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Bug fix for SE analytical derivatives when TAPER was ON. Bug fix for SE-QMMM: never

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switch on the TAPER function.. added 1 regtest


svn-origin-rev: 6306
This commit is contained in:
Teodoro Laino 2007-08-18 21:03:07 +00:00
parent 10f17602f0
commit 8918f632fc
7 changed files with 284 additions and 9 deletions
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20
src/semi_empirical_int_ana.F
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@ -1050,18 +1050,22 @@ CONTAINS
END IF
ssss = ri(1)
! Tapering function
ft = taper ( rij )
core(:,:) = ft*core(:,:)
ssss = ft*ssss
ft = 1.0_dp
dft= 0.0_dp
IF (itype/=0) THEN
ft = taper ( rij )
dft= dtaper_ana ( rij )
END IF
! If no orbitals are present on the atom let's zero the integral contribution
IF (sepi%natorb == -1) core(:,1) = 0.0_dp
IF (sepj%natorb == -1) core(:,2) = 0.0_dp
!
dssss = dri(1)
! Tapering function
dft= dtaper_ana ( rij )
! First derivatives..
dssss = dri(1)
dcore(:,:) = ft*dcore(:,:)+dft*core(:,:)
dssss = ft*dssss+dft*ssss
dssss = ft*dssss+dft*ssss
! Then values of functions
core(:,:) = ft*core(:,:)
ssss = ft*ssss
! If no orbitals are present on the atom let's zero the integral contribution
IF (sepi%natorb == -1) dcore(:,1) = 0.0_dp
IF (sepj%natorb == -1) dcore(:,2) = 0.0_dp

3
src/semi_empirical_integrals.F
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@ -1394,7 +1394,8 @@ CONTAINS
ssss = ri(1)
! Tapering function
ft = taper ( rij )
ft = 1.0_dp
IF (itype /=0) ft = taper ( rij )
core(:,:) = ft*core(:,:)
ssss = ft*ssss
! If no orbitals are present on the atom let's zero the integral contribution

1
tests/QMMM/SE/regtest/TEST_FILES
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@ -16,3 +16,4 @@ water_3_full.inp 7
#QMMM Walls
water_3_NOwalls.inp 2
water_3_walls.inp 2
zwitt.inp 2

100
tests/QMMM/SE/regtest/zwitt.inp Normal file
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@ -0,0 +1,100 @@
&FORCE_EVAL
METHOD QMMM
&DFT
&QS
METHOD AM1
EXTRAPOLATION USE_PREV_WF
&END QS
&SCF
SCF_GUESS ATOMIC
MAX_SCF 50
EPS_SCF 1.0E-6
&OT
PRECONDITIONER NONE
MINIMIZER DIIS
&END
&OUTER_SCF
MAX_SCF 5
EPS_SCF 1.0E-6
&END
&END SCF
&END DFT
&MM
&FORCEFIELD
parm_file_name ../sample_pot/zwitt.pot
parmtype CHM
&END FORCEFIELD
&POISSON
&EWALD
EWALD_TYPE spme
ALPHA .4
GMAX 60
&END EWALD
&END POISSON
&END MM
&QMMM
&CELL
ABC 15.0 15.0 15.0
UNIT ANGSTROM
&END CELL
ECOUPL COULOMB
NOCENTER
&MM_KIND H1
RADIUS 0.44
&END MM_KIND
&MM_KIND H2
RADIUS 0.44
&END MM_KIND
&MM_KIND O
RADIUS 0.78
&END MM_KIND
&QM_KIND H
MM_INDEX 2 3 4 7
&END QM_KIND
&QM_KIND O
MM_INDEX 8
&END QM_KIND
&QM_KIND N
MM_INDEX 1 6
&END QM_KIND
&QM_KIND C
MM_INDEX 5
&END QM_KIND
&END QMMM
&SUBSYS
&CELL
ABC 50.0 50.0 50.0
UNIT ANGSTROM
&END CELL
&TOPOLOGY
CONN_FILE ../sample_psf/zwitt.psf
CONNECTIVITY PSF
COORD_FILE_NAME ../sample_pdb/zwitt.pdb
COORDINATE PDB
&END TOPOLOGY
&END SUBSYS
&END FORCE_EVAL
&GLOBAL
FFTLIB FFTSG
PRINT_LEVEL LOW
PROJECT DEBUG
RUN_TYPE MD
&END GLOBAL
&MOTION
&MD
ENSEMBLE NVE
STEPS 5
TIMESTEP 0.5
TEMPERATURE 300
&END MD
&PRINT
&TRAJECTORY
ADD_LAST NO
&END
&VELOCITIES OFF
&END
&END
&END MOTION

