NWChem Version 3.3.1 Release Notes

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# NWChem Version 3.3 and 3.3.1 Release Notes NOTE: These release notes are not a substitute for reading the User Manual! They are meant to give a thumbnail sketch of the new capabilities and bug fixes that are available in NWChem Version 3.3. When there is a conflict between the release notes and the User Manual, the User Manual takes precedence. NWChem 3.3.1 changes from NWChem 3.3 Several new major capabilities are available in NWChem, including several new modules. The new modules are: Car-Parrinello simulations (the PSPW module), Python interface (the PYTHON module), and analysis of trajectory information during a molecular dynamics calculation and of ESP calculations(the ANALYSIS module). For each of these capabilities, the user is referred to the User Manual for more information. Additional major additions to the capabilities include: GIAO NMR chemical shift capabilities for closed shells (GIAO in the PROPERTY module), The DRIVER module has been greatly improved, with many new features, Several new DFT functionals have been added: Exchange Perdew91, Gill96, and PBE96 functionals Correlation PBE96 functional Exchange-Correlation Becke97, Becke97-1, and HCTH functionals The ElectroStatic Potential (ESP) module has several new features, Automatic recognition of molecular symmetry (AUTOSYM in the GEOMETRY module), Addition of Hondo 1e- energy and gradient integrals, Increased accuracy in the integral API. Again, for each of these capabilities, the user is referred to the User Manual for more information. Listed below are the other major and many minor changes for each module with significant changes. These descriptions are somewhat terse and more information is generally available in the User Manual. Task level directives: Unrecognized directives will now cause NWChem to stop and print an error message Task analysis added for MD runs Task python added for python interface Task pspw added for pseudopotential plane-wave (Car-Parrinello) runs Initial orbital Guess: New code from Paul Sherwood to generate reasonable initial atomic guesses for heavy elements with ECPs. This generates guess densities for those atoms that previously didn't work and produces much better guess densities than the previous version. The atomic guess code now generates f orbital density fragments in the correct order for both cartesian and spherical basis sets. Higher accuracy is now used in the initial guess to accomodate large basis sets. If linear dependencies are found, even higher accuracy is used. Users are warned if initial guess can lead to symmetry problems. BUG FIX: UHF projections of small basis sets to large basis sets will now work Basis Sets: Basis set library has been updated to include all new basis sets at the EMSL Gaussian Basis Set Order Form page of David Feller BUG FIX: Some of the Stuttgart ECPs which had the coefficients and exponents switched are now correct. Geometry: Extended redundant internals to allow user constraints. Adjustable geometries. AUTOZ is now the default. A tolerance is now available in SYMMETRY directive of GEOMETRY directive. AUTOSYM is now available (with a tolerance) on the GEOMETRY line directive. Optional velocity input for Car Parinello code. More robust z-matrix code. C7 and D6 symmetries are properly set up. DFT: Introduced X Perdew91, Gill96, and PB96 functionals. Introduced C PB96 functional. Introduced XC Becke97, Becke97-1, and HCTH. DFT is now able to use spherical basis functions as well as cartesian. DFT gradients can now use the Texas integrals. Linear scaling is acheived in the exchange contribution when charge fitting basis sets are used with hybrid density functionals. If the vectors directive is used with SCF or DFT and a problem occurs, the atomic guess will be used. Lebedev grids have been significantly modified. Delley weights are no longer allowed. Modified grid input: you can now add nrad nang accqrad. Better screening on the exchange correlation numerical grid, which improves performance by at least 20%. Default convergence parameters was modified to produce more robust results. Introduced check on integrated density: a warning message is printed if the claimed accuracy criteria for the XC numerical grid are not met. Default finite difference step for nuclear hessian generation for DFT changed to 0.01 au and for all other methods it is 0.001 au. BUG FIX: In cases in which the spin polarization is large in open shell systems, wrong wave functions and gradients were obtained using