[gmx-developers] short range energies
Mehmet Suezen
suzen at theochem.tu-muenchen.de
Fri Mar 22 19:17:04 CET 2002
David van der Spoel wrote:
> >May be it is related, does return value of nbf_index in src/mdlib/ns.c
> >affect energy calculation? Appears to be ? And what one must expect
> >behaviour of this returns? it was not the case for me.
> >
> >since that file has an error statement;
> >"Call your Gromacs dealer for assistance"
>
> and also a comment:
> * No error checking here!
>
> maybe you should also print the result of nbf_index routine, and verify
> that it points to your routine.
after verifing that, nbf_index and do_fnbf functions called correct
inner loop id at fnbf.c, except then lj potential other potentials (bham
and bhamlj) still giving
zero energy. any idea !. log file that has beed produced in my tests
attached.
cheerz,
Mehmet
-------------- next part --------------
frnbfp at force.c 0
functype[0] at force.c 14
functype[1] at force.c 14
functype[2] at force.c 14
functype[3] at force.c 14
frbBHAM at force.c 0
frbBHAMLJ at force.c 0
logicals at mknbfp at force.c BHAM 1 BHAMLJ 0
idef>iparams at force.c par 0 is 84170000000.000000
idef>iparams at force.c par 0 is 152.207000
idef>iparams at force.c par 0 is 0.002248
idef>iparams at force.c par 1 is 1034469.617000
idef>iparams at force.c par 1 is 47.959330
idef>iparams at force.c par 1 is 0.006825
idef>iparams at force.c par 2 is 1034469.617000
idef>iparams at force.c par 2 is 47.959330
idef>iparams at force.c par 2 is 0.006825
idef>iparams at force.c par 3 is 169512.294000
idef>iparams at force.c par 3 is 28.464078
idef>iparams at force.c par 3 is 0.020719
fr>bBHAM at force.c after mk_nbfp call 1
fr>bBHAMLJ at force.c after mk_nbfp call 0
ener[i] at mdrunner.c 0.000000 and i is 0
ener[i] at mdrunner.c 0.000000 and i is 1
ener[i] at mdrunner.c 0.000000 and i is 2
ener[i] at mdrunner.c 0.000000 and i is 3
ener[i] at mdrunner.c 0.000000 and i is 4
ener[i] at mdrunner.c 0.000000 and i is 5
ener[i] at mdrunner.c 0.000000 and i is 6
ener[i] at mdrunner.c 0.000000 and i is 7
ener[i] at mdrunner.c 0.000000 and i is 8
ener[i] at mdrunner.c 0.000000 and i is 9
ener[i] at mdrunner.c 0.000000 and i is 10
ener[i] at mdrunner.c 0.000000 and i is 11
ener[i] at mdrunner.c 0.000000 and i is 12
ener[i] at mdrunner.c 0.000000 and i is 13
ener[i] at mdrunner.c 0.000000 and i is 14
ener[i] at mdrunner.c 0.000000 and i is 15
ener[i] at mdrunner.c 0.000000 and i is 16
ener[i] at mdrunner.c 0.000000 and i is 17
ener[i] at mdrunner.c 0.000000 and i is 18
ener[i] at mdrunner.c 0.000000 and i is 19
ener[i] at mdrunner.c 0.000000 and i is 20
ener[i] at mdrunner.c 0.000000 and i is 21
ener[i] at mdrunner.c 0.000000 and i is 22
ener[i] at mdrunner.c 0.000000 and i is 23
ener[i] at mdrunner.c 0.000000 and i is 24
ener[i] at mdrunner.c 0.000000 and i is 25
ener[i] at mdrunner.c 0.000000 and i is 26
ener[i] at mdrunner.c 0.000000 and i is 27
ener[i] at mdrunner.c 0.000000 and i is 28
ener[i] at mdrunner.c 0.000000 and i is 29
