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LIST OF ALL COMPILE KEYWORDS IN CHARMMΒΆ

By employing appropriate preprocessor keys, one can generate a variant of CHARMM. This document list the preprocessor keywords used in the CHARMM source code. This list is still under construction and requires developers to update upon modifying and indroducing codes.

In the listing, note the following description keys. - member: keyword grouping - required: list of keywords required for this keyword to be used properly. - conflicting: list of keywords/groups that cannot be used with this keyword. - availability: If/How this keyword is generated by install.com - note: Any additional information about usage

CHARMM Element doc/commands.doc $Revision: 1.6 $

File: preflx_list, Node: Top, Up: (chmdoc/developer.doc), Next:


* Menu:

* Include::     Include File Directory
* Platform::    Machine Type
* OS::          Operating System
* Size::        Size Directive
* Archi::       Machine Architecture
* Parallel::    Parallel CHARMM descriptors
* Feature::     Feature Directives
* Graphics::    Graphics Directives
* Unnorm::      Keywords not for normal use
* NOINC::       Major Blocks that can be Removed
* Control::     Control Directives
* Unknown::     Undocumented keywords (must done soon)

File: preflx_list, Node: Include, Up: Top, Previous: Top, Next: Platform

[1] Include File Directory

    FCMDIR=directory_name   ! point to a particular directory
    FCMDIR=CURRENT          ! use what is specified in the include line.
    FCMDIR=LOCAL            ! use the local directory.


File: preflx_list, Node: Platform, Up: Top, Previous: Include, Next: OS

[2] Machine Type (choose exactly one)

    ALLIANT     = Alliant
                  member: machine-types, machines
                  required: ????
                  conflicting: machines
                  availability: none

    ALPHA       = DEC alpha workstation
                  member: machine-types, machines
                  required: ????
                  conflicting: machines
                  availability: ALPHA, ALPHAMP

    ALTIX       = SGI Altix
                  member: machine-types, machines
                  required: ????
                  conflicting: machines
                  availability: altix, ALTIX

    APOLLO      = HP-Apollo, both AEGIS and UNIX
                  member: machine-types, machines
                  required: ????
                  conflicting: machines
                  availability: none

    ARDENT      = Stardent, Titan series
                  member: machine-types, machines
                  required: ????
                  conflicting: machines
                  availability: STARDENT

    CONVEX      = Convex Computer
                  member: machine-types, machines
                  required: ????
                  conflicting: machines
                  availability: CONVEX

    CRAY        = Cray Research Inc.
                  member: machine-types, machines
                  required: ????
                  conflicting: machines
                  availability: CRAY

    DEC         = DEC ULTRIX
                  member: machine-types, machines
                  required: ????
                  conflicting: machines
                  availability: DEC

    HAL         = Sun computer port - special
                  member: machine-types, machines
                  required: ????
                  conflicting: machines
                  availability: HAL
    GWS         = intel-type machines using pg, g77, absoft, intel compilers
                         or any machine using gnu compiler
                  member: machine-types, machines
                  required: ????
                  conflicting: machines
                  availability: gnu

    GWS         = Sun Global Works System
                  member: machine-types, machines
                  required: ????
                  conflicting: machines
                  availability: GWS

    HPUX        = Hewlett-Packard series 700.
                  member: machine-types, machines
                  required: ????
                  conflicting: machines
                  availability: CSPP, HPUX


    HPITANIUM   = HP Itanium
                  member: machine-types, machines
                  required: ????
                  conflicting: machines
                  availability: hpitanium

    IBM         = IBM-3090 running AIX
                  member: machine-types, machines
                  required: ????
                  conflicting: machines
                  availability: none

    IBMRS       = IBM-RS
                  member: machine-types, machines
                  required: ????
                  conflicting: machines
                  availability: none, was IBMSP3, IBMRS

    IBMAIX      = All current IBM platforms running current AIX
                  member: machine-types, machines
                  required: ????
                  conflicting: machines
                  availability: IBMAIX,ibmaix

    IRIS        = Silicon Graphics
                  member: machine-types, machines
                  required: ????
                  conflicting: machines
                  availability: sgi, SGI64

    MACINTOSH   = Apple Macintosh computers (system 7)
                  member: machine-types, machines
                  required: ????
                  conflicting: machines
                  availability: none

    OSX         = Apple Macintosh computers OSX
                  member: machine-types, machines
                  required: ????
                  conflicting: machines
                  availability: OSX, osx

    SUN         = Sun Microsystems
                  member: machine-types, machines
                  required: ????
                  conflicting: machines
                  availability: SUN, SUNMPI, SUN64
                  availability: GWS

