" CG_ :" , A10)' , advance=tag) merge(".true. <==",".false. ",CG_ )
If( CG_ ) write(10,'(" Top_Selection = " , I0)') Top_Selection
write(10,'(" profiling :" , A10)') merge(".true. <==",".false. ",profiling)
end if
if( nuclear_matter == "MDynamics" ) then
write(10,'('' '')')
write(10,'(''<====== ############### ==>'')')
write(10,'(''<==== parameters_MM ====>'')')
write(10,'(''<== ############### ======>'')')
write(10,*)
write(10, '(" VDOS_ :" , A10)') merge(".true. <==",".false. ",VDOS_)
tag = merge("no ","yes",driver_MM == "MM_Dynamics")
write(10 , '(" driver_MM : " , A11)' , advance=tag) driver_MM
If( driver_MM == "MM_Dynamics" ) then
write(10,'(" <== thermostat = " , A14)' ) thermostat
If( thermostat /= "Microcanonical" ) then
write( number_string , '(F6.2)' ) temperature
write(10,'(t36,"temperature (K) = " , A6)') adjustl(number_string)
write( number_string , '(F8.5)' ) thermal_relaxation_time
write(10,'(t36,"relax time (ps) = " , A7)') adjustl(number_string)
write( number_string , '(F6.2)' ) pressure
write(10,'(t36,"pressure (atm) = " , A6)') adjustl(number_string)
write( number_string , '(E12.5)' ) pressure_relaxation_time
write(10,'(t36,"pressure_relax time (ps) = " , A7)') merge( adjustl(number_string) , "P-fixed" , pressure_relaxation_time < large )
end If
write(10,'(t36,"read_velocities :" , A10)') merge(".true. <==",".false. ",read_velocities)
end IF
write( number_string , '(F6.2)' ) cutoff_radius
write(10,'(" Wolf_cutoff : " , A6)') adjustl(number_string)
write( number_string , '(F8.5)' ) damping_Wolf
write(10,'(" Wolf_damping : " , A8)') adjustl(number_string)
write(10,'(" MM_input_format : " , A4)') MM_input_format
write(10,'(" MM_log_step : " , I0)') MM_log_step
write(10,'(" MM_frame_step : " , I0)') MM_frame_step
write(10,*)
end if
close (10)
if( ad_hoc ) then
open (10, file='log.trunk/driver_parms_and_tuning.log', status='old', access='append')
write(10,'(''<====== ############### ==>'')')
write(10,'(''<==== TUNING ====>'')')
write(10,'(''<== ############### ======>'')')
write(10,*)
close (10)
if( DRIVER /= "MM_Dynamics" ) then
open (10, file='log.trunk/driver_parms_and_tuning.log', status='old', access='append')
write(10,'("== Electronic Tuning ==")')
write(10,'(/" ad_hoc :" , A10)') merge(".true. <==",".false. ",ad_hoc)
!=========================
open(33, file='card.inpt', status='old', iostat=ioerr)
read_loop: do
read(33,'(A)',iostat=ioerr) line
if ( ioerr /= 0 ) exit read_loop
read(line,*,iostat=ioerr) keyword ! <== keyword = first contiguous string from line
keyword = to_upper_case(keyword)
if( index(keyword,"!") /= 0 ) cycle read_loop
if( keyword == "AD_HOC" ) then
do
read(33,'(A)',iostat=ioerr) line
CALL get_line_apart( line , done , EH_MM )
if( ioerr /= 0 ) exit
if( done ) cycle
if( EH_MM == "QM" ) &
then
write(10,'(t2,A80)') adjustl(line)
end if
!this prevents double reading in the case of blank lines ...
line = "XXXXXXXXXXXXXXXXXXXXXX"
end do
end if
!this prevents double reading in the case of blank lines ...
keyword = "XXXXXXXXXXXXXXXXXXXXXX"
end do read_loop
close(33)
!=========================
CALL system("awk '/univ/ && NR >= 50 && NR <= 85' < $DYNEMOLDIR/tuning.f | awk '!/ !/' >> log.trunk/driver_parms_and_tuning.log")
close(10)
end if
if( nuclear_matter == "MDynamics" ) then
open (10, file='log.trunk/driver_parms_and_tuning.log', status='old', access='append')
write(10,*)
write(10,'("== Nuclear Tuning ==")')
write(10,*)
CALL system("awk '/atom/&&/%/&&/=/' < $DYNEMOLDIR/tuning.f | awk '!/univ/' | awk '!/ !/' | awk '{gsub(/^[ \t]+/,x); print}' >> log.trunk/driver_parms_and_tuning.log")
close(10)
end if
end if
include 'formats.h'
end subroutine dump_driver_parameters_and_tuning
!
!
!
