NWCHEM Programmer's Guide, Release 5.1

High Performance Computational Chemistry Group

8 January 2009

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• DISCLAIMER
• Glossary of NWChem Terms
• About This Guide
  • Purpose
  • Scope
  • Prerequisites
  • How to Use This Guide
  • Organization
    • Chapter 1: NWChem Overview
    • Chapter 2: Generic Task Interface
    • Chapter 3: Molecular Calculation Modules
    • Chapter 4: The Molecular Modeling Toolkit
    • Chapter 6: The Software Development Toolkit
    • Chapter 7: Utilities
    • Chapter 8: Installing NWChem
    • Chapter 9: Developing New Modules and Enhancements
    • Chapter 10: Testing the Program
    • Chapter 11: Documenting New Modules and Code Enhancements
    • Appendix A. The Integral Application Programmer's Interface
    • Appendix B. Performance Statistics Collection - PSTAT
    • Appendix C. Integral File I/O
    • Appendix D. Error Messages
  • Related Product Information
  • Notation Conventions
  
  
• Contents
• 1. NWChem Overview
  • 1.1 Introduction
  • 1.2 NWChem Architecture
    • 1.2.1 Object Oriented Design
    • 1.2.2 Non-Uniform Memory Access
    • 1.2.3 The Five-Tiered Modular Architecture
      • 1.2.3.1 The Generic Task Interface
      • 1.2.3.2 The Molecular Calculation Modules
      • 1.2.3.3 The Molecular Modeling Toolkit
      • 1.2.3.4 The Software Development Toolkit
      • 1.2.3.5 The Utility Routines
  
  
• 2. Generic Task Interface
  • 2.1 Flow of Control in NWChem
  • 2.2 Task Execution in NWChem
    • 2.2.1 Task Routines for NWChem Operations
      • 2.2.1.1 task
      • 2.2.1.2 task_energy
      • 2.2.1.3 task_gradient
      • 2.2.1.4 task_freq
      • 2.2.1.5 task_hessian
      • 2.2.1.6 task_optimize
      • 2.2.1.7 task_num_grad
      • 2.2.1.8 task_save_state and task_restore_state
  
  
• 3. Molecular Calculation Modules
  • 3.1 Theories
    • 3.1.1 Self-Consistent Field Module - SCF
    • 3.1.2 Gaussian Density Functional Theory Module - DFT
    • 3.1.3 Møllier-Plesset Module - MP2
    • 3.1.4 Resolution of the Identity Approximate Integral Method
      • 3.1.4.1 RI-MP2
      • 3.1.4.2 RISCF
    • 3.1.5 CCSD
    • 3.1.6 MCSCF
    • 3.1.7 CI
    • 3.1.8 Molecular Mechanics (MM)
  • 3.2 Operations
    • 3.2.1 Energy
    • 3.2.2 Gradient
    • 3.2.3 Optimization
    • 3.2.4 Frequencies
    • 3.2.5 Properties
    • 3.2.6 Dynamics
  