ener[i] at mdrunner.c 0.000000 and i is 30
ener[i] at mdrunner.c 0.000000 and i is 31
ener[i] at mdrunner.c 0.000000 and i is 32
ener[i] at mdrunner.c 0.000000 and i is 33
ener[i] at mdrunner.c 0.000000 and i is 34
ener[i] at mdrunner.c 0.000000 and i is 35
top->idef.functype[0] at runner.c 14
top->idef.functype[1] at runner.c 14
top->idef.functype[2] at runner.c 14
top->idef.functype[3] at runner.c 14
boolens bLR 0 bLJLR 0 bBHAM 1 bBHAMLJ 0 b14 0 at runner.c
after set_pot_bools at init_md of runner.c bBHAM 1 bBHAMLJ 0 bLJLR 0
ener[i] at md.c 0.000000 and i is 0
ener[i] at md.c 0.000000 and i is 1
ener[i] at md.c 0.000000 and i is 2
ener[i] at md.c 0.000000 and i is 3
ener[i] at md.c 0.000000 and i is 4
ener[i] at md.c 0.000000 and i is 5
ener[i] at md.c 0.000000 and i is 6
ener[i] at md.c 0.000000 and i is 7
ener[i] at md.c 0.000000 and i is 8
ener[i] at md.c 0.000000 and i is 9
ener[i] at md.c 0.000000 and i is 10
ener[i] at md.c 0.000000 and i is 11
ener[i] at md.c 0.000000 and i is 12
ener[i] at md.c 0.000000 and i is 13
ener[i] at md.c 0.000000 and i is 14
ener[i] at md.c 0.000000 and i is 15
ener[i] at md.c 0.000000 and i is 16
ener[i] at md.c 0.000000 and i is 17
ener[i] at md.c 0.000000 and i is 18
ener[i] at md.c 0.000000 and i is 19
ener[i] at md.c 0.000000 and i is 20
ener[i] at md.c 0.000000 and i is 21
ener[i] at md.c 0.000000 and i is 22
ener[i] at md.c 0.000000 and i is 23
ener[i] at md.c 0.000000 and i is 24
ener[i] at md.c 0.000000 and i is 25
ener[i] at md.c 0.000000 and i is 26
ener[i] at md.c 0.000000 and i is 27
ener[i] at md.c 0.000000 and i is 28
ener[i] at md.c 0.000000 and i is 29
ener[i] at md.c 0.000000 and i is 30
ener[i] at md.c 0.000000 and i is 31
ener[i] at md.c 0.000000 and i is 32
ener[i] at md.c 0.000000 and i is 33
ener[i] at md.c 0.000000 and i is 34
ener[i] at md.c 0.000000 and i is 35
epot[i] at sim_util.c reset_energies() 0.000000 and i is 0
epot[i] at sim_util.c reset_energies() 0.000000 and i is 1
epot[i] at sim_util.c reset_energies() 0.000000 and i is 2
epot[i] at sim_util.c reset_energies() 0.000000 and i is 3
epot[i] at sim_util.c reset_energies() 0.000000 and i is 4
epot[i] at sim_util.c reset_energies() 0.000000 and i is 5
epot[i] at sim_util.c reset_energies() 0.000000 and i is 6
epot[i] at sim_util.c reset_energies() 0.000000 and i is 7
epot[i] at sim_util.c reset_energies() 0.000000 and i is 8
epot[i] at sim_util.c reset_energies() 0.000000 and i is 9
epot[i] at sim_util.c reset_energies() 0.000000 and i is 10
epot[i] at sim_util.c reset_energies() 0.000000 and i is 11
epot[i] at sim_util.c reset_energies() 0.000000 and i is 12
epot[i] at sim_util.c reset_energies() 0.000000 and i is 13
epot[i] at sim_util.c reset_energies() 0.000000 and i is 14
epot[i] at sim_util.c reset_energies() 0.000000 and i is 15
epot[i] at sim_util.c reset_energies() 0.000000 and i is 16
epot[i] at sim_util.c reset_energies() 0.000000 and i is 17
epot[i] at sim_util.c reset_energies() 0.000000 and i is 18
epot[i] at sim_util.c reset_energies() 0.000000 and i is 19
