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# Global include file for Psi3
# Includes the basics to get you started
# Other Ruby modules that are required
require 'stringio'
# Please note that not all the objects are given here. Any commands that communicate directly to
# any Psi3 library function is implemented in the source for psirb.
module Psi
module SupportsAnalyticalGradients
def supports_analytical_gradients
true
end
end
module NoAnalyticalGradients
def supports_analytical_gradients
false
end
end
module Commands
INPUT = "input"
INPUTKEEP = "input --keepoutput"
UINPUT = "input --chkptgeom"
INPUTCHKPT = "input --keepchkpt --keepoutput"
INIT = INPUT
DONE = "psiclean"
INTS = "cints"
SCF = "cscf"
LOCALIZE = "localize"
DERIV = "cints --deriv1"
DERIV2 = "cints --deriv2"
PROPINT = "cints --oeprop"
TRANSQT = "transqt"
CCTRANS = "transqt2"
BACKTRANSQT = "transqt --backtr"
CPHF = "cphf"
RESPONSE = "response"
NORMCO = "normco"
OEPROP = "oeprop"
OPTKING = "optking"
STABLE = "stable"
CIS = "cis"
UGEOM = "ugeom"
CCSORT = "ccsort"
CCRESET = "ccsort --reset"
CCENERGY = "ccenergy"
CCTRIPLES = "cctriples"
CCHBAR = "cchbar"
CCLAMBDA = "cclambda"
CCEOM = "cceom"
CCRESPONSE = "ccresponse"
CCDENSITY = "ccdensity"
MP2 = "mp2"
DETCI = "detci"
CCLAMBDA_EXCITED = "cclambda"
CCLAMBDA_ZETA = "cclambda --zeta"
CCDENSITY_CALC_XI = "ccdensity --calc_xi"
CCDENSITY_USE_ZETA = "ccdensity --use_zeta" # --excited
# Things for optimizations
FINDIF_DISP_SYMM = "optking --disp_irrep --irrep 1"
FINDIF_NEXT = "optking --disp_load"
FINDIF_INPUT = "input --keepchkpt --chkptgeom --noreorient"
FINDIF_ENERGY_SAVE = "optking --energy_save"
FINDIF_GRAD_ENERGY = "optking --grad_energy"
GEOMUPDATE = "optking --opt_step"
# Things for frequencies
FINDIF_DISP_FREQ_ENERGY_CART = "optking --disp_freq_energy_cart"
FINDIF_FREQ_ENERGY_CART = "optking --freq_energy_cart"
FINDIF_DISP_FREQ_GRAD_CART = "optking --disp_freq_grad_cart"
FINDIF_GRAD_SAVE = "optking --grad_save"
FINDIF_FREQ_GRAD_CART = "optking --freq_grad_cart"
end
# Access to the global task object. The first time it is retrieved the object is created.
def self.global_task=(val)
@global_task = val
end
def self.global_task
if @global_task == nil
# Creat the global task
@global_task = Psi::Task.new
end
@global_task
end
def self.memory=(val)
Psi::global_task.memory=val
end
def self.memory
Psi::global_task.memory
end
def self.prefix=(val)
Psi::global_task.prefix=val
end
def self.prefix
Psi::global_task.prefix
end
def self.scratch=(val)
Psi::global_task.scratch=val
end
def self.scratch
Psi::global_task.scratch
end
def self.check_commands=(val)
Psi::global_task.check_commands = val
end
def self.check_commands
Psi::global_task.check_commands
end
def self.print_toc(unit)
Psi::global_task.print_toc unit
end
def self.units=(val)
Psi::global_task.units = val
end
def self.units
Psi::global_task.units
end
# Routines to set active geometry, referred to only by Input
def self.geometry=(val)
Psi::global_task.geometry = val
end
def self.geometry
Psi::global_task.geometry
end
# Routines to set active zmat, referred to only by Input
def self.zmat=(val)
Psi::global_task.zmat = val
end
def self.zmat
Psi::global_task.zmat
end
# Routines to remember basis
def self.basis=(val)
Psi::global_task.basis = val
end
def self.basis
Psi::global_task.basis
end
# Set the label
def self.label=(val)
Psi::global_task.label = val
end
def self.label
Psi::global_task.label
end
# Set the label
def self.wavefunction=(val)
Psi::global_task.wavefunction = val
end
def self.wavefunction
Psi::global_task.wavefunction
end
# Set the flag for analytical gradients
def self.analytical_gradients=(val)
Psi::global_task.analytical_gradients=val
end
def self.analytical_gradients
Psi::global_task.analytical_gradients
end
# Set the global reference
def self.reference=(val)
Psi::global_task.reference = val
end
def self.reference
Psi::global_task.reference
end
# Additions to the Task class
class Task
def check_commands=(val)
@check_commands = val
end
def check_commands
if @check_commands == nil
@check_commands = false
end
@check_commands
end
def reference=(val)
@reference = val
end
def reference
if @reference == nil
puts "Warning: Reference not set. Assuming RHF."
return "RHF"
end
@reference
end
def wavefunction=(val)
@wavefunction = val
end
def wavefunction
if @wavefunction == nil
# Was never set, assume SCF
puts "Warning: Wavefunction not set. Assuming SCF."