Perdew86 C functionals. This has been fixed. BUG FIX: If the user has a CD fitting basis set with a shell larger than any shell in the AO basis set, the program would stop. This no longer applies. BUG FIX: All hybrid functionals were giving incorrect results when using open shell wavefunctions because the total density was being used instead of separate alpha and beta Hartree-Fock exchange contributions. This is now fixed. (It was also fixed in later releases of 3.2.1.) SCF: Eliminated or tightened screening options to make integral selection threshold more consistent between file and direct routines. Improved precision in linear solve to stabilize direct SCF. If the vectors directive is used with SCF or DFT and a problem occurs, the atomic guess will be used. Driver: Revamped Driver capabilities. Ensure constraints are imposed after geometry step. Extended redundant internals to allow user constraints. AUTOZ is now the default. Properties: Note that spherical functions do not work yet with properties. Input for the NBO program are produced. Addition of GIAO NMR chemical shift calculations. Added "all" keyword. BUG FIX:Property package will correctly skip property evaluation for generally contracted basis sets and basis sets with pure sp functions (to get the properties use the "segement" keyword when specifying a basis set). MP2: TIGHT directive MP2 for higher precision energy and gradients BUG FIX: Non-abelian point groups are now handled properly in the MP2 gradient code. Make RI-MP2 compute SCF reference if it is not already done (or done with sufficient accuracy). BUG FIX: RIMP2 - Fix overflow memory problem for large jobs. Hessian and Frequencies: Default finite difference step for nuclear hessian generation for DFT changed to 0.01 au and for all other methods it is 0.001 au. BUG FIX: Numerical hessian restarts now work properly. ESP: Use of fast routines for ESP calculations. Write name.xyz and name.plt file (plot with gOpenMol). Write name.er file to recover previous runs. Write name.q file with partial charges. Added Schwarz screening - screen option in ESP block. Added option to read in previous esp grid, if name.grid is present, it will automatically get used unless you give a command recalculate. Print atom radii. Additional constraint options. Prepare module: Changed topology and restart format printed out. New ALTLOC, MODEL, LINK, and CHAIN commands. Allow comment lines in sequence file - begin line with #. Always recalculate grid if ESP required on a fragment. Implement 'modify segment' and 'update lists' commands. Force PDB link cards. Add modify commands for bonded interaction parameters. Recode pre_mklist to allow and identify multiple node (greater than 3) bonded interactions. Automatically identifies cysteine-sulphur bridges. Default HIS to HID for amber when reading PDB without hydrogens. Write out segment charges when writing topology file. Add support for DNA and RNA with AMBER force field. Add ignore keyword so that bonded parameters between quantum atoms do not need to be defined in the database. Make 1.0 default scaling for ESP fitted charges. BUG FIX:Multiple node bonded interaction error takes care of itself. BUG FIX:If last segment was a single atom, the atom would be lost. This is now fixed. KNOWN BUG:In some systems, when converting a restart file to a PDB file, the restart file gets corrupted. This is fixed in version 3.3.1. MD: Changed topology format - cannot use old files with the new code!! Added ability to analyze the trajectory on the fly - see the ANALYSIS module of User Manual. Implement periodic boundary conditions for bonded interactions. Improved load balancing. Dynamic assignment of subset of nodes for performing the FFT calculation. Split PME calculation now default - see pme keyword in MD block. Improved periodic boundary condition scheme. Exclude constraints between atoms fixed in space - improves reliability of Shake algorithm. Remove the restriction that bonded interactions can involve atoms on at most two segments. Improved printing SHAKE dev-too-large error message identifying the atoms that are involved. BUG FIX: Fix J-Box or I-Box is Illegal problem. Prevent dimension problems if box index list from previous run exceeds current dimension. Integral changes: Inclusion of energy and gradient one-electron integrals from HONDO. Turn off SP integral code due to accuracy problems. Several fixes to the integral code with respect to memory and bugs in TEXAS when high angular momentum and large exponents are present in the basis set. Fix of ECP integral bug when the ECP