  
• 4. Molecular Modeling Toolkit
  • 4.1 The Geometry Object
    • 4.1.1 Creating, destroying, loading and storing geometries
      • 4.1.1.1 geom_create
      • 4.1.1.2 geom_destroy
      • 4.1.1.3 geom_check_handle
      • 4.1.1.4 geom_rtdb_load
      • 4.1.1.5 geom_rtdb_store
      • 4.1.1.6 geom_rtdb_delete
    • 4.1.2 Information About the Geometry
      • 4.1.2.1 geom_ncent
      • 4.1.2.2 geom_nuc_charge
      • 4.1.2.3 geom_nuc_rep_energy
      • 4.1.2.4 geom_include_bqbq
      • 4.1.2.5 geom_set_bqbq
    • 4.1.3 Information About Centers and Coordinates
      • 4.1.3.1 geom_cart_set
      • 4.1.3.2 geom_cart_get
      • 4.1.3.3 geom_cent_get
      • 4.1.3.4 geom_cent_set
      • 4.1.3.5 geom_cent_tag
      • 4.1.3.6 geom_check_cent
    • 4.1.4 Support for Periodic Systems
      • 4.1.4.1 geom_systype_get
      • 4.1.4.2 geom_latvec_get
      • 4.1.4.3 geom_latang_get
      • 4.1.4.4 geom_recipvec_get
      • 4.1.4.5 geom_recipang_get
      • 4.1.4.6 geom_volume_get
      • 4.1.4.7 geom_amatrix_get and geom_amatinv_get
    • 4.1.5 Printing and Miscellaneous Routines
      • 4.1.5.1 geom_print and geom_print_xyz
      • 4.1.5.2 geom_set_user_units
      • 4.1.5.3 geom_tag_to_element
      • 4.1.5.4 geom_charge_center
      • 4.1.5.5 geom_num_core
      • 4.1.5.6 geom_freeze
  • 4.2 The Basis Set Object
    • 4.2.1 Creating, Destroying, Loading and Storing Basis Sets
      • 4.2.1.1 bas_create
      • 4.2.1.2 bas_destroy
      • 4.2.1.3 bas_check_handle
      • 4.2.1.4 bas_rtdb_load
      • 4.2.1.5 bas_rtdb_store
    • 4.2.2 Information About the Entire Basis
      • 4.2.2.1 bas_high_angular
      • 4.2.2.2 bas_numbf
      • 4.2.2.3 bas_name
      • 4.2.2.4 bas_numcont
      • 4.2.2.5 bas_nbf_cn_max
      • 4.2.2.6 bas_nbf_ce_max
    • 4.2.3 Mapping Between Centers, Shells/Contractions and Functions
      • 4.2.3.1 bas_cn2ce
      • 4.2.3.2 bas_cn2bfr
      • 4.2.3.3 bas_ce2bfr
      • 4.2.3.4 bas_ce2cnr
      • 4.2.3.5 bas_bf2ce
      • 4.2.3.6 bas_bf2cn
    • 4.2.4 Printing Basis Sets
      • 4.2.4.1 bas_print
      • 4.2.4.2 bas_print_all
      • 4.2.4.3 gbs_map_print
    • 4.2.5 Miscellaneous Other Functions for Basis Sets
      • 4.2.5.1 bas_continfo
      • 4.2.5.2 bas_get_exponent and bas_set_exponent
      • 4.2.5.3 bas_get_coeff and bas_set_coeff
    • 4.2.6 Other -- unique contraction information and adding centers
  • 4.3 Linear Algebra Routines
    • 4.3.1 Simple linear operations
      • 4.3.1.1 ga_get_diag
      • 4.3.1.2 ga_maxelt
      • 4.3.1.3 ga_ran_fill
      • 4.3.1.4 ga_screen
      • 4.3.1.5 ga_mat2col and ga_col2mat
    • 4.3.2 Linear algebra and transformations
      • 4.3.2.1 ga_mix
      • 4.3.2.2 two_index_transf
      • 4.3.2.3 ga_matpow
      • 4.3.2.4 mk_fit_xf
      • 4.3.2.5 ga_orthog
      • 4.3.2.6 ga_orthog_vec
    • 4.3.3 Iterative linear algebra operations
      • 4.3.3.1 ga_iter_diag
      • 4.3.3.2 ga_iter_lsolve
      • 4.3.3.3 ga_iter_orthog
      • 4.3.3.4 ga_iter_project
    • 4.3.4 Miscellaneous
      • 4.3.4.1 ga_pcg_minimize
      • 4.3.4.2 int_1e_ga
      • 4.3.4.3 int_2c_ga
  • 4.4 Symmetry
    • 4.4.1 Symmetry Group and Operations Functions
      • 4.4.1.1 sym_group_name
      • 4.4.1.2 sym_number_ops
      • 4.4.1.3 sym_center_map
      • 4.4.1.4 sym_inv_op
      • 4.4.1.5 sym_apply_op
      • 4.4.1.6 sym_apply_cart_op
      • 4.4.1.7 sym_get_cart_op
      • 4.4.1.8 sym_ops_get
      • 4.4.1.9 sym_op_mult_table
    • 4.4.2 Geometries and Gradients
      • 4.4.2.1 sym_geom_project
      • 4.4.2.2 sym_grad_symmetrize
    • 4.4.3 Character Tables
      • 4.4.3.1 sym_char_table
      • 4.4.3.2 sym_op_classify
    • 4.4.4 Atomic/Molecular Orbitals
      • 4.4.4.1 sym_bas_irreps
      • 4.4.4.2 sym_movecs_adapt
      • 4.4.4.3 sym_movecs_apply_op
      • 4.4.4.4 sym_bas_op
    • 4.4.5 `Skeleton' integral lists
      • 4.4.5.1 sym_atom_pair
      • 4.4.5.2 sym_atom_quartet and sym_atom_gen_quartet
      • 4.4.5.3 sym_shell_pair
      • 4.4.5.4 sym_shell_quartet
      • 4.4.5.5 sym_symmetrize
    • 4.4.6 Printing Symmetry Information
      • 4.4.6.1 sym_print_all
      • 4.4.6.2 sym_print_char_table
      • 4.4.6.3 sym_print_ops
    • 4.4.7 Internal symmetry stuff that might be useful
      • 4.4.7.1 sym_op_type
      • 4.4.7.2 sym_op_class_name
    • 4.4.8 Miscellaneous
      • 4.4.8.1 cross_product
      • 4.4.8.2 deter3
  
