mirror of
https://github.com/Electrostatics/apbs.git
synced 2026-06-04 20:54:22 +08:00
107 lines
2.5 KiB
Python
107 lines
2.5 KiB
Python
from .vgrid import (
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startVio,
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Vgrid_ctor,
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Vgrid_readDX,
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Vgrid_value,
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Vgrid_gradient,
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)
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import sys
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from sys import stdout, stderr
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"""
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read.py - An example script for interfacing Python with APBS
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Vgrid routines
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"""
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header = "\n\n\
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----------------------------------------------------------------------\n\
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Adaptive Poisson-Boltzmann Solver (APBS)\n\
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----------------------------------------------------------------------\n\
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\n\n"
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usage = "python[2] read.py file.dx\n"
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NMAX = 5
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def main():
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inpath = ""
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value = 0.0
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data = []
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startVio()
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if len(sys.argv) != 2:
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stderr.write(
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"\n*** Syntax error: got %d arguments, expected 2.\n\n"
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% len(sys.argv)
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)
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stderr.write("%s\n" % usage)
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sys.exit(2)
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else:
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inpath = sys.argv[1]
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stdout.write(header)
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stdout.write("main: Reading data from %s... \n" % inpath)
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grid = Vgrid_ctor(0, 0, 0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, data)
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Vgrid_readDX(grid, "FILE", "ASC", "", inpath)
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nx = grid.nx
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ny = grid.ny
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nz = grid.nz
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hx = grid.hx
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hy = grid.hy
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hzed = grid.hzed
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xmin = grid.xmin
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ymin = grid.ymin
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zmin = grid.zmin
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stdout.write("main: nx = %d, ny = %d, nz = %d\n" % (nx, ny, nz))
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stdout.write("main: hx = %g, hy = %g, hz = %g\n" % (hx, hy, hzed))
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stdout.write(
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"main: xmin = %g, ymin = %g, zmin = %g\n" % (xmin, ymin, zmin)
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)
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# Read off some values
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stdout.write("main: Moving along x-axis...\n")
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for i in range(nx):
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inval = 0.0
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pt = [
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xmin + i * hx,
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ymin + 0.5 * (ny - 1) * hy,
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zmin + 0.5 * (nz - 1) * hzed,
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]
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ret, value = Vgrid_value(grid, pt, inval)
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if ret:
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stdout.write(
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"main: u(%g, %g, %g) = %g\n" % (pt[0], pt[1], pt[2], value)
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)
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# Integrate
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stdout.write("main: Integrating...\n")
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sum = 0
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pt = 0
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for i in range(nx):
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for j in range(ny):
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for k in range(nz):
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inval = 0.0
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pt = [xmin + i * hx, ymin + j * hy, zmin + k * hzed]
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ret, value = Vgrid_value(grid, pt, inval)
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if ret:
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sum = sum + value
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stdout.write(
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"main: Integral over grid = %1.12E\n" % (sum * hx * hy * hzed)
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)
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grad = [0.0, 0.0, 0.0]
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Vgrid_gradient(grid, pt, grad)
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if __name__ == "__main__":
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main()
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