NAMD: File Members

_ | a | b | c | d | e | f | g | i | l | m | n | o | p | r | s | t | u | v | w

- _ -

_initCharm() : BackEnd.C
_registerExternalModules() : moduleinit.C
_registerNeighborLB() : moduleinit.C

- a -

AddAtom() : FreeEnergyParse.h, FreeEnergyParse.C
AddAtoms() : FreeEnergyParse.h, FreeEnergyParse.C
AddAtomsInResidues() : FreeEnergyParse.h, FreeEnergyParse.C
AddResidues() : FreeEnergyParse.h, FreeEnergyParse.C
all_init() : BackEnd.C
atobool() : SimParameters.C
average() : HomePatch.C

- b -

build12Excls() : CompressPsf.C
build13Excls() : CompressPsf.C
build14Excls() : CompressPsf.C
buildExclusions() : CompressPsf.C

- c -

calc_fulldirect() : ComputeFullDirect.C
cast_array() : varsizemsg.h
cast_size() : varsizemsg.h
cfftb() : pub3dfft.C
cfftb1() : pub3dfft.C
cfftf() : pub3dfft.C
cfftf1() : pub3dfft.C
cffti() : pub3dfft.C
cffti1() : pub3dfft.C
CheckParentheses() : FreeEnergyParse.h, FreeEnergyParse.C
checkSum() : MStream.C
clearGlobalVectors() : CompressPsf.C
close_dcd_read() : dcdlib.h, dcdlib.C
close_dcd_write() : dcdlib.h, dcdlib.C
compDistance() : HomePatch.C
compLoad() : ProxyMgr.C
compress_psf_file() : CompressPsf.h, CompressPsf.C
compute_b_moduli() : PmeKSpace.C
compute_b_spline() : PmeBase.h, PmeBase.C
convert() : ParseOptions.h, ParseOptions.C
CpvDeclare() : ProcessorPrivate.C
CpvExtern() : ProcessorPrivate.h
CpvStaticDeclare() : Communicate.C, BackEnd.C
CreateNamdCentLB() : NamdCentLB.h, NamdCentLB.C
CreateNamdNborLB() : NamdNborLB.h, NamdNborLB.C
crossterm_setup() : Parameters.C, ComputeCrossterms.C
CsmHandler() : Communicate.C

- d -

dataelement_cons_macro() : ParseOptions.C
dataelement_cons_macro_default() : ParseOptions.C
dftmod() : PmeKSpace.C
dummy_erf() : erf.C
dump_param() : DumpBench.C
dumpbench() : DumpBench.h, DumpBench.C

- e -

endd() : DataStream.h
endi() : InfoStream.h, InfoStream.C
ETITLE() : Controller.C
EXCLUDED() : ComputeNonbondedBase2.h, ComputeNonbondedBase.h
exit_sched() : BackEnd.C

- f -

Fclose() : common.h, common.C
FEP() : ComputeNonbondedBase2.h, ComputeNonbondedBase.h
fep_vdw_forceandenergies() : ComputeNonbondedFEP.C
FEPTITLE() : Controller.C
fill_header() : imd.C
find_free_port() : GlobalMasterIMD.C
Fopen() : common.h, common.C
FORMAT() : Controller.C
forward_back_sub() : ComputeCrossterms.C

- g -

G_q() : HomePatch.C
generateAtomTypeTable() : ComputeEwald.C
generatePmePeList() : ComputePme.C
generatePmePeList2() : ComputePme.C
getAcceptorData() : CompressPsf.C
getAngleData() : CompressPsf.C
getAtomData() : CompressPsf.C
GetAtomName() : FreeEnergyParse.h, FreeEnergyParse.C
getBondData() : CompressPsf.C
getCrosstermData() : CompressPsf.C
getDihedralData() : CompressPsf.C
getDonorData() : CompressPsf.C
getExclusionData() : CompressPsf.C
getExtraBonds() : CompressPsf.C
getImproperData() : CompressPsf.C
GetResNum() : FreeEnergyParse.h, FreeEnergyParse.C
GetResRange() : FreeEnergyParse.h, FreeEnergyParse.C
GetRestraint() : FreeEnergyParse.h, FreeEnergyParse.C
GetSegName() : FreeEnergyParse.h, FreeEnergyParse.C
GetTime() : FreeEnergyParse.h, FreeEnergyParse.C