  
• 5. Integral Application Programmer's Interface
  • 5.1 Overview
  • 5.2 Adding a new base integral code to the NWChem INT-API
  
  
• 6. Software Development Toolkit
  • 6.1 Non-Uniform Memory Allocation (NUMA)
    • 6.1.1 Message Passing
    • 6.1.2 Memory Allocator (MA)
      • 6.1.2.1 MA Data Types
      • 6.1.2.2 Implementation
      • 6.1.2.3 List of MA routines
      • 6.1.2.4 MA Errors
    • 6.1.3 Global Arrays (GA)
      • 6.1.3.1 Interaction Between GA and MA
      • 6.1.3.2 List of GA Routines
      • 6.1.3.3 New(?) Stuff
      • 6.1.3.4 Use of TCGMSG global operation routines
      • 6.1.3.5 Interaction between GA and message-passing
    • 6.1.4 ChemI/O
      • 6.1.4.1 Elementary I/O Library (ELIO)
      • 6.1.4.2 Disk Resident Arrays
      • 6.1.4.3 Exclusive Access Files (EAF)
      • 6.1.4.4 Shared Files (SF)
  • 6.2 The Run Time Data Base (RTDB)
    • 6.2.1 Functions to Control Access to the Runtime Database
      • 6.2.1.1 rtdb_parallel
      • 6.2.1.2 rtdb_open
      • 6.2.1.3 rtdb_close
      • 6.2.1.4 rtdb_put
      • 6.2.1.5 rtdb_get
      • 6.2.1.6 rtdb_cput and rtdb_cget
      • 6.2.1.7 rtdb_ma_get
      • 6.2.1.8 rtdb_get_info
      • 6.2.1.9 rtdb_first and rtdb_next
      • 6.2.1.10 rtdb_delete
      • 6.2.1.11 rtdb_print
  
