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new syntax for mapping section of free energy methods.. fixing info for dumping

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particles info for several methods.. added 1 regtest..


svn-origin-rev: 6283
This commit is contained in:
Teodoro Laino 2007-08-13 22:53:39 +00:00
parent 51c933b08a
commit d927326fa2
8 changed files with 236 additions and 35 deletions
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2
src/eip_environment.F
View file

@ -287,7 +287,7 @@ CONTAINS
! *** Print the atomic coordinates
CALL write_qs_particle_coordinates(particle_set, cell=cell, &
subsys_section=subsys_section, &
error=error)
label="EIP",error=error)
CALL write_particle_distances(particle_set, cell=cell, &
subsys_section=subsys_section, &
error=error)

74
src/force_env_methods.F
View file

@ -1507,10 +1507,10 @@ END SUBROUTINE mixed_energy_forces
CHARACTER(len=*), PARAMETER :: routineN = 'get_subsys_map_index', &
routineP = moduleN//':'//routineN
INTEGER :: i, ival, j, jval, k, n_rep, &
n_rep_loc, n_rep_sys, stat, &
tmp
INTEGER, DIMENSION(:), POINTER :: index_glo, index_loc
INTEGER :: i, iatom, ival, j, jval, k, &
n_rep, n_rep_loc, n_rep_map, &
n_rep_sys, stat, tmp
INTEGER, DIMENSION(:), POINTER :: index_glo, index_loc, list
LOGICAL :: check, explicit, failure
TYPE(section_vals_type), POINTER :: fragments_loc, fragments_sys, &
map_force_ev, map_full_sys
@ -1542,30 +1542,58 @@ END SUBROUTINE mixed_energy_forces
fragments_sys => section_vals_get_subs_vals(map_full_sys,"FRAGMENT",error=error)
fragments_loc => section_vals_get_subs_vals(map_force_ev,"FRAGMENT",i_rep_section=i,error=error)
!Perform few check on the structure of the input mapping section. as provided by the user
CALL section_vals_get(fragments_loc, explicit=explicit, n_repetition=n_rep_loc, error=error)
CPPrecondition(explicit,cp_failure_level,routineP,error,failure)
CALL section_vals_get(fragments_loc, n_repetition=n_rep_loc, error=error)
CALL section_vals_get(fragments_sys, explicit=explicit, n_repetition=n_rep_sys, error=error)
CPPrecondition(explicit,cp_failure_level,routineP,error,failure)
CPPrecondition(n_rep_sys>=n_rep_loc,cp_failure_level,routineP,error,failure)
!Loop over the fragment of the force_eval
DO i = 1, n_rep_loc
CALL section_vals_val_get(fragments_loc,"_SECTION_PARAMETERS_",i_rep_section=i,i_val=ival,error=error)
CALL section_vals_val_get(fragments_loc,"MAP",i_rep_section=i,i_val=jval,error=error)
! Index corresponding to the mixed_force_eval fragment
DO j = 1, n_rep_sys
CALL section_vals_val_get(fragments_sys,"_SECTION_PARAMETERS_",i_rep_section=j,i_val=tmp,error=error)
IF (tmp==jval) EXIT
END DO
CPPrecondition(j<=n_rep_sys,cp_failure_level,routineP,error,failure)
CALL section_vals_val_get(fragments_loc,"_DEFAULT_KEYWORD_",i_rep_section=i,i_vals=index_loc,error=error)
CALL section_vals_val_get(fragments_sys,"_DEFAULT_KEYWORD_",i_rep_section=j,i_vals=index_glo,error=error)
check = ((index_loc(2)-index_loc(1))==(index_glo(2)-index_glo(1)))
IF (n_rep_loc==0) THEN
NULLIFY(list)
! We expect an easier syntax in this case..
CALL section_vals_val_get(map_force_ev,"DEFINE_FRAGMENTS",i_rep_section=i,n_rep_val=n_rep_map,&
error=error)
check = (n_rep_map/=0)
CPPrecondition(check,cp_failure_level,routineP,error,failure)
! Now let's build the real mapping
DO k = 0, index_loc(2)-index_loc(1)
map_index(index_loc(1)+k) = index_glo(1)+k
CALL section_vals_val_get(map_force_ev,"DEFINE_FRAGMENTS",i_rep_section=i,i_vals=list,&
error=error)
CPPrecondition(SIZE(list)>0,cp_failure_level,routineP,error,failure)
iatom = 0
DO i = 1, SIZE(list)
jval = list(i)
DO j = 1, n_rep_sys
CALL section_vals_val_get(fragments_sys,"_SECTION_PARAMETERS_",i_rep_section=j,i_val=tmp,error=error)
IF (tmp==jval) EXIT
END DO
CALL section_vals_val_get(fragments_sys,"_DEFAULT_KEYWORD_",i_rep_section=j,i_vals=index_glo,error=error)
DO k = 0, index_glo(2)-index_glo(1)
iatom = iatom + 1
CPPrecondition(iatom<=natom,cp_failure_level,routineP,error,failure)
map_index(iatom) = index_glo(1)+k
END DO
END DO
END DO
check = (iatom==natom)
CPPrecondition(check,cp_failure_level,routineP,error,failure)
ELSE
! General syntax..
!Loop over the fragment of the force_eval
DO i = 1, n_rep_loc
CALL section_vals_val_get(fragments_loc,"_SECTION_PARAMETERS_",i_rep_section=i,i_val=ival,error=error)
CALL section_vals_val_get(fragments_loc,"MAP",i_rep_section=i,i_val=jval,error=error)
! Index corresponding to the mixed_force_eval fragment
DO j = 1, n_rep_sys
CALL section_vals_val_get(fragments_sys,"_SECTION_PARAMETERS_",i_rep_section=j,i_val=tmp,error=error)
IF (tmp==jval) EXIT
END DO
CPPrecondition(j<=n_rep_sys,cp_failure_level,routineP,error,failure)
CALL section_vals_val_get(fragments_loc,"_DEFAULT_KEYWORD_",i_rep_section=i,i_vals=index_loc,error=error)
CALL section_vals_val_get(fragments_sys,"_DEFAULT_KEYWORD_",i_rep_section=j,i_vals=index_glo,error=error)
check = ((index_loc(2)-index_loc(1))==(index_glo(2)-index_glo(1)))
CPPrecondition(check,cp_failure_level,routineP,error,failure)
! Now let's build the real mapping
DO k = 0, index_loc(2)-index_loc(1)
map_index(index_loc(1)+k) = index_glo(1)+k
END DO
END DO
END IF
END IF
END SUBROUTINE get_subsys_map_index

