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pes_generators [2020/07/15 15:28]
qianli
pes_generators [2022/02/28 08:35] (current)
rauhutmoschneide [Scaling of individual coordinates]
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 |Surface extension  |  4.30  |  4.69  |  5.05  |  5.39  | |Surface extension  |  4.30  |  4.69  |  5.05  |  5.39  |
  
 +  * **''ORIENT''** Allows to specify a certain orientation of the molecule. With ''ORIENT=//yes//'' (Default) the orientation is choosed automatically according to the asymmetric parameter of the molecule. To choose a certain orientation, ''ORIENT=//XC//'' need to be set. X represents a number from 1 to 3 (in arabic or roman letters), and C need to be set to **r** or **l**. For example, ''ORIENT=//IIl//'' orientates the molecule according to the **IIl** convention. ''ORIENT=//old//'' does not rotate the molecule at all. 
   * **''PLOT''=//n//** ''PLOT''=//n// plots all //n//D surfaces and a corresponding Gnuplot script in a separate subdirectory (''plots1'') in the //home//-directory in order to allow for visualization of the computed //n//D surfaces. E.g. the command "gnuplot plotV1D.gnu" in the ''plots1'' directory produces .eps files for all 1D surfaces. Default: ''PLOT=0''.   * **''PLOT''=//n//** ''PLOT''=//n// plots all //n//D surfaces and a corresponding Gnuplot script in a separate subdirectory (''plots1'') in the //home//-directory in order to allow for visualization of the computed //n//D surfaces. E.g. the command "gnuplot plotV1D.gnu" in the ''plots1'' directory produces .eps files for all 1D surfaces. Default: ''PLOT=0''.
   * **''SADDLE''=//n//** Standard ''SURF'' calculations expect the reference structure to be a (local) minimum on the PES, i.e. ''SADDLE=0'' (default). Alternatively, one may start the PES generation from a transition state, which is recommended for the calculation of double-minimum potentials. This situation is not recognized automatically and thus requires the keyword ''SADDLE=1''. Within ''XSURF'' calculations, this keyword needs not to be provided.   * **''SADDLE''=//n//** Standard ''SURF'' calculations expect the reference structure to be a (local) minimum on the PES, i.e. ''SADDLE=0'' (default). Alternatively, one may start the PES generation from a transition state, which is recommended for the calculation of double-minimum potentials. This situation is not recognized automatically and thus requires the keyword ''SADDLE=1''. Within ''XSURF'' calculations, this keyword needs not to be provided.
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 The ''SCALE'' option of the ''SURF'' program enables a modification of the extension of all difference potentials by a common factor. In contrast to that the ''SCALNM'' directive allows for the scaling with respect to the individual normal coordinates. This is the recommended choice for potentials dominated by quartic rather than quadratic terms. At most 3N-6 individual scale factors and shift parameters can be provided. In particular the ''AUTO'' option was found to be very helpful in practical applications. The ''SCALE'' option of the ''SURF'' program enables a modification of the extension of all difference potentials by a common factor. In contrast to that the ''SCALNM'' directive allows for the scaling with respect to the individual normal coordinates. This is the recommended choice for potentials dominated by quartic rather than quadratic terms. At most 3N-6 individual scale factors and shift parameters can be provided. In particular the ''AUTO'' option was found to be very helpful in practical applications.
  
