diff --git a/regtest/rt41/Makefile b/regtest/rt41/Makefile
new file mode 120000
index 0000000000000000000000000000000000000000..a19fbb5e94242934cf3be817c2bd68f92897f19d
--- /dev/null
+++ b/regtest/rt41/Makefile
@@ -0,0 +1 @@
+../scripts/test.make
\ No newline at end of file
diff --git a/regtest/rt41/colvar.reference b/regtest/rt41/colvar.reference
new file mode 100644
index 0000000000000000000000000000000000000000..14ce541c160f8075eba6f4d89353692c0f9a1879
--- /dev/null
+++ b/regtest/rt41/colvar.reference
@@ -0,0 +1,29 @@
+#! FIELDS time r1.X r2.X r2.Y r2.zzz
+ 0.000000 1.9434 1.9434 2.9434 0.0001
+ 5.000000 1.3261 1.3261 2.3261 0.0001
+ 10.000000 3.1900 3.1900 4.1900 0.0001
+ 15.000000 5.5554 5.5554 6.5554 0.0001
+ 20.000000 6.8811 6.8811 7.8811 0.0000
+ 25.000000 8.1518 8.1518 9.1518 0.0000
+ 30.000000 10.1206 10.1206 11.1206 0.0000
+ 35.000000 10.9254 10.9254 11.9254 0.0001
+ 40.000000 13.4767 13.4767 14.4767 0.0001
+ 45.000000 14.5201 14.5201 15.5201 0.0001
+ 50.000000 15.0187 15.0187 16.0187 0.0000
+ 55.000000 15.7926 15.7926 16.7926 0.0001
+ 60.000000 19.5301 19.5301 20.5301 0.0000
+ 65.000000 20.1734 20.1734 21.1734 0.0001
+ 70.000000 22.1538 22.1538 23.1538 0.0001
+ 75.000000 23.5398 23.5398 24.5398 0.0001
+ 80.000000 24.3638 24.3638 25.3638 0.0001
+ 85.000000 26.9164 26.9164 27.9164 0.0000
+ 90.000000 28.4074 28.4074 29.4074 0.0001
+ 95.000000 29.6254 29.6254 30.6254 0.0001
+ 100.000000 31.1434 31.1434 32.1434 0.0001
+ 105.000000 33.3878 33.3878 34.3878 0.0000
+ 110.000000 34.5353 34.5353 35.5353 0.0001
+ 115.000000 36.8600 36.8600 37.8600 0.0001
+ 120.000000 37.7380 37.7380 38.7380 0.0001
+ 125.000000 38.9521 38.9521 39.9521 0.0000
+ 130.000000 41.9895 41.9895 42.9895 0.0001
+ 135.000000 41.9978 41.9978 42.9978 0.0001
diff --git a/regtest/rt41/config b/regtest/rt41/config
new file mode 100644
index 0000000000000000000000000000000000000000..2c148d2022107d8a8fc489c0fb6bb16dc38cf45f
--- /dev/null
+++ b/regtest/rt41/config
@@ -0,0 +1,2 @@
+type=driver
+arg="--plumed plumed.dat --trajectory-stride 50 --timestep 0.005 --noatoms"
diff --git a/regtest/rt41/input_colvar b/regtest/rt41/input_colvar
new file mode 100644
index 0000000000000000000000000000000000000000..5ef6c8256607307d3ad74f6c909127bb4e48fd88
--- /dev/null
+++ b/regtest/rt41/input_colvar
@@ -0,0 +1,547 @@
+#! FIELDS time p2.X p2.Y p2.zzz p3.X p3.Y p3.zzz
+ 0.000000 1.9434 2.9434 0.0001 1.9434 2.9434 0.0001
+ 0.250000 1.0090 2.0090 0.0001 1.0090 2.0090 0.0001
+ 0.500000 1.0579 2.0579 0.0001 1.0579 2.0579 0.0001
+ 0.750000 1.0331 2.0331 0.0000 1.0331 2.0331 0.0000
+ 1.000000 1.3768 2.3768 0.0001 1.3768 2.3768 0.0001
+ 1.250000 1.4149 2.4149 0.0000 1.4149 2.4149 0.0000
+ 1.500000 1.0652 2.0652 0.0001 1.0652 2.0652 0.0001
+ 1.750000 1.0157 2.0157 0.0000 1.0157 2.0157 0.0000
+ 2.000000 1.1453 2.1453 0.0001 1.1453 2.1453 0.0001
+ 2.250000 1.3270 2.3270 0.0000 1.3270 2.3270 0.0000
+ 2.500000 1.0513 2.0513 0.0000 1.0513 2.0513 0.0000
+ 2.750000 1.3269 2.3269 0.0000 1.3269 2.3269 0.0000
+ 3.000000 1.0317 2.0317 0.0001 1.0317 2.0317 0.0001
+ 3.250000 3.1167 4.1167 0.0001 3.1167 4.1167 0.0001
+ 3.500000 1.2525 2.2525 0.0001 1.2525 2.2525 0.0001
+ 3.750000 1.2615 2.2615 0.0001 1.2615 2.2615 0.0001
+ 4.000000 1.4116 2.4116 0.0001 1.4116 2.4116 0.0001
+ 4.250000 2.2825 3.2825 0.0001 2.2825 3.2825 0.0001
+ 4.500000 2.0832 3.0832 0.0000 2.0832 3.0832 0.0000
+ 4.750000 1.5973 2.5973 0.0001 1.5973 2.5973 0.0001
+ 5.000000 1.3261 2.3261 0.0001 1.3261 2.3261 0.0001
+ 5.250000 2.4515 3.4515 0.0001 2.4515 3.4515 0.0001
+ 5.500000 2.5412 3.5412 0.0001 2.5412 3.5412 0.0001
+ 5.750000 1.8538 2.8538 0.0000 1.8538 2.8538 0.0000
+ 6.000000 1.3933 2.3933 0.0001 1.3933 2.3933 0.0001
+ 6.250000 1.7948 2.7948 0.0000 1.7948 2.7948 0.0000
+ 6.500000 3.8916 4.8916 0.0001 3.8916 4.8916 0.0001
+ 6.750000 2.4106 3.4106 0.0001 2.4106 3.4106 0.0001
+ 7.000000 2.9130 3.9130 0.0000 2.9130 3.9130 0.0000
+ 7.250000 2.7856 3.7856 0.0000 2.7856 3.7856 0.0000
+ 7.500000 3.0248 4.0248 0.0001 3.0248 4.0248 0.0001
+ 7.750000 3.0256 4.0256 0.0001 3.0256 4.0256 0.0001
+ 8.000000 2.8465 3.8465 0.0001 2.8465 3.8465 0.0001
+ 8.250000 1.7385 2.7385 0.0001 1.7385 2.7385 0.0001
+ 8.500000 3.2267 4.2267 0.0001 3.2267 4.2267 0.0001
+ 8.750000 3.4119 4.4119 0.0000 3.4119 4.4119 0.0000
+ 9.000000 2.6281 3.6281 0.0000 2.6281 3.6281 0.0000
+ 9.250000 2.4505 3.4505 0.0001 2.4505 3.4505 0.0001
+ 9.500000 2.9935 3.9935 0.0001 2.9935 3.9935 0.0001
+ 9.750000 4.2826 5.2826 0.0001 4.2826 5.2826 0.0001
+ 10.000000 3.1900 4.1900 0.0001 3.1900 4.1900 0.0001