15
tests/QMMM/SE/sample_pdb/zwitt.pdb Normal file
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@ -0,0 +1,15 @@
CRYST1 34.781 35.010 35.149 90.00 90.00 90.00 P 1 1
ATOM 1 N1 MOL M 1 18.347 16.987 18.758 1.00 0.00 ML01 N
ATOM 2 H1 MOL M 1 19.231 16.392 18.981 1.00 0.00 ML01 H
ATOM 3 H2 MOL M 1 17.567 16.604 19.364 1.00 0.00 ML01 H
ATOM 4 H3 MOL M 1 18.496 17.955 19.163 1.00 0.00 ML01 H
ATOM 5 C1 MOL M 1 18.047 17.026 17.206 1.00 0.00 ML01 C
ATOM 6 N2 MOL M 1 18.253 15.958 16.315 1.00 0.00 ML01 N
ATOM 7 H4 MOL M 1 18.060 15.850 15.299 1.00 0.00 ML01 H
ATOM 8 O1 MOL M 1 17.507 18.020 16.842 1.00 0.00 ML01 O
ATOM 54 O WAT M 17 2.133 35.301 11.605 1.00 0.00 ML02 O
ATOM 55 H1 WAT M 17 1.968 34.389 11.774 1.00 0.00 ML02 H
ATOM 56 H2 WAT M 17 1.664 35.484 10.785 1.00 0.00 ML02 H
ATOM 60 O WAT M 19 32.501 32.805 6.785 1.00 0.00 ML02 O
ATOM 61 H1 WAT M 19 31.756 33.342 6.964 1.00 0.00 ML02 H
ATOM 62 H2 WAT M 19 32.473 32.647 5.803 1.00 0.00 ML02 H