10
src/input_cp2k.F
View file

@ -1680,6 +1680,16 @@ END SUBROUTINE create_cpot_section
n_keywords=1, n_subsections=0, repeats=.TRUE., required=.TRUE.,&
error=error)
CALL keyword_create(keyword, name="DEFINE_FRAGMENTS",&
description="Specify the fragments definition of the force_eval through the fragments of the"//&
" force_eval_mixed. This avoids the pedantic definition of the fragments for the force_eval,"//&
" assuming the order of the fragments for the specified force_eval is the same as the sequence "//&
" of integers provided. Easier to USE should be preferred to the specification of the single fragments.",&
usage="DEFINE_FRAGMENTS <INTEGER> .. <INTEGER>", type_of_var=integer_t, n_var=-1,&
error=error)
CALL section_add_keyword(sub2section,keyword,error=error)
CALL keyword_release(keyword,error=error)
CALL keyword_create(keyword, name="_SECTION_PARAMETERS_",&
description="Defines the index of the force_eval for which fragments and mappings are provided",&
usage="<INTEGER>", type_of_var=integer_t, n_var=1, required=.TRUE.,error=error)

2
src/kg_environment.F
View file

@ -295,7 +295,7 @@ CONTAINS
CALL write_total_numbers(atomic_kind_set,particle_set,kg_env%input,error)
! Print the atomic coordinates
CALL write_qs_particle_coordinates(particle_set,cell,subsys_section,error)
CALL write_qs_particle_coordinates(particle_set,cell,subsys_section,label="KIM-GORDON",error=error)
! Print the interatomic distances ***
CALL write_particle_distances(particle_set,cell,subsys_section,error)

