towhee-users Mailing List for MCCCS Towhee

On Mon, Feb 23, 2009 at 11:52 AM, Amir Vahid <av...@ua...> wrote:

> I have installed the latest version of towhee on a fedora machine w/o any
> problem but when I want to install it on a RedHat system it generates many
> errors that are enclosed to this email. Does the software need to be
> installed on a root directory, i.e. su –root? Thanks

This is a long-standing problem with the double underscore in some
version of the GNU compiler.  It began affecting Towhee in recent
releases due to the movement of many subroutines from Fortran to C.
Starting with version 6.2.2 there is a configure option that resolves
this issue.

./configure --enable-fix-GNU
cd Source
make clean
make towhee

That "enable" option has worked for all reported cases (so far) and
this occurs most often with Cygwin for windows and certain Linux
distributions.

Marcus
-- 
Marcus G. Martin
Director, Useful Bias Incorporated
88 Martinez Road
Edgewood NM 87015-8222
ph. (505) 286-4457
www.usefulbias.com
www.photobirder.com

finalize.o(.text+0x135):/home/avahid/towhee/Source/finalize.F:60: undefined reference to `twh_moltyp__'
finalize.o(.text+0x144):/home/avahid/towhee/Source/finalize.F:61: undefined reference to `twh_nboxi__'
finalize.o(.text+0x153):/home/avahid/towhee/Source/finalize.F:63: undefined reference to `twh_acnvol__'
finalize.o(.text+0x162):/home/avahid/towhee/Source/finalize.F:64: undefined reference to `twh_acsvol__'
finalize.o(.text+0x171):/home/avahid/towhee/Source/finalize.F:66: undefined reference to `twh_cubeletweight__'
finalize.o(.text+0x180):/home/avahid/towhee/Source/finalize.F:68: undefined reference to `twh_coordfield__'
finalize.o(.text+0x18f):/home/avahid/towhee/Source/finalize.F:69: undefined reference to `twh_coordstorage__'
finalize.o(.text+0x19e):/home/avahid/towhee/Source/finalize.F:70: undefined reference to `twh_coordtemp__'
findtarget.o(.text+0x1a7): In function `twh_findtarget__':
/home/avahid/towhee/Source/findtarget.F:74: undefined reference to `twh_moltyp__'
findtarget.o(.text+0x478):/home/avahid/towhee/Source/findtarget.F:98: undefined reference to `twh_moltyp__'
findtarget.o(.text+0x634):/home/avahid/towhee/Source/findtarget.F:192: undefined reference to `twh_moltyp__'
findtarget.o(.text+0x77c):/home/avahid/towhee/Source/findtarget.F:279: undefined reference to `twh_moltyp__'
findtarget.o(.text+0x1465):/home/avahid/towhee/Source/findtarget.F:366: undefined reference to `twh_moltyp__'
findtarget.o(.text+0x147f):/home/avahid/towhee/Source/findtarget.F:367: more undefined references to `twh_moltyp__' follow
getcbangle.o(.text+0x19e): In function `twh_getcbangle__':
/home/avahid/towhee/Source/getcbangle.F:162: undefined reference to `twh_grownum__'
getcbangle.o(.text+0x1b8):/home/avahid/towhee/Source/getcbangle.F:163: undefined reference to `twh_growfrom__'
getcbangle.o(.text+0x2ba):/home/avahid/towhee/Source/getcbangle.F:189: undefined reference to `twh_growprev__'
getcbbond.o(.text+0x15c): In function `twh_getcbbond__':
/home/avahid/towhee/Source/getcbbond.F:122: undefined reference to `twh_grownum__'
getcbbond.o(.text+0x176):/home/avahid/towhee/Source/getcbbond.F:123: undefined reference to `twh_growfrom__'
getcbbond.o(.text+0x204):/home/avahid/towhee/Source/getcbbond.F:138: undefined reference to `twh_growprev__'
getcbbond.o(.text+0x652):/home/avahid/towhee/Source/getcbbond.F:222: undefined reference to `twh_glist__'
getcbdihed.o(.text+0x30d): In function `twh_getcbdihed__':
/home/avahid/towhee/Source/getcbdihed.F:151: undefined reference to `twh_growprev__'
globalaccess.o(.text+0x1163): In function `twh_get_growvalidcount__':
/home/avahid/towhee/Source/globalaccess.F:929: undefined reference to `twh_growvalidcount__'
globalaccess.o(.text+0x1cbf): In function `twh_get_nboxi__':
/home/avahid/towhee/Source/globalaccess.F:2110: undefined reference to `twh_nboxi__'
globaldata.o(.text+0x902d): In function `twh_coordinates__':
/home/avahid/towhee/Source/globaldata.F:5043: undefined reference to `twh_coordtemp__'
