# Explanation of the 'properties':
#
# It is cheap to compute r^2, and the kernels require various other functions of r for
# different kinds of interaction. Depending on the needs of the kernel and the available
# processor instructions, this will be done in different ways.
#
# 'rinv' means we need 1/r, which is calculated as 1/sqrt(r^2).
# 'rinvsq' means we need 1/(r*r). This is calculated as rinv*rinv if we already did rinv, otherwise 1/r^2.
# 'r' is similarly calculated as r^2*rinv when needed
# 'table' means the interaction is tabulated, in which case we will calculate a table index before the interaction
# 'shift' means the interaction will be modified by a constant to make it zero at the cutoff.
# 'cutoff' means the interaction is set to 0.0 outside the cutoff
#
FileHeader = create_copyright_header('2012,2013,2014')
FileHeader += """/*
* Note: this file was generated by the GROMACS """+Arch+""" kernel generator.
*/
"""
###############################################
# ELECTROSTATICS
# Interactions and flags for them
###############################################
ElectrostaticsList = {
'None' : [],
'Coulomb' : ['rinv','rinvsq'],
'ReactionField' : ['rinv','rinvsq'],
'GeneralizedBorn' : ['rinv','r'],
'CubicSplineTable' : ['rinv','r','table'],
# Explanation of the 'properties':
#
# It is cheap to compute r^2, and the kernels require various other functions of r for
# different kinds of interaction. Depending on the needs of the kernel and the available
# processor instructions, this will be done in different ways.
#
# 'rinv' means we need 1/r, which is calculated as 1/sqrt(r^2).
# 'rinvsq' means we need 1/(r*r). This is calculated as rinv*rinv if we already did rinv, otherwise 1/r^2.
# 'r' is similarly calculated as r^2*rinv when needed
# 'table' means the interaction is tabulated, in which case we will calculate a table index before the interaction
# 'shift' means the interaction will be modified by a constant to make it zero at the cutoff.
# 'cutoff' means the interaction is set to 0.0 outside the cutoff
#
FileHeader = create_copyright_header("2012,2013,2014")
FileHeader += (
"""/*
* Note: this file was generated by the GROMACS """
+ Arch
+ """ kernel generator.
*/
"""
)
###############################################
# ELECTROSTATICS
# Interactions and flags for them
###############################################
ElectrostaticsList = {
"None": [],
# Note that while functions for both nbnxn kernel structures are
# compiled and built into an mdrun executable, because that executable
# is not portable, only the functions for the useful nbnxn kernel
# structure for the hardware selected at CMake time contain real
# kernel logic. A run-time error occurs if an inappropriate kernel
# dispatcher function is called (but that is normally impossible).
import re
import sys
import os
os.chdir(os.path.dirname(os.path.abspath(__file__)))
import collections # Requires Python 2.7
sys.path.append('../../../../../admin')
from copyright import create_copyright_header
FileHeader = create_copyright_header('2012,2013,2014')
FileHeader += """/*
* Note: this file was generated by the Verlet kernel generator for
* kernel type {0}.
*/
"""
def read_kernel_template(filename):
with open(filename, "r") as TemplateFile:
TemplateText = TemplateFile.read()
copyright_re = r'/\*\n \* This file is part of the GROMACS molecular simulation package\.\n( \*.*\n)* \*/\n'
match = re.match(copyright_re, TemplateText)
if match:
TemplateText = TemplateText[match.end():]
# Explanation of the 'properties':
#
# It is cheap to compute r^2, and the kernels require various other functions of r for
# different kinds of interaction. Depending on the needs of the kernel and the available
# processor instructions, this will be done in different ways.
#
# 'rinv' means we need 1/r, which is calculated as 1/sqrt(r^2).
# 'rinvsq' means we need 1/(r*r). This is calculated as rinv*rinv if we already did rinv, otherwise 1/r^2.
# 'r' is similarly calculated as r^2*rinv when needed
# 'table' means the interaction is tabulated, in which case we will calculate a table index before the interaction
# 'shift' means the interaction will be modified by a constant to make it zero at the cutoff.
# 'cutoff' means the interaction is set to 0.0 outside the cutoff
#
FileHeader = create_copyright_header('2012,2013,2014,2015,2017,2018')
FileHeader += """/*
* Note: this file was generated by the GROMACS """+Arch+""" kernel generator.
*/
"""
###############################################
# ELECTROSTATICS
# Interactions and flags for them
###############################################
ElectrostaticsList = {
'None' : [],
'Coulomb' : ['rinv','rinvsq'],
'ReactionField' : ['rinv','rinvsq'],
'CubicSplineTable' : ['rinv','r','table'],
'Ewald' : ['rinv','rinvsq','r'],
# Explanation of the 'properties':
#
# It is cheap to compute r^2, and the kernels require various other functions of r for
# different kinds of interaction. Depending on the needs of the kernel and the available
# processor instructions, this will be done in different ways.
#
# 'rinv' means we need 1/r, which is calculated as 1/sqrt(r^2).
# 'rinvsq' means we need 1/(r*r). This is calculated as rinv*rinv if we already did rinv, otherwise 1/r^2.
# 'r' is similarly calculated as r^2*rinv when needed
# 'table' means the interaction is tabulated, in which case we will calculate a table index before the interaction
# 'shift' means the interaction will be modified by a constant to make it zero at the cutoff.
# 'cutoff' means the interaction is set to 0.0 outside the cutoff
#
FileHeader = create_copyright_header('2012,2013,2014,2015,2017,2018')
FileHeader += """/*
* Note: this file was generated by the GROMACS """ + Arch + """ kernel generator.
*/
"""
###############################################
# ELECTROSTATICS
# Interactions and flags for them
###############################################
ElectrostaticsList = {
'None': [],
'Coulomb': ['rinv', 'rinvsq'],
'ReactionField': ['rinv', 'rinvsq'],
'CubicSplineTable': ['rinv', 'r', 'table'],
'Ewald': ['rinv', 'rinvsq', 'r'],