    ULTRA       = For modern Sun compilers circa 2000.
                  member: machine-types, machines
                  required: ????
                  conflicting: machines
                  availability: none

    VAX         = Digital Equipment Corp. VAX VMS.
                  member: machine-types, machines
                  required: ????
                  conflicting: machines
                  availability: none


  Other machine descriptors
    IBMMVS      = IBM's MVS platform
                  member: machine-descriptors, machines
                  required: ????
                  conflicting: machines
                  availability: none

    IBMVM       = IBM's VM platform
                  member: machine-descriptors, machines
                  required: ????
                  conflicting: machines
                  availability: none

    GNU         = using GNU Fortran compiler
                  member: machine-descriptors, machines
                  required: ????
                  conflicting: machines
                  availability: GNU

    CMEM        = A convex option?
                  member: machine-descriptors, machines
                  required: ????
                  conflicting: machines
                  availability: none

    GRAPE       = Use MD-GRAPE-II board to speedup nonbond calculations
                  member: machine-descriptors, machines
                  required: ????
                  conflicting: machines
                  availability: none

    LOBOS       = LoBoS cluster specific code
                  member: machine-descriptors, machines
                  required: ????
                  conflicting: machines
                  availability: none

  Parallel machine types
    ALPHAMP     = DEC Alpha Multi Processor machines
                  member: parallel-machines, machines
                  required: ????
                  conflicting: machines
                  availability: ALPHAMP

    CM5         = Machine type            = TMC's CM-5 machine
                  member: parallel-machines, machines
                  required: ????
                  conflicting: machines
                  availability: CM5

    CSPP        = Convex PA-RISC parallel system (HP chip)
                  member: parallel-machines, machines
                  required: HPUX
                  conflicting: machines
                  availability: CSPP

    CSPPMPI     = Convec SPP using proprietary MPI library
                  member: parallel-machines, machines
                  required: ????
                  conflicting: machines
                  availability: CSPP

    DELTA       = machine type            = Intel delta (Caltech) machine
                  member: parallel-machines, machines
                  required: ????
                  conflicting: machines
                  availability: none

    IBMSP       = machine type            = IBM's SPn cluster machines
                  member: parallel-machines, machines
                  required: ????
                  conflicting: machines
                  availability: none, use IBMAIXMP

    IBMSP1      = machine type            = IBM's SP1 cluster machines
                  member: parallel-machines, machines
                  required: ????
                  conflicting: machines
                  availability: none, use IBMAIXMP

    INTEL       = machine type            = Intel iPSC Hypercube
                  member: parallel-machines, machines
                  required: ????
                  conflicting: machines
                  availability: none

    PARAGON     = machine type            = Intel Paragon machine
                  member: parallel-machines, machines
                  required: ????
                  conflicting: machines
                  availability: none

    SGIMP       = machine type            = SGI Power Challenge
                  member: parallel-machines, machines
                  required: ????
                  conflicting: machines
                  availability: none

    T3D         = Cray massively parallel (DEC Alpha chip)
                  member: parallel-machines, machines
                  required: ????
                  conflicting: machines
                  availability: none

    T3E         = Cray massively parallel (DEC Alpha chip)
                  member: parallel-machines, machines
                  required: ????
                  conflicting: machines
                  availability: T3E

    TERRA       = multiprocessor DEC Alpha chip system
                  member: parallel-machines, machines
                  required: ????
                  conflicting: machines
                  availability: none



File: preflx_list, Node: OS, Up: Top, Previous: Platform, Next: Size

[3] Operating system (choose at most one)

    AIX370      = IBM UNIX
                  member: operating-system
                  required: IBM*  ???
                  conflicting: ???
                  availability: none

    UNIX        = UNIX
                  member: operating-system
                  required: ???
                  conflicting: ???
                  availability: ALPHA, ALPHAMP, ALTIX
                  availability: CONVEX, CSPP, DEC, GNU, HPUX, IBMAIX
                  availability: IBMAIXMP,
                  availability: SGI64, SUN, SUNMPI
                  availability: SUN64, HAL, GWS, T3E

    UNICOS      = Cray UNIX
                  member: operating-system
                  required: ???
                  conflicting: ???
                  availability: none

    OS2         = IBM pre-emptive multitasking
                  member: operating-system
                  required: IBM* ???
                  conflicting: ???
                  availability: none


File: preflx_list, Node: Size, Up: Top, Previous: OS, Next: Archi

[4] Size directive (must choose exactly one)

    HUGE        = 1,000,000 atom limit
                  member: size-directives
                  required: none
                  conflicting: size-directives
                  availability: huge

    XXLARGE     =360720 atom limit
                  member: size-directives
                  required: none
                  conflicting: size-directives
                  availability: XXLARGE