globaldata.o(.text+0x9081):/home/avahid/towhee/Source/globaldata.F:5043: undefined reference to `twh_coordtemp__'
globaldata.o(.text+0x90a9):/home/avahid/towhee/Source/globaldata.F:5032: undefined reference to `twh_coordtemp__'
globaldata.o(.text+0x90dc):/home/avahid/towhee/Source/globaldata.F:5005: undefined reference to `twh_coordstorage__'
globaldata.o(.text+0x9130):/home/avahid/towhee/Source/globaldata.F:5049: undefined reference to `twh_coordtemp__'
globaldata.o(.text+0x91a5):/home/avahid/towhee/Source/globaldata.F:4987: undefined reference to `twh_coordstorage__'
globaldata.o(.text+0x9208):/home/avahid/towhee/Source/globaldata.F:5012: undefined reference to `twh_coordtemp__'
globaldata.o(.text+0xa75b): In function `twh_eam_rho__':
/home/avahid/towhee/Source/globaldata.F:5873: undefined reference to `twh_eam_rho_temp__'
globaldata.o(.text+0xa799):/home/avahid/towhee/Source/globaldata.F:5870: undefined reference to `twh_eam_rho_real__'
globaldata.o(.text+0xbc8c): In function `twh_fieldcoordinates__':
/home/avahid/towhee/Source/globaldata.F:6585: undefined reference to `twh_coordfield__'
globaldata.o(.text+0xbcf3):/home/avahid/towhee/Source/globaldata.F:6583: undefined reference to `twh_coordfield__'
globaldata.o(.text+0xc8de): In function `twh_getatomnum__':
/home/avahid/towhee/Source/globaldata.F:7023: undefined reference to `twh_globalpos__'
globaldata.o(.text+0x12978): In function `twh_lexsched__':
/home/avahid/towhee/Source/globaldata.F:10184: undefined reference to `twh_logical_exsched__'
globaldata.o(.text+0x129a5):/home/avahid/towhee/Source/globaldata.F:10184: undefined reference to `twh_logical_exsched__'
globaldata.o(.text+0x12a70): In function `twh_lexist__':
/home/avahid/towhee/Source/globaldata.F:10250: undefined reference to `twh_logical_exist__'
globaldata.o(.text+0x12a9d):/home/avahid/towhee/Source/globaldata.F:10250: undefined reference to `twh_logical_exist__'
globaldata.o(.text+0x12b68): In function `twh_lmoveme__':
/home/avahid/towhee/Source/globaldata.F:10314: undefined reference to `twh_logical_moveme__'
globaldata.o(.text+0x12b95):/home/avahid/towhee/Source/globaldata.F:10314: undefined reference to `twh_logical_moveme__'
globaldata.o(.text+0x12f14): In function `twh_lperiodic__':
/home/avahid/towhee/Source/globaldata.F:10521: undefined reference to `twh_logical_periodic__'
globaldata.o(.text+0x12f41):/home/avahid/towhee/Source/globaldata.F:10521: undefined reference to `twh_logical_periodic__'
globaldata.o(.text+0x15cba): In function `twh_oldgetatomnum__':
/home/avahid/towhee/Source/globaldata.F:12510: undefined reference to `twh_globalpos__'
globaldata.o(.text+0xa777): In function `twh_eam_rho__':
/home/avahid/towhee/Source/globaldata.F:5874: undefined reference to `twh_eam_rho_real__'
globaldata.o(.text+0xa78a):/home/avahid/towhee/Source/globaldata.F:5874: undefined reference to `twh_eam_rho_real__'
globaldata.o(.text+0xa7b5):/home/avahid/towhee/Source/globaldata.F:5871: undefined reference to `twh_eam_rho_temp__'
globaldata.o(.text+0xa7cd):/home/avahid/towhee/Source/globaldata.F:5871: undefined reference to `twh_eam_rho_temp__'
initconf.o(.text+0x77a): In function `twh_initconf__':
/home/avahid/towhee/Source/initconf.F:206: undefined reference to `twh_ewald_kmax__'
initconf.o(.text+0x816):/home/avahid/towhee/Source/initconf.F:215: undefined reference to `twh_nboxi__'
initconf.o(.text+0x845):/home/avahid/towhee/Source/initconf.F:220: undefined reference to `twh_globalpos__'
initconf.o(.text+0xfcc):/home/avahid/towhee/Source/initconf.F:422: undefined reference to `twh_nboxi__'
initconf.o(.text+0x106a):/home/avahid/towhee/Source/initconf.F:455: undefined reference to `twh_moltyp__'
initconf.o(.text+0x10dd):/home/avahid/towhee/Source/initconf.F:462: undefined reference to `twh_globalpos__'
initconf.o(.text+0x20f2):/home/avahid/towhee/Source/initconf.F:613: undefined reference to `twh_nboxi__'
initconf.o(.text+0x2112):/home/avahid/towhee/Source/initconf.F:614: undefined reference to `twh_moltyp__'