epot[i] at sim_util.c reset_energies() 0.000000 and i is 20
epot[i] at sim_util.c reset_energies() 0.000000 and i is 21
epot[i] at sim_util.c reset_energies() 0.000000 and i is 22
epot[i] at sim_util.c reset_energies() 0.000000 and i is 23
epot[i] at sim_util.c reset_energies() 0.000000 and i is 24
epot[i] at sim_util.c reset_energies() 0.000000 and i is 25
epot[i] at sim_util.c reset_energies() 0.000000 and i is 26
epot[i] at sim_util.c reset_energies() 0.000000 and i is 27
epot[i] at sim_util.c reset_energies() 0.000000 and i is 28
epot[i] at sim_util.c reset_energies() 0.000000 and i is 29
epot[i] at sim_util.c reset_energies() 0.000000 and i is 30
epot[i] at sim_util.c reset_energies() 0.000000 and i is 31
epot[i] at sim_util.c reset_energies() 0.000000 and i is 32
epot[i] at sim_util.c reset_energies() 0.000000 and i is 33
epot[i] at sim_util.c reset_energies() 0.000000 and i is 34
epot[i] at sim_util.c reset_energies() 0.000000 and i is 35
at ns.c frbBHAM 1 frbBHAMLJ 0 at bvdw
eNR_INL0500 12
eNR_INL1500 33
eNR_INL0400 8
eNR_INL0300 4
eNR_INL0200 2
eNR_INL1200 21
eNR_INL0100 0
eNR_INL1100 17
===================================================
innerloop index is 8 and nn 21
bcoul 1 bvdw 1 at ns.c
innerloop nn is 21 at ns.c ivdw is 2 icoul is 1
===================================================
at ns.c frbBHAM 1 frbBHAMLJ 0 at bvdw
eNR_INL0500 12
eNR_INL1500 33
eNR_INL0400 8
eNR_INL0300 4
eNR_INL0200 2
eNR_INL1200 21
eNR_INL0100 0
eNR_INL1100 17
===================================================
innerloop index is 2 and nn 2
bcoul 0 bvdw 1 at ns.c
innerloop nn is 2 at ns.c ivdw is 2 icoul is 0
===================================================
at ns.c frbBHAM 1 frbBHAMLJ 0 at bvdw
eNR_INL0500 12
eNR_INL1500 33
eNR_INL0400 8
eNR_INL0300 4
eNR_INL0200 2
eNR_INL1200 21
eNR_INL0100 0
eNR_INL1100 17
===================================================
innerloop index is 6 and nn 13
bcoul 1 bvdw 0 at ns.c
innerloop nn is 13 at ns.c ivdw is 0 icoul is 1
===================================================
at ns.c frbBHAM 1 frbBHAMLJ 0 at bvdw
eNR_INL0500 12
eNR_INL1500 33
eNR_INL0400 8
eNR_INL0300 4
eNR_INL0200 2
eNR_INL1200 21
eNR_INL0100 0
eNR_INL1100 17
===================================================
innerloop index is 8 and nn 22
bcoul 1 bvdw 1 at ns.c
innerloop nn is 22 at ns.c ivdw is 2 icoul is 1
===================================================
at ns.c frbBHAM 1 frbBHAMLJ 0 at bvdw
eNR_INL0500 12
eNR_INL1500 33
eNR_INL0400 8
eNR_INL0300 4
eNR_INL0200 2
eNR_INL1200 21
eNR_INL0100 0
eNR_INL1100 17
===================================================
innerloop index is 2 and nn 3
bcoul 0 bvdw 1 at ns.c
innerloop nn is 3 at ns.c ivdw is 2 icoul is 0
===================================================
at ns.c frbBHAM 1 frbBHAMLJ 0 at bvdw
eNR_INL0500 12
eNR_INL1500 33
eNR_INL0400 8
eNR_INL0300 4
eNR_INL0200 2
eNR_INL1200 21
eNR_INL0100 0
eNR_INL1100 17
===================================================
innerloop index is 6 and nn 14