return "SCF"
end
@wavefunction
end
# What are the units for the geometry
def units=(val)
@units = val
end
def units
if @units == nil
return "angstroms"
end
@units
end
# Routines to set active geometry, referred to only by Input
def geometry=(val)
@geometry = val
end
def geometry
@geometry
end
# Routines to set active zmat, referred to only by Input
def zmat=(val)
@zmat = val
end
def zmat
@zmat
end
# Routines to remember basis
def basis=(val)
puts val.to_s
@basis = val
end
def basis
puts val.to_s
@basis
end
# Set the label
def label=(val)
@label = val
end
def label
@label
end
def gradients=(val)
@gradients = val
end
def set_gradients(val)
@gradients = val
end
def get_gradients
@gradients
end
def gradients
if @gradients == nil
return false
end
@gradients
end
def second_deriv=(val)
@second_deriv = val
end
def set_second_deriv(val)
@second_deriv = val
end
def get_second_deriv
@second_deriv
end
def second_deriv
if @second_deriv == nil
return false
end
@second_deriv
end
def set_optimization_complete(val)
@optimization_complete = val
end
def get_optimization_complete
if @optimization_complete == nil
return false
end
@optimization_complete
end
# Memory is given in megabytes
def get_memory
if @memory == nil
return 256
end
@memory
end
def set_memory=(val)
@memory=val
end
def memory=(val)
@memory=val
end
def memory
if @memory == nil
return 256
end
@memory
end
def self.create(*args)
args_hash = args[0]
t = Psi::Task.new args_hash
if t == nil
puts "Error: Unable to create Task object."
exit 1
end
if block_given?
yield t
else
t
end
end
end # of Task
module InputGenerator
def set_task(val)
@task = val
end
def get_task
@task
end
def set_psi_module_name(val)
@psi_module_name = val
end
def get_psi_module_name
if @psi_module_name == nil
self.class.name.slice!(5..-1)
else
@psi_module_name
end
end
def generate_value(item)
result = StringIO.new("", "w")
if item.kind_of?(Array)
# Encompass an array with ()
result.printf "("
item.each do |x|
sub_result = generate_value(x)
result.printf(sub_result.string)
end
# close off the array
result.puts ")"
elsif item.kind_of?(Hash)
item.each do |key,value|
result.puts "#{key} = #{generate_value(value).string}"
end
elsif item.kind_of?(Symbol)
# 1. Get the name of the symbol :name (without colon) and tack on a $ to the front
# making it a global variable.
# 2. eval the global variable for it's value
value = eval("$" + item.id2name)
result.printf "#{value.to_s} "
else
# Tell everything else to convert to a string
result.printf "#{item.to_s} "
end
return result
end
def generate_scratch_input(input)
# Make sure the scratch location stuff is included
input.puts "psi:("
input.puts " files:("
input.puts " default:("
input.puts " nvolume=1"
input.puts " volume1=\\\"#{@task.scratch}\\\""
input.puts " )"
input.puts " file32: (nvolume=1 volume1=\\\"./\\\")"
input.puts " )"
input.puts ")"
end
# Set the input parameters that are needed to run the given psi module
# Expects a hash containing properties to be set
# { "jobtype" => "sp", "dertype" => "none" }
# Uses the name of the encompassing class to name the module for psi3 input file
def generate_input(input_hash)
input = StringIO.new("", "w")
# Generate file sections
generate_scratch_input(input)
# Begin the input
input.puts "#{get_psi_module_name}:("
# Go through the hash and add entries into the input
sub_result = generate_value(input_hash)
input.puts(sub_result.string)
# Put in the memory keyword
input.puts "memory = (#{@task.get_memory} MB)"
# Close off the input
input.puts ")"
return input
end
end
module Executor
def set_binary_command(binary)
@program = binary
end
def get_binary_command
@program
end
def execute_internal(input_file, binary=nil)
puts "DEBUG: For #{binary} would have used:\n#{input_file.string}" if Psi::check_commands == true and binary != nil
if Psi::check_commands == true and get_binary_command != nil
puts "DEBUG: For #{get_binary_command} would have used:\n#{input_file.string}"
end
if Psi::check_commands != true
prefix = ""
prefix = "-p #{get_task.prefix}" if get_task.prefix != nil
if binary != nil
if Psi::quiet
`echo "#{input_file.string}" | #{binary} #{prefix} -f - >& /dev/null`
else
`echo "#{input_file.string}" | #{binary} #{prefix} -f -`
end
elsif get_binary_command != nil
if Psi::quiet
`echo "#{input_file.string}" | #{get_binary_command} #{prefix} -f - >& /dev/null`
else
`echo "#{input_file.string}" | #{get_binary_command} #{prefix} -f -`
end
else
puts "Error: Executor.execute: Unable to determine which module to run."
exit 1
end
# Check to see if the above line worked
status = $?
# Note for optking a specialized execute is needed
if status != 0
puts "Module exited with an error."
puts "Error code: #{status}"
puts "Used:\n#{input_file.string}"
exit 1
end
end
end
# This function requires that InputGenerator be used
def execute(input_hash, binary=nil)
# Form the input file
input_file = generate_input input_hash
# execute the module
execute_internal(input_file, binary)
end
end
end
require 'color'
require 'input'
require 'cints'
require 'scf'
require 'optking'
require 'clean'
require 'pes'
require 'transqt'
require 'ccsort'
require 'ccenergy'
require 'cctriples'
require 'symbols'
require 'chkpt'
require 'mp2'
require 'cchbar'
require 'ccdensity'
require 'cclambda'
require 'oeprop'
require 'deriv'
require 'detci'
require 'deriv2'
require 'propint'
require 'cphf'
require 'frequencies'
require 'cceom'
if File.exist?( File.expand_path("~/.psi.rb"))
load "~/.psi.rb"
end
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