initconf.o(.text+0x218a):/home/avahid/towhee/Source/initconf.F:621: undefined reference to `twh_globalpos__'
mainloop.o(.text+0x8fd): In function `twh_mainloop__':
/home/avahid/towhee/Source/mainloop.F:473: undefined reference to `twh_moltyp__'
mainloop.o(.text+0x917):/home/avahid/towhee/Source/mainloop.F:474: undefined reference to `twh_nboxi__'
mainloop.o(.text+0xd07):/home/avahid/towhee/Source/mainloop.F:747: undefined reference to `twh_acnvol__'
mainloop.o(.text+0xd36):/home/avahid/towhee/Source/mainloop.F:750: undefined reference to `twh_acsvol__'
mainloop.o(.text+0xd4b):/home/avahid/towhee/Source/mainloop.F:752: undefined reference to `twh_acnvol__'
mainloop.o(.text+0x5702):/home/avahid/towhee/Source/mainloop.F:517: undefined reference to `twh_v_semigrand__'
mainloop.o(.text+0x5744):/home/avahid/towhee/Source/mainloop.F:521: undefined reference to `twh_tmmc_weight__'
mainloop.o(.text+0x57f5):/home/avahid/towhee/Source/mainloop.F:539: undefined reference to `twh_tmmc_weight__'
mainloop.o(.text+0x5810):/home/avahid/towhee/Source/mainloop.F:540: undefined reference to `twh_tmmc_weight__'
mainloop.o(.text+0x5919):/home/avahid/towhee/Source/mainloop.F:550: undefined reference to `twh_tmmc_weight__'
mainloop.o(.text+0x6aea):/home/avahid/towhee/Source/mainloop.F:761: undefined reference to `twh_acnvol__'
mainloop.o(.text+0x6b3a):/home/avahid/towhee/Source/mainloop.F:771: undefined reference to `twh_acsvol__'
mainloop.o(.text+0x7135):/home/avahid/towhee/Source/mainloop.F:579: undefined reference to `twh_v_semigrand__'
mainloop.o(.text+0x71b2):/home/avahid/towhee/Source/mainloop.F:763: undefined reference to `twh_acsvol__'
mainloop.o(.text+0x71df):/home/avahid/towhee/Source/mainloop.F:476: undefined reference to `twh_gyration__'
mainloop.o(.text+0x72b9):/home/avahid/towhee/Source/mainloop.F:532: undefined reference to `twh_tmmc_weight__'
mapconf.o(.text+0xad): In function `twh_mapconf__':
/home/avahid/towhee/Source/mapconf.F:75: undefined reference to `twh_moltyp__'
mapconf.o(.text+0x2b7):/home/avahid/towhee/Source/mapconf.F:113: undefined reference to `twh_glist__'
mapconf.o(.text+0x531):/home/avahid/towhee/Source/mapconf.F:196: undefined reference to `twh_cubeletweight__'
mapconf.o(.text+0x66c):/home/avahid/towhee/Source/mapconf.F:149: undefined reference to `twh_cubeletweight__'
mapconf.o(.text+0x6b1):/home/avahid/towhee/Source/mapconf.F:155: undefined reference to `twh_cubeletweight__'
mapconf.o(.text+0x73e):/home/avahid/towhee/Source/mapconf.F:135: undefined reference to `twh_cubeletweight__'
mapconf.o(.text+0x90c):/home/avahid/towhee/Source/mapconf.F:174: undefined reference to `twh_cubeletweight__'
pivot.o(.text+0x1fb): In function `twh_pivot__':
/home/avahid/towhee/Source/pivot.F:123: undefined reference to `twh_nboxi__'
readclassical.o(.text+0x3ba): In function `twh_readclassical__':
/home/avahid/towhee/Source/readclassical.F:253: undefined reference to `twh_ewald_kmax__'
readclassical.o(.text+0xe40):/home/avahid/towhee/Source/readclassical.F:282: undefined reference to `twh_ewald_kmax__'
readclassical.o(.text+0xf12):/home/avahid/towhee/Source/readclassical.F:313: undefined reference to `twh_ewald_kmax__'
readlammps.o(.text+0x24e): In function `twh_readlammps__':
/home/avahid/towhee/Source/readlammps.F:118: undefined reference to `twh_coordtemp__'
readtowhee.o(.text+0xf67): In function `twh_readtowhee__':
/home/avahid/towhee/Source/readtowhee.F:923: undefined reference to `twh_ewald_kmax__'
readtowhee.o(.text+0x170a):/home/avahid/towhee/Source/readtowhee.F:485: undefined reference to `twh_v_semigrand__'
readtowhee.o(.text+0x172d):/home/avahid/towhee/Source/readtowhee.F:487: undefined reference to `twh_tmmc_weight__'
readtowhee.o(.text+0x179e):/home/avahid/towhee/Source/readtowhee.F:505: undefined reference to `twh_tmmc_weight__'
readtowhee.o(.text+0x17bf):/home/avahid/towhee/Source/readtowhee.F:506: undefined reference to `twh_tmmc_weight__'
