The odata file

Input is keyword driven with sensible defaults in most cases. The last keyword will usually be POINTS, after which the starting geometry is specified, one atom per line, by the atomic symbol (case insensitive) and the corresponding x, y and z coordinates. For potentials that are coded within OPTIM there will always be an assumed unit system. OPTIM determines the potential to be used from the atomic symbol of the last atom, and various symbols have evolved for different systems, as described in §II. Free format may be used within each line. Blank lines are ignored.

The following keywords are recognized, where n and x are integer and real data, respectively.

• 2D: restrict the system to the x-y plane.
• ADM n: will cause the interatomic distance matrix to be printed every n cycles; the default for n is 20. This matrix is not printed by default.
• AXIS n: specifies the highest symmetry axis to search for in routine symmetry; default is six.
• AXTELL Z^*: specifies that the Axilrod-Teller potential with coefficient Z^* is to be added to the potential specified by the atom type.
• BINARY ntypea epsab epsbb sigmaab sigmabb: specifies a binary Lennard-Jones system for use with the Lp or Ls atom types. ntypea is the number of type A atoms--the rest are assumed to be type B and appear at the end of the list of coordinates. 2#2 define the units of energy and length, and epsab=3#3, epsbb=4#4,sigmaab=5#5, sigmabb=6#6.
• CADPAC system exec: tells the program to read derivative information in CADPAC format. system is a string to identify the system and exec is the name of an executable which will generate a CADPAC input deck from a points file. If exec is omitted its name is assumed to be editit.system.
• CGCONV qmax gmax: qmax is the convergence criterion for the energy change between successive steps, default 0.001. gmax is the convergence criterion for the root-mean-square gradient, default 0.001. These are the convergence criteria for the subspace minimizations in hybrid EF/CG transition state searches, for use with CGTS.
• CHECKINDEX nevs ceig nevl: instructs the program to check the Hessian index after a conjugate gradient minimization or conjugate gradient hybrid transition state search. This keyword now works with NOHESS. The parameters are the same as for CGTS below, and need not be set if they have already been specified by that keyword.
• CHECKCONT: if CHECKINDEX is specified then CHECKCONT instructs the program to take a pushoff and continue if convergence to a stationary point with the wrong Hessian index is detected.
• CGMIN qmax gmax: instructs the program to perform a conjugate gradient minimization. qmax is the convergence criterion for the energy change between successive steps, default 0.001. gmax is the convergence criterion for the root-mean-square gradient, default 0.001.
• CGSTEP: instructs the program to step off a saddle point along the eigenvector corresponding to the smallest negative eigenvalue without diagonalizing the Hessian to find this eigenvector. It is possible to step off parallel and antiparallel to this eigenvector by specifying positive or negative values for the MODE parameter. CGTS must be set too.
• CGTS nevs ncgmax ceig nevl: instructs the program to perform a hybrid conjugate gradient/eigenvector-following transition state search. nevs is an integer which defines the largest number of iterations allowed in the calculation of the smallest Hessian eigenvalue; default 500. ncgmax is an integer which defines the largest number of conjugate gradient steps allowed in the subspace optimization; default 100. ceig is a double precision parameter which governs the convergence criterion for the eigenvalue of the eigenvector which will be searched uphill; default 1.0. ceig is compared to the percentage change in the eigenvalue between successive steps. nevl is an integer which defines the largest number of iterations allowed in the calculation of the largest Hessian eigenvalue; default 100. Not needed if NOHESS is set.
• COMMENT or NOTE: the rest of the line is ignored.
• CONVERGE x y: overrides the default convergence conditions for eigenvector-following and steepest-descent calculations described in §V. If one number is supplied then convergence depends only upon the maximum unscaled step falling below the specified value (and the right number of negative Hessian eigenvalues). If two numbers are supplied the second is the required threshold for the RMS force which must also be satisfied.
• DCHECK ON/OFF: turns on/off warning messages when atoms approach to within 0.5 distance units units. Default is ON.
• DBRENT: if set then all line minimizations will use Brent's method based upon first derivatives rather than just energies. This can be significantly slower and does not seem to improve the accuracy.