+ 10.250000 3.5456 4.5456 0.0000 3.5456 4.5456 0.0000
+ 10.500000 3.5451 4.5451 0.0000 3.5451 4.5451 0.0000
+ 10.750000 4.1587 5.1587 0.0001 4.1587 5.1587 0.0001
+ 11.000000 3.9178 4.9178 0.0000 3.9178 4.9178 0.0000
+ 11.250000 3.8826 4.8826 0.0001 3.8826 4.8826 0.0001
+ 11.500000 3.2615 4.2615 0.0001 3.2615 4.2615 0.0001
+ 11.750000 4.2869 5.2869 0.0001 4.2869 5.2869 0.0001
+ 12.000000 4.5757 5.5757 0.0000 4.5757 5.5757 0.0000
+ 12.250000 3.2142 4.2142 0.0000 3.2142 4.2142 0.0000
+ 12.500000 3.9086 4.9086 0.0001 3.9086 4.9086 0.0001
+ 12.750000 3.7618 4.7618 0.0001 3.7618 4.7618 0.0001
+ 13.000000 4.8157 5.8157 0.0001 4.8157 5.8157 0.0001
+ 13.250000 3.9568 4.9568 0.0001 3.9568 4.9568 0.0001
+ 13.500000 4.8524 5.8524 0.0000 4.8524 5.8524 0.0000
+ 13.750000 4.4105 5.4105 0.0000 4.4105 5.4105 0.0000
+ 14.000000 4.9450 5.9450 0.0001 4.9450 5.9450 0.0001
+ 14.250000 4.7719 5.7719 0.0001 4.7719 5.7719 0.0001
+ 14.500000 4.5365 5.5365 0.0001 4.5365 5.5365 0.0001
+ 14.750000 4.0972 5.0972 0.0001 4.0972 5.0972 0.0001
+ 15.000000 5.5554 6.5554 0.0001 5.5554 6.5554 0.0001
+ 15.250000 5.1352 6.1352 0.0001 5.1352 6.1352 0.0001
+ 15.500000 4.2067 5.2067 0.0000 4.2067 5.2067 0.0000
+ 15.750000 4.5249 5.5249 0.0001 4.5249 5.5249 0.0001
+ 16.000000 4.7725 5.7725 0.0001 4.7725 5.7725 0.0001
+ 16.250000 5.9837 6.9837 0.0001 5.9837 6.9837 0.0001
+ 16.500000 4.7753 5.7753 0.0000 4.7753 5.7753 0.0000
+ 16.750000 6.0804 7.0804 0.0001 6.0804 7.0804 0.0001
+ 17.000000 5.7243 6.7243 0.0000 5.7243 6.7243 0.0000
+ 17.250000 6.0755 7.0755 0.0001 6.0755 7.0755 0.0001
+ 17.500000 5.7907 6.7907 0.0000 5.7907 6.7907 0.0000
+ 17.750000 5.5556 6.5556 0.0001 5.5556 6.5556 0.0001
+ 18.000000 5.4734 6.4734 0.0001 5.4734 6.4734 0.0001
+ 18.250000 6.8349 7.8349 0.0001 6.8349 7.8349 0.0001
+ 18.500000 6.1115 7.1115 0.0001 6.1115 7.1115 0.0001
+ 18.750000 5.4763 6.4763 0.0001 5.4763 6.4763 0.0001
+ 19.000000 6.0577 7.0577 0.0000 6.0577 7.0577 0.0000
+ 19.250000 5.8285 6.8285 0.0001 5.8285 6.8285 0.0001
+ 19.500000 5.8165 6.8165 0.0001 5.8165 6.8165 0.0001
+ 19.750000 5.4695 6.4695 0.0000 5.4695 6.4695 0.0000
+ 20.000000 6.8811 7.8811 0.0000 6.8811 7.8811 0.0000
+ 20.250000 7.1282 8.1282 0.0000 7.1282 8.1282 0.0000
+ 20.500000 7.0992 8.0992 0.0001 7.0992 8.0992 0.0001
+ 20.750000 6.0105 7.0105 0.0001 6.0105 7.0105 0.0001
+ 21.000000 6.8671 7.8671 0.0000 6.8671 7.8671 0.0000
+ 21.250000 6.2864 7.2864 0.0001 6.2864 7.2864 0.0001
+ 21.500000 7.2471 8.2471 0.0000 7.2471 8.2471 0.0000
+ 21.750000 7.2481 8.2481 0.0000 7.2481 8.2481 0.0000
+ 22.000000 5.9782 6.9782 0.0001 5.9782 6.9782 0.0001
+ 22.250000 6.8523 7.8523 0.0001 6.8523 7.8523 0.0001
+ 22.500000 6.8326 7.8326 0.0001 6.8326 7.8326 0.0001
+ 22.750000 6.5175 7.5175 0.0000 6.5175 7.5175 0.0000
+ 23.000000 6.4000 7.4000 0.0000 6.4000 7.4000 0.0000
+ 23.250000 8.0028 9.0028 0.0000 8.0028 9.0028 0.0000
+ 23.500000 8.1695 9.1695 0.0000 8.1695 9.1695 0.0000
+ 23.750000 7.9851 8.9851 0.0001 7.9851 8.9851 0.0001
+ 24.000000 6.8908 7.8908 0.0001 6.8908 7.8908 0.0001
+ 24.250000 7.4686 8.4686 0.0001 7.4686 8.4686 0.0001
+ 24.500000 7.0070 8.0070 0.0001 7.0070 8.0070 0.0001
+ 24.750000 8.5092 9.5092 0.0001 8.5092 9.5092 0.0001
+ 25.000000 8.1518 9.1518 0.0000 8.1518 9.1518 0.0000
+ 25.250000 7.3926 8.3926 0.0001 7.3926 8.3926 0.0001
+ 25.500000 7.9078 8.9078 0.0001 7.9078 8.9078 0.0001
+ 25.750000 7.3901 8.3901 0.0001 7.3901 8.3901 0.0001
+ 26.000000 7.5108 8.5108 0.0000 7.5108 8.5108 0.0000
+ 26.250000 7.3993 8.3993 0.0000 7.3993 8.3993 0.0000
+ 26.500000 9.0054 10.0054 0.0000 9.0054 10.0054 0.0000
+ 26.750000 9.0212 10.0212 0.0001 9.0212 10.0212 0.0001
+ 27.000000 9.2067 10.2067 0.0000 9.2067 10.2067 0.0000
+ 27.250000 7.3974 8.3974 0.0001 7.3974 8.3974 0.0001
+ 27.500000 8.4983 9.4983 0.0000 8.4983 9.4983 0.0000
+ 27.750000 8.4074 9.4074 0.0001 8.4074 9.4074 0.0001
+ 28.000000 9.4812 10.4812 0.0000 9.4812 10.4812 0.0000
+ 28.250000 8.9480 9.9480 0.0000 8.9480 9.9480 0.0000
+ 28.500000 8.8156 9.8156 0.0001 8.8156 9.8156 0.0001
+ 28.750000 9.3383 10.3383 0.0001 9.3383 10.3383 0.0001
+ 29.000000 8.6766 9.6766 0.0001 8.6766 9.6766 0.0001
+ 29.250000 8.8167 9.8167 0.0001 8.8167 9.8167 0.0001
+ 29.500000 8.8586 9.8586 0.0000 8.8586 9.8586 0.0000
+ 29.750000 9.7681 10.7681 0.0000 9.7681 10.7681 0.0000
+ 30.000000 10.1206 11.1206 0.0000 10.1206 11.1206 0.0000
+ 30.250000 10.2048 11.2048 0.0000 10.2048 11.2048 0.0000
+ 30.500000 8.8600 9.8600 0.0000 8.8600 9.8600 0.0000
+ 30.750000 9.2746 10.2746 0.0000 9.2746 10.2746 0.0000
+ 31.000000 9.5056 10.5056 0.0001 9.5056 10.5056 0.0001