readtowhee.o(.text+0x22de):/home/avahid/towhee/Source/readtowhee.F:514: undefined reference to `twh_tmmc_weight__'
readtowhee.o(.text+0x22f1):/home/avahid/towhee/Source/readtowhee.F:515: undefined reference to `twh_v_semigrand__'
readtowhee.o(.text+0x2708):/home/avahid/towhee/Source/readtowhee.F:498: undefined reference to `twh_tmmc_weight__'
readtowhee.o(.text+0x964a):/home/avahid/towhee/Source/readtowhee.F:2706: undefined reference to `twh_ewald_kmax__'
readtowhee.o(.text+0x9764):/home/avahid/towhee/Source/readtowhee.F:2734: undefined reference to `twh_coordfield__'
readtowhee.o(.text+0x97b5):/home/avahid/towhee/Source/readtowhee.F:2738: undefined reference to `twh_moltyp__'
readtowhee.o(.text+0x9add):/home/avahid/towhee/Source/readtowhee.F:2695: undefined reference to `twh_ewald_kmax__'
readtowhee.o(.text+0x9d8d):/home/avahid/towhee/Source/readtowhee.F:2793: undefined reference to `twh_moltyp__'
readtowhee.o(.text+0x9e58):/home/avahid/towhee/Source/readtowhee.F:2757: undefined reference to `twh_moltyp__'
readtowhee.o(.text+0xa961):/home/avahid/towhee/Source/readtowhee.F:2924: undefined reference to `twh_growvalidcount__'
recippress.o(.text+0x24a): In function `twh_recippress__':
/home/avahid/towhee/Source/recippress.F:73: undefined reference to `twh_moltyp__'
recipsum.o(.text+0x8c): In function `twh_recipsum__':
/home/avahid/towhee/Source/recipsum.F:58: undefined reference to `twh_ewald_kmax__'
recipsum.o(.text+0x4e0):/home/avahid/towhee/Source/recipsum.F:125: undefined reference to `twh_moltyp__'
resetcoulomb.o(.text+0x45): In function `twh_resetcoulomb__':
/home/avahid/towhee/Source/resetcoulomb.F:45: undefined reference to `twh_ewald_kmax__'
resetcoulomb.o(.text+0x54):/home/avahid/towhee/Source/resetcoulomb.F:46: undefined reference to `twh_ewald_kmax__'
resetcoulomb.o(.text+0x16c):/home/avahid/towhee/Source/resetcoulomb.F:78: undefined reference to `twh_ewald_kmax__'
resetcoulomb.o(.text+0x2a5):/home/avahid/towhee/Source/resetcoulomb.F:63: undefined reference to `twh_ewald_kmax__'
rosenbluth.o(.text+0x546): In function `twh_rosenbluth_main__':
/home/avahid/towhee/Source/rosenbluth.F:211: undefined reference to `twh_growfrom__'
rosenbluth.o(.text+0x561):/home/avahid/towhee/Source/rosenbluth.F:212: undefined reference to `twh_grownum__'
rosenbluth.o(.text+0x57c):/home/avahid/towhee/Source/rosenbluth.F:213: undefined reference to `twh_growprev__'
rotate.o(.text+0x193): In function `twh_rotate__':
/home/avahid/towhee/Source/rotate.F:109: undefined reference to `twh_nboxi__'
rotate.o(.text+0x4a2):/home/avahid/towhee/Source/rotate.F:162: undefined reference to `twh_rcmu__'
rotationmatrix.o(.text+0x3e): In function `twh_rotationmatrix__':
/home/avahid/towhee/Source/rotationmatrix.F:52: undefined reference to `twh_moltyp__'
rwcbmc.o(.text+0x27a5): In function `twh_rwcbmc__':
/home/avahid/towhee/Source/rwcbmc.F:294: undefined reference to `twh_cubeletweight__'
rwconf.o(.text+0x117a): In function `twh_rwconf__':
/home/avahid/towhee/Source/rwconf.F:444: undefined reference to `twh_moltyp__'
rwconf.o(.text+0x1d45):/home/avahid/towhee/Source/rwconf.F:451: undefined reference to `twh_moltyp__'
rwconf.o(.text+0x1da1):/home/avahid/towhee/Source/rwconf.F:460: undefined reference to `twh_nboxi__'
rwconf.o(.text+0x1e93):/home/avahid/towhee/Source/rwconf.F:587: undefined reference to `twh_moltyp__'
rwconf.o(.text+0x20a3):/home/avahid/towhee/Source/rwconf.F:470: undefined reference to `twh_nboxi__'
rwconf.o(.text+0x21e6):/home/avahid/towhee/Source/rwconf.F:486: undefined reference to `twh_nboxi__'
rwconf.o(.text+0x2215):/home/avahid/towhee/Source/rwconf.F:493: undefined reference to `twh_nboxi__'
rwconf.o(.text+0x2249):/home/avahid/towhee/Source/rwconf.F:495: undefined reference to `twh_moltyp__'
rwconf.o(.text+0x2429):/home/avahid/towhee/Source/rwconf.F:521: undefined reference to `twh_nboxi__'
rwconf.o(.text+0x2443):/home/avahid/towhee/Source/rwconf.F:522: undefined reference to `twh_moltyp__'
rwconf.o(.text+0x2505):/home/avahid/towhee/Source/rwconf.F:576: undefined reference to `twh_moltyp__'