!=================================================
subroutine get_line_apart( line , done , EH_MM )
!=================================================
implicit none
character(*) , intent(in) :: line
logical , intent(out) :: done
character(*) , intent(out) :: EH_MM
! local variables ...
integer :: ioerr
character(len=40) :: command , command1 , command2
done = .false.
read(line,*,iostat=ioerr) command , command1 , command2
command = to_upper_case(command)
If( command(1:6) /= "AD_HOC" ) then
done = .true.
return
endif
EH_MM = command(8:9)
end subroutine get_line_apart
!
!
!
!================================================================
function Checking_Topology( bonds , angs , diheds ) result(TorF)
!================================================================
implicit none
integer , intent(in) :: bonds (:,:)
integer , intent(in) :: angs (:,:)
integer , intent(in) :: diheds(:,:)
logical :: TorF
! local variables ...
integer :: i , x , y , z
integer :: Nbonds , Nangs , Ndiheds , KeyLeft , KeyRight
integer , allocatable :: BondKeys(:) , AngKeys(:)
logical :: flag
Nbonds = size(bonds (:,1))
Nangs = size(angs (:,1))
Ndiheds = size(diheds(:,1))
! checking bonds topology ...
allocate( BondKeys(Nbonds) )
do i = 1 , Nbonds
x = bonds(i,1) ; y = bonds(i,2)
BondKeys(i) = PairingFunction( x , y , verbose = .true. )
end do
! checking angs topology ...
do i = 1 , Nangs
flag = .false.
x = angs(i,1) ; y = angs(i,2)
KeyLeft = PairingFunction(x,y)
If( .not. any(KeyLeft == BondKeys) ) call error_message(i,angs,flag,instance="ang")
x = angs(i,2) ; y = angs(i,3)
KeyRight = PairingFunction(x,y)
If( .not. any(KeyRight == BondKeys) ) call error_message(i,angs,flag,instance="ang")
If( KeyLeft == KeyRight ) call error_message(i,angs,flag,instance="ang")
end do
! checking diheds topology ...
allocate( AngKeys(Nangs) )
do i = 1 , Nangs
x = angs(i,1) ; y = angs(i,2) ; z = angs(i,3)
AngKeys(i) = CantorPairing( x , y , z )
end do
do i = 1 , Ndiheds
flag = .false.
x = diheds(i,1) ; y = diheds(i,2) ; z = diheds(i,3)
KeyLeft = CantorPairing( x , y , z )
If( .not. any(KeyLeft == AngKeys) ) call error_message(i,diheds,flag,instance="dihed")
x = diheds(i,2) ; y = diheds(i,3) ; z = diheds(i,4)
KeyRight = CantorPairing( x , y , z )
If( .not. any(KeyRight == AngKeys) ) call error_message(i,diheds,flag,instance="dihed")
end do
! prepare to leave ...
if( done ) then
TorF = .true. ! <== error detected
close(10)
else
TorF = .false. ! <== NO error detected
end If
end function Checking_Topology
!
!
!
!
!========================================
function CantorPairing(i,j,k) result(R)
! 3-tupling Cantor Function ...
! f(i,j,k) = f(k,j,i)
!========================================
implicit none
integer , intent(in) :: i,j,k
! local variables ...
integer :: R , L , a , b
! Symmetric Pairing for (i,k)-tuple ...
a = max(i,k) ; b = min(i,k)
L = a*(a+1)/2 + b
! Cantor pairing with the center pairing ...
R = (L+j)*(L+j+1)/2 + L
end function CantorPairing
!
!
!
!===============================================
function PairingFunction(i,j,verbose) result(k)
!===============================================
implicit none
integer , intent(in) :: i,j
logical , optional , intent(in) :: verbose
! local variables ...
integer :: k , a , b
If( (i == j) .and. present(verbose) ) then
Print 232, i , j
stop
end If
! the symmetric pairing satisfies f(i,j)=f(j,i) ...
! Symmetric Cantor Pairing ...
!k = (i+j)*(i+j+1)/2 + (i*j)
! Symmetric Pairing ...
a = max(i,j) ; b = min(i,j)
k = a*(a+1)/2 + b
include 'formats.h'
end function PairingFunction
!
!
!
!==================================================
subroutine error_message(i , a , flag , instance )
!==================================================
implicit none
integer , intent(in) :: i
integer , intent(in) :: a(:,:)
logical , intent(inout) :: flag
character(len=*) , intent(in) :: instance
If( .not. done ) open (10, file='log.trunk/Topology.test.log', status='unknown')
done = .true.
If( flag == .true. ) return
select case (instance)
case("ang")
write(10,231) a(i,1) , a(i,2) , a(i,3)
case("dihed")
write(10,233) a(i,1) , a(i,2) , a(i,3) , a(i,4)
end select
flag = .true.
include 'formats.h'
end subroutine error_message
!
!
!
!
end MODULE setup_checklist