    XLARGE      =240480 atom limit
                  member: size-directives
                  required: none
                  conflicting: size-directives
                  availability: none

    LARGE       = 60120 atom limit
                  member: size-directives
                  required: none
                  conflicting: size-directives
                  availability: LARGE

    MEDIUM      = 25140 atom limit
                  member: size-directives
                  required: none
                  conflicting: size-directives
                  availability: MEDIUM

    REDUCE      = 15000 atom limit, and most memory at mimimums
                  member: size-directives
                  required: none
                  conflicting: size-directives
                  availability: REDUCE

    SMALL       =  6120 atom limit
                  member: size-directives
                  required: none
                  conflicting: size-directives
                  availability: SMALL

    XSMALL      =  2040 atom limit
                  member: size-directives
                  required: none
                  conflicting: size-directives
                  availability: XSMALL


File: preflx_list, Node: Archi, Up: Top, Previous: Size, Next: Parallel

[5] Machine Architecture (may choose several)

    SCALAR      = machine characteristics = default for scalar machines
                  member: machine-character
                  required: none
                  conflicting: none
                  availability: MPISET, ALPHA, ALPHAMP, CM5
                  availability: DEC, GNU, CSPP, HPUX, IBMAIX
                  availability: IBMAIXMP, IBMRS, IBMSP, IBMSP3, INTEL
                  availability: INTEL, SGI64, SUN, SUNMPI, SUN64, HAL
                  availability: GWS, T3D, T3E, TERRA
                  availability: NIH

    VECTOR      = feature directive *     = Vectorized routines
                  member: machine-character
                  required: none
                  conflicting: none
                  availability: CONVEX, CRAY, STARDENT
                  availability: NIH

    PARVECT     = Parallel vector code (multi processor vector machines)
                  member: machine-character
                  required: none
                  conflicting: none
                  availability: CONVEX
                  availability: NIH

    CRAYVEC     = Fast vector code (standard vector code)
                  member: machine-character
                  required: none
                  conflicting: none
                  availability: CRAY
                  availability: NIH

    SINGLE      = specifies single precision version (primarily used for CRAY)
                  member: machine-character
                  required: none
                  conflicting: ???
                  availability: CRAY

    SGIF90      = Used to compile CHARMM using F90 compiler on SGI machines
                  member: machine-character
                  required: ???
                  conflicting: ???
                  availability: none

    64          = use 64 bit pointers
                  member: machine-character
                  required: ????
                  conflicting: ???
                  availability: 64 with {sgi,sgi64, ibmaix, ibmaixmp}


    I8          = use 64 bit integers or uses only 64 bit integers
                  member: machine-character
                  required: ????
                  conflicting: ???
                  availability: i8, I8

    T3ETRAJ     = Used to read t3e trajectories on IEEE machines w/ 32 bit integers
                  member: machine-character
                  required: T3E ???
                  conflicting: ???
                  availability: none

    I4BINARY    = Insures integer*4 binary files are written
                  member: machine-character
                  required:
                  conflicting: ???
                  availability: all 64 bit compiles

    TESTENDIAN  = Check endian-ness of trajectories when reading
                  non-native trajectories
                  member: machine-character
                  required:
                  conflicting: ???
                  availability: only by manual addition to pref.dat



File: preflx_list, Node: Parallel, Up: Top, Previous: Archi, Next: Feature


[6] Parallel CHARMM descriptors  (see parallel.doc)

    (all require the PARALLEL keyword)

    COMMEASURE  = enable parallel communications timing code
                  member: parallel-option
                  required: PARALLEL, ???
                  conflicting: ???
                  availability: none

    GENCOMM     = Use general communications scheme
                  member: parallel-option
                  required: PARALLEL, ???
                  conflicting: ???
                  availability: PVMSET, SOCKET, MPISET

    MANYNODES   = use options that are more efficient with many nodes
                  member: parallel-option
                  required: PARALLEL, ???
                  conflicting: ???
                  availability: none

    MPI         = Using MPI communication primitives
                  member: parallel-option
                  required: PARALLEL, ???
                  conflicting: ???
                  availability: MPISET

    PARAFULL    = Full communication parallel scheme.
                  member: parallel-option
                  required: PARALLEL, ???
                  conflicting: ???
                  availability: PVMSET, SOCKET, MPISET, SUNMPI, GWS
                  availability: CSPP, TERRA, CM5, IBMSP, IBMSP3, IBMAIX
                  availability: T3D, T3E, ALPHAMP