rwconf.o(.text+0x2992):/home/avahid/towhee/Source/rwconf.F:549: undefined reference to `twh_globalpos__'
rwconf.o(.text+0x29f1):/home/avahid/towhee/Source/rwconf.F:560: undefined reference to `twh_moltyp__'
rwconf.o(.text+0x2a54):/home/avahid/towhee/Source/rwconf.F:566: undefined reference to `twh_globalpos__'
schedule.o(.text+0x4bf): In function `twh_schedule__':
/home/avahid/towhee/Source/schedule.F:841: undefined reference to `twh_growfrom__'
schedule.o(.text+0x4f4):/home/avahid/towhee/Source/schedule.F:844: undefined reference to `twh_grownum__'
schedule.o(.text+0x650):/home/avahid/towhee/Source/schedule.F:864: undefined reference to `twh_growprev__'
schedule.o(.text+0x76d):/home/avahid/towhee/Source/schedule.F:176: undefined reference to `twh_growfrom__'
schedule.o(.text+0x925):/home/avahid/towhee/Source/schedule.F:324: undefined reference to `twh_grownum__'
schedule.o(.text+0x9cb):/home/avahid/towhee/Source/schedule.F:376: undefined reference to `twh_growfrom__'
schedule.o(.text+0xa0a):/home/avahid/towhee/Source/schedule.F:379: undefined reference to `twh_growprev__'
schedule.o(.text+0xa74):/home/avahid/towhee/Source/schedule.F:886: undefined reference to `twh_growfrom__'
schedule.o(.text+0xa99):/home/avahid/towhee/Source/schedule.F:891: undefined reference to `twh_grownum__'
schedule.o(.text+0xb46):/home/avahid/towhee/Source/schedule.F:897: undefined reference to `twh_growfrom__'
schedule.o(.text+0xcff):/home/avahid/towhee/Source/schedule.F:906: undefined reference to `twh_growprev__'
schedule.o(.text+0xd47):/home/avahid/towhee/Source/schedule.F:910: undefined reference to `twh_growprev__'
schedule.o(.text+0xd6f):/home/avahid/towhee/Source/schedule.F:924: undefined reference to `twh_grownum__'
schedule.o(.text+0xdb5):/home/avahid/towhee/Source/schedule.F:929: undefined reference to `twh_grownum__'
schedule.o(.text+0xdd0):/home/avahid/towhee/Source/schedule.F:931: undefined reference to `twh_grownum__'
schedule.o(.text+0xea7):/home/avahid/towhee/Source/schedule.F:943: undefined reference to `twh_grownum__'
schedule.o(.text+0xecc):/home/avahid/towhee/Source/schedule.F:946: undefined reference to `twh_growfrom__'
schedule.o(.text+0xee7):/home/avahid/towhee/Source/schedule.F:947: undefined reference to `twh_growfrom__'
schedule.o(.text+0xf01):/home/avahid/towhee/Source/schedule.F:948: undefined reference to `twh_growprev__'
schedule.o(.text+0xf1c):/home/avahid/towhee/Source/schedule.F:949: undefined reference to `twh_growprev__'
schedule.o(.text+0xf36):/home/avahid/towhee/Source/schedule.F:950: undefined reference to `twh_grownum__'
schedule.o(.text+0xf51):/home/avahid/towhee/Source/schedule.F:951: undefined reference to `twh_grownum__'
schedule.o(.text+0x10a3):/home/avahid/towhee/Source/schedule.F:973: undefined reference to `twh_grownum__'
schedule.o(.text+0x1176):/home/avahid/towhee/Source/schedule.F:981: undefined reference to `twh_growfrom__'
schedule.o(.text+0x1191):/home/avahid/towhee/Source/schedule.F:984: undefined reference to `twh_grownum__'
schedule.o(.text+0x12c1):/home/avahid/towhee/Source/schedule.F:1002: undefined reference to `twh_grownum__'
schedule.o(.text+0x14cd):/home/avahid/towhee/Source/schedule.F:1051: undefined reference to `twh_growfrom__'
schedule.o(.text+0x14f9):/home/avahid/towhee/Source/schedule.F:1053: undefined reference to `twh_growprev__'
schedule.o(.text+0x1512):/home/avahid/towhee/Source/schedule.F:1055: undefined reference to `twh_growfrom__'
schedule.o(.text+0x1605):/home/avahid/towhee/Source/schedule.F:1063: undefined reference to `twh_growprev__'
schedule.o(.text+0x1772):/home/avahid/towhee/Source/schedule.F:1098: undefined reference to `twh_grownum__'
schedule.o(.text+0x178c):/home/avahid/towhee/Source/schedule.F:1105: undefined reference to `twh_grownum__'
schedule.o(.text+0x1a11):/home/avahid/towhee/Source/schedule.F:1132: undefined reference to `twh_growfrom__'
schedule.o(.text+0x1b3b):/home/avahid/towhee/Source/schedule.F:730: undefined reference to `twh_growfrom__'
