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Resolution function and PARAMETERS for SANS (#972)
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* Add resolution function and PARAMETERSFILE keyword

* Fix warning and improve reading from PARAMETERFILE

* Allows reading PARAMETERS for SANS

* Fix resolution function units

* Remove dot from bibliography

* Add test to SANS with resolution function reading PARAMETERS from file

* astyle changes
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@hmcezar
hmcezar authored Sep 25, 2023
1 parent 3be5aa0 commit 948e8df
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1 change: 1 addition & 0 deletions regtest/isdb/rt-sans/Makefile
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include ../../scripts/test.make
2 changes: 2 additions & 0 deletions regtest/isdb/rt-sans/colvar.reference
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#! FIELDS time sans.q-0 sans.q-1 sans.q-2 sans.q-3 sans.q-4 sans.q-5 sans.q-6 sans.q-7 sans.q-8 sans.q-9 sans.q-10 sans.q-11 sans.q-12 sans.q-13 sans.q-14 sans.exp-0 sans.exp-1 sans.exp-2 sans.exp-3 sans.exp-4 sans.exp-5 sans.exp-6 sans.exp-7 sans.exp-8 sans.exp-9 sans.exp-10 sans.exp-11 sans.exp-12 sans.exp-13 sans.exp-14
0.000000 0.987712 0.972288 0.957710 0.911071 0.850477 0.778757 0.698772 0.528043 0.442987 0.366106 0.293353 0.232892 0.178651 0.133932 0.058760 0.567780 0.538400 0.637740 0.570090 0.544870 0.473150 0.398940 0.296550 0.263370 0.212490 0.161590 0.133300 0.095560 0.054072 0.029263
3 changes: 3 additions & 0 deletions regtest/isdb/rt-sans/config
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mpiprocs=4
type=driver
arg="--plumed plumed.dat --timestep 0.005 --mf_pdb template.pdb"
820 changes: 820 additions & 0 deletions regtest/isdb/rt-sans/forces.reference
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42 changes: 42 additions & 0 deletions regtest/isdb/rt-sans/plumed.dat
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MOLINFO STRUCTURE=template.pdb

# SANS
SANS ...

LABEL=sans
ATOMS=1-270
N=11

# Read parameters from file
PARAMETERSFILE=scatlens.plumed

QVALUE1=0.0110113 EXPINT1=0.56778 SIGMARES1=0.001
QVALUE2=0.0169278 EXPINT2=0.5384 SIGMARES2=0.001
QVALUE3=0.0209899 EXPINT3=0.63774 SIGMARES3=0.002
QVALUE4=0.031085 EXPINT4=0.57009 SIGMARES4=0.002
QVALUE5=0.040975 EXPINT5=0.54487 SIGMARES5=0.003
QVALUE6=0.050954 EXPINT6=0.47315 SIGMARES6=0.003
QVALUE7=0.060951 EXPINT7=0.39894 SIGMARES7=0.003
QVALUE8=0.080938 EXPINT8=0.29655 SIGMARES8=0.004
QVALUE9=0.091069 EXPINT9=0.26337 SIGMARES9=0.005
QVALUE10=0.100795 EXPINT10=0.21249 SIGMARES10=0.006
QVALUE11=0.110893 EXPINT11=0.16159 SIGMARES11=0.007
QVALUE12=0.120377 EXPINT12=0.1333 SIGMARES12=0.008
QVALUE13=0.130277 EXPINT13=0.09556 SIGMARES13=0.009
QVALUE14=0.140141 EXPINT14=0.054072 SIGMARES14=0.01
QVALUE15=0.161951 EXPINT15=0.029263 SIGMARES15=0.01

# METAINFERENCE
# Uncomment the following keywords and adjust parameters to activate METAINFERENCE
# DOSCORE NOENSEMBLE SIGMA_MEAN0=0
# REGRES_ZERO=500
# SIGMA0=5 SIGMA_MIN=0.001 SIGMA_MAX=5.00
# NOISETYPE=MGAUSS