• DEBUG: causes unscaled steps, gradients, Hessian eigenvalues and summary information to be printed every cycle. Turned off by default.
• DOUBLE: adds a double-well potential as per J. Chem. Phys., 110, 6617, 1999. The energy and derivatives add to the potential specified by the atom type. Only atom type 'LS' (not binary) has the 1,2 interaction removed as well. At low density some atoms may not interact with any others and problems result due to additional zero eigenvalues.
• DUMPVECTOR [ALLSTEPS] [ALLVECTORS]: if present the Hessian eigenvectors will be written to file vector.dump after each OPTIMization step, preceded by the corresponding eigenvalue for each one. The eigenvectors corresponding to zero eigenvalues are excluded. For hybrid eigenvector-following/conjugate-gradient transition state searches only the results corresponding to the smallest non-zero eigenvalue are dumped. The default is to dump only the vector corresponding to the smallest non-zero eigenvalue for the last step. If ALLSTEPS is present then vectors are dumped at every step. If ALLVECTORS is present then all the vectors corresponding to non-zero eigenvalues are dumped, rather than just one of them. ALLSTEPS and ALLVECTORS can be present in either order.
• EFSTEPS n: prints the unscaled steps in the Hessian eigenvector basis every n steps--turned off by default.
• EVCUT x: sets a cutoff value for eigenvalues. Eigenvalues of magnitude less than x are treated as zeros and steps along such directions are omitted.
• GAUSSIAN: tells the program to read derivative information in Gaussian92 format.
• GDIIS x y z: initiates geometry direct inversion of the invariant subspace. This option always seems to give poorer convergence if analytic second derivatives are available at every step. It requires three real parameters which are read after the GDIIS keyword. The first is the RMS force below which GDIIS will be used, the second is the dimension of the DIIS problem to solve and the third is the interval between GDIIS steps.
• GRADIENT n: causes the gradients along the Hessian eigenvectors to be printed every n cycles. Gradient printing is turned off by default.
• HUPDATE nstart ninterval: uses Powell's Hessian update procedure[11] instead of calculating the analytic second derivatives at every step. nstart is the first step at which analytic derivatives will be calculated; by default nstart=0, the Hessian is initialized to the identity and no analytic second derivatives are ever calculated. ninterval is the interval at which analytic Hessians are calculated; the default is 0 which means that no additional analytic Hessians are ever found. A transition state search starting from a minimum seems unlikely to work unless we calculate analytic Hessians at regular intervals including the first step.
• MASS: Specifies the use of mass-weighting for the steps; the input and output coordinates are not affected.
• MAXSTEP x: specifies the maximum step size for eigenvector-following and steepest-descent calculations, default value 0.2. The precise implementation of this constraint depends upon the step scaling method employed (see §VI).
• MAXMAX x: specifies the maximum value that the maximum step size is allowed to rise to. The default value is 0.5.
• MINMAX x: specifies the minimum value that the maximum step size is allowed to fall to. The default value is 0.01.
• MODE n: in an eigenvector-following transition state search specifies the eigenvector to be followed uphill, where 1 means the softest mode, 2 means the next softest, and so on. Setting n to 0 means that the softest mode is followed uphill at every step, otherwise a maximum overlap criterion is used to determine the mode followed after the first step. The sign of n is used to determine the direction in which we step along the eigenvector if we are starting from a stationary point. This enables one to start transition state searches from minima along any of the eigendirections in either sense. If a minimization is started from a converged transition state then setting n to 7#7 enables one to walk down the two sides of the pathway. This is true for runs based on conjugate gradient techniques too if the keyword CGSTEP is used. MODE is now also used in EF/CG searches so long as an analytical Hessian is calculated.
• MYLINMIN: specifies that an alternative line minimization procedure should be used in conjugate gradient calculations rather than the default method. See also POWER.
• NOHESS: perform a hybrid EF/CG transition state search without a Hessian. The smallest eigenvalue and the corresponding eigenvector are found from a separate minimization problem for every combined EF/CG step.