schedule.o(.text+0x1b6a):/home/avahid/towhee/Source/schedule.F:733: undefined reference to `twh_grownum__'
schedule.o(.text+0x1c19):/home/avahid/towhee/Source/schedule.F:742: undefined reference to `twh_growprev__'
schedule.o(.text+0x1ce7):/home/avahid/towhee/Source/schedule.F:336: undefined reference to `twh_growfrom__'
schedule.o(.text+0x1d25):/home/avahid/towhee/Source/schedule.F:340: undefined reference to `twh_growprev__'
schedule.o(.text+0x1dcf):/home/avahid/towhee/Source/schedule.F:224: undefined reference to `twh_growfrom__'
schedule.o(.text+0x1f50):/home/avahid/towhee/Source/schedule.F:266: undefined reference to `twh_grownum__'
schedule.o(.text+0x26d0):/home/avahid/towhee/Source/schedule.F:605: undefined reference to `twh_growfrom__'
schedule.o(.text+0x28aa):/home/avahid/towhee/Source/schedule.F:643: undefined reference to `twh_growprev__'
schedule.o(.text+0x28cb):/home/avahid/towhee/Source/schedule.F:647: undefined reference to `twh_growfrom__'
schedule.o(.text+0x2aa5):/home/avahid/towhee/Source/schedule.F:685: undefined reference to `twh_growprev__'
schedule.o(.text+0x2b5d):/home/avahid/towhee/Source/schedule.F:698: undefined reference to `twh_growprev__'
schedule.o(.text+0x2c6a):/home/avahid/towhee/Source/schedule.F:716: undefined reference to `twh_grownum__'
schedule.o(.text+0x2e97):/home/avahid/towhee/Source/schedule.F:238: undefined reference to `twh_growprev__'
schedule.o(.text+0x2eb0):/home/avahid/towhee/Source/schedule.F:239: undefined reference to `twh_grownum__'
schedule.o(.text+0x2fe2):/home/avahid/towhee/Source/schedule.F:347: undefined reference to `twh_grownum__'
schedule.o(.text+0x3203):/home/avahid/towhee/Source/schedule.F:327: undefined reference to `twh_growprev__'
schedule.o(.text+0x3616):/home/avahid/towhee/Source/schedule.F:319: undefined reference to `twh_growprev__'
setcbdihed.o(.text+0x1278): In function `twh_setcbdihed__':
/home/avahid/towhee/Source/setcbdihed.F:333: undefined reference to `twh_growprev__'
setclassical.o(.text+0x53c): In function `twh_setclassical__':
/home/avahid/towhee/Source/setclassical.F:148: undefined reference to `twh_ewald_kmax__'
stresstensor.o(.text+0x34a): In function `twh_stresstensor__':
/home/avahid/towhee/Source/stresstensor.F:120: undefined reference to `twh_moltyp__'
stresstensor.o(.text+0x3a7):/home/avahid/towhee/Source/stresstensor.F:123: undefined reference to `twh_rcmu__'
stresstensor.o(.text+0x41d):/home/avahid/towhee/Source/stresstensor.F:128: undefined reference to `twh_moltyp__'
stresstensor.o(.text+0x539):/home/avahid/towhee/Source/stresstensor.F:142: undefined reference to `twh_rcmu__'
swapmoves.o(.text+0xa40): In function `twh_swapmoves__':
/home/avahid/towhee/Source/swapmoves.F:636: undefined reference to `twh_moltyp__'
swapmoves.o(.text+0xa58):/home/avahid/towhee/Source/swapmoves.F:637: undefined reference to `twh_nboxi__'
swapmoves.o(.text+0x28b1):/home/avahid/towhee/Source/swapmoves.F:1279: undefined reference to `twh_nboxi__'
swapmoves.o(.text+0x2cbf):/home/avahid/towhee/Source/swapmoves.F:1100: undefined reference to `twh_tmmc_weight__'
swapmoves.o(.text+0x2cd4):/home/avahid/towhee/Source/swapmoves.F:1102: undefined reference to `twh_tmmc_weight__'
swapmoves.o(.text+0x3427):/home/avahid/towhee/Source/swapmoves.F:1086: undefined reference to `twh_tmmc_weight__'
swapmoves.o(.text+0x343c):/home/avahid/towhee/Source/swapmoves.F:1087: undefined reference to `twh_tmmc_weight__'
swapmoves.o(.text+0x38ca): In function `twh_initial_atom_insertion__':
/home/avahid/towhee/Source/swapmoves.F:1670: undefined reference to `twh_glist__'
swapmoves.o(.text+0x3a35):/home/avahid/towhee/Source/swapmoves.F:1482: undefined reference to `twh_glist__'
swapmoves.o(.text+0x3a53):/home/avahid/towhee/Source/swapmoves.F:1486: undefined reference to `twh_rcmu__'
swapmoves.o(.text+0x3c0c):/home/avahid/towhee/Source/swapmoves.F:1557: undefined reference to `twh_glist__'