    PARALLEL    = Multi-machine (Intel, workstation clusters,...)
                  member: parallel-option
                  required: none
                  conflicting: (see doc/parallel.doc )
                  availability: PVMSET, SOCKET, MPISET, SUNMPI, GWS
                  availability: CSPP, TERRA, CM5, IBMSP, IBMSP3, IBMAIX
                  availability: T3D, T3E, ALPHAMP

    PARASCAL    = Scalable method (coordinates and forces not global)
                  member: parallel-option
                  required: PARALLEL, ???
                  conflicting: ???
                  availability: none

    PVM         = use PVM parallel communcations library
                  member: parallel-option
                  required: PARALLEL, ???
                  conflicting: ???
                  availability: PVMSET

    PVMC        = use PVM parallel communcations library; alt. method
                  member: parallel-option
                  required: PARALLEL, ???
                  conflicting: ???
                  availability: PVMSET

    SHMEM       = Shared memory put & get
                  member: parallel-option
                  required: PARALLEL, ???
                  conflicting: ???
                  availability: none

    SOCKET      = Use socket calls for communication
                  member: parallel-option
                  required: PARALLEL, ???
                  conflicting: ???
                  availability: SOCKET

    BUFFERED    = Buffered communication (may speed up TCP/IP transfer)
                  member: parallel-option
                  required: PARALLEL, ???
                  conflicting: ???
                  availability: none

    CMPI        = CHARMM implementation of the MPI standard (still needed)
                  member: parallel-option
                  required: PARALLEL, ???
                  conflicting: ???
                  availability: PVMSET, SOCKET, MPISET, CM5

    CMPIx       = Easy way to temporarily exclude some code. Should be cleaned
                  member: parallel-option
                  required: PARALLEL, ???
                  conflicting: ???
                  availability: none

    CONCURR     = Enables documented parallel concurent
                  member: parallel-option
                  required: PARALLEL, ???
                  conflicting: ???
                  availability: none

    ETHER       = Parallel platform which was never used
                  (should go away at some point)
                  member: parallel-option
                  required: PARALLEL, ???
                  conflicting: ???
                  availability: none

    RING        = Parallel platform which was never used
                  (should go away at some point)
                  member: parallel-option
                  required: PARALLEL, ???
                  conflicting: ???
                  availability: none

    SCHED       = Used on clusters to change the scheduling mechanism in kernel
                  member: parallel-option
                  required: PARALLEL, ???
                  conflicting: ???
                  availability: none

    TIMESTAMP   = Precise timing of the communication
                  member: parallel-option
                  required: PARALLEL, ???
                  conflicting: ???
                  availability: none

    PRLLOUT     = Specify to direct output from processors to separate files
                  member: parallel-option
                  required: PARALLEL, ???
                  conflicting: ???
                  availability: none

    CRAY_1DFFT  = Used for parallel PME on Cray T3E
                  member: parallel-option
                  required: PARALLEL, ???
                  conflicting: ???
                  availability: none

    MPIFFT      = Faster FFT transpose using asynchronous MPI send/recv
                  member: parallel-option
                  required: PARALLEL, ???
                  conflicting: ???
                  availability: none

    MPIFFT      = Faster FFT transpose using asynchronous MPI send/recv
                  member: parallel-option
                  required: PARALLEL, ???
                  conflicting: ???
                  availability: none

    IBMAIX_MPI64 = Correct calls to mpi routines for 64 bit compiles
                  member: parallel-option
                  required: PARALLEL, ???
                  conflicting: ???
                  availability: IBMAIXMP with 64

    MPIFFT      = Faster FFT transpose using asynchronous MPI send/recv
                  member: parallel-option
                  required: PARALLEL, ???
                  conflicting: ???
                  availability: none



File: preflx_list, Node: Feature, Up: Top, Previous: Parallel, Next: Graphics


[7] Feature directives

    ACE         = Generalzied Born model from M Schaefer.
                  member: features
                  required: ???
                  conflicting: ???
                  availability: FULL

    AMBER       = Use to get different CCELEC compatable with Amber
                  member: features
                  required: none
                  conflicting: none
                  availability: none

    ASPENER     = Atomic Solvation Parameter energy term
                  member: features
                  required: ???
                  conflicting: ???
                  availability: FULL

    BLOCK       = Energy partition and free energy code
                  member: features
                  required: none
                  conflicting: none
                  availability: FULL

    CGENFF      = make top and par arrays larger for General Force Field
                  member: features
                  required: none
                  conflicting: possibly but unlikely: MMFF, CFF, YAMMP
                  availability: FULL

    CMAP        = ???
                  member: features
                  required: ???
                  conflicting: ???
                  availability: IBMSP, IBMSP3, IBMAIX, T3D, T3E
                  availability: FULL