• POWER n: n is an integer which determines how small an initial displacement to try in the first line minimization of a conjugate gradient search. The larger the value of power, the smaller the order of magnitude of the displacement; default 5. This only does something if MYLINMIN is also set in odata.
• NOPRINTPARAMS: specifies that the parameters which were read following the PARAMS keyword should not be printed at the top of each set of points in the output files.
• NORESET: specifies that periodic images should not be returned to the primary supercell for calculations involving periodic boundary conditions.
• PARAMS: enables additional parameters to be set for specific potentials, e.g. Z^* for LJAT, 8#8 for Morse, n, m, the box lengths L_x, L_y and L_z and the cutoff for ME, the box lengths L_x, L_y and L_z and the cutoff for JM, SC and P6, and 9#9, c and 10#10 for Au, Ag and Ni. Note that all the numbers are read as real.
• POINTS: this must be the last keyword and introduces the coordinate information which is read one atom per line. Each line must consist of the atomic symbol of the atom followed by its three Cartesian coordinates. Leading spaces before the atomic symbol should be avoided.
• PRESSURE: if present tells the program to perform a constant pressure optimization for SC, ME, MP, MS and P6. The default is a constant volume optimization.
• PRINT n: sets the print level. The default value is zero. Use of this option is not recommended, since more specific print control is possible (see below).
• PUSHOFF x: sets the magnitude of a step away from a stationary point of the wrong order (see §IX for default action). Default value is 0.01.
• PUSHTOL x: sets the threshold for the RMS force below which the system may apply a PUSHOFF to escape from a stationary point of the wrong Hessian index. Default value is 0.00001. Using a negative value prevents pushoffs from occurring.
• READVEC: if present the Hessian eigenvector corresponding to the smallest eigenvalue will be read from file vector.dump. The latter file can be generated using the DUMPVECTOR keyword in a previous run.
• RESIZE x: scales all the coordinates by x before the first step is taken. Default is 1.0.
• RESTART: tells OPTIM to continue a previous run archived in an ARCHIVE file.
• ROT: if present a rotational kinetic energy term is added to the Hamiltonian. Either constant angular momentum (ROT JZ x) or constant angular velocity (ROT OMEGA x) may be used to specify J_z or 11#11.
• SCALE n: sets the scaling algorithm as described in §VI. The default is n=10.
• SEARCH n: specifies the search type for eigenvector-following and steepest-descent calculations, default is type 0. The most common options are 0, a minimization, and 2, a transition state search. See §IV for full details.
• SHIFT x: specifies the shift applied to eigenvectors corresponding to normal modes that conserve the energy. The default is 10⁶. The shift must be large enough to move the eigenvalues in question to the top of the spectrum.
• STEPS n: sets the maximum number of optimization steps per call to OPTIM. The default is n=1. Setting n to zero at the start of a run means that only a point group analysis is performed.
• SUMMARY n: prints a summary of the steps and derivatives every n steps. The default is n=20.
• SYMCUT x: specifies the RMS force below which the point group symmetry subroutine will be called. The default is x=0.001.
• TITLE: this option has been removed due to lack of demand.
• TOLBRENT x: specifies the tolerance for the dbrent line minimization part of conjugate gradient optimizations; default is x=0.1.
• TOLD x: sets the initial distance tolerance for points to be considered the same after rotations and reflections in point group determination. The default is 0.0001.
• TOLE x: sets the initial distance tolerance for eigenvalues of the inertia tensor to be considered equivalent in point group determination. The default is 0.0001.
• TOSI 12#12: specifies a Born-Mayer potential with the parameters indicated (see §III).
• TRAD x: sets the trust radius (see §VI). The default value is 2.0.
• VALUES n: prints the Hessian eigenvalues every n steps. The default is n=20.
• VECTORS n: prints the Hessian eigenvectors every n steps. Eigenvector printing is turned off by default.
• WELCH 13#13: specifies a Welch binary salt potential with the parameters indicated (see §III).
• ZEROS n: sets the number of zero Hessian eigenvalues to be assumed--useful for general optimization problems specified by VARIABLES.