+ 31.250000 10.3959 11.3959 0.0000 10.3959 11.3959 0.0000
+ 31.500000 10.0084 11.0084 0.0001 10.0084 11.0084 0.0001
+ 31.750000 9.8521 10.8521 0.0000 9.8521 10.8521 0.0000
+ 32.000000 10.3120 11.3120 0.0001 10.3120 11.3120 0.0001
+ 32.250000 9.5696 10.5696 0.0001 9.5696 10.5696 0.0001
+ 32.500000 10.2229 11.2229 0.0001 10.2229 11.2229 0.0001
+ 32.750000 9.2246 10.2246 0.0000 9.2246 10.2246 0.0000
+ 33.000000 11.0408 12.0408 0.0000 11.0408 12.0408 0.0000
+ 33.250000 10.9355 11.9355 0.0001 10.9355 11.9355 0.0001
+ 33.500000 11.0212 12.0212 0.0001 11.0212 12.0212 0.0001
+ 33.750000 9.9950 10.9950 0.0000 9.9950 10.9950 0.0000
+ 34.000000 10.8371 11.8371 0.0000 10.8371 11.8371 0.0000
+ 34.250000 10.7630 11.7630 0.0000 10.7630 11.7630 0.0000
+ 34.500000 11.3749 12.3749 0.0000 11.3749 12.3749 0.0000
+ 34.750000 10.8268 11.8268 0.0000 10.8268 11.8268 0.0000
+ 35.000000 10.9254 11.9254 0.0001 10.9254 11.9254 0.0001
+ 35.250000 11.4695 12.4695 0.0001 11.4695 12.4695 0.0001
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+ 35.750000 11.2141 12.2141 0.0001 11.2141 12.2141 0.0001
+ 36.000000 10.9006 11.9006 0.0001 10.9006 11.9006 0.0001
+ 36.250000 12.3187 13.3187 0.0000 12.3187 13.3187 0.0000
+ 36.500000 12.0581 13.0581 0.0001 12.0581 13.0581 0.0001
+ 36.750000 12.1095 13.1095 0.0001 12.1095 13.1095 0.0001
+ 37.000000 10.9742 11.9742 0.0000 10.9742 11.9742 0.0000
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+ 38.750000 11.1104 12.1104 0.0001 11.1104 12.1104 0.0001
+ 39.000000 11.8881 12.8881 0.0001 11.8881 12.8881 0.0001
+ 39.250000 11.8041 12.8041 0.0000 11.8041 12.8041 0.0000
+ 39.500000 13.5494 14.5494 0.0000 13.5494 14.5494 0.0000
+ 39.750000 13.2306 14.2306 0.0001 13.2306 14.2306 0.0001
+ 40.000000 13.4767 14.4767 0.0001 13.4767 14.4767 0.0001
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+ 41.000000 13.6144 14.6144 0.0001 13.6144 14.6144 0.0001
+ 41.250000 12.9117 13.9117 0.0001 12.9117 13.9117 0.0001
+ 41.500000 12.9911 13.9911 0.0000 12.9911 13.9911 0.0000
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+ 42.000000 12.6076 13.6076 0.0001 12.6076 13.6076 0.0001
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+ 43.000000 14.4720 15.4720 0.0001 14.4720 15.4720 0.0001
+ 43.250000 14.6719 15.6719 0.0001 14.6719 15.6719 0.0001
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+ 44.250000 14.8745 15.8745 0.0000 14.8745 15.8745 0.0000
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+ 45.000000 14.5201 15.5201 0.0001 14.5201 15.5201 0.0001
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+ 45.500000 14.5934 15.5934 0.0001 14.5934 15.5934 0.0001
+ 45.750000 13.4843 14.4843 0.0001 13.4843 14.4843 0.0001
+ 46.000000 15.4321 16.4321 0.0000 15.4321 16.4321 0.0000
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+ 46.500000 15.6806 16.6806 0.0001 15.6806 16.6806 0.0001
+ 46.750000 13.9386 14.9386 0.0000 13.9386 14.9386 0.0000
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+ 48.250000 15.5412 16.5412 0.0002 15.5412 16.5412 0.0002
+ 48.500000 14.3423 15.3423 0.0001 14.3423 15.3423 0.0001
+ 48.750000 15.2094 16.2094 0.0001 15.2094 16.2094 0.0001
+ 49.000000 15.1168 16.1168 0.0001 15.1168 16.1168 0.0001
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+ 49.500000 16.2539 17.2539 0.0001 16.2539 17.2539 0.0001
+ 49.750000 16.3489 17.3489 0.0001 16.3489 17.3489 0.0001
+ 50.000000 15.0187 16.0187 0.0000 15.0187 16.0187 0.0000
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+ 50.500000 16.0528 17.0528 0.0001 16.0528 17.0528 0.0001
+ 50.750000 16.4196 17.4196 0.0001 16.4196 17.4196 0.0001
+ 51.000000 16.8259 17.8259 0.0001 16.8259 17.8259 0.0001
+ 51.250000 15.5587 16.5587 0.0000 15.5587 16.5587 0.0000
+ 51.500000 16.3950 17.3950 0.0001 16.3950 17.3950 0.0001
+ 51.750000 15.2996 16.2996 0.0001 15.2996 16.2996 0.0001
+ 52.000000 16.0925 17.0925 0.0001 16.0925 17.0925 0.0001
+ 52.250000 16.4335 17.4335 0.0001 16.4335 17.4335 0.0001
+ 52.500000 17.1829 18.1829 0.0000 17.1829 18.1829 0.0000
+ 52.750000 17.5384 18.5384 0.0001 17.5384 18.5384 0.0001
+ 53.000000 17.2631 18.2631 0.0001 17.2631 18.2631 0.0001
+ 53.250000 16.2614 17.2614 0.0001 16.2614 17.2614 0.0001
+ 53.500000 17.0032 18.0032 0.0000 17.0032 18.0032 0.0000
+ 53.750000 17.5027 18.5027 0.0001 17.5027 18.5027 0.0001
+ 54.000000 17.0522 18.0522 0.0001 17.0522 18.0522 0.0001
+ 54.250000 17.3532 18.3532 0.0001 17.3532 18.3532 0.0001
+ 54.500000 16.6059 17.6059 0.0000 16.6059 17.6059 0.0000
+ 54.750000 16.9281 17.9281 0.0001 16.9281 17.9281 0.0001
+ 55.000000 15.7926 16.7926 0.0001 15.7926 16.7926 0.0001