    DIMB        = Iterative diagonalization, reduced basis (normal modes)
                  member: features
                  required: ???
                  conflicting: NOVIBRAN
                  availability: FULL

    DMCONS      = Contact map umbrella potential routine
                  member: features
                  required: ???
                  conflicting: ???
                  availability: FULL

    DOCK        = modification of block to include assymetric matrix
                  member: features
                  required: ???
                  conflicting: ???
                  availability: FULL

    EISPACK     = Use the EISPACK code for diagonalization
                  member: features
                  required: ???
                  conflicting: ???
                  availability: none

    FACTS       = Generalized Born model
                  (Fully Analytical Continuum Treatment of Solvation)
                  member: features
                  required: ???
                  conflicting: ???
                  availability: FULL

    FASTENBFS8  = Reordered loops for faster non-PME nonbond energy.
                  member: features
                  required: None
                  conflicting: None, but see note
                  availability: ALTIX, SGI, SGI64
                  note: This is purely a performance optimization.
                        It was designed for software pipelining architectures.

    FASTEW      = Reordered loops for faster direct sum in PME
                  member: features
                  required: None
                  conflicting: None, but see note
                  availability: ALTIX, SGI, SGI64
                  note: This is purely a performance optimization.
                        It was designed for software pipelining architectures.
                        Some keywords, like DRUDE, ruin the performance on
                        some platforms.

    FILEINPUT   = Use to take standard in from charmm.inp
                  member: features
                  required: ???
                  conflicting: ???
                  availability: none

    FILEOUTPUT  = Use to send standard out to charmm.out
                  member: features
                  required: ???
                  conflicting: ???
                  availability: none

    FMA         = Fast Multipole method
                  member: features
                  required: ???
                  conflicting: ???
                  availability: FULL

    FOURD       = minimization and dynamics in 4 dimensions
                  member: features
                  required: ???
                  conflicting: ???
                  availability: FULL

    FSSHK       = Use to get optimized SHAKE for non CRAYVEC machines
                  member: features
                  required: ???
                  conflicting: ???
                  availability: IBMSP3, IBMAIX
                  availability: FULL

    GAMESS      = Include the GAMESS QM package
                  member: features, quantum-method
                  required: ???
                  conflicting: quantum-method, ???
                  availability: GAMESS

    GENETIC     = Use to include Genetc algorithm and internal
                    coordinate MC sampling
                  member: features
                  required: ???
                  conflicting: ???
                  availability: FULL

    GRID        = Set-up and use grid based potentials for docking
                  member: features
                  required: ???
                  conflicting: ???
                  availability: FULL

    BANBA       = Generalized Born module and lambda dynamics
                  member: features
                  required: GENBORN ???
                  conflicting: ???
                  availability: FULL

    GBBLCK      = Generalized Born module
                  member: features
                  required: GENBORN ???
                  conflicting: ???
                  availability: FULL

    GBFIXAT     = Generalized Born module
                  member: features
                  required: GENBORN ???
                  conflicting: ???
                  availability: FULL

    GBINLINE    = Generalized Born module
                  member: features
                  required: GENBORN ???
                  conflicting: ???
                  availability: IBMSP3, IBMAIX, TSRI
                  availability: FULL

    GBNOLIST    = Generalized Born module
                  member: features
                  required: GENBORN ???
                  conflicting: ???
                  availability: none

    GBSWIT      = Generalized Born module
                  member: features
                  required: GENBORN ???
                  conflicting: ???
                  availability: IBMSP3, IBMAIX, TSRI
                  availability: FULL

    GENBORN     = Generalized Born module
                  member: features
                  required: GENBORN ???
                  conflicting: ???
                  availability: IBMSP3, IBMAIX, TSRI
                  availability: FULL

    GBMV        = Generalized Born Molecular Volume module
                  member: features
                  required: GENBORN ???
                  conflicting: ???
                  availability: IBMSP, IBMSP3, IBMAIX, T3D, T3E
                  availability: FULL

    HMCM        = HArmonic restraints to center of mass
                  member: features
                  required: ???
                  conflicting: ???
                  availability: FULL

    IMCUBES     = Include to use image cubes list algorithm
                  member: features
                  required: ???
                  conflicting: NOIMAGES
                  availability: IBMSP3, IBMAIX, TSRI
                  availability: FULL

    LATTICE     = Module to read/write Skolnick lattice files
                  member: features
                  required: ???
                  conflicting: ???
                  availability: FULL

    LDM         = Lambda-dynamics module
                  member: features
                  required: ???
                  conflicting: ???
                  availability: FULL

    LDLAN       = Lambda-dynamics module
                  member: features
                  required: LDM ???
                  conflicting: ???
                  availability: FULL