contained a zero r-exponent. Routines for relativistic integral code (include?) Generates relativistic one-electron integrals (include?) Tests, manuals and misc script changes: Updated User's Manual to reflect new and modified functionality in NWChem. QA tests have been updated to reflect the new functionality in NWChem. Updated scripts to run NWChem in LoadLeveller and NQE and to test results. Addition of some scripts to create animated gifs based on using RASMOL and files printed out by NWChem during optimizations and frequency calculations. Updates in the Programmer's Manual (much more is still left to come!). Installation availability: The current tested platforms and O/S versions are: IBM SP with P2SC nodes, AIX 4.2.1, and PSSP 2.3 IBM SP with silver nodes (SMP nodes with two 604e processors), AIX 4.3.2, and PSSP 3.1. IBM RS6000 workstation, AIX 3.2, 4.1. and 4.3 Cray T3E, 2.0.4.61 UNICOSMK SGI R8000/10000, IRIX 6.2, 6.5 SGI R4000, IRIX 5.3 SUN workstations, SunOS 4.1.3 and Solaris 5.5 Compaq DEC alpha workstion (600 MHz EV6), Digital UNIX V4.0E Rev. 1091, DEC C V5.8-009, Digital Fortran V5.2 Linux. Since there are at least 8 popular distributions of the Linux operating system and numerous others in existence, including downloading everything and building your own Linux OS, it is impossible to test all possible versions of Linux with NWChem. NWChem Release 3.3 has been tested on Slackware 3.4, 3.5, 4.0, RedHat 5.1, 5.2, and 6.0, Mandrake based on RedHat 6.0, and LinuxPPC 4.0 for the Power PC Macintosh. These all use the EGCS compilers at different levels. Those distributed from Slackware are somewhat different than those distributed from RedHat but the code is configured to run on all of them. The Linux Alpha version 5.2 from Red Hat fails to compile the code as well as the beta release of the Digital Fortran compiler for Linux based Alpha systems. NOTE:In releases of NWChem prior to 3.3 additional processes had to be created on workstation clusters to support remote access to shared memory. This is no longer the case. The TCGMSG process group file just needs to refer to processes running NWChem. ## Changes from NWChem 3.3 to NWChem 3.3.1 Fix for PB96 functionals. Note that all previous calculations with this functional are incorrect. Do NOT rely on results using any version previous to 3.3.1 Slightly looser value of EPREC in DRIVER for DFT calculations. (5e-6 instead of 1e-7) Improved screening on the grid for DFT which only effects large calculations (usually those that have molecules that are "spread out"). The periodic boundary conditions for an MD run now checks for images more than one cell away. Fix in the PREPARE module so that some solvents that were not being written out correctly in the PDB file now are. Fix in the solvate box command. Fix for periodic boundary conditions for solvation. Fix for the passing of character strings in the PSPW code. Dramatically improved parallel efficiency of the Lagrange multipliers and the non-local pseudopotentials on high-latency parallel platforms in the PSPW code. Improved persistence of tolerance changes when linear dependence is found. This had caused some convergence problems. Improved eigensolver for large linear dependencies. Please note that the current algorithm in PEigS requires more memory. You may need to increase the amount of memory needed for a particular calcuation. This problem will be rectified in the next version. The TIGHT option has replaced AOTOL and MOTOL in MP2 (undocumented feature of version 3.3). Fix in the CCSD calculation to add some synchronization which provided more stability. Fix for message passing with Linux. This fixes a known performance problem. Modifications in the GA tools which were causing performance problems between workstations. Fix tools makefiles to allow for larger than 2 GB files on the SP and to fix a diagonalization problem which was causing problems with the scalability of DFT. Fix for the T3E makefile so that the make works cleanly. Work arounds to LAPI problems that have been identified on the SP. The symptoms generally showed up as jobs that would hang. Additional printing of information in the ecce.out file to be compatible with Ecce 1.5. The examples directory has been updated and the tests directory has been deleted because the input files were obsolete. NWChem | Capabilities | Platforms | Download | User's Manual | Programmer's Manual | Release Notes | FAQ Known Bugs | Support | Tutorial | Contributors | Benchmarks | Search | Mol Sci. Soft. Group | Citation Contact: NWChem Support Updated: March 8, 2005