-  * **''AUTO''=//on / off//** ''AUTO''=//on// (defaulr) switches on an automatic scaling procedure of the potential in order to determine meaningful elongations and ''SHIFT'' values with respect to all coordinates, i.e. for each normal mode an optimized scaling parameter ''SFAC'' and ''SHIFT'' parameter will be determined. Usually this results in an increased number of 1D grid points. The ''AUTO'' keyword intrinsically depends on the thresholds and parameters, which can be controlled by the keywords ''THRSHIFT'', ''ITMAX'', ''LEVMAX'', ''DENSMAX'', and ''DENSMIN''.+  * **''AUTO''=//on / off//** ''AUTO''=//on// (default) switches on an automatic scaling procedure of the potential in order to determine meaningful elongations and ''SHIFT'' values with respect to all coordinates, i.e. for each normal mode an optimized scaling parameter ''SFAC'' and ''SHIFT'' parameter will be determined. Usually this results in an increased number of 1D grid points. The ''AUTO'' keyword intrinsically depends on the thresholds and parameters, which can be controlled by the keywords ''THRSHIFT'', ''ITMAX'', ''LEVMAX'', ''DENSMAX'', and ''DENSMIN''.
   * **''DENSMAX''=//value//** Threshold for the maximum vibrational density on the edges of the potential needed for the automated upscaling of the potentials (see keyword ''AUTO'').   * **''DENSMAX''=//value//** Threshold for the maximum vibrational density on the edges of the potential needed for the automated upscaling of the potentials (see keyword ''AUTO'').
   * **''DENSMIN''=//value//** Threshold for the minimum vibrational density on the edges of the potential needed for the automated downscaling of the potentials (see keyword ''AUTO'').   * **''DENSMIN''=//value//** Threshold for the minimum vibrational density on the edges of the potential needed for the automated downscaling of the potentials (see keyword ''AUTO'').
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-[\tt Problem:]+**Problem:**
 The Surf calculation crashes with an error message like The Surf calculation crashes with an error message like
 <code> <code>
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  CURRENT STACK:      MAIN  CURRENT STACK:      MAIN
 </code> </code>
-[\tt Solution:]+ 
 +**Solution:**
 The program has problems in the symmetry conversion when restarting a Hartree-Fock calculation from the reference calculation at the equilibrium geometry. You need to start the Hartree-Fock calculations independently by using the keywords ''%%start,atden%%''. The program has problems in the symmetry conversion when restarting a Hartree-Fock calculation from the reference calculation at the equilibrium geometry. You need to start the Hartree-Fock calculations independently by using the keywords ''%%start,atden%%''.
  
  
-[\tt Problem:]+**Problem:**
 In parallel calculations (mppx) the CPU-time of a ''SURF'' calculation differs considerably from the real-time (wallclock time). In parallel calculations (mppx) the CPU-time of a ''SURF'' calculation differs considerably from the real-time (wallclock time).
-[\tt Solution:]+ 
 +**Solution:**
 There may be two reasons for this: (1) Usually a ''SURF'' calculation spends a significant amount of the total time in the Hartree-Fock program and the 2-electron integrals program. As the integrals are stored on disk, 2 processes on the same machine may write on disk at the same time and thus the calculation time depends to some extend on the disk controller. It is more efficient to stripe several disks and to use several controllers. This problem can be circumvented by distributing the job over several machines, but limiting the number of processors for each machine to 1. (2) The integrals program buffers the integrals. Parallel jobs may require too much memory (factor of 2 plus the shared memory) and thus the integrals buffering will be inefficient. Try to reduce the memory as much as you can. It might be advantageous to separate the memory demanding ''VCI'' calculation from the ''SURF'' calculation. There may be two reasons for this: (1) Usually a ''SURF'' calculation spends a significant amount of the total time in the Hartree-Fock program and the 2-electron integrals program. As the integrals are stored on disk, 2 processes on the same machine may write on disk at the same time and thus the calculation time depends to some extend on the disk controller. It is more efficient to stripe several disks and to use several controllers. This problem can be circumvented by distributing the job over several machines, but limiting the number of processors for each machine to 1. (2) The integrals program buffers the integrals. Parallel jobs may require too much memory (factor of 2 plus the shared memory) and thus the integrals buffering will be inefficient. Try to reduce the memory as much as you can. It might be advantageous to separate the memory demanding ''VCI'' calculation from the ''SURF'' calculation.
  