swapmoves.o(.text+0x3ec2):/home/avahid/towhee/Source/swapmoves.F:1604: undefined reference to `twh_glist__'
switch.o(.text+0x685): In function `twh_switch__':
/home/avahid/towhee/Source/switch.F:175: undefined reference to `twh_rcmu__'
tranatom.o(.text+0x1dd): In function `twh_tranatom__':
/home/avahid/towhee/Source/tranatom.F:98: undefined reference to `twh_nboxi__'
trancom.o(.text+0x1ab): In function `twh_trancom__':
/home/avahid/towhee/Source/trancom.F:110: undefined reference to `twh_nboxi__'
trancom.o(.text+0x476):/home/avahid/towhee/Source/trancom.F:172: undefined reference to `twh_rcmu__'
updatethreebondbias.o(.text+0xad): In function `twh_updatethreebondbias__':
/home/avahid/towhee/Source/updatethreebondbias.F:59: undefined reference to `twh_nboxi__'
updatethreebondbias.o(.text+0xca):/home/avahid/towhee/Source/updatethreebondbias.F:61: undefined reference to `twh_moltyp__'
updatetwobondbias.o(.text+0xad): In function `twh_updatetwobondbias__':
/home/avahid/towhee/Source/updatetwobondbias.F:59: undefined reference to `twh_nboxi__'
updatetwobondbias.o(.text+0xca):/home/avahid/towhee/Source/updatetwobondbias.F:61: undefined reference to `twh_moltyp__'
updatevolmaxdisp.o(.text+0x1a9): In function `twh_updatevolmaxdisp__':
/home/avahid/towhee/Source/updatevolmaxdisp.F:76: undefined reference to `twh_acnvol__'
updatevolmaxdisp.o(.text+0x1be):/home/avahid/towhee/Source/updatevolmaxdisp.F:77: undefined reference to `twh_acsvol__'
veefone.o(.text+0x50): In function `twh_veefone__':
/home/avahid/towhee/Source/veefone.F:72: undefined reference to `twh_moltyp__'
volnpt.o(.text+0x2af): In function `twh_volnpt__':
/home/avahid/towhee/Source/volnpt.F:146: undefined reference to `twh_moltyp__'
volnpt.o(.text+0xb1d):/home/avahid/towhee/Source/volnpt.F:230: undefined reference to `twh_rcmu__'
volnpt.o(.text+0xbfc):/home/avahid/towhee/Source/volnpt.F:253: undefined reference to `twh_moltyp__'
volnpt.o(.text+0x10e9):/home/avahid/towhee/Source/volnpt.F:402: undefined reference to `twh_moltyp__'
volnvt.o(.text+0x3d4): In function `twh_volnvt__':
/home/avahid/towhee/Source/volnvt.F:163: undefined reference to `twh_moltyp__'
volnvt.o(.text+0x464):/home/avahid/towhee/Source/volnvt.F:169: undefined reference to `twh_nboxi__'
volnvt.o(.text+0x84f):/home/avahid/towhee/Source/volnvt.F:309: undefined reference to `twh_nboxi__'
volnvt.o(.text+0x8c8):/home/avahid/towhee/Source/volnvt.F:321: undefined reference to `twh_moltyp__'
volnvt.o(.text+0xbed):/home/avahid/towhee/Source/volnvt.F:361: undefined reference to `twh_rcmu__'
volnvt.o(.text+0x145f):/home/avahid/towhee/Source/volnvt.F:532: undefined reference to `twh_moltyp__'
vsasa.o(.text+0x48): In function `twh_vsasa__':
/home/avahid/towhee/Source/vsasa.F:50: undefined reference to `twh_moltyp__'
writedlpoly.o(.text+0x4b5): In function `twh_writedlpoly__':
/home/avahid/towhee/Source/writedlpoly.F:123: undefined reference to `twh_moltyp__'
writedlpoly.o(.text+0x1192):/home/avahid/towhee/Source/writedlpoly.F:188: undefined reference to `twh_moltyp__'
writedlpoly.o(.text+0x151f):/home/avahid/towhee/Source/writedlpoly.F:286: undefined reference to `twh_moltyp__'
writedlpoly.o(.text+0x1873):/home/avahid/towhee/Source/writedlpoly.F:372: more undefined references to `twh_moltyp__' follow
writepdb.o(.text+0x4df): In function `twh_writepdb__':
/home/avahid/towhee/Source/writepdb.F:141: undefined reference to `twh_nboxi__'
writepdb.o(.text+0x505):/home/avahid/towhee/Source/writepdb.F:143: undefined reference to `twh_moltyp__'
writepdb.o(.text+0xb0b):/home/avahid/towhee/Source/writepdb.F:124: undefined reference to `twh_moltyp__'
writetowhee.o(.text+0x734c): In function `twh_writetowhee__':
/home/avahid/towhee/Source/writetowhee.F:371: undefined reference to `twh_ewald_kmax__'
writetramonto.o(.text+0x34c): In function `twh_writetramonto__':
/home/avahid/towhee/Source/writetramonto.F:100: undefined reference to `twh_moltyp__'
collect2: ld returned 1 exit status
make: *** [towhee] Error 1
[avahid@polymer1 Source]$ 
[avahid@polymer1 Source]$ 