bcoul 1 bvdw 0 at ns.c
innerloop nn is 14 at ns.c ivdw is 0 icoul is 1
===================================================
at ns.c frbBHAM 1 frbBHAMLJ 0 at bvdw
eNR_INL0500 12
eNR_INL1500 33
eNR_INL0400 8
eNR_INL0300 4
eNR_INL0200 2
eNR_INL1200 21
eNR_INL0100 0
eNR_INL1100 17
===================================================
innerloop index is 8 and nn 23
bcoul 1 bvdw 1 at ns.c
innerloop nn is 23 at ns.c ivdw is 2 icoul is 1
===================================================
at ns.c frbBHAM 1 frbBHAMLJ 0 at bvdw
eNR_INL0500 12
eNR_INL1500 33
eNR_INL0400 8
eNR_INL0300 4
eNR_INL0200 2
eNR_INL1200 21
eNR_INL0100 0
eNR_INL1100 17
===================================================
innerloop index is 6 and nn 15
bcoul 1 bvdw 0 at ns.c
innerloop nn is 15 at ns.c ivdw is 0 icoul is 1
===================================================
at ns.c frbBHAM 1 frbBHAMLJ 0 at bvdw
eNR_INL0500 12
eNR_INL1500 33
eNR_INL0400 8
eNR_INL0300 4
eNR_INL0200 2
eNR_INL1200 21
eNR_INL0100 0
eNR_INL1100 17
===================================================
innerloop index is 8 and nn 24
bcoul 1 bvdw 1 at ns.c
innerloop nn is 24 at ns.c ivdw is 2 icoul is 1
===================================================
at ns.c frbBHAM 1 frbBHAMLJ 0 at bvdw
eNR_INL0500 12
eNR_INL1500 33
eNR_INL0400 8
eNR_INL0300 4
eNR_INL0200 2
eNR_INL1200 21
eNR_INL0100 0
eNR_INL1100 17
===================================================
innerloop index is 6 and nn 16
bcoul 1 bvdw 0 at ns.c
innerloop nn is 16 at ns.c ivdw is 0 icoul is 1
===================================================
i is 0 bHaveLJ at nc.c 1 and frBHAM 1 frBHAMLJ 0
i is 0 bHaveLJ at nc.c 1 and frBHAM 1 frBHAMLJ 0
i is 1 bHaveLJ at nc.c 1 and frBHAM 1 frBHAMLJ 0
i is 1 bHaveLJ at nc.c 1 and frBHAM 1 frBHAMLJ 0
bBHAM 1 bBHAMLJ 0 at force.c Call the short range functions
before call do_fnbf bBHAM force.c
before call do_fnbf egBHAM force.c grpsestat -1.993435
before call do_fnbf egCOUL force.c grpsestat 0.000000
in fnbf.c value of nrnb_ind 21
in fnbf.c INL1200
after call do_fnbf bBHAM force.c
in tgroup sum_epot() epot[F_LR] 0.000000 epot[F_BHAM] 0.000000 epot[F_BHAMLJ] 0.000000
ener[i] at md.c 0.000000 and i is 0
ener[i] at md.c 0.000000 and i is 1
ener[i] at md.c 0.000000 and i is 2
ener[i] at md.c 0.000000 and i is 3
ener[i] at md.c 0.000000 and i is 4
ener[i] at md.c 0.000000 and i is 5
ener[i] at md.c 0.000000 and i is 6
ener[i] at md.c 0.000000 and i is 7
ener[i] at md.c 0.000000 and i is 8
ener[i] at md.c 0.000000 and i is 9
ener[i] at md.c 0.000000 and i is 10
ener[i] at md.c 0.000000 and i is 11
ener[i] at md.c 0.000000 and i is 12
ener[i] at md.c 0.000000 and i is 13
ener[i] at md.c 0.000000 and i is 14
ener[i] at md.c 0.000000 and i is 15
ener[i] at md.c 0.000000 and i is 16
ener[i] at md.c 0.000000 and i is 17
ener[i] at md.c -185584.826214 and i is 18
ener[i] at md.c 0.000000 and i is 19
ener[i] at md.c 0.000000 and i is 20
ener[i] at md.c 0.000000 and i is 21
ener[i] at md.c 0.000000 and i is 22
ener[i] at md.c 0.000000 and i is 23