    LDMGEN      = Lambda-dynamics module
                  member: features
                  required: LDM ???
                  conflicting: ???
                  availability: FULL

    NOLDMUP     = Lambda-dynamics module
                  member: features
                  required: LDM ???
                  conflicting: ???
                  availability: none

    LMC         = Lambda-dynamics module
                  member: features
                  required: LDM ???
                  conflicting: ???
                  availability: FULL

    LRST        = Lambda-dynamics module
                  member: features
                  required: LDM ???
                  conflicting: ???
                  availability: FULL

    QBLOCK      = Lambda-dynamics module
                  member: features
                  required: LDM ???
                  conflicting: ???
                  availability: none

    LRVDW       = Long-range vdw correction to energy and pressure
                  member: features
                  required: ???
                  conflicting: ???
                  availability: none

    MCSS        = Multiple Copy Simultaneous Search
                  member: features
                  required: ???
                  conflicting: ???
                  availability: none

    MMFF        = Merck's Molecular Force Field
                  member: features
                  required: ???
                  conflicting: ???
                  availability: FULL

    MOLVIB      = MOLVIB vibrational analysis code
                  member: features
                  required: ???
                  conflicting: NOVIBRAN
                  availability: FULL

    MULTCAN     = AN implementation of multi-canonical sampling
                  member: features
                  required: ???
                  conflicting: ???
                  availability: FULL

    MTS         = Multiple time step code
                  member: features
                  required: ???
                  conflicting: ???
                  availability: FULL???

    NIH         = NIH default specs code
                  member: features
                  required: ???
                  conflicting: ???
                  availability: CSPP, MPISET, GWS
                  availability: NIH

    NEWTIMER    = New timing routines to be included as default
                  member: features
                  required: ???
                  conflicting: ???
                  availability: IBMSP3, IBMAIX
                  availability: FULL

    NOPARASWAP  = inhibit ASP parameter swap method (requires ASPENER)
                  member: features
                  required: ???
                  conflicting: ???
                  availability: none

    OLDDYN      = Old dynamics integrator
                  member: features
                  required: none
                  conflicting: none
                  availability: FULL??, LITE

    PBEQ        = Poisson Boltzmann equation solver
                  member: features
                  required: ???
                  conflicting: ???
                  availability: FULL

    PBOUND      = Simple periodic boundary method
                  member: features
                  required: ???
                  conflicting: NOIMAGES
                  availability: FULL??, LITE

    PBOUNDC     = Additional keyword for pbound in cray vector code
                  member: features
                  required: ???
                  conflicting: ???
                  availability: none

    PERT        = NIH free energy code
                  member: features
                  required: none
                  conflicting: none
                  availability: FULL

    PM1         = PM1 polarization water model
                  member: features
                  required: ???
                  conflicting: ???
                  availability: FULL

    PMEPLSMA    = Used in PME for charged system correction with plasma
                  Replaces the accurate calculation of net charge correction.
                  member: features
                  required: ???
                  conflicting: ???
                  availability: IBMSP3, IBMAIX, TSRI
                  availability: FULL
                  note: This code gives wrong answers - BRB

    POLAR       = Feynman path integral simulations and PM6 or PM1
                  member: features
                  required: ???
                  conflicting: ???
                  availability: none

    PRIMSH      = Shell option in MMFP?
                  member: features
                  required: ???
                  conflicting: ???
                  availability: FULL

    PREFMSI     = Includes pref.dat keys in accessible CHARMM data structure
                  member: features
                  required: ???
                  conflicting: ???
                  availability: IBMSP3

    PSSP        = Compile specialized soft sphere energy routines
                  to be used together with PERT free energy calculations
                  member: features
                  required: ???
                  conflicting: ???
                  availability: FULL

    QUANTA      = Quanta interface code
                  member: features
                  required: ???
                  conflicting: ???
                  availability: none

    QUANTUM     = AM1 QM/MM method using MopacXX (not with GAMESS or CADPAC)
                  member: features, quantum-method
                  required: ???
                  conflicting: quantum-method, ???
                  availability: FULL unless other quantum-method

    RCFFT       = Key word for real-to-complex ffts in parallel PME
                  member: features
                  required: ???
                  conflicting: ???
                  availability: TERRA, IBMSP, IBMSP3, IBMAIX, T3D, T3E, ALPHAMP
                  availability: FULL

    REPLICA     = Replica code  (requirs BLOCK)
                  member: features
                  required: BLOCK
                  conflicting: none
                  availability: FULL

    RGYCONS     = Umbrella potential in radius of gyration
                  member: features
                  required: ???
                  conflicting: ???
                  availability: FULL

    RISM        = RISM solvation code
                  member: features
                  required: ???
                  conflicting: ???
                  availability: FULL

