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more examples and improved readability
This commit is contained in:
Robert Harrison
parent
a0efeceb24
commit
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1 changed files with 96 additions and 86 deletions
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@ -77,6 +77,9 @@ your program may deadlock (i.e., cease to make progress).
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\item When writing to the database (\verb+rtdb_put()+) it is the data
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from node zero that is written.
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\item NWChem overrides certain default signal handlers so care
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must be taken when creating processes (see Section \ref{sec:sigchld}).
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\end{itemize}
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\section{NWChem extensions}
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@ -149,23 +152,18 @@ This input prints the traditional greeting from each parallel process.
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\subsection{Scanning a basis exponent}
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\begin{verbatim}
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geometry units au noprint
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O 0 0 0
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H 0 1.430 -1.107
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H 0 -1.430 -1.107
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geometry units au
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O 0 0 0; H 0 1.430 -1.107; H 0 -1.430 -1.107
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end
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python noprint
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python
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exponent = 0.1
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while (exponent <= 2.01):
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input_parse('''
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basis noprint
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H library 3-21g
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O library 3-21g
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O d; %f 1.0
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H library 3-21g; O library 3-21g; O d; %f 1.0
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end
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''' % (exponent))
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print ' exponent = ', exponent, ' energy = ', task_energy('scf')
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exponent = exponent + 0.1
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end
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@ -192,12 +190,11 @@ Note that execution in parallel may produce unwanted output since
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all process execute the print statement inside the Python program.
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\subsection{Scanning a basis exponent revisited.}
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\label{sec:scan2}
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\begin{verbatim}
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geometry units au
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O 0 0 0
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H 0 1.430 -1.107
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H 0 -1.430 -1.107
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O 0 0 0; H 0 1.430 -1.107; H 0 -1.430 -1.107
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end
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print none
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@ -208,12 +205,9 @@ all process execute the print statement inside the Python program.
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def energy_at_exponent(exponent):
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input_parse('''
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basis noprint
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H library 3-21g
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O library 3-21g
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O d; %f 1.0
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H library 3-21g; O library 3-21g; O d; %f 1.0
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end
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''' % (exponent))
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return task_energy('scf')
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exponent = 0.1
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@ -246,10 +240,8 @@ file. When the loop is finished the additional output file is closed.
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\begin{verbatim}
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python
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geometry = '''
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geometry noprint
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symmetry d2h
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C 0 0 %f
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H 0 0.916 1.224
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geometry noprint; symmetry d2h
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C 0 0 %f; H 0 0.916 1.224
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end
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'''
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x = 0.6
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@ -260,10 +252,7 @@ file. When the loop is finished the additional output file is closed.
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x = x + 0.01
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end
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basis
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C library 6-31g*
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H library 6-31g*
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end
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basis; C library 6-31g*; H library 6-31g*; end
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print none
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@ -272,15 +261,15 @@ file. When the loop is finished the additional output file is closed.
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This scans the bond length in ethene from 1.2 to 1.44 in steps
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of 0.2 computing the energy at each geometry. Since it is using
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$D_{2h}$ symmetry the program actually uses a variable (verb+x+) that is
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$D_{2h}$ symmetry the program actually uses a variable (\verb+x+) that is
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half the bond length.
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\subsection{Scan using the BSSE counterpoise corrected energy}
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\begin{verbatim}
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basis spherical noprint
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Ne library cc-pvdz; He library cc-pvdz
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BqNe library Ne cc-pvdz; BqHe library He cc-pvdz
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basis spherical
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Ne library cc-pvdz; BqNe library Ne cc-pvdz
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He library cc-pvdz; BqHe library He cc-pvdz
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end
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mp2; tight; freeze core atomic; end
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@ -288,38 +277,23 @@ half the bond length.
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print none
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python noprint
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supermolecule = '''
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geometry noprint
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Ne 0 0 0
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He 0 0 %f
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end
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'''
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fragment1 = '''
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geometry noprint
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Ne 0 0 0
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BqHe 0 0 %f
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end
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'''
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fragment2 = '''
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geometry noprint
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BqNe 0 0 0
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He 0 0 %f
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end
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'''
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def geom_energy(geometry):
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input_parse(geometry)
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input_parse('scf; vectors atomic; end\n')
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supermolecule = 'geometry noprint; Ne 0 0 0; He 0 0 %f; end\n'
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fragment1 = 'geometry noprint; Ne 0 0 0; BqHe 0 0 %f; end\n'
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fragment2 = 'geometry noprint; BqNe 0 0 0; He 0 0 %f; end\n'
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def energy(geometry):
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input_parse(geometry + 'scf; vectors atomic; end\n')
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return task_energy('mp2')
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def bsse_energy(z):
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return geom_energy(supermolecule % z) - \
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geom_energy(fragment1 % z) - \
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geom_energy(fragment2 % z)
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return energy(supermolecule % z) - \
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energy(fragment1 % z) - \
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energy(fragment2 % z)
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z = 3.3
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while (z < 4.301):
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energy = bsse_energy(z)
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e = bsse_energy(z)
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if (ga_nodeid() == 0):
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print ' z = %5.2f energy = %10.7f ' % (z, energy)
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print ' z = %5.2f energy = %10.7f ' % (z, e)
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z = z + 0.1
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end
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@ -356,7 +330,6 @@ package.