+ 55.250000 17.2110 18.2110 0.0000 17.2110 18.2110 0.0000
+ 55.500000 17.5846 18.5846 0.0001 17.5846 18.5846 0.0001
+ 55.750000 17.8666 18.8666 0.0001 17.8666 18.8666 0.0001
+ 56.000000 18.2468 19.2468 0.0001 18.2468 19.2468 0.0001
+ 56.250000 18.1218 19.1218 0.0001 18.1218 19.1218 0.0001
+ 56.500000 16.9705 17.9705 0.0001 16.9705 17.9705 0.0001
+ 56.750000 17.7506 18.7506 0.0000 17.7506 18.7506 0.0000
+ 57.000000 18.1285 19.1285 0.0001 18.1285 19.1285 0.0001
+ 57.250000 18.0247 19.0247 0.0001 18.0247 19.0247 0.0001
+ 57.500000 18.0924 19.0924 0.0001 18.0924 19.0924 0.0001
+ 57.750000 17.9847 18.9847 0.0001 17.9847 18.9847 0.0001
+ 58.000000 17.8135 18.8135 0.0001 17.8135 18.8135 0.0001
+ 58.250000 17.0656 18.0656 0.0001 17.0656 18.0656 0.0001
+ 58.500000 17.6905 18.6905 0.0001 17.6905 18.6905 0.0001
+ 58.750000 18.5188 19.5188 0.0001 18.5188 19.5188 0.0001
+ 59.000000 18.9824 19.9824 0.0000 18.9824 19.9824 0.0000
+ 59.250000 19.1426 20.1426 0.0000 19.1426 20.1426 0.0000
+ 59.500000 19.0595 20.0595 0.0001 19.0595 20.0595 0.0001
+ 59.750000 18.7700 19.7700 0.0001 18.7700 19.7700 0.0001
+ 60.000000 19.5301 20.5301 0.0000 19.5301 20.5301 0.0000
+ 60.250000 19.3457 20.3457 0.0001 19.3457 20.3457 0.0001
+ 60.500000 19.0527 20.0527 0.0000 19.0527 20.0527 0.0000
+ 60.750000 19.1799 20.1799 0.0001 19.1799 20.1799 0.0001
+ 61.000000 18.9106 19.9106 0.0000 18.9106 19.9106 0.0000
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+ 132.250000 40.9555 41.9555 0.0001 40.9555 41.9555 0.0001
+ 132.500000 40.6201 41.6201 0.0000 40.6201 41.6201 0.0000
+ 132.750000 41.5831 42.5831 0.0001 41.5831 42.5831 0.0001
+ 133.000000 41.1452 42.1452 0.0000 41.1452 42.1452 0.0000
+ 133.250000 41.9675 42.9675 0.0001 41.9675 42.9675 0.0001
+ 133.500000 41.8360 42.8360 0.0001 41.8360 42.8360 0.0001
+ 133.750000 41.9216 42.9216 0.0000 41.9216 42.9216 0.0000
+ 134.000000 41.8315 42.8315 0.0001 41.8315 42.8315 0.0001
+ 134.250000 41.3247 42.3247 0.0001 41.3247 42.3247 0.0001
+ 134.500000 41.9998 42.9998 0.0001 41.9998 42.9998 0.0001
+ 134.750000 41.0553 42.0553 0.0001 41.0553 42.0553 0.0001
+ 135.000000 41.9978 42.9978 0.0001 41.9978 42.9978 0.0001
+ 135.250000 41.9695 42.9695 0.0000 41.9695 42.9695 0.0000
+ 135.500000 41.9529 42.9529 0.0001 41.9529 42.9529 0.0001
+ 135.750000 41.8093 42.8093 0.0000 41.8093 42.8093 0.0000
+ 136.000000 41.9968 42.9968 0.0001 41.9968 42.9968 0.0001
+ 136.250000 41.9985 42.9985 0.0001 41.9985 42.9985 0.0001
diff --git a/regtest/rt41/plumed.dat b/regtest/rt41/plumed.dat
new file mode 100644
index 0000000000000000000000000000000000000000..f6acab8e81dec4e0da687224c68eb2d7c4977209
--- /dev/null
+++ b/regtest/rt41/plumed.dat
@@ -0,0 +1,3 @@
+r1: READ VALUES=p2.X FILE=input_colvar
+r2: READ VALUES=p3.* FILE=input_colvar
+PRINT ARG=r1.*,r2.* STRIDE=1000 FILE=colvar FMT=%8.4f
diff --git a/src/basic/ActionAtomistic.cpp b/src/basic/ActionAtomistic.cpp
index aa54b740dcbfcb8ef510e98febc45ca291b5cc00..b430a561ebc73f25dd4588173a40521f62af0643 100644
--- a/src/basic/ActionAtomistic.cpp
+++ b/src/basic/ActionAtomistic.cpp
@@ -48,6 +48,7 @@ lockRequestAtoms(false),
atoms(plumed.getAtoms())
{
atoms.add(this);
+ if(atoms.getNatoms()==0) error("Cannot perform calculations involving atoms without atoms");
}
void ActionAtomistic::registerKeywords( Keywords& keys ){
diff --git a/src/basic/ColvarEnergy.cpp b/src/basic/ColvarEnergy.cpp
index 848603ebc15590168070592d01cb6d977dba0e6a..2b0b295e511b5e5ead6b6bf680bdef68c0575052 100644
--- a/src/basic/ColvarEnergy.cpp
+++ b/src/basic/ColvarEnergy.cpp
@@ -22,6 +22,7 @@
#include "Colvar.h"
#include "ActionRegister.h"
#include "PlumedMain.h"
+#include "Atoms.h"
#include <string>
#include <cmath>
@@ -53,6 +54,7 @@ class ColvarEnergy : public Colvar {
public:
ColvarEnergy(const ActionOptions&);
// active methods:
+ void prepare();
virtual void calculate();
static void registerKeywords( Keywords& keys );
};
@@ -80,6 +82,9 @@ void ColvarEnergy::registerKeywords( Keywords& keys ){
keys.remove("NUMERICAL_DERIVATIVES");
}
+void ColvarEnergy::prepare(){
+ plumed.getAtoms().setCollectEnergy(true);
+}
// calculator
void ColvarEnergy::calculate(){
diff --git a/src/basic/GenericRead.cpp b/src/basic/GenericRead.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..4e1d95e48f1b80ba3d5ceadedcd4defec6afe2e8
--- /dev/null
+++ b/src/basic/GenericRead.cpp
@@ -0,0 +1,179 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ Copyright (c) 2012 The plumed team
+ (see the PEOPLE file at the root of the distribution for a list of names)
+
+ See http://www.plumed-code.org for more information.