- i -

iDEBUG() : InfoStream.h, InfoStream.C
iERROR() : InfoStream.h, InfoStream.C
iINFO() : InfoStream.h, InfoStream.C
imd_disconnect() : imd.h, imd.C
imd_go() : imd.C
imd_handshake() : imd.h, imd.C
imd_htonl() : imd.C
imd_kill() : imd.h, imd.C
imd_ntohl() : imd.C
imd_pause() : imd.h, imd.C
imd_readn() : imd.C
imd_recv_energies() : imd.h, imd.C
imd_recv_fcoords() : imd.h, imd.C
imd_recv_handshake() : imd.h, imd.C
imd_recv_header() : imd.h, imd.C
imd_recv_header_nolengthswap() : imd.C
imd_recv_mdcomm() : imd.h, imd.C
imd_send_energies() : imd.h, imd.C
imd_send_fcoords() : imd.h, imd.C
imd_send_mdcomm() : imd.h, imd.C
imd_trate() : imd.h, imd.C
imd_writen() : imd.C
init_exp() : ComputeEwald.C
integrateAllAtomSigs() : CompressPsf.C
iPE() : InfoStream.h, InfoStream.C
IsAResidue() : FreeEnergyParse.h, FreeEnergyParse.C
IsAtom() : FreeEnergyParse.h, FreeEnergyParse.C
IsAtomName() : FreeEnergyParse.h, FreeEnergyParse.C
IsAtomNameList() : FreeEnergyParse.h, FreeEnergyParse.C
IsEndGroup() : FreeEnergyParse.h, FreeEnergyParse.C
isPmeProcessor() : NamdCentLB.C, ComputePme.C, AlgSeven.C
IsResidue() : FreeEnergyParse.h, FreeEnergyParse.C
IsResidueRange() : FreeEnergyParse.h, FreeEnergyParse.C
IsStartGroup() : FreeEnergyParse.h, FreeEnergyParse.C
iWARN() : InfoStream.h, InfoStream.C

- l -

LdbCoordinator_initproc() : LdbCoordinator.h, LdbCoordinator.C
LOCALDECOUPLE() : ComputeNonbondedBase2.h
lookupCstPool() : CompressPsf.h
lu_decomp_nopivot() : ComputeCrossterms.C
lubksb() : HomePatch.C
ludcmp() : HomePatch.C

- m -

main() : mainfunc.C, loaddcd.c, FreeEnergyMain.C, flipdcd.c, flipbinpdb.c, fixdcd.c, dumpdcd.c
mat_multiply_vec() : NamdOneTools.h, NamdOneTools.C
MatrixFitRMS() : fitrms.h, fitrms.C
memusage() : memusage.h, memusage.C
memusage_mallinfo() : memusage.C
memusage_mstats() : memusage.C
memusage_ps() : memusage.C
mollify() : HomePatch.C
my_assert() : FreeEnergyAssert.C
my_imd_connect() : GlobalMasterIMD.C
my_sigint_handler() : Controller.C

- n -

NAMD_backup_file() : common.h, common.C
NAMD_blank_string() : strlib.h, strlib.C
NAMD_bug() : common.h, common.C
NAMD_die() : common.h, common.C
NAMD_err() : common.h, common.C
NAMD_find_first_word() : strlib.h, strlib.C
NAMD_find_word() : strlib.h, strlib.C
NAMD_new_handler() : BackEnd.C
NAMD_pad() : strlib.h, strlib.C
NAMD_quit() : common.h, common.C
NAMD_read_int() : strlib.h, strlib.C
NAMD_read_line() : strlib.h, strlib.C
NAMD_remove_comment() : strlib.h, strlib.C
NAMD_stringdup() : common.h, common.C
NAMD_truncate() : strlib.h, strlib.C
NAMD_write() : dcdlib.C, common.h, common.C, dcdlib.C
new_array() : packmsg.h
new_PDBData() : PDBData.h, PDBData.C
next() : ParseOptions.C
noInterNode() : ProxyMgr.C
normalize3d() : fitrms.C

- o -

open_dcd_read() : dcdlib.h, dcdlib.C
open_dcd_write() : dcdlib.h, dcdlib.C
open_dcd_write_par_slave() : dcdlib.h, dcdlib.C
operator!=() : CompressPsf.C
operator<<() : InfoStream.h, InfoStream.C, DataStream.h, DataStream.C
operator==() : CompressPsf.C
outer() : Tensor.h
outputPsfFile() : CompressPsf.C

- p -

PACK_MSG() : ProxyMgr.C, MigrateAtomsMsg.C, ComputeGlobalMsgs.C, ComputeDPMEMsgs.C, packmsg.h
pad() : dcdlib.C
pairlist_from_pairlist() : ComputeNonbondedInl.h
parse_input_macro() : ParseOptions.C
parse_input_macro_b() : ParseOptions.C
parse_input_macro_default() : ParseOptions.C
parse_input_macro_default_b() : ParseOptions.C
parse_stringlist_macro() : ParseOptions.C
passb() : pub3dfft.C
passb2() : pub3dfft.C
passb3() : pub3dfft.C
passb4() : pub3dfft.C
passb5() : pub3dfft.C
passf() : pub3dfft.C
passf2() : pub3dfft.C
passf3() : pub3dfft.C
passf4() : pub3dfft.C
passf5() : pub3dfft.C
pp_clamp() : PressureProfile.h
pp_reduction() : PressureProfile.h
ProblemParsing() : FreeEnergyParse.h, FreeEnergyParse.C
processCpuLoad() : ProxyMgr.C
ProcessorPrivateInit() : ProcessorPrivate.h, ProcessorPrivate.C
pubd3di() : pub3dfft.h, pub3dfft.C
pubdz3d() : pub3dfft.h, pub3dfft.C
pubz3d() : pub3dfft.h, pub3dfft.C
pubz3di() : pub3dfft.h, pub3dfft.C
pubzd3d() : pub3dfft.h, pub3dfft.C