7
src/particle_types.F
View file

@ -661,7 +661,7 @@ END SUBROUTINE clone_particle
unit_of_length_name=unit_of_length_name)
WRITE (UNIT=iw,FMT="(/,/,T2,A)")&
"ATOMIC COORDINATES IN "//TRIM(unit_of_length_name)
"MODULE FIST: ATOMIC COORDINATES IN "//TRIM(unit_of_length_name)
WRITE (UNIT=iw,&
FMT="(/,T3,A,7X,2(A1,11X),A1,8X,A8,5X,A6,/)")&
"Atom Kind ATM_TYP","X","Y","Z"," q(eff)"," Mass"
@ -686,7 +686,7 @@ END SUBROUTINE clone_particle
END SUBROUTINE write_fist_particle_coordinates
SUBROUTINE write_qs_particle_coordinates(particle_set,cell,subsys_section,error)
SUBROUTINE write_qs_particle_coordinates(particle_set,cell,subsys_section,label,error)
! Purpose: Write the atomic coordinates to the output unit.
! History: - Creation (05.06.2000,MK)
@ -695,6 +695,7 @@ END SUBROUTINE clone_particle
POINTER :: particle_set
TYPE(cell_type), POINTER :: cell
TYPE(section_vals_type), POINTER :: subsys_section
CHARACTER(LEN=*), INTENT(IN) :: label
TYPE(cp_error_type), INTENT(INOUT) :: error
CHARACTER(LEN=2) :: element_symbol
@ -715,7 +716,7 @@ END SUBROUTINE clone_particle
unit_of_length_name=unit_of_length_name)
WRITE (UNIT=iw,FMT="(/,/,T2,A)")&
"ATOMIC COORDINATES IN "//TRIM(unit_of_length_name)
"MODULE "//TRIM(label)//": ATOMIC COORDINATES IN "//TRIM(unit_of_length_name)
WRITE (UNIT=iw,&
FMT="(/,T3,A,7X,2(A1,11X),A1,8X,A8,5X,A6,/)")&
"Atom Kind Element","X","Y","Z"," Z(eff)"," Mass"

11
src/qs_environment.F
View file

@ -26,21 +26,19 @@
!******************************************************************************
MODULE qs_environment
USE bibliography, ONLY: cite_reference, Iannuzzi2007
USE atomic_kind_list_types, ONLY: atomic_kind_list_create,&
atomic_kind_list_release,&
atomic_kind_list_type
USE atomic_kind_types, ONLY: atomic_kind_type,&
check_atomic_kind_set,&
get_atomic_kind,&
get_atomic_kind_set,&
init_atomic_kind_set,&
init_gapw_basis_set,&
read_atomic_kind_set,&
write_atomic_kind_set,&
write_gto_basis_sets
USE basis_set_types, ONLY: get_gto_basis_set,&
gto_basis_set_type
USE bibliography, ONLY: Iannuzzi2007,&
cite_reference
USE cell_types, ONLY: cell_clone,&
cell_create,&
cell_release,&
@ -212,6 +210,7 @@ CONTAINS
CHARACTER(len=*), PARAMETER :: routineN = 'qs_init', &
routineP = moduleN//':'//routineN
INTEGER :: max_set, natom
LOGICAL :: do_et, do_hf, harris_flag, &
my_qmmm, my_qmmm_periodic, &
use_ref_cell
@ -233,8 +232,6 @@ CONTAINS
POINTER :: particle_set
TYPE(section_vals_type), POINTER :: cell_section, colvar_section, &
et_coupling_section, harris_section, hf_section, kind_section
INTEGER :: iatom, natom, nseta, iset,&
max_set
NULLIFY(my_subsystem, molecule_kind_set, molecule_set, atomic_kind_set,&
particle_set,atomic_kinds,particles,mols,mol_kinds,my_cell,my_cell_ref,&
@ -921,7 +918,7 @@ CONTAINS
CALL write_total_numbers(atomic_kind_set,particle_set,qs_env%input,error)
! Print the atomic coordinates
CALL write_qs_particle_coordinates(particle_set,cell,subsys_section,error)
CALL write_qs_particle_coordinates(particle_set,cell,subsys_section,label="QUICKSTEP",error=error)
! Print the interatomic distances
CALL write_particle_distances(particle_set,cell,subsys_section,error)