Hello all:

  I want to use towhee to do some MC simulations.

  I tried to compile towhee but failed because there are so many undefined
subroutines in the source files.

  For example in the allocate.F I got the below messages:
allocate.o: In function `twh_allocate_eam__':
~/towhee-6.2.2/Source/allocate.F:39: undefined reference to
`twh_eam_rho_real__'
~/towhee-6.2.2/Source/allocate.F:40: undefined reference to
`twh_eam_rho_temp__'

  In fact there are so many above like messages that I can not show them
all. I doubt maybe the source files are not complete. 
  Can anyone tell me the place where these undefined subroutines are? 

  Best regards

Caoch
Tokyo Institute Technology

On Fri, Feb 6, 2009 at 5:05 PM, Sebastien groh <gr...@ca...> wrote:

> I am interested to look at the effect of hydrogen on the dislocation
> activity in magnesium, using different concentration of hydrogen. Using
> a simulation box with a dislocation in the middle, I am interested to
> do some monte carlo to charge the magnesium simulation cell with
> hydrogen. After that, I want to use the output file generated with the
> monte carlo run to perform some molecular statics and molecular
> dynamics calculations.

You are unlikely to get much of anything useful from Towhee related to
that problem.  You will first need a forcefield that has been
parameterized for the interaction of hydrogen with magnesium.  I do
not believe any of the currently implemented forcefields are likely to
produce meaningful results for that system.  You instead need to find
a literature forcefield developed for that system - although one would
expect that paper (if it existed) would likely contain the answers you
are looking for as well.

> (1) Could you tell me if in the example directory I can find something
> similar to what I want to do? I does not have to be hydrogen. It can be
> a metal X that you want to charge with a gas Y.

There are examples loading light gasses into porous materials such as
zeolites.  Catlow_Zeolite_4a or Dubb_Zeolite.

> (2) Can I do monte carlo at 0K? (probably no, but I want confirmation).

There is no such thing as Monte Carlo molecular simulation at 0K.
That would be some sort of minimization procedure instead, or a search
for the lowest energy states.  Without a positive temperature Towhee
will not function.

In theory, Towhee can be compiled with a quantum code and use them to
generate the energies.  Some of the framework for that exists in
Towhee, but it has never been truly functional and would require
someone to do a fair bit of code work to make it all work properly.
Such a procedure is insanely expensive and only a handful of groups
have managed to get it working with their own codes (not Towhee): for
example, Ilja Siepmann or Lev Gelb.

Marcus
-- 
Marcus G. Martin
Director, Useful Bias Incorporated
88 Martinez Road
Edgewood NM 87015-8222
ph. (505) 286-4457
www.usefulbias.com
www.photobirder.com

Dear Towhee users and developers,

I never used monte carlo simulation before so I apologize if my 
questions are too easy.

What I want to do?
I am interested to look at the effect of hydrogen on the dislocation 
activity in magnesium, using different concentration of hydrogen. Using 
a simulation box with a dislocation in the middle, I am interested to 
do some monte carlo to charge the magnesium simulation cell with 
hydrogen. After that, I want to use the output file generated with the 
monte carlo run to perform some molecular statics and molecular 
dynamics calculations.

(1) Could you tell me if in the example directory I can find something 
similar to what I want to do? I does not have to be hydrogen. It can be 
a metal X that you want to charge with a gas Y.
(2) Can I do monte carlo at 0K? (probably no, but I want confirmation).

Thanks,
Sebastien