+
+ This file is part of plumed, version 2.0.
+
+ plumed is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Lesser General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ plumed is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with plumed. If not, see <http://www.gnu.org/licenses/>.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#include "ActionPilot.h"
+#include "ActionWithValue.h"
+#include "ActionRegister.h"
+#include "PlumedMain.h"
+#include "ActionSet.h"
+#include "Atoms.h"
+
+namespace PLMD{
+
+//+PLUMEDOC GENERIC READ
+/*
+Read quantities from a colvar file.
+
+\par Examples
+
+*/
+//+ENDPLUMEDOC
+
+class GenericRead :
+public ActionPilot,
+public ActionWithValue
+{
+friend class ActionPilot;
+private:
+ bool cloned_file;
+ unsigned nlinesPerStep;
+ std::string filename;
+ PlumedIFile* ifile;
+ std::vector<Value*> readvals;
+public:
+ static void registerKeywords( Keywords& keys );
+ GenericRead(const ActionOptions&);
+ ~GenericRead();
+ void prepare();
+ void apply(){};
+ void calculate();
+ void update();
+ std::string getFilename() const;
+ PlumedIFile* getFile();
+};
+
+PLUMED_REGISTER_ACTION(GenericRead,"READ")
+
+void GenericRead::registerKeywords(Keywords& keys){
+ Action::registerKeywords(keys);
+ ActionPilot::registerKeywords(keys);
+ ActionWithValue::registerKeywords(keys);
+ keys.add("compulsory","STRIDE","1","the frequency with which the file should be read.");
+ keys.add("compulsory","EVERY","1","only read every ith line of the colvar file. This should be used if the colvar was written more frequently than the trajectory.");
+ keys.add("compulsory","VALUES","the values to read from the file");
+ keys.add("compulsory","FILE","the name of the file from which to read these quantities");
+ keys.remove("NUMERICAL_DERIVATIVES");
+}
+
+GenericRead::GenericRead(const ActionOptions&ao):
+Action(ao),
+ActionPilot(ao),
+ActionWithValue(ao),
+nlinesPerStep(1)
+{
+ // Read the file name from the input line
+ parse("FILE",filename);
+ // Open the file if it is not already opened
+ cloned_file=false;
+ std::vector<GenericRead*> other_reads=plumed.getActionSet().select<GenericRead*>();
+ for(unsigned i=0;i<other_reads.size();++i){
+ if( other_reads[i]->getFilename()==filename ){
+ ifile=other_reads[i]->getFile();
+ cloned_file=true;
+ }
+ }
+ if( !cloned_file ){
+ ifile=new PlumedIFile();
+ if( !ifile->FileExist(filename) ) error("could not find file named " + filename);
+ ifile->link(*this);
+ ifile->open(filename);
+ ifile->allowIgnoredFields();
+ }
+ parse("EVERY",nlinesPerStep);
+ if(nlinesPerStep>1) log.printf(" only reading every %dth line of file %s\n",nlinesPerStep,filename.c_str() );
+ else log.printf(" reading data from file %s\n",filename.c_str() );
+ // Find out what we are reading
+ std::vector<std::string> valread; parseVector("VALUES",valread);
+
+ std::size_t dot=valread[0].find_first_of('.');
+ if( valread[0].find(".")!=std::string::npos ){
+ std::string label=valread[0].substr(0,dot);
+ std::string name=valread[0].substr(dot+1);
+ if( name=="*" ){
+ if( valread.size()>1 ) error("all values must be from the same Action when using READ");
+ std::vector<std::string> fieldnames;
+ ifile->scanFieldList( fieldnames );
+ for(unsigned i=0;i<fieldnames.size();++i){
+ if( fieldnames[i].substr(0,dot)==label ){
+ readvals.push_back(new Value(this, fieldnames[i], false) );
+ addComponent( fieldnames[i].substr(dot+1) ); componentIsNotPeriodic( fieldnames[i].substr(dot+1) );
+ }
+ }
+ } else {
+ readvals.push_back(new Value(this, valread[0], false) );
+ addComponent( name ); componentIsNotPeriodic( valread[0].substr(dot+1) );
+ for(unsigned i=1;i<valread.size();++i) {
+ if( valread[i].substr(0,dot)!=label ) error("all values must be from the same Action when using READ");;
+ readvals.push_back(new Value(this, valread[i], false) );
+ addComponent( valread[i].substr(dot+1) ); componentIsNotPeriodic( valread[i].substr(dot+1) );
+ }
+ }
+ } else {
+ if( valread.size()!=1 ) error("all values must be from the same Action when using READ");
+ readvals.push_back(new Value(this, valread[0], false) );
+ addValue(); setNotPeriodic();
+ log.printf(" reading value %s and storing as %s\n",valread[0].c_str() ,getLabel().c_str() );
+ }
+ checkRead();
+}
+
+GenericRead::~GenericRead(){
+ if( !cloned_file ){ ifile->close(); delete ifile; }
+ for(unsigned i=0;i<readvals.size();++i) delete readvals[i];
+}
+
+std::string GenericRead::getFilename() const {
+ return filename;
+}
+
+PlumedIFile* GenericRead::getFile(){
+ return ifile;
+}
+
+void GenericRead::prepare(){
+ if( !cloned_file ){
+ double du_time;
+ if( !ifile->scanField("time",du_time) ){
+ error("Reached end of file " + filename + " before end of trajectory");