ener[i] at md.c 0.000000 and i is 24
ener[i] at md.c 0.000000 and i is 25
ener[i] at md.c 0.000000 and i is 26
ener[i] at md.c 0.000000 and i is 27
ener[i] at md.c 0.000000 and i is 28
ener[i] at md.c 0.000000 and i is 29
ener[i] at md.c 0.000000 and i is 30
ener[i] at md.c 0.000000 and i is 31
ener[i] at md.c 0.000000 and i is 32
ener[i] at md.c 0.000000 and i is 33
ener[i] at md.c 0.000000 and i is 34
ener[i] at md.c -185584.826214 and i is 35
epot[i] at sim_util.c reset_energies() 0.000000 and i is 0
epot[i] at sim_util.c reset_energies() 0.000000 and i is 1
epot[i] at sim_util.c reset_energies() 0.000000 and i is 2
epot[i] at sim_util.c reset_energies() 0.000000 and i is 3
epot[i] at sim_util.c reset_energies() 0.000000 and i is 4
epot[i] at sim_util.c reset_energies() 0.000000 and i is 5
epot[i] at sim_util.c reset_energies() 0.000000 and i is 6
epot[i] at sim_util.c reset_energies() 0.000000 and i is 7
epot[i] at sim_util.c reset_energies() 0.000000 and i is 8
epot[i] at sim_util.c reset_energies() 0.000000 and i is 9
epot[i] at sim_util.c reset_energies() 0.000000 and i is 10
epot[i] at sim_util.c reset_energies() 0.000000 and i is 11
epot[i] at sim_util.c reset_energies() 0.000000 and i is 12
epot[i] at sim_util.c reset_energies() 0.000000 and i is 13
epot[i] at sim_util.c reset_energies() 0.000000 and i is 14
epot[i] at sim_util.c reset_energies() 0.000000 and i is 15
epot[i] at sim_util.c reset_energies() 0.000000 and i is 16
epot[i] at sim_util.c reset_energies() 0.000000 and i is 17
epot[i] at sim_util.c reset_energies() 0.000000 and i is 18
epot[i] at sim_util.c reset_energies() 0.000000 and i is 19
epot[i] at sim_util.c reset_energies() 0.000000 and i is 20
epot[i] at sim_util.c reset_energies() 0.000000 and i is 21
epot[i] at sim_util.c reset_energies() 0.000000 and i is 22
epot[i] at sim_util.c reset_energies() 0.000000 and i is 23
epot[i] at sim_util.c reset_energies() 0.000000 and i is 24
epot[i] at sim_util.c reset_energies() 0.000000 and i is 25
epot[i] at sim_util.c reset_energies() 0.000000 and i is 26
epot[i] at sim_util.c reset_energies() 0.000000 and i is 27
epot[i] at sim_util.c reset_energies() 0.000000 and i is 28
epot[i] at sim_util.c reset_energies() 0.000000 and i is 29
epot[i] at sim_util.c reset_energies() 0.000000 and i is 30
epot[i] at sim_util.c reset_energies() 0.000000 and i is 31
epot[i] at sim_util.c reset_energies() 0.000000 and i is 32
epot[i] at sim_util.c reset_energies() 0.000000 and i is 33
epot[i] at sim_util.c reset_energies() 0.000000 and i is 34
epot[i] at sim_util.c reset_energies() 0.000000 and i is 35
bBHAM 1 bBHAMLJ 0 at force.c Call the short range functions
before call do_fnbf bBHAM force.c
before call do_fnbf egBHAM force.c grpsestat -1.993435
before call do_fnbf egCOUL force.c grpsestat 0.000000
in fnbf.c value of nrnb_ind 21
in fnbf.c INL1200
after call do_fnbf bBHAM force.c
in tgroup sum_epot() epot[F_LR] 0.000000 epot[F_BHAM] 0.000000 epot[F_BHAMLJ] 0.000000
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