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print ' y z energy gradient'
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print ' ----- ----- ---------- ------------------------------------'
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y = 1.2
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elo = 0.0
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while y <= 1.61:
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z = 1.0
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while z <= 1.21:
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@ -370,10 +343,6 @@ package.
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(energy,gradient) = task_gradient('scf')
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if (energy < elo):
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elo = energy
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ylo = y
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zlo = z
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print ' %5.2f %5.2f %9.6f' % (y, z, energy),
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i = 0
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while (i < len(gradient)):
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@ -382,9 +351,6 @@ package.
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print ''
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z = z + 0.1
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y = y + 0.1
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print ''
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print ' Lowest energy =',elo,' at y=',ylo,', z =',zlo
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print ' '
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end
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print none
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@ -396,7 +362,7 @@ This program illustrates evaluating the energy and gradient
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by calling \verb+task_gradient()+. A water molecule is scanned
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through several $C_{2v}$ geometries by varying the y and z coordinates
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of the two hydrogen atoms. At each geometry the coordinates, energy
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and gradient are printed. The lowest energy geometry is recorded.
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and gradient are printed.
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The basis set (sto-3g) is input as usual. The two while loops vary
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the y and z coordinates. These are then substituted into a geometry
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@ -416,26 +382,11 @@ end-of-line.
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python
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energies = {}
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c2h4 = '''
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geometry noprint
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symmetry d2h
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C 0 0 0.672
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H 0 0.935 1.238
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end
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'''
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ch4 = '''
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geometry noprint
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symmetry td
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C 0 0 0
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H 0.634 0.634 0.634
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end
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'''
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h2 = '''
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geometry noprint
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H 0 0 0.378
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H 0 0 -0.378
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end
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'''
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c2h4 = 'geometry noprint; symmetry d2h; \
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C 0 0 0.672; H 0 0.935 1.238; end\n'
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ch4 = 'geometry noprint; symmetry td; \
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C 0 0 0; H 0.634 0.634 0.634; end\n'
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h2 = 'geometry noprint; H 0 0 0.378; H 0 0 -0.378; end\n'
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def energy(basis, geometry):
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input_parse('''
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@ -447,9 +398,8 @@ end-of-line.
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return task_energy('mp2')
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for basis in ('sto-3g', '6-31g', '6-31g*', 'cc-pvdz', 'cc-pvtz'):
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energies[basis] = 2*energy(basis, ch4) - \
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2*energy(basis, h2) - \
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energy(basis, c2h4)
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energies[basis] = 2*energy(basis, ch4) \
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- 2*energy(basis, h2) - energy(basis, c2h4)
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if (ga_nodeid() == 0): print basis, ' %8.6f' % energies[basis]
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end
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@ -521,6 +471,66 @@ If your Python program detects an error, raise an unhandled
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exception. Do not call \verb+exit(1)+ since this may circumvent
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necessary clean-up of the NWChem execution environment.
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\subsection{Scaning a basis exponent yet again --- plotting and
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handling child processes}
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\label{sec:sigchld}
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\begin{verbatim}
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geometry units au
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O 0 0 0; H 0 1.430 -1.107; H 0 -1.430 -1.107
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end
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print none
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python
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import Gnuplot, time, signal
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def energy_at_exponent(exponent):
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input_parse('''
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basis noprint
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H library 3-21g; O library 3-21g; O d; %f 1.0
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end
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''' % (exponent))
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return task_energy('scf')
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data = []
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exponent = 0.5
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while exponent <= 0.6:
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energy = energy_at_exponent(exponent)
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print ' exponent = ', exponent, ' energy = ', energy
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data = data + [[exponent,energy]]
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exponent = exponent + 0.02
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if (ga_nodeid() == 0):
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signal.signal(signal.SIGCHLD, signal.SIG_DFL)
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g = Gnuplot.Gnuplot()
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g('set data style linespoints')
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g.plot(data)
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time.sleep(30) # 30s to look at the plot
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end
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task python
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\end{verbatim}
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This illustrates how to handle signals from terminating child
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processes and how to generate simple plots on UNIX systems. The
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example from Section \ref{sec:scan2} is modified so that instead of
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writing the data to a file for subsequent visualization, it is saved
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for subsequent visualization with Gnuplot (you'll need both Gnuplot
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and the corresponding package for Python in your \verb+PYTHONPATH+.
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Look at http://monsoon.harvard.edu/~mhagger/download).
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The issue is that NWChem traps various signals from the O/S that
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usually indicate bad news in order to provide better error handling
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and reliable clean-up of shared, parallel resources. One of these
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signals is \verb+SIGCHLD+ which is generated whenever a child process
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terminates. If you want to create child processes within Python, then
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the NWChem handler for \verb+SIGCHLD+ must be replaced with the
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default handler. There seems to be no easy way to restore the
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NWChem handler after the child has completed, but this should have
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no serious side effect.
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\section{Troubleshooting}
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Common problems with Python programs inside NWChem.
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