+ } else if( fabs( du_time-getTime() )>epsilon ){
+ std::string str_dutime,str_ptime; Tools::convert(du_time,str_dutime); Tools::convert(getTime(),str_ptime);
+ error("mismatched times in colvar files : colvar time=" + str_dutime + " plumed time=" + str_ptime );
+ }
+ }
+}
+
+void GenericRead::calculate(){
+ for(unsigned i=0;i<readvals.size();++i){
+ ifile->scanField( readvals[i] );
+ getPntrToComponent(i)->set( readvals[i]->get() );
+ }
+}
+
+void GenericRead::update(){
+ if( !cloned_file ){
+ for(unsigned i=0;i<nlinesPerStep;++i){
+ ifile->scanField(); double du_time;
+ if( plumed.getAtoms().getNatoms()==0 && !ifile->scanField("time",du_time) ) plumed.stop();
+ }
+ }
+}
+
+}
diff --git a/src/basic/PlumedMain.cpp b/src/basic/PlumedMain.cpp
index 886e84c40b8fb28ec611dc24c316a61a3993f552..8c3ce20ac66a40fd66ea2603973f004ff70e4cbf 100644
--- a/src/basic/PlumedMain.cpp
+++ b/src/basic/PlumedMain.cpp
@@ -29,7 +29,6 @@
#include "Atoms.h"
#include <set>
#include "config/PlumedConfig.h"
-#include "Colvar.h"
#include <cstdlib>
#include "ActionRegister.h"
#include "GREX.h"
@@ -63,7 +62,9 @@ PlumedMain::PlumedMain():
bias(0.0),
exchangePatterns(*new(ExchangePatterns)),
novirial(false),
- restart(false)
+ restart(false),
+ stopFlag(NULL),
+ stopNow(false)
{
log.link(comm);
log.setLinePrefix("PLUMED: ");
@@ -272,6 +273,10 @@ void PlumedMain::cmd(const std::string & word,void*val){
CHECK_NOTINIT(initialized,word);
CHECK_NULL(val,word);
log.open(static_cast<char*>(val),"w");
+ } else if(word=="setStopFlag"){
+ CHECK_NOTINIT(initialized,word);
+ CHECK_NULL(val,word);
+ stopFlag=static_cast<int*>(val);
} else if(word=="getExchangesFlag"){
CHECK_INIT(initialized,word);
CHECK_NULL(val,word);
@@ -455,16 +460,11 @@ void PlumedMain::prepareDependencies(){
};
// also, if one of them is the total energy, tell to atoms that energy should be collected
- bool collectEnergy=false;
for(ActionSet::iterator p=actionSet.begin();p!=actionSet.end();++p){
if((*p)->isActive()){
- if(Colvar *c=dynamic_cast<Colvar*>(*p)) {
- if(c->checkIsEnergy()) collectEnergy=true;
- }
if((*p)->checkNeedsGradients()) (*p)->setOption("GRADIENTS");
}
}
- atoms.setCollectEnergy(collectEnergy);
stopwatch.stop("1 Prepare dependencies");
@@ -541,6 +541,11 @@ void PlumedMain::justApply(){
for(ActionSet::iterator p=actionSet.begin();p!=actionSet.end();++p){
if((*p)->isActive()) (*p)->update();
}
+// Check that no action has told the calculation to stop
+ if(stopNow){
+ if(stopFlag) (*stopFlag)=1;
+ else plumed_merror("your md code cannot handle plumed stop events - add a call to plumed.comm(stopFlag,stopCondition)");
+ }
stopwatch.stop("5 Applying (backward loop)");
}
@@ -614,6 +619,9 @@ void PlumedMain::eraseFile(PlumedFileBase&f){
files.erase(&f);
}
+void PlumedMain::stop(){
+ stopNow=true;
+}
diff --git a/src/basic/PlumedMain.h b/src/basic/PlumedMain.h
index b3fc8ab5c97f66d0293d889019a08bc68262a92f..164f0253d6137c2061addeb863f8caea10679193 100644
--- a/src/basic/PlumedMain.h
+++ b/src/basic/PlumedMain.h
@@ -129,6 +129,10 @@ private:
std::set<PlumedFileBase*> files;
typedef std::set<PlumedFileBase*>::iterator files_iterator;
+/// Stuff to make plumed stop the MD code cleanly
+ int* stopFlag;
+ bool stopNow;
+
public:
/// Flag to switch off virial calculation (for debug)
bool novirial;
@@ -237,6 +241,8 @@ public:
void fflush();
/// Check if restarting
bool getRestart()const;
+/// Stop the calculation cleanly (both the MD code and plumed)
+ void stop();
};
/////
diff --git a/src/cltools/CLToolDriver.cpp b/src/cltools/CLToolDriver.cpp
index a8b6a0f5aeb2e5895b1e567a7501e3fdcb2f4031..36641c791cfe0e67b7759f71122aed2b5c42f7dd 100644
--- a/src/cltools/CLToolDriver.cpp
+++ b/src/cltools/CLToolDriver.cpp
@@ -80,6 +80,7 @@ void CLToolDriver<real>::registerKeywords( Keywords& keys ){
keys.add("compulsory","--plumed","plumed.dat","specify the name of the plumed input file");
keys.add("compulsory","--timestep","1.0","the timestep that was used in the calculation that produced this trajectory in picoseconds");
keys.add("compulsory","--trajectory-stride","1","the frequency with which frames were output to this trajectory during the simulation");
+ keys.addFlag("--noatoms",false,"don't read in a trajectory. Just use colvar files as specified in plumed.dat");
keys.add("atoms","--ixyz","the trajectory in xyz format");
keys.add("optional","--length-units","units for length, either as a string or a number");
keys.add("optional","--dump-forces","dump the forces on a file");
@@ -124,6 +125,9 @@ int CLToolDriver<real>::main(FILE* in,FILE*out,PlumedCommunicator& pc){
);
return 0;
}
+ // Are we reading trajectory data
+ bool noatoms; parseFlag("--noatoms",noatoms);
+
std::string fakein;
