CHARMM Element doc/test.doc 1.1#File: Test, Node: Top, Up: (chmdoc/commands.doc) Test commands: Commands to test various conditions in CHARMM[SYNTAX TEST]Syntax of the TEST commands:TEST FIRSt [TOL real] [STEP real] [UNIT int] [MASS int] [atom-selection] (0.005) (0.0001) (6) (0) [ CRYStal [ HOMOgeneous ] ]TEST SECOnd [TOL real] [STEP real] [UNIT int] (0.005) (0.0001) (OUTU (6)) TEST COORdinates [COMP]TEST CONNectvity [SUBSet atom-selection] [COMMon atom-selection] [PRINt]TEST PSFTEST PARAmeter TRIGonometry { DIHEdral } { CDIHedral } { VDIHedral } { IMPRoper }TEST HEAPTEST STACkGETHeap integerTEST INITializationRESETTEST NOCOmmunication { READ UNIT int STEP int MEMO int } { WRITE UNIT int STEP int MEMO int } { CLOSE }TEST STAMp LEVEl int The TEST FIRSt command, tests the first derivative of theenergy by finite differences. It uses the GETE subroutine, so that beforethis command is invoked, the UPDAte command must be invoked. Sincetwo energy evaluations are done for each degree of freedom, an atomselection should be used for large systems. The TOL keyword may beused to list only those terms which differ by more than a particulartolerance factor. The STEP keyword gives the finite difference stepsize in angstroms. The MASS integer value determines how mass weightingwill be used with regards to rigid or SHAKE constraints (0= no massweighting, 1= mass weighting, -1=ignore water hydrogen masses).This command is analogous to the second derivative test command underthe vibrational analysis (VIBRAN:: WRITE SECOnd derivatives CARDFINIte). The CRYStal keyword also causes the forces along the crystaldegrees of freedom to be checked. The HOMOgeneous keyword causes thecauses all of the atoms to be scaled in a homogeneous fashion whenthe box size/shape changes.The TEST SECOnd command, tests the second derivative of theenergy by finite difference of the forces. It is thus assumed that thefirst derivative is wright. UPDAte should be invoked before use. Noselection is allowed and the whole 3Nx(3N+1)/2 second derivativematrices are created by analytic and finite difference methods. Sodon't use a too big system (a few hundred atoms depending on yourcomputer). TOL and STEP have the same meaning than for TEST FIRSt. The TEST COORdinates command will test to insure that allcoordinates are in range and defined. The comparison coordinates may betested. The TEST CONNectivity command tests the structure for properconnectivity between the selected set of atoms. This is to facilitatefinding loose pieces of a molecule after a DELEte ATOM command. Thealgorithm checks to make sure that some connective bonding, bonds,angles or torsions, exist between atoms in the selection SUBSet andatoms in the COMMon set selection. For example, if a sequence ofamino acid residues, say 1-5, were selected as the SUBSet and only residue5 was selected for the COMMon set the CONNectivity between the two setsis true. If, say, residue 10 was selected for the common set then thetest would prove false and the message "One disconnected segment found"would be printed. The TEST PSF command tests most of the data in the structure file.The data is sorted and duplications are found as well.The TEST PARAmeter command write out the tables used by energyroutines. DIHEdral, CDIHedral and IMPRoper TRIGonometry tables are theparameters listed in the order they are stocked. Number,Force-constant, Periodicity, Reference Angle, Cosine and sine arelisted. The VDIHedral option lists the dihedral energy term series asthey are used in the PARVect dihedral energy routines. Term-number,Parameter-number (cf DIHEdral), Force-constant, Periodicity,Reference Angle, Cosine and sine are listed. TEST PARAmeter is mostlyfor developing purposes. An unknown option will be ignored. The TEST HEAP command causes the heap data to be printedbetween non-miscellaneous commands. This will continue untiljob termination. This makes it easy to see where space allocationwent wrong during program development. The TEST STACk command performsthe same function for stack space usage. The GETHeap routine allocates and then frees a block of memoryspecified in words. This command is used to prevent fragmentation ofmemory, or to preallocate disk space for a long run that will needspace later. The TEST INITialization command will initialize just abouteverything. Its use is in testing the program when making majorchanges or additions. The RESEt command deletes all atoms and calls the initializationroutine. It should be called before TEST INIT to reset everything. The TEST NOCOmmunication performs parallel run reading datafrom memory instead. TEST NOCO WRITE command has to be performed on asingle CPU and writes all the necessary data from memory to a filespecified by UNIT keyword. The STEP keyword specifies the number ofsteps for which the information will be saved to a file. MEMOrykeyword reserves the memory needed for this operation. TEST NOCO READhas the same parameters as WRITE, but the complete information isstored to the memory from the file for the number of steps specifiedwith the STEP keyword. TEST NOCO CLOSe has to be specified after WRITEcommand and before STOP. The TEST STAMp command outputs a time stamp in microsecondprecision of the following events: level= 0 - OFF -1 - from input script 1 - report from dynamics 2 - report from paral1 routines 4 - report from paral3 routinesNOTE: It is possible to combine reports, ie level=6 is the same as level.eq.4 or