164
tests/FE/regtest-1/Solv_alch_chng_simpl.inp Normal file
View file

@ -0,0 +1,164 @@
&MULTIPLE_FORCE_EVALS
FORCE_EVAL_ORDER 2 3
MULTIPLE_SUBSYS T
&END
&FORCE_EVAL
METHOD MIXED
&MIXED
MIXING_TYPE GENMIX
&GENERIC
# X: Energy force_eval 2
# Y: Energy force_eval 3
MIXING_FUNCTION k*X+(1.0-k)*Y
VARIABLES X Y
PARAMETERS k
VALUES 0.5
&END
&MAPPING
&FORCE_EVAL_MIXED
&FRAGMENT 1
1 6
&END
&FRAGMENT 2
7 16
&END
&FRAGMENT 3
17 22
&END
&FRAGMENT 4
23 33
&END
&FRAGMENT 5
34 1851
&END
&END
&FORCE_EVAL 1
DEFINE_FRAGMENTS 1 2 3 5
&END
&FORCE_EVAL 2
DEFINE_FRAGMENTS 1 4 3 5
&END
&END
&END
&SUBSYS
&TOPOLOGY
CONNECTIVITY OFF
COORDINATE PDB
COORD_FILE_NAME full.pdb
&END TOPOLOGY
&CELL
ABC 30.9751780 30.8599250 30.7278700
UNIT ANGSTROM
&END CELL
&END SUBSYS
&END FORCE_EVAL
&FORCE_EVAL
METHOD FIST
&MM
&FORCEFIELD
PARM_FILE_NAME ala.pot
parmtype CHM
&SPLINE
EMAX_SPLINE 100000000.0
&END
&END FORCEFIELD
&POISSON
&EWALD
EWALD_TYPE spme
ALPHA .5
GMAX 36
O_SPLINE 6
&END EWALD
&END POISSON
&END MM
&SUBSYS
&TOPOLOGY
CONNECTIVITY PSF
CONN_FILE_NAME ala.psf
COORDINATE PDB
COORD_FILE_NAME ala.pdb
&END TOPOLOGY
&CELL
ABC 30.9751780 30.8599250 30.7278700
UNIT ANGSTROM
&END CELL
&END SUBSYS
&END FORCE_EVAL
&FORCE_EVAL
METHOD FIST
&MM
&FORCEFIELD
PARM_FILE_NAME ser.pot
parmtype CHM
&SPLINE
EMAX_SPLINE 100000000.0
&END
&END FORCEFIELD
&POISSON
&EWALD
EWALD_TYPE spme
ALPHA .5
GMAX 36
O_SPLINE 6
&END EWALD
&END POISSON
&END MM
&SUBSYS
&TOPOLOGY
CONNECTIVITY PSF
CONN_FILE_NAME ser.psf
COORDINATE PDB
COORD_FILE_NAME ser.pdb
&END TOPOLOGY
&CELL
ABC 30.9751780 30.8599250 30.7278700
UNIT ANGSTROM
&END CELL
&END SUBSYS
&END FORCE_EVAL
&GLOBAL
FFTLIB FFTSG
PROJECT DDG_SOLVATION
RUN_TYPE MD
PRINT_LEVEL LOW
&END GLOBAL
&MOTION
&MD
ENSEMBLE NVE
STEPS 20
TIMESTEP 0.5
TEMPERATURE 200.0
&NOSE
LENGTH 3
YOSHIDA 3
TIMECON 300
MTS 2
&END NOSE
&PRINT
&ENERGY
EACH 1
&END
&END
&END MD
&PRINT
&TRAJECTORY
EACH 100
&END
&VELOCITIES OFF
&END
&FORCES OFF
&END
&RESTART_HISTORY OFF
&END
&RESTART
EACH 10
&END
&END
&FREE_ENERGY
METHOD AC
&ALCHEMICAL_CHANGE
PARAMETER k
&END
&END
&END MOTION

1
tests/FE/regtest-1/TEST_FILES
View file

@ -6,3 +6,4 @@
#
Solv_alch_chng.inp 2
Solv_alch_chng_dist.inp 2
Solv_alch_chng_simpl.inp 2