    RXNCOR      = RXNCOR code
                  member: features
                  required: ???
                  conflicting: ???
                  availability: FULL

    SHAPES      = NIH shape descriptor code (under development)
                  member: features
                  required: none
                  conflicting: none
                  availability: FULL

    SOFTVDW     = Use to permit soft vdw and electrostatic short range
                    potentials
                  member: features
                  required: ???
                  conflicting: ???
                  availability: FULL

    TNPACK      = truncated Newton minimization
                  member: features
                  required: ???
                  conflicting: ???
                  availability: FULL

    TRAVEL      = PATH and TRAVEL code
                  member: features
                  required: ???
                  conflicting: ???
                  availability: FULL

    TSM         = TSM and ICPERT code
                  member: features
                  required: none
                  conflicting: none
                  availability: FULL

    YAMMP       = Key for compatability in use with YAMMP from Steve Harvey
                  member: features
                  required: ???
                  conflicting: ???
                  availability: none


File: preflx_list, Node: Graphics, Up: Top, Previous: Feature, Next: Unnorm

[8] Graphics keywords;

    NOGRAPHICS  = graphics code not compiled
                  member: graphics-option, major-feature-remove
                  required: none
                  conflicting: none
                  availability: .not.(XREQ|NODSP)

    GLDISPLAY   = use the GL display code for the graphics window (*)
                  The GL code is relatively untested, and may have problems
                  member: graphics-option
                  required: none
                  conflicting: NOGRAPHICS NODISPLAY APOLLO XDISPLAY
                  availability: none

    NODISPLAY   = no graphics window; PostScript, other files produced
                  member: graphics-option
                  required: none
                  conflicting: NOGRAPHICS NODISPLAY XDISPLAY
                  availability: NODSP

    XDISPLAY    = use the X11 display code for the graphics window
                  member: graphics-option
                  required: none
                  conflicting: NOGRAPHICS NODISPLAY APOLLO GLDISPLAY
                  availability: XREQ


File: preflx_list, Node: Unnorm, Up: Top, Previous: Graphcis, Next: NOINC

[9] Keywords Not for Normal Use

    JUNK        = Code with problems or unused (but not ready for discard)
                  member: unused-code
                  required: ???
                  conflicting: ???
                  availability: none

    DEBUG       = Extra print statements.
                  member: unused-code
                  required: ???
                  conflicting: ???
                  availability: none

    IPRESS      = Pressure code in suspended development (for PBOUND)
                  member: unused-code
                  required: none
                  conflicting: none

                  availability: none
    REPDEB      = debug replica code.
                  member: unused-code
                  required: REPLICA BLOCK
                  conflicting: ???
                  availability: none

    DEBUGGB     = debug in GB code.
                  member: unused-code
                  required: ???
                  conflicting: ???
                  availability: none

    UNUSED      = isolate code apparently not used
                  member: unused-code
                  required: ???
                  conflicting: ???
                  availability: none

    CKSHKTOL    = debugging for fast shake
                  member: unused-code
                  required: ???
                  conflicting: ???
                  availability: none


File: preflx_list, Node: NOINC, Up: Top, Previous: Unnorm, Next: Control

[10] Major Blocks that can be Removed, but normally are not

    NOCORREL    = removes time series analysis
                  member: major-feature-remove
                  required: none
                  conflicting: none
                  availability: TERRA, CM5, T3D, T3E, ALPHAMP

    NOGRAPHICS  = removes all graphics code (see above in graphics)

    NOIMAGES    = removes image and crystal fascility
                  member: major-feature-remove
                  required: none
                  conflicting: none

    NOST2       = removes ST2 water model routines
                  member: major-feature-remove
                  required: none
                  conflicting: none
                  availability: TERRA, CM5, T3D, T3E, ALPHAMP

    NOVIBRAN    = removes vibrational analysis and all Hessian code
                  member: major-feature-remove
                  required: none
                  conflicting: none
                  availability: TERRA, CM5, T3D, T3E, ALPHAMP

    NOMISC      = removes miscellaneous stuff:
                    BARR, DRAWSP, HBUILD, PATH, QUICKA, SBOUND, SURFAC,
                    XRAY, TESTCH, RXNCOR
                  member: major-feature-remove
                  required: none
                  conflicting: none

    NO_BYCC     = removes BYCC list option for memory savings
                  member: major-feature-remove
                  required: none
                  conflicting: none
                  availability: IBMSP3, IBMAIX, T3E

    NO_BYCU     = removes BYCU list option for memory savings
                  member: major-feature-remove
                  required: none
                  conflicting: none
                  availability: IBMSP3, IBMAIX, T3E