104
tests/QMMM/SE/sample_pot/zwitt.pot Normal file
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@ -0,0 +1,104 @@
*>>>>>>> AMBER FF Converted into CHARMM FF style <<<<<<<
*>>>>>>> Generated on :: 20070525 192950.667 +0200 by :: teo <<<<<<<
*>>>>>>> pcihpc07 <<<<<<<
*>>>>>>> Leap Title :: MOL <<<<<<<
*>>>>>>> Send all comments related to the FFs conversion to <<<<<<<
*>>>>>>> teodoro.laino@gmail.com <<<<<<<
BONDS
!
!V(bond) = Kb(b - b0)**2
!
!Kb: kcal/mole/A**2
!b0: A
!
!atom type Kb b0
!
n4 hn1 369.000000000 1.033000000
n2 hn2 375.500000000 1.029000000
HW OW 553.000000000 0.957200000
HW HW 553.000000000 1.513600000
n4 c 255.500000000 1.546000000
c n2 374.600000000 1.420000000
c o 648.000000000 1.214000000
ANGLES
!
!V(angle) = Ktheta(Theta - Theta0)**2
!
!V(Urey-Bradley) = Kub(S - S0)**2
!
!Ktheta: kcal/mole/rad**2
!Theta0: degrees
!Kub: kcal/mole/A**2 (Urey-Bradley)
!S0: A
!
!atom types Ktheta Theta0 Kub S0
!
hn1 n4 hn1 40.500000000 108.110046161
hn1 n4 c 44.700000000 110.860047626
c n2 hn2 51.500000000 126.500054215
n4 c n2 64.700000000 114.640049017
n4 c o 69.600000000 118.830050985
n2 c o 73.000000000 122.500052501
DIHEDRALS
!
!V(dihedral) = Kchi(1 + cos(n(chi) - delta))
!
!Kchi: kcal/mole
!n: multiplicity
!delta: degrees
!
!atom types Kchi n delta
!
n4 c n2 hn2 4.150000000 2 180.000077144
hn1 n4 c n2 0.188888889 3 0.000000000
hn1 n4 c o 0.188888889 3 0.000000000
hn2 n2 c o 4.150000000 2 180.000077144
n4 n2 c o 10.500000000 2 180.000077144
IMPROPER
!
!V(improper) = Kpsi(psi - psi0)**2
!
!Kpsi: kcal/mole/rad**2
!psi0: degrees
!note that the second column of numbers (0) is ignored
!
!atom types Kpsi psi0
!
NONBONDED
!
!V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6]
!
!epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j)
!Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j
!
!atom ignored epsilon Rmin/2 ignored eps,1-4 Rmin/2,1-4
!
n4 0.000000000 0.170000000 1.824000000
hn1 0.000000000 0.015700000 0.600000000
c 0.000000000 0.086000000 1.908000000
n2 0.000000000 0.170000000 1.824000000
hn2 0.000000000 0.015700000 0.600000000
o 0.000000000 0.210000000 1.661200000
OW 0.000000000 0.152000000 1.768300000
HW 0.000000000 0.000000000 0.000000000
END
!
! This Section can be cutted & pasted into the Fist input file..
!
CHARGES
n4 -0.353000000
hn1 0.283000000
c 0.801000000
n2 -1.024000000
hn2 0.408000000
o -0.681000000
OW -0.834000000
HW 0.417000000
END CHARGES

50
tests/QMMM/SE/sample_psf/zwitt.psf Normal file
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@ -0,0 +1,50 @@
PSF EXT
1 !NTITLE
Conversion from AMBER PARMTOP ::MOL
14 !NATOM
1 MOL01 1 MOL N1 n4 -0.353000 14.010 0
2 MOL01 1 MOL H1 hn1 0.283000 1.008 0
3 MOL01 1 MOL H2 hn1 0.283000 1.008 0
4 MOL01 1 MOL H3 hn1 0.283000 1.008 0
5 MOL01 1 MOL C1 c 0.801000 12.010 0
6 MOL01 1 MOL N2 n2 -1.024000 14.010 0
7 MOL01 1 MOL H4 hn2 0.408000 1.008 0
8 MOL01 1 MOL O1 o -0.681000 16.000 0
9 MOL02 2 WAT O OW -0.834000 16.000 0
10 MOL02 2 WAT H1 HW 0.417000 1.008 0
11 MOL02 2 WAT H2 HW 0.417000 1.008 0
12 MOL02 3 WAT O OW -0.834000 16.000 0
13 MOL02 3 WAT H1 HW 0.417000 1.008 0
14 MOL02 3 WAT H2 HW 0.417000 1.008 0
13 !NBOND
1 2 1 3 1 4 6 7
10 9 11 9 11 10 13 12
14 12 14 13 1 5 5 6
5 8
10 !NTHETA
2 1 3 2 1 4 2 1 5
3 1 4 3 1 5 4 1 5
5 6 7 1 5 6 1 5 8
6 5 8
9 !NPHI
1 5 6 7 2 1 5 6
2 1 5 8 3 1 5 6
3 1 5 8 4 1 5 6
4 1 5 8 7 6 5 8
1 6 5 8
0 !NIMPHI
0 !NDON
0 !NACC
0 !NNB
0 !NGRP