  
• 7. Utilities
  • 7.1 Input Parser
    • 7.1.1 Free-format Fortran Input Routines - INP
    • 7.1.2 Initialization
      • 7.1.2.1 inp_init
    • 7.1.3 Basic Input Routines
      • 7.1.3.1 inp_read
      • 7.1.3.2 inp_i
      • 7.1.3.3 inp_f
      • 7.1.3.4 inp_a
      • 7.1.3.5 inp_a_trunc
      • 7.1.3.6 inp_line
      • 7.1.3.7 inp_cline
      • 7.1.3.8 inp_irange
      • 7.1.3.9 inp_ilist
      • 7.1.3.10 inp_search
    • 7.1.4 Routines concerning fields within a line
      • 7.1.4.1 inp_n_field
      • 7.1.4.2 inp_cur_field
      • 7.1.4.3 inp_set_field
      • 7.1.4.4 inp_prev_field
    • 7.1.5 String routines
      • 7.1.5.1 inp_strlen
      • 7.1.5.2 inp_lcase
      • 7.1.5.3 inp_ucase
      • 7.1.5.4 inp_compare
      • 7.1.5.5 inp_match
      • 7.1.5.6 inp_strtok
    • 7.1.6 Error handling routines
      • 7.1.6.1 inp_errout
      • 7.1.6.2 inp_outrec
      • 7.1.6.3 inp_clear_err
      • 7.1.6.4 inp_eof
  • 7.2 NWChem Ouput to Ecce
    • 7.2.1 Contents of Output for Ecce
    • 7.2.2 Format of Output
    • 7.2.3 NWChem Ecce Output API
      • 7.2.3.1 routine ecce_print_module_entry(module)
      • 7.2.3.2 routine ecce_print_module_exit(module, status)
      • 7.2.3.3 routine ecce_print1(keyword, ma_type, data, dim1)
      • 7.2.3.4 routine ecce_print2(keyword, ma_type, data, dim1, dim2)
      • 7.2.3.5 routine ecce_print1_char(keyword, data, dim1)
      • 7.2.3.6 routine ecce_print2_dbl_tol
      • 7.2.3.7 routine ecce_print_control(status, old)
      • 7.2.3.8 routine ecce_print_file_open(filename)
      • 7.2.3.9 routine ecce_print_file_close()
      • 7.2.3.10 routine ecce_print_echo_input
      • 7.2.3.11 routine ecce_print_echo_string
      • 7.2.3.12 routine is_ecce_print_on
      • 7.2.3.13 subroutine movecs_ecce_print_on
      • 7.2.3.14 subroutine movecs_ecce_print_off
      • 7.2.3.15 subroutine movecs_ecce
      • 7.2.3.16 bas_ecce_print_basis
      • 7.2.3.17 geom_print_rtdb_ecce
      • 7.2.3.18 geom_print_ecce
    • 7.2.4 Standard exit status
    • 7.2.5 Standard keywords
      • 7.2.5.1 Converged/final energies
      • 7.2.5.2 Converged/final properties
      • 7.2.5.3 Convergence information
      • 7.2.5.4 Timing and performance information
  • 7.3 Utility routines
    • 7.3.1 Printing utilities
      • 7.3.1.1 util_print_centered
      • 7.3.1.2 banner
      • 7.3.1.3 output
    • 7.3.2 Error Routines
      • 7.3.2.1 errquit
    • 7.3.3 Parallel Communication
      • 7.3.3.1 util_char_ga_brdcst
      • 7.3.3.2 fcsnd and fcrcv
    • 7.3.4 Naming Files
      • 7.3.4.1 util_file_name
      • 7.3.4.2 util_file_prefix
      • 7.3.4.3 util_pname
    • 7.3.5 Sequential Fortran Files
      • 7.3.5.1 util_flush
      • 7.3.5.2 sread and swrite
    • 7.3.6 Parallel file operations
      • 7.3.6.1 begin_seq_output, write_seq, and end_seq_output
    • 7.3.7 Data packing and unpacking
    • 7.3.8 Checksums
      • 7.3.8.1 Checksum C and Fortran interface
    • 7.3.9 Source version information
      • 7.3.9.1 util_version
    • 7.3.10 Times and dates
      • 7.3.10.1 util_cpusec
      • 7.3.10.2 util_wallsec
      • 7.3.10.3 util_date
    • 7.3.11 System operations and information
      • 7.3.11.1 util_hostname
      • 7.3.11.2 util_file_unlink
      • 7.3.11.3 util_file_copy
      • 7.3.11.4 util_system
    • 7.3.12 C to Fortran interface
      • 7.3.12.1 string_to_fortchar and fortchar_to_string
    • 7.3.13 Debugging aids
      • 7.3.13.1 ieeetrap
    • 7.3.14 Miscellaneous BLAS-like operations
      • 7.3.14.1 Initializing arrays -- dfill and ifill
  • 7.4 Print Control
    • 7.4.1 Other Relevant Routines
      • 7.4.1.1 util_print
      • 7.4.1.2 util_print_input
      • 7.4.1.3 util_print_push
      • 7.4.1.4 util_print_pop
      • 7.4.1.5 util_print_rtdb_load
      • 7.4.1.6 util_print_set_level
  