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 ==== Options ==== ==== Options ====
  
 +    **''AUTOFIT''=//n//** (=0 Default) If ''AUTOFIT''=1, the number of basis function for fitting the grid points is determined automatically. To do so, the fine grid of the energy is compared to the coarse grid points. If the deviation is too high, another basis function is added. The procedure starts with 8 basis functions and stops at the latest at ''FITXD_MAX'' basis functions. Once 'AUTOFIT' is used, the keywords ''FITXD'' does not have any use.
   * **''CORRECT''=//n//** (=1 (on) Default) If a certain subsurface does not converge despite increasing the number of ab initio calculations, symmetry in this subsurface (if any) will be neglected in order to avoid any errors due to inaccuracies in the displacement vectors and the subsurface will be recalculated accordingly. This option is automatically switched off in any Taylor expansions of the PES.   * **''CORRECT''=//n//** (=1 (on) Default) If a certain subsurface does not converge despite increasing the number of ab initio calculations, symmetry in this subsurface (if any) will be neglected in order to avoid any errors due to inaccuracies in the displacement vectors and the subsurface will be recalculated accordingly. This option is automatically switched off in any Taylor expansions of the PES.
 +  * **''FITXD_MAX''=//n//**(=10 Default) For the automated procedure with ''AUTOFIT'' an upper limit for the number of basis functions can be set with this keyword.
   * **''FITMETHOD''=//n//** (=1 Default) Within the iterative build-up of the individual subsurfaces, intermediate fitting will be used. This can be based on true multidimensional Kronecker product fitting (''FITMETHOD''=1) or on fitting along one-dimensional cuts (''FITMETHOD''=2).   * **''FITMETHOD''=//n//** (=1 Default) Within the iterative build-up of the individual subsurfaces, intermediate fitting will be used. This can be based on true multidimensional Kronecker product fitting (''FITMETHOD''=1) or on fitting along one-dimensional cuts (''FITMETHOD''=2).
   * **''INFO''=//n//** (=1 Default) ''INFO''=0 suppresses any information about the program parameters and symmetry information. ''INFO''=1 refers to the standard output, while ''INFO''=2 provides additional information about the symmetry recognition.   * **''INFO''=//n//** (=1 Default) ''INFO''=0 suppresses any information about the program parameters and symmetry information. ''INFO''=1 refers to the standard output, while ''INFO''=2 provides additional information about the symmetry recognition.
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   * **''THRSED''=//value//** (=1.0d-6 Default) Threshold for determining symmetry elements of the molecule.   * **''THRSED''=//value//** (=1.0d-6 Default) Threshold for determining symmetry elements of the molecule.
   * **''THRSYMx''=//value//** ($x$=1,2,...) Threshold used for recognizing symmetry within a subsurface of the PES expansion - in dependence on the order of the expansion term. The defaults are ''THRSYM1''=5.0d-5, ''THRSYM2''=1.0d-5,''THRSYM3''=5.0d-6,''THRSYM4''=5.0d-6,''THRSYM5''=1.0d-7.   * **''THRSYMx''=//value//** ($x$=1,2,...) Threshold used for recognizing symmetry within a subsurface of the PES expansion - in dependence on the order of the expansion term. The defaults are ''THRSYM1''=5.0d-5, ''THRSYM2''=1.0d-5,''THRSYM3''=5.0d-6,''THRSYM4''=5.0d-6,''THRSYM5''=1.0d-7.
 +  * **''DELAUTO''=//variable//**(=//off// Default) If ''DELAUTO''=//on//, all not converged surfaces of the highest considered dimension are deleted. It only works after a restart from an external potfile.
  
 +==== Selection of Modes ====
 +''VIBMODE'',//options//
 +
 +The ''VIBMODE'' directive allows to span the PES only with predefined modes. The following options can be combined in various ways.
 +
 +  * **''ENERGHIGH''=//x//** Modes with a frequency lower than **x** are used to span the surface (according to the harmonic frequencies)
 +  * **''ENERGLOW''=//x//** Modes with a frequency higher than **x** are used to span the surface (according to the harmonic frequencies)
 +  * **''HIGH''=//n//** the highest **n** modes are used to span the surface
 +  * **''LOW''=//n//** the lowest **n** modes are used to span the surface
 +  * **''MODE''=//n//** Mode which is used to span the surface (can be used multiple times)
 ==== Visualisation and interfaces ==== ==== Visualisation and interfaces ====
  
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   * **''MEMORY''=//n//** Memory request of the individual single point calculations in MW.   * **''MEMORY''=//n//** Memory request of the individual single point calculations in MW.
   * **''WFU''=//file name//** If additional information need to be read in from a .wfu file, this can be specified here.   * **''WFU''=//file name//** If additional information need to be read in from a .wfu file, this can be specified here.
 +