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fixing input references..

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svn-origin-rev: 6315
This commit is contained in:
Teodoro Laino 2007-08-28 13:13:23 +00:00
parent e575c7adff
commit dce78a92e1
4 changed files with 289 additions and 5 deletions
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10
src/input_cp2k_mm.F
View file

@ -502,7 +502,7 @@ CONTAINS
IF (.NOT. failure) THEN
CALL section_create(section,name="TORSION",&
description="specifies the torsion potential of the MM system."//&
"Functional Form (CHARMM): K*[1+cos[M*PHI-PHI0]].",&
"Functional Form (CHARMM): K * [ 1 + cos[M*PHI] * cos[PHI0]].",&
n_keywords=1, n_subsections=0, repeats=.TRUE., required=.TRUE.,&
error=error)
@ -530,14 +530,14 @@ CONTAINS
CALL keyword_release(keyword,error=error)
CALL keyword_create(keyword, name="PHI0",&
description="Defines the phase of the potential",&
description="Defines the phase of the potential.",&
usage="PHI0 {real}", required=.TRUE., type_of_var=real_t,&
n_var=1, unit_str="rad", error=error)
CALL section_add_keyword(section,keyword,error=error)
CALL keyword_release(keyword,error=error)
CALL keyword_create(keyword, name="M",&
description="Defines the multiplicity of the potential",&
description="Defines the multiplicity of the potential.",&
usage="M {integer}", required=.TRUE., type_of_var=integer_t,&
n_var=1, error=error)
CALL section_add_keyword(section,keyword,error=error)
@ -585,7 +585,7 @@ CONTAINS
CALL section_create(section,name="BEND",&
description="specifies the bend potential of the MM system."//&
"Functional Form (G96): K*(COS(THETA)-THETA0)^2"//&
"Functional Form (HARMONIC/CHARMM/G87): K*(THETA-THETA0)^2",&
"Functional Form (HARMONIC/CHARMM/G87): 1/2*K*(THETA-THETA0)^2",&
n_keywords=1, n_subsections=1, repeats=.TRUE., required=.TRUE.,&
error=error)
@ -698,7 +698,7 @@ CONTAINS
description="specifies the bond potential the MM system"//&
"Functional Form (QUARTIC): (1/2*K1+[1/3*K2+1/4*K3*|R-R0|]*|R-R0|)(R-R0)^2"//&
"Functional Form (G96): 1/4*K*(R-R0)^2"//&
"Functional Form (HARMONIC|CHARMM|G87): K*(R-R0)^2",&
"Functional Form (HARMONIC|CHARMM|G87): 1/2*K*(R-R0)^2",&
n_keywords=1, n_subsections=0, repeats=.TRUE., required=.TRUE.,&
error=error)

2
tests/Fist/regtest/TEST_FILES
View file

@ -57,3 +57,5 @@ argon_msst_damped.inp 2
h2.inp 7
# parser test
h2_parse.inp 7
# complex torsion potential
TNF2.inp 7