  
• 8. Installing NWChem
  • 8.1 How to Obtain NWChem
  • 8.2 Supported Platforms
    • 8.2.1 Porting Notes
  • 8.3 Environmental Variables
  • 8.4 Makefiles and Libraries
  • 8.5 Managing NWChem
    • 8.5.1 Introduction to CVS
    • 8.5.2 The CVS Model
    • 8.5.3 The CVS Program
    • 8.5.4 Summary of CVS commands
    • 8.5.5 Troubleshooting CVS
  
  
• 9. Developing New Modules and Enhancements
  • 9.1 General Design Guidelines
  • 9.2 Coding Style
    • 9.2.1 Version information
    • 9.2.2 Standard interface for top-level modules
    • 9.2.3 No globally defined common blocks
    • 9.2.4 Naming of routines and common blocks
    • 9.2.5 Inclusion of common block definitions
    • 9.2.6 Convention for naming include files
    • 9.2.7 Syntax for including files using the C preprocessor
    • 9.2.8 No implicitly typed variables
    • 9.2.9 Use double precision rather than real*8
    • 9.2.10 C macro definitions should be in upper case
    • 9.2.11 Fortran source should be in lower or mixed case
    • 9.2.12 Naming of variables holding handles/pointers obtained from MA/GA
    • 9.2.13 Fortran unit numbers
    • 9.2.14 Use standard print control
    • 9.2.15 Error handling
    • 9.2.16 Comments
    • 9.2.17 Message IDs
    • 9.2.18 Bit operations -- bitops.fh
    • 9.2.19 Blockdata statements and linking
  
  
• 10. Testing the Program
• 11. Documenting New Modules and Code Enhancements
  • 11.1 Content of the Documentation
    • 11.1.1 Documentation of a Molecular Calculation Module
      • 11.1.1.1 Module Documentation Template
    • 11.1.2 Documentation of Modeling or Development Tools
      • 11.1.2.1 Modeling Tools Documentation Template
    • 11.1.3 Content for In-Source Documentation of Routines
  
