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Add xSPRINT coordinates CV
1 parent 2e6f01f commit 78d4d5a

26 files changed

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‎regtest/.gitignore‎

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!/wham
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!/metatomic
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!/sizeshape
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!/xsprint
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# These files we just want to ignore completely
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tmp

‎regtest/xsprint/Makefile‎

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include ../scripts/module.make

‎regtest/xsprint/rt-xsprint-1shell/Makefile‎

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include ../../scripts/test.make

‎regtest/xsprint/rt-xsprint-1shell/colvar.reference‎

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#! FIELDS time xs_coord-0 xs_coord-1 xs_coord-2 xs_coord-3 xs_coord-4 xs_coord-5 xs_coord-6 xs_coord-7 xs_coord-8 xs_coord-9 xs_coord-10 xs_coord-11 xs_coord-12 xs_coord-13
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0.000000 4.6419 6.0632 6.1581 6.1588 6.4828 6.4895 6.8567 2.7487 2.7496 3.2158 3.2972 3.3002 3.5708 3.5727
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1.000000 5.8879 5.9824 6.0344 6.0796 6.4405 6.9432 7.1897 3.0307 3.0555 3.1203 3.3415 3.5160 3.6172 4.0368
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2.000000 5.5023 5.8045 5.9213 5.9916 6.1783 6.3161 6.4699 2.8745 3.1502 3.3023 3.4359 3.5402 3.7582 4.0200
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3.000000 5.4075 5.5786 5.8003 6.0605 6.1389 6.6391 6.7378 2.8069 3.1223 3.1291 3.3933 3.6409 4.0698 4.2879
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4.000000 5.4487 5.4653 5.6167 5.9594 6.4644 6.6199 6.9774 2.7674 2.9206 3.1827 3.4475 3.5723 4.2203 4.5450
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5.000000 5.8821 5.8821 5.8845 5.8845 5.8861 5.8963 5.8963 3.3549 3.3584 3.3584 3.3784 3.3784 3.4041 3.4041
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6.000000 5.7865 5.9230 6.0762 6.3384 6.4910 7.4292 7.8610 2.7869 2.8071 2.8072 3.0500 3.6363 3.7908 4.4693
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7.000000 5.6959 5.7783 6.4257 6.5346 6.6417 7.3627 7.5493 2.6189 2.6695 3.1743 3.1848 3.7441 3.8198 3.8911
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8.000000 3.9801 6.1602 6.5242 6.5244 6.6727 7.3000 7.3007 2.2038 2.2054 3.0656 3.1561 3.1562 3.8773 3.8775
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9.000000 3.1441 5.1850 6.1753 6.1753 6.7558 6.7559 7.3867 1.7190 1.9932 3.1433 3.1433 3.4588 3.4589 4.5090
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10.000000 2.6856 4.5889 6.2007 6.3569 6.6190 6.9819 7.0862 1.5286 1.5286 3.2115 3.2167 3.4300 4.2474 4.2476
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11.000000 1.9044 2.7928 4.1486 4.9250 5.5725 6.1807 6.4234 1.1614 1.1658 3.1261 3.3631 3.6928 4.0992 4.1208
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12.000000 3.8279 5.3013 6.0450 6.0450 6.3891 6.3892 7.1793 2.1907 2.3741 2.9944 3.0827 3.0827 3.3256 3.3257
15+
13.000000 3.1948 4.8342 6.1370 6.4611 6.5331 7.1671 7.3430 1.4230 2.8196 3.1100 3.3468 3.3518 4.2910 4.2920
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14.000000 3.5386 5.4587 6.1050 6.1173 6.7973 6.8382 7.6329 1.5730 3.0701 3.0761 3.1049 3.5010 3.5059 4.5673
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15.000000 5.2389 5.5466 5.8188 5.9540 6.1001 6.5796 6.9787 2.8276 3.0649 3.2850 3.3500 3.3500 3.6339 3.7524
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16.000000 6.5160 6.5164 6.8251 6.8254 7.5418 7.6267 8.0331 2.8615 2.8621 3.0705 3.0707 4.0205 4.2613 4.2614

‎regtest/xsprint/rt-xsprint-1shell/config‎

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type=driver
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plumed_modules="adjmat sprint xsprint"
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arg="--plumed plumed.dat --ixyz isomers.xyz --dump-forces forces --dump-forces-fmt=%8.4f"
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extra_files="../../trajectories/isomers.xyz"

‎regtest/xsprint/rt-xsprint-1shell/forces.reference‎

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X 0.0500 0.3019 -0.0073
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X 0.4229 0.0082 0.0011
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X 0.0994 -0.3504 0.0089
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X 0.4437 -0.3234 0.5632
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X 0.6089 0.5389 -0.0105
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14
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‎regtest/xsprint/rt-xsprint-1shell/plumed.dat‎