bool debugfloat=parse("--debug-float",fakein);
if(debugfloat && sizeof(real)!=sizeof(float)){
@@ -136,12 +140,14 @@ int CLToolDriver<real>::main(FILE* in,FILE*out,PlumedCommunicator& pc){
bool debug_pd=parse("--debug-pd",fakein);
bool debug_dd=parse("--debug-dd",fakein);
+ if( debug_pd || debug_dd ) plumed_massert(!noatoms,"cannot debug without atoms");
int multi=1;
FILE*multi_log=NULL;
bool debug_grex=parse("--debug-grex",fakein);
PlumedCommunicator intracomm;
PlumedCommunicator intercomm;
if(debug_grex){
+ plumed_massert( !noatoms, "must have atoms to debug_grex");
Tools::convert(fakein,multi);
int ntot=pc.Get_size();
int nintra=ntot/multi;
@@ -168,58 +174,68 @@ int CLToolDriver<real>::main(FILE* in,FILE*out,PlumedCommunicator& pc){
unsigned stride; parse("--trajectory-stride",stride);
// are we writing forces
string dumpforces(""), dumpforcesFmt("%f");;
- parse("--dump-forces",dumpforces);
+ if(!noatoms) parse("--dump-forces",dumpforces);
if(dumpforces!="") parse("--dump-forces-fmt",dumpforcesFmt);
// Read in an xyz file
- string trajectoryFile("");
- std::string traj_xyz; parse("--ixyz",traj_xyz);
- if(traj_xyz.length()>0 && trajectoryFile.length()==0) trajectoryFile=traj_xyz;
- if(trajectoryFile.length()==0){
- fprintf(out,"ERROR: missing trajectory data\n");
- return 0;
- }
- string lengthUnits(""); parse("--length-units",lengthUnits);
- if(lengthUnits.length()>0) units.setLength(lengthUnits);
-
- string pdbfile; parse("--pdb",pdbfile);
- if(pdbfile.length()>0){
- bool check=pdb.read(pdbfile,false,1.0);
- plumed_massert(check,"error reading pdb file");
- }
+ string trajectoryFile(""), pdbfile("");
+ bool pbc_cli_given=false; vector<double> pbc_cli_box(9,0.0);
+ if(!noatoms){
+ std::string traj_xyz; parse("--ixyz",traj_xyz);
+ if(traj_xyz.length()>0 && trajectoryFile.length()==0) trajectoryFile=traj_xyz;
+ if(trajectoryFile.length()==0){
+ fprintf(stderr,"ERROR: missing trajectory data\n");
+ return 1;
+ }
+ string lengthUnits(""); parse("--length-units",lengthUnits);
+ if(lengthUnits.length()>0) units.setLength(lengthUnits);
+
+ parse("--pdb",pdbfile);
+ if(pdbfile.length()>0){
+ bool check=pdb.read(pdbfile,false,1.0);
+ plumed_massert(check,"error reading pdb file");
+ }
- string pbc_cli_list; parse("--box",pbc_cli_list);
- bool pbc_cli_given=false;
- vector<double> pbc_cli_box(9,0.0);
- if(pbc_cli_list.length()>0) {
- pbc_cli_given=true;
- vector<string> words=Tools::getWords(pbc_cli_list,",");
- if(words.size()==3){
- for(int i=0;i<3;i++) sscanf(words[i].c_str(),"%lf",&(pbc_cli_box[4*i]));
- } else if(words.size()==9) {
- for(int i=0;i<9;i++) sscanf(words[i].c_str(),"%lf",&(pbc_cli_box[i]));
- } else {
- string msg="ERROR: cannot parse command-line box "+pbc_cli_list;
- fprintf(stderr,"%s\n",msg.c_str());
- return 1;
- }
+ string pbc_cli_list; parse("--box",pbc_cli_list);
+ if(pbc_cli_list.length()>0) {
+ pbc_cli_given=true;
+ vector<string> words=Tools::getWords(pbc_cli_list,",");
+ if(words.size()==3){
+ for(int i=0;i<3;i++) sscanf(words[i].c_str(),"%lf",&(pbc_cli_box[4*i]));
+ } else if(words.size()==9) {
+ for(int i=0;i<9;i++) sscanf(words[i].c_str(),"%lf",&(pbc_cli_box[i]));
+ } else {
+ string msg="ERROR: cannot parse command-line box "+pbc_cli_list;
+ fprintf(stderr,"%s\n",msg.c_str());
+ return 1;
+ }
+ }
}
-
+
plumed_massert(!(debug_dd&debug_pd),"cannot use debug-dd and debug-pd at the same time");
if(debug_pd || debug_dd) plumed_massert(PlumedCommunicator::initialized(),"needs mpi for debug-pd");
- if(trajectoryFile.length()==0){
- string msg="ERROR: please specify a trajectory";
- fprintf(stderr,"%s\n",msg.c_str());
- return 1;
- }
-
Plumed p;
int rr=sizeof(real);
p.cmd("setRealPrecision",&rr);
- int checknatoms=0;
+ int checknatoms=-1;
+ int plumedStopCondition=0;
+ p.cmd("setStopFlag",&plumedStopCondition);
int step=0;
+ if(PlumedCommunicator::initialized()){
+ if(multi>1){
+ if(intracomm.Get_rank()==0) p.cmd("GREX setMPIIntercomm",&intercomm.Get_comm());
+ p.cmd("GREX setMPIIntracomm",&intracomm.Get_comm());
+ p.cmd("GREX init");
+ }
+ p.cmd("setMPIComm",&intracomm.Get_comm());
+ }
+ p.cmd("setMDLengthUnits",&units.getLength());
+ p.cmd("setMDEngine","driver");
+ p.cmd("setTimestep",×tep);
+ p.cmd("setPlumedDat",plumedFile.c_str());
+ p.cmd("setLog",out);
if(debug_grex){
string n;
@@ -227,29 +243,29 @@ int CLToolDriver<real>::main(FILE* in,FILE*out,PlumedCommunicator& pc){
trajectoryFile+="."+n;
}
- FILE* fp;
- if (trajectoryFile=="-")
- fp=in;
- else {
- fp=fopen(trajectoryFile.c_str(),"r");
- if(!fp){
- string msg="ERROR: Error opening XYZ file "+trajectoryFile;
- fprintf(stderr,"%s\n",msg.c_str());
- return 1;
- }
- }
-
-
- FILE* fp_forces=NULL;
- if(dumpforces.length()>0){
- if(PlumedCommunicator::initialized() && pc.Get_size()>1){