265
tests/Fist/regtest/TNF2.inp Normal file
View file

@ -0,0 +1,265 @@
&FORCE_EVAL
METHOD FIST
&MM
&FORCEFIELD
#####################################################
&BOND
ATOMS C F
KIND CHARMM
K [kjmol*angstrom^-2] 3697.
R0 [angstrom] 1.323
&END BOND
&BOND
ATOMS C S
KIND CHARMM
K [kjmol*angstrom^-2] 1970.
R0 [angstrom] 1.818
&END BOND
&BOND
ATOMS S O
KIND CHARMM
K [kjmol*angstrom^-2] 5331.
R0 [angstrom] 1.442
&END BOND
&BOND
ATOMS S N
KIND CHARMM
K [kjmol*angstrom^-2] 3113.
R0 [angstrom] 1.570
&END BOND
#####################################################
&BEND
ATOMS F C F
K [kjmol*rad^-2] 781.
THETA0 [deg] 107.1
&END BEND
&BEND
ATOMS F C S
K [kjmol*rad^-2] 694.
THETA0 [deg] 111.8
&END BEND
&BEND
ATOMS C S O
K [kjmol*rad^-2] 870.
THETA0 [deg] 102.6
&END BEND
&BEND
ATOMS O S O
K [kjmol*rad^-2] 969.
THETA0 [deg] 118.5
&END BEND
&BEND
ATOMS S N S
K [kjmol*rad^-2] 671.
THETA0 [deg] 125.6
&END BEND
&BEND
ATOMS O S N
K [kjmol*rad^-2] 789.
THETA0 [deg] 113.6
&END BEND
&BEND
ATOMS N S C
K [kjmol*rad^-2] 816.
THETA0 [deg] 100.2
&END BEND
#####################################################
&TORSION
ATOMS F C S O
K [kjmol] .725500
PHI0 [deg] 0.00
M 3
&END TORSION
&TORSION
ATOMS S N S O
K [kjmol] -0.0075
PHI0 [deg] 0.00
M 3
&END TORSION
&TORSION
ATOMS F C S N
K [kjmol] .661
PHI0 [deg] 0.00
M 3
&END TORSION
&TORSION
ATOMS S N S C
K [kjmol] 16.3865
PHI0 [deg] 0.00
M 1
&END TORSION
&TORSION
ATOMS S N S C
K [kjmol] -5.21
PHI0 [deg] 180.00
M 2
&END TORSION
&TORSION
ATOMS S N S C
K [kjmol] -1.5975
PHI0 [deg] 0.00
M 3
&END TORSION
#####################################################
&CHARGE
ATOM F
CHARGE -0.16
&END CHARGE
&CHARGE
ATOM C
CHARGE 0.35
&END CHARGE
&CHARGE
ATOM S
CHARGE 1.02
&END CHARGE
&CHARGE
ATOM O
CHARGE -0.53
&END CHARGE
&CHARGE
ATOM N
CHARGE -0.66
&END CHARGE
#####################################################
&NONBONDED
&LENNARD-JONES
ATOMS F C
EPSILON [kjmol] .98982054939266642808
SIGMA [angstrom] 3.225
RCUT 9.0
&END LENNARD-JONES
&LENNARD-JONES
ATOMS F F
EPSILON [kjmol] .88700000000000000000
SIGMA [angstrom] 2.95
RCUT 9.0
&END LENNARD-JONES
&LENNARD-JONES
ATOMS C C
EPSILON [kjmol] 1.10456000000000000000
SIGMA [angstrom] 3.50
RCUT 9.0
&END LENNARD-JONES
&LENNARD-JONES
ATOMS F S
EPSILON [kjmol] 1.92644958407947961536
SIGMA [angstrom] 3.250
RCUT 9.0
&END LENNARD-JONES
&LENNARD-JONES
ATOMS F O
EPSILON [kjmol] 1.76562020831208204652
SIGMA [angstrom] 2.955
RCUT 9.0
&END LENNARD-JONES
&LENNARD-JONES
ATOMS C S
EPSILON [kjmol] 2.14976255433012880448
SIGMA [angstrom] 3.525
RCUT 9.0
&END LENNARD-JONES
&LENNARD-JONES
ATOMS C O
EPSILON [kjmol] 1.97028992627988635308
SIGMA [angstrom] 3.230
RCUT 9.0
&END LENNARD-JONES
&LENNARD-JONES
ATOMS S S
EPSILON [kjmol] 4.18400000000000000000
SIGMA [angstrom] 3.55
RCUT 9.0
&END LENNARD-JONES
&LENNARD-JONES
ATOMS S O
EPSILON [kjmol] 3.83469934153904691748
SIGMA [angstrom] 3.255
RCUT 9.0
&END LENNARD-JONES
&LENNARD-JONES
ATOMS O O
EPSILON [kjmol] 3.51456000000000000000
SIGMA [angstrom] 2.96
RCUT 9.0
&END LENNARD-JONES
&LENNARD-JONES
ATOMS N N
EPSILON [kjmol] 2.84512000000000000000
SIGMA [angstrom] 3.25
RCUT 9.0
&END LENNARD-JONES
&LENNARD-JONES
ATOMS N C
EPSILON [kjmol] 1.77273961630014914040
SIGMA [angstrom] 3.375
RCUT 9.0
&END LENNARD-JONES
&LENNARD-JONES
ATOMS N F
EPSILON [kjmol] 1.58859102351738095168
SIGMA [angstrom] 3.10
RCUT 9.0
&END LENNARD-JONES
&LENNARD-JONES
ATOMS N S
EPSILON [kjmol] 3.45021478751685834808
SIGMA [angstrom] 3.40
RCUT 9.0
&END LENNARD-JONES
&LENNARD-JONES
ATOMS N O
EPSILON [kjmol] 3.16217408553039660128
SIGMA [angstrom] 3.105
RCUT 9.0
&END LENNARD-JONES
&END NONBONDED
#####################################################
&END FORCEFIELD
&POISSON
&EWALD
EWALD_TYPE spme
ALPHA .44
GMAX 24
O_SPLINE 6
&END EWALD
&END POISSON
&END MM
&SUBSYS
&CELL
ABC 10.0 10.0 10.0
UNIT ANGSTROM
&END CELL
&TOPOLOGY
COORDINATE XYZ
COORD_FILE_NAME ../sample_xyz/TNF2.xyz
CONNECTIVITY GENERATE
&GENERATE
CREATE_MOLECULES
REORDER
&END
&DUMP_PDB
&END
&DUMP_PSF
&END
&END TOPOLOGY
&END SUBSYS
&END FORCE_EVAL
&GLOBAL
FFTLIB FFTSG
PROJECT ionic
RUN_TYPE GEO_OPT
PRINT_LEVEL LOW
&END GLOBAL
&MOTION
&MD
ENSEMBLE NVE
STEPS 10
TIMESTEP 0.5
TEMPERATURE 298
&END MD
&GEOOPT
MAX_ITER 1000
MINIMIZER BFGS
&END
&END MOTION

17
tests/Fist/sample_xyz/TNF2.xyz Normal file
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@ -0,0 +1,17 @@
15
molecular structure
C 2.941257 -1.635788 -0.600313
F 2.086340 -2.551304 -1.077166
S 2.180025 0.116190 -0.654305
O 3.275874 0.999499 -0.216950
N 0.893229 -0.023374 0.333077
S 0.902994 0.323318 1.923455
C 0.384503 2.163043 1.954339
O -0.248675 -0.356946 2.540279
O 2.205461 0.300892 2.612890
O 1.680121 0.219186 -2.035966
F 4.048782 -1.666551 -1.362973
F 3.281998 -1.986955 0.644600
F 0.344238 2.596812 3.227160
F 1.247272 2.930136 1.278641
F -0.833949 2.331990 1.421787