- r -

read_binary_coors() : NamdState.C, NamdOneTools.h, NamdOneTools.C
read_binary_file() : NamdOneTools.h, NamdOneTools.C
read_dcdheader() : dcdlib.h
read_dcdstep() : dcdlib.h
ReadAlpha() : FreeEnergyParse.h, FreeEnergyParse.C
ReadAlphaNum() : FreeEnergyParse.h, FreeEnergyParse.C
ReadAValue() : FreeEnergyParse.h, FreeEnergyParse.C
ReadBound() : FreeEnergyParse.h, FreeEnergyParse.C
ReadChar() : FreeEnergyParse.h, FreeEnergyParse.C
ReadDigits() : FreeEnergyParse.h, FreeEnergyParse.C
ReadInput() : FreeEnergyParse.h, FreeEnergyParse.C
ReadNextItem() : FreeEnergyParse.h, FreeEnergyParse.C
ReadNextPmfSpec() : FreeEnergyParse.h, FreeEnergyParse.C
ReadNextRestraintType() : FreeEnergyParse.h, FreeEnergyParse.C
ReadParentheses() : FreeEnergyParse.h, FreeEnergyParse.C
ReadPmfBlock() : FreeEnergyParse.h, FreeEnergyParse.C
readPsfFile() : CompressPsf.C
ReadRestraints() : FreeEnergyParse.h, FreeEnergyParse.C
ReadTaskType() : FreeEnergyParse.h, FreeEnergyParse.C
ReadTimeUnits() : FreeEnergyParse.h, FreeEnergyParse.C
readtoeoln() : PDB.C, parm.C
ReadWhite() : FreeEnergyParse.h, FreeEnergyParse.C
ReadWord() : FreeEnergyParse.h, FreeEnergyParse.C
register_cb() : ScriptTcl.C
register_exit_sched() : BackEnd.C
registerUserEventsForAllComputeObjs() : Node.C, ComputeMgr.C
rstring() : ParseOptions.C

- s -

scale_coordinates() : ComputePme.C
scale_forces() : ComputePme.C
SELF() : ComputeNonbondedBase.h
send_dgram() : main.C
set_macro() : ParseOptions.C
SetEqual() : FreeEnergyVector.C
settle1() : Settle.h, Settle.C
settle1init() : Settle.h, Settle.C
settle1isinitted() : Settle.h, Settle.C
settle2() : Settle.h, Settle.C
settlev() : Settle.C
shiftedpotential() : ComputeNonbondedFEP.C
SIMPARAM() : DumpBenchParams.h, DumpBench.C
simple_set_macro() : ParseOptions.C
sizeof_element() : packmsg.h
slave_init() : BackEnd.C
Strdup() : ParseOptions.C
swap4() : imd.C
swap_header() : imd.C

- t -

tbsoft_sendusage() : main.C
ti_vdw_force_energy_dUdl() : ComputeNonbondedFEP.C
TITITLE() : Controller.C
ToLower() : FreeEnergyParse.h, FreeEnergyParse.C

- u -

ustring() : ParseOptions.C

- v -

vec_rotation_matrix() : NamdOneTools.h, NamdOneTools.C
vmdsock_accept() : vmdsock.h, vmdsock.C
vmdsock_bind() : vmdsock.h, vmdsock.C
vmdsock_connect() : vmdsock.h, vmdsock.C
vmdsock_create() : vmdsock.h, vmdsock.C
vmdsock_destroy() : vmdsock.h, vmdsock.C
vmdsock_init() : vmdsock.h, vmdsock.C
vmdsock_listen() : vmdsock.h, vmdsock.C
vmdsock_read() : vmdsock.h, vmdsock.C
vmdsock_selread() : vmdsock.h, vmdsock.C
vmdsock_selwrite() : vmdsock.h, vmdsock.C
vmdsock_write() : vmdsock.h, vmdsock.C

- w -

wrap_coor() : Output.C
wrap_coor_int() : Output.C
write_dcdheader() : dcdlib.h, dcdlib.C
write_dcdstep() : dcdlib.h, dcdlib.C
write_dcdstep_par_header() : dcdlib.h, dcdlib.C
write_dcdstep_par_slave() : dcdlib.h, dcdlib.C
write_dcdstep_par_units() : dcdlib.h, dcdlib.C

Generated on Thu Jul 3 04:08:16 2008 for NAMD by

1.3.9.1