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xs: XSPRINT ...
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GROUP1=1-7 GROUP2=8-14
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SWITCH11={RATIONAL R_0=2.6 NN=6 MM=12}
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SWITCH12={RATIONAL R_0=2.2 NN=6 MM=12}
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SWITCH22={RATIONAL R_0=2.2 NN=6 MM=12}
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NSHELLS=1
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...
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PRINT ARG=xs_coord-0,xs_coord-1,xs_coord-2,xs_coord-3,xs_coord-4,xs_coord-5,xs_coord-6,xs_coord-7,xs_coord-8,xs_coord-9,xs_coord-10,xs_coord-11,xs_coord-12,xs_coord-13 FILE=colvar FMT=%8.4f
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BIASVALUE ARG=xs_coord-0

‎regtest/xsprint/rt-xsprint-3shell/Makefile‎

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include ../../scripts/test.make

‎regtest/xsprint/rt-xsprint-3shell/colvar.reference‎

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#! FIELDS time xs_coord-0 xs_coord-1 xs_coord-2 xs_coord-3 xs_coord-4 xs_coord-5 xs_coord-6 xs_coord-7 xs_coord-8 xs_coord-9 xs_coord-10 xs_coord-11 xs_coord-12 xs_coord-13
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0.000000 0.3093 0.3234 0.3235 0.3331 0.3331 0.3345 0.3352 0.3352 0.3357 0.3357 0.3547 0.3548 0.3557 0.3557
3+
1.000000 0.3165 0.3220 0.3221 0.3225 0.3235 0.3262 0.3343 0.3454 0.3499 0.3511 0.3609 0.3615 0.3622 0.3640
4+
2.000000 0.3208 0.3219 0.3252 0.3261 0.3285 0.3290 0.3330 0.3458 0.3543 0.3555 0.3557 0.3577 0.3605 0.3613
5+
3.000000 0.3204 0.3227 0.3227 0.3242 0.3263 0.3306 0.3328 0.3436 0.3513 0.3516 0.3591 0.3591 0.3593 0.3639
6+
4.000000 0.3223 0.3227 0.3228 0.3247 0.3260 0.3299 0.3301 0.3518 0.3531 0.3537 0.3573 0.3591 0.3604 0.3627
7+
5.000000 0.3280 0.3280 0.3280 0.3280 0.3281 0.3281 0.3282 0.3494 0.3494 0.3495 0.3495 0.3497 0.3497 0.3498
8+
6.000000 0.3058 0.3116 0.3245 0.3254 0.3285 0.3291 0.3338 0.3393 0.3506 0.3578 0.3578 0.3598 0.3612 0.3614
9+
7.000000 0.3086 0.3118 0.3243 0.3245 0.3256 0.3298 0.3318 0.3527 0.3535 0.3547 0.3584 0.3590 0.3640 0.3654
10+
8.000000 0.3139 0.3179 0.3180 0.3375 0.3375 0.3377 0.3380 0.3402 0.3403 0.3492 0.3696 0.3696 0.3734 0.3734
11+
9.000000 0.2996 0.3052 0.3125 0.3137 0.3230 0.3319 0.3319 0.3348 0.3348 0.3386 0.3386 0.3497 0.3787 0.3787
12+
10.000000 0.2940 0.2940 0.3020 0.3094 0.3155 0.3289 0.3306 0.3321 0.3324 0.3364 0.3401 0.3726 0.3726 0.3762
13+
11.000000 0.2039 0.2178 0.2217 0.2628 0.2745 0.2820 0.2906 0.2979 0.3027 0.3102 0.3197 0.3303 0.3560 0.3578
14+
12.000000 0.2984 0.3092 0.3188 0.3204 0.3346 0.3346 0.3347 0.3347 0.3347 0.3347 0.3447 0.3506 0.3723 0.3723
15+
13.000000 0.2973 0.3069 0.3196 0.3222 0.3262 0.3310 0.3321 0.3323 0.3368 0.3370 0.3421 0.3633 0.3633 0.3656
16+
14.000000 0.3075 0.3217 0.3228 0.3288 0.3323 0.3361 0.3378 0.3387 0.3446 0.3449 0.3513 0.3642 0.3686 0.3707
17+
15.000000 0.3096 0.3169 0.3186 0.3257 0.3299 0.3321 0.3346 0.3348 0.3359 0.3424 0.3424 0.3507 0.3545 0.3560
18+
16.000000 0.3015 0.3130 0.3187 0.3187 0.3200 0.3229 0.3229 0.3599 0.3621 0.3621 0.3628 0.3628 0.3628 0.3628

‎regtest/xsprint/rt-xsprint-3shell/config‎

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type=driver
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plumed_modules="adjmat sprint xsprint"
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arg="--plumed plumed.dat --ixyz isomers.xyz --dump-forces forces --dump-forces-fmt=%8.4f"
4+
extra_files="../../trajectories/isomers.xyz"

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