  
• A. Integral Application Programmer's Interface
  • A.1 INT-API: Initialization, Integral Accuracy and Termination
    • A.1.1 int_init
    • A.1.2 intd_init
    • A.1.3 int_terminate
    • A.1.4 intd_terminate
    • A.1.5 intdd_terminate
    • A.1.6 int_acc_std
    • A.1.7 int_acc_high
    • A.1.8 int_acc_get
    • A.1.9 int_acc_set
  • A.2 INT-API: Memory Managment Routines
    • A.2.1 int_mem
    • A.2.2 int_mem_1e
    • A.2.3 int_mem_2e4c
    • A.2.4 int_mem_h1
    • A.2.5 int_mem_2eec
    • A.2.6 int_mem_2e2c
    • A.2.7 int_mem_3ov
    • A.2.8 int_mem_print
    • A.2.9 intb_mem_2e4c
  • A.3 INT-API: Integral Routines
    • A.3.1 int_1estv
    • A.3.2 int_1eov
    • A.3.3 int_1eke
    • A.3.4 int_1epe
    • A.3.5 int_1eh1
    • A.3.6 int_1eall
    • A.3.7 int_1cg
    • A.3.8 int_1e3ov
    • A.3.9 int_l1e3ov
    • A.3.10 int_l1eall
    • A.3.11 int_pgen1e
    • A.3.12 int_l1eh1
    • A.3.13 int_l1eke
    • A.3.14 int_l1eov
    • A.3.15 int_l1epe
    • A.3.16 int_l1gen1e
    • A.3.17 int_2e2c
    • A.3.18 int_2e2c
    • A.3.19 int_l2e3c
    • A.3.20 int_2e3c
    • A.3.21 int_2e4c
    • A.3.22 int_l2e4c
    • A.3.23 intb_init4c
    • A.3.24 intb_2e4c
    • A.3.25 intb_nw_2e4c
  • A.4 INT-API: Property Integral Routines
    • A.4.1 int_mpole
    • A.4.2 int_projpole
  • A.5 INT-API: Miscellaneous Routines
    • A.5.1 exact_mem
    • A.5.2 emem_3ov
    • A.5.3 emem_1e
    • A.5.4 emem_1e_dk
    • A.5.5 emem_1e_rel
    • A.5.6 emem_2e4c
    • A.5.7 emem_2e3c
    • A.5.8 emem_2e2c
    • A.5.9 emem_2e4c_full
    • A.5.10 int_nbf_max
    • A.5.11 int_mem_zero
    • A.5.12 api_is_ecp_basis
    • A.5.13 emem_1e_pvp
    • A.5.14 exactd_mem
    • A.5.15 emem_d1e
    • A.5.16 emem_d1e_rel
    • A.5.17 emem_d2e4c
    • A.5.18 emem_d2e4c_full
    • A.5.19 int_canon
    • A.5.20 int_chk_init
    • A.5.21 int_chk_sh
    • A.5.22 int_nospherical_check
    • A.5.23 int_nogencont_check
    • A.5.24 int_nospshell_check
    • A.5.25 int_bothsp_gc_check
    • A.5.26 int_hf1sp
    • A.5.27 int_hf1sp_ecp
    • A.5.28 int_1psp
    • A.5.29 int_1dsp
    • A.5.30 int_1spsp
    • A.5.31 int_1spa
    • A.5.32 int_sp1b
    • A.5.33 int_nint
    • A.5.34 int_unint
    • A.5.35 int_nint_cart
    • A.5.36 int_unint_cart
  
  
• B. Performance Statistics Collection -- PSTAT
  • B.1 Model
  • B.2 API
    • B.2.1 Include files
    • B.2.2 pstat_init
    • B.2.3 pstat_terminate
    • B.2.4 pstat_allocate
    • B.2.5 pstat_free
    • B.2.6 pstat_on
    • B.2.7 pstat_off
    • B.2.8 pstat_acc
    • B.2.9 pstat_print_all and pstat_print
    • B.2.10 Usage Notes
  • B.3 Closing Comment
  
  
• C. Integral File I/O - INT2E
  • C.1 Application- and I/O-Level Views of the Data Stream
  • C.2 Internal Data Structures (all are node-private)
    • C.2.1 Cache
  • C.3 Subprograms
    • C.3.1 sread, swrite (in util directory)
    • C.3.2 int2e_file_open (API)
    • C.3.3 int2e_file_close (API)
    • C.3.4 int2e_file_rewind (API)
    • C.3.5 int2e_file_read (API)
    • C.3.6 int2e_file_write (API)
    • C.3.7 int2e_file_write_big (internal)
    • C.3.8 int2e_buf_read, int2e_buf_write (mostly internal)
    • C.3.9 int2e_buf_clear (internal)
    • C.3.10 int2e_buf_cntr_pack, int2e_buf_cntr_unpack (internal)
    • C.3.11 int2e_buf_pack, int2e_buf_unpack (internal)
    • C.3.12 int2e_set_bf_range, int2e_get_bf_range (API)
  
  
• D. NWChem Error Messages
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