... SANS

PRINT ARG=(sans\.q-.*),(sans\.exp-.*) FILE=colvar STRIDE=1

DUMPDERIVATIVES ARG=(sans\.q-.*) FILE=forces FMT=%.4f

ENDPLUMED
270 changes: 270 additions & 0 deletions regtest/isdb/rt-sans/scatlens.plumed
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PARAMETERS1=109.3554
PARAMETERS2=48.3351
PARAMETERS3=79.9724
PARAMETERS4=79.9724
PARAMETERS5=86.6434
PARAMETERS6=109.3554
PARAMETERS7=48.3351
PARAMETERS8=79.9724
PARAMETERS9=79.9724
PARAMETERS10=86.6434
PARAMETERS11=109.3554
PARAMETERS12=48.3351
PARAMETERS13=79.9724
PARAMETERS14=79.9724
PARAMETERS15=86.6434
PARAMETERS16=109.3554
PARAMETERS17=48.3351
PARAMETERS18=79.9724
PARAMETERS19=79.9724
PARAMETERS20=86.6434
PARAMETERS21=109.3554
PARAMETERS22=48.3351
PARAMETERS23=79.9724
PARAMETERS24=79.9724
PARAMETERS25=86.6434
PARAMETERS26=109.3554
PARAMETERS27=48.3351
PARAMETERS28=79.9724
PARAMETERS29=79.9724
PARAMETERS30=86.6434
PARAMETERS31=109.3554
PARAMETERS32=48.3351
PARAMETERS33=79.9724
PARAMETERS34=79.9724
PARAMETERS35=86.6434
PARAMETERS36=109.3554
PARAMETERS37=48.3351
PARAMETERS38=79.9724
PARAMETERS39=79.9724
PARAMETERS40=86.6434
PARAMETERS41=109.3554
PARAMETERS42=48.3351
PARAMETERS43=79.9724
PARAMETERS44=79.9724
PARAMETERS45=86.6434
PARAMETERS46=109.3554
PARAMETERS47=48.3351
PARAMETERS48=79.9724
PARAMETERS49=79.9724
PARAMETERS50=86.6434
PARAMETERS51=109.3554
PARAMETERS52=48.3351
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PARAMETERS55=86.6434
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PARAMETERS60=86.6434
PARAMETERS61=109.3554
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PARAMETERS65=86.6434
PARAMETERS66=109.3554
PARAMETERS67=48.3351
PARAMETERS68=79.9724
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PARAMETERS71=109.3554
PARAMETERS72=48.3351
PARAMETERS73=79.9724
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PARAMETERS75=86.6434
PARAMETERS76=109.3554
PARAMETERS77=48.3351
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PARAMETERS80=86.6434
PARAMETERS81=109.3554
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PARAMETERS85=86.6434
PARAMETERS86=109.3554
PARAMETERS87=48.3351
PARAMETERS88=79.9724
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PARAMETERS90=86.6434
PARAMETERS91=109.3554
PARAMETERS92=48.3351
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PARAMETERS95=86.6434
PARAMETERS96=109.3554
PARAMETERS97=48.3351
PARAMETERS98=79.9724
PARAMETERS99=79.9724
PARAMETERS100=86.6434
PARAMETERS101=109.3554
PARAMETERS102=48.3351
PARAMETERS103=79.9724
PARAMETERS104=79.9724
PARAMETERS105=86.6434
PARAMETERS106=109.3554
PARAMETERS107=48.3351
PARAMETERS108=79.9724
PARAMETERS109=79.9724
PARAMETERS110=86.6434
PARAMETERS111=109.3554
PARAMETERS112=48.3351
PARAMETERS113=79.9724
PARAMETERS114=79.9724
PARAMETERS115=86.6434
PARAMETERS116=109.3554
PARAMETERS117=48.3351
PARAMETERS118=79.9724
PARAMETERS119=79.9724
PARAMETERS120=86.6434
PARAMETERS121=109.3554
PARAMETERS122=48.3351
PARAMETERS123=79.9724
PARAMETERS124=79.9724
PARAMETERS125=86.6434
PARAMETERS126=109.3554
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PARAMETERS131=109.3554
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PARAMETERS268=79.9724
PARAMETERS269=79.9724
PARAMETERS270=86.6434
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Found broken examples in automatic/a-masterclass-22-09.txt
Found broken examples in automatic/a-masterclass-22-11.txt
Found broken examples in automatic/a-masterclass-22-12.txt
Found broken examples in automatic/performance-optimization.txt
Found broken examples in automatic/a-trieste-6.txt
Found broken examples in automatic/munster.txt
Found broken examples in automatic/ANN.tmp
Found broken examples in automatic/EDS.tmp
Found broken examples in automatic/EMMI.tmp
Found broken examples in automatic/ENVIRONMENTSIMILARITY.tmp
Found broken examples in automatic/FOURIER_TRANSFORM.tmp
Found broken examples in automatic/FUNCPATHGENERAL.tmp
Found broken examples in automatic/FUNCPATHMSD.tmp
Found broken examples in automatic/FUNNEL.tmp
Found broken examples in automatic/FUNNEL_PS.tmp
Found broken examples in automatic/GHBFIX.tmp
Found broken examples in automatic/INCLUDE.tmp
Found broken examples in automatic/MAZE_MEMETIC_SAMPLING.tmp
Found broken examples in automatic/MAZE_OPTIMIZER_BIAS.tmp
Found broken examples in automatic/MAZE_RANDOM_ACCELERATION_MD.tmp
Found broken examples in automatic/MAZE_RANDOM_WALK.tmp
Found broken examples in automatic/MAZE_SIMULATED_ANNEALING.tmp
Found broken examples in automatic/MAZE_STEERED_MD.tmp
Found broken examples in automatic/PIV.tmp
Found broken examples in automatic/PLUMED.tmp
Found broken examples in MiscelaneousPP.md

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