    NO_DQS      = removes DQS loption from NMR module for memory savings
                  member: major-feature-remove
                  required: none
                  conflicting: none


File: preflx_list, Node: Control, Up: Top, Previous: NOINC, Next: Unknown

[11] Other Control Directives

    EXPAND      = Do semi-automatic code expansion
                  member: compile-directive
                  required: none
                  conflicting: none
                  availability: NIH

    LONGLINE    = Allows a longer line output format (>80 characters).
                  member: compile-directive
                  required: none
                  conflicting: none
                  availability: NIH

    SAVEFCM     = Include all SAVE statements in .fcm files
                  member: compile-directive
                  required: none
                  conflicting: none
                  availability: NIH

    SINGLE      = Conversion to single precision (SINGLE is a keyword)
                  member: compile-directive
                  required: none
                  conflicting: ???
                  availability: CRAY

    PUTFCM      = Include files are to be copied into fortran files
                  member: compile-directive
                  required: none
                  conflicting: none
                  availability: FULL, LITE, always

    VMS         = Use VMS directory names (from DEC's DCL)
                  member: compile-directive
                  required: VAX???
                  conflicting: none

    REMIMPNON   = Remove any "IMPLICIT NONE" lines found in the source
                  member: compile-directive
                  required: none
                  conflicting: none

    UPPERCASE   = Convert all non-text code to uppercase Fortran
                  member: compile-directive
                  required: none
                  conflicting: none


File: preflx_list, Node: Unknown, Up: Top, Previous: Control, Next: Top

[12] Undocumented keywords (coming soon)

    ADUMB       =
                  availability: FULL

    CADPAC      =
                  member: features, quantum-method
                  required: ???
                  conflicting: quantum-method, ???
                  availability: CADPAC

    CFF         =
                  availability: FULL

    CHARMMRATE  =
                  availability: POLYRATE

    CHEMPERT    =
                  availability: none

    CHEQ        =
                  availability: none

    DISCOVER    =
                  availability: none

    EMAP        =
                  availability: FULL

    ESTATS      =
                  availability: FULL

    FLUCQ       =
                  availability: none

    GAMESSUK    =
                  member: features, quantum-method
                  required: ???
                  conflicting: quantum-method, ???
                  availability: GAMESSUK

    GAUSSIAN    =
                  availability: none

    GBSW        =
                  availability: none
                  note: Is this supposed to be GBSWIT?

    GCMC        =
                  availability: none

    GNUALPHA    =
                  availability: none

    GOMODEL     =
                  availability: none

    GRAPE1      =
                  availability: none

    GSBP        =
                  availability: FULL

    IBMAIX      =
                  member: machine-types, machines
                  required: UNIX, SCALAR
                  conflicting: machines
                  availability: IBMAIX

    IBMAIXMP    =
                  member: machine-types, machines
                  required: UNIX, SCALAR
                  conflicting: machines
                  availability: IBMAIXMP

    INSIGHT     =
                  availability: none

    INTEGER8    =
                  member: ???
                  required:
                  conflicting:
                  availability: LONGINT

    LIBGRAPE    =
                  availability: none

    LONEPAIR    =
                  availability: FULL

    MBOND       =
                  availability: none

    MC          =
                  availability: FULL

    MEHMC       =
                  availability: none

    NEWRNG      =
                  availability: none

    NOSKULL     = Do not print the Skull and crossbones when CHARMM dies.
                  availability: none

    NOTDEF      =
                  availability: none

    OLDGRAPE    =
                  availability: none

    OLD_IMCUBES =
                  availability: none

    OVERLAP     =
                  availability: none

    PARALLELSHK =
                  availability: none

    PARALLELx   =
                  availability: none

    PARASCC     =
                  availability: none

    PATHINT     =
                  availability: FULL

    PBC         =
                  availability: none

    PNOE        =
                  availability: FULL

    POINTER_KEY =
                  availability: none

    POSIX       =
                  availability: CRAY&'TS'

    QCHEM       =
                  member: features, quantum-method
                  required: ???
                  conflicting: quantum-method, ???
                  availability: none

    QDYN        =
                  availability: none

    RDFSOL      =
                  availability: none

    SASAE       =
                  availability: FULL

    SCCDFTB     =
                  member: features, quantum-method
                  required: ???
                  conflicting: quantum-method, ???


    SHELL       =
                  availability: none

    SPAS        =
                  availability: none

    SSH         =
                  availability: none

    SUN64       =
                  member: machine-types, machines
                  required: UNIX, SCALAR
                  conflicting: machines
                  availability: SUN64


    TMD         =
                  availability: none

    TPS         =
                  availability: none

    TSALLIS     =
                  availability: FULL