- string n;
- Tools::convert(pc.Get_rank(),n);
- dumpforces+="."+n;
- }
- fp_forces=fopen(dumpforces.c_str(),"w");
+ FILE* fp=NULL; FILE* fp_forces=NULL;
+ if(!noatoms){
+ if (trajectoryFile=="-")
+ fp=in;
+ else {
+ fp=fopen(trajectoryFile.c_str(),"r");
+ if(!fp){
+ string msg="ERROR: Error opening XYZ file "+trajectoryFile;
+ fprintf(stderr,"%s\n",msg.c_str());
+ return 1;
+ }
+ }
+
+ if(dumpforces.length()>0){
+ if(PlumedCommunicator::initialized() && pc.Get_size()>1){
+ string n;
+ Tools::convert(pc.Get_rank(),n);
+ dumpforces+="."+n;
+ }
+ fp_forces=fopen(dumpforces.c_str(),"w");
+ }
}
-
+
std::string line;
std::vector<real> coordinates;
std::vector<real> forces;
@@ -272,29 +288,16 @@ int CLToolDriver<real>::main(FILE* in,FILE*out,PlumedCommunicator& pc){
// random stream to choose decompositions
Random rnd;
- while(Tools::getline(fp,line)){
+ while(true){
+ if(!noatoms){
+ if(!Tools::getline(fp,line)) break;
+ } else if ( plumedStopCondition ) break;
int natoms;
bool ok;
bool first_step=false;
- sscanf(line.c_str(),"%d",&natoms);
- if(checknatoms==0){
- checknatoms=natoms;
- if(PlumedCommunicator::initialized()){
- if(multi>1){
- if(intracomm.Get_rank()==0) p.cmd("GREX setMPIIntercomm",&intercomm.Get_comm());
- p.cmd("GREX setMPIIntracomm",&intracomm.Get_comm());
- p.cmd("GREX init");
- }
- p.cmd("setMPIComm",&intracomm.Get_comm());
- }
- p.cmd("setMDLengthUnits",&units.getLength());
- p.cmd("setNatoms",&natoms);
- p.cmd("setMDEngine","driver");
- p.cmd("setTimestep",×tep);
- p.cmd("setPlumedDat",plumedFile.c_str());
- p.cmd("setLog",out);
- p.cmd("init");
+ if(!noatoms) sscanf(line.c_str(),"%d",&natoms);
+ if(checknatoms<0 && !noatoms){
pd_nlocal=natoms;
pd_start=0;
first_step=true;
@@ -309,7 +312,13 @@ int CLToolDriver<real>::main(FILE* in,FILE*out,PlumedCommunicator& pc){
charges[index]=pdb.getBeta()[i];
}
}
-
+ } else if( checknatoms<0 && noatoms ){
+ natoms=0;
+ }
+ if( checknatoms<0 ){
+ checknatoms=natoms;
+ p.cmd("setNatoms",&natoms);
+ p.cmd("init");
}
plumed_massert(checknatoms==natoms,"number of atom changed");
@@ -371,61 +380,63 @@ int CLToolDriver<real>::main(FILE* in,FILE*out,PlumedCommunicator& pc){
}
}
- ok=Tools::getline(fp,line);
- plumed_massert(ok,"premature end of file");
-
- std::vector<double> celld(9,0.0);
- if(pbc_cli_given==false) {
- std::vector<std::string> words;
- words=Tools::getWords(line);
- if(words.size()==3){
- sscanf(line.c_str(),"%lf %lf %lf",&celld[0],&celld[4],&celld[8]);
- } else if(words.size()==9){
- sscanf(line.c_str(),"%lf %lf %lf %lf %lf %lf %lf %lf %lf",
- &celld[0], &celld[1], &celld[2],
- &celld[3], &celld[4], &celld[5],
- &celld[6], &celld[7], &celld[8]);
- } else plumed_merror("needed box in second line");
- } else { // from command line
- celld=pbc_cli_box;
- }
- for(unsigned i=0;i<9;i++)cell[i]=real(celld[i]);
-
- // Read coordinates
- for(int i=0;i<natoms;i++){
- ok=Tools::getline(fp,line);
- plumed_massert(ok,"premature end of file");
- char dummy[1000];
- double cc[3];
- std::sscanf(line.c_str(),"%s %lf %lf %lf",dummy,&cc[0],&cc[1],&cc[2]);
- if(!debug_pd || ( i>=pd_start && i<pd_start+pd_nlocal) ){
- coordinates[3*i]=real(cc[0]);
- coordinates[3*i+1]=real(cc[1]);
- coordinates[3*i+2]=real(cc[2]);
- }
- if(debug_dd){
- for(int i=0;i<dd_nlocal;++i){
- int kk=dd_gatindex[i];
- dd_coordinates[3*i+0]=coordinates[3*kk+0];
- dd_coordinates[3*i+1]=coordinates[3*kk+1];
- dd_coordinates[3*i+2]=coordinates[3*kk+2];
- }
- }
- }
+ if(!noatoms){
+ ok=Tools::getline(fp,line);
+ plumed_massert(ok,"premature end of file");
+
+ std::vector<double> celld(9,0.0);
+ if(pbc_cli_given==false) {
+ std::vector<std::string> words;
+ words=Tools::getWords(line);
+ if(words.size()==3){
+ sscanf(line.c_str(),"%lf %lf %lf",&celld[0],&celld[4],&celld[8]);
+ } else if(words.size()==9){
+ sscanf(line.c_str(),"%lf %lf %lf %lf %lf %lf %lf %lf %lf",
+ &celld[0], &celld[1], &celld[2],
+ &celld[3], &celld[4], &celld[5],
+ &celld[6], &celld[7], &celld[8]);
+ } else plumed_merror("needed box in second line");
+ } else { // from command line
+ celld=pbc_cli_box;
+ }
+ for(unsigned i=0;i<9;i++)cell[i]=real(celld[i]);
+
+ // Read coordinates
+ for(int i=0;i<natoms;i++){
+ ok=Tools::getline(fp,line);
+ plumed_massert(ok,"premature end of file");
+ char dummy[1000];
+ double cc[3];
+ std::sscanf(line.c_str(),"%s %lf %lf %lf",dummy,&cc[0],&cc[1],&cc[2]);
+ if(!debug_pd || ( i>=pd_start && i<pd_start+pd_nlocal) ){
+ coordinates[3*i]=real(cc[0]);
+ coordinates[3*i+1]=real(cc[1]);
+ coordinates[3*i+2]=real(cc[2]);
+ }
+ if(debug_dd){
+ for(int i=0;i<dd_nlocal;++i){
+ int kk=dd_gatindex[i];
+ dd_coordinates[3*i+0]=coordinates[3*kk+0];
+ dd_coordinates[3*i+1]=coordinates[3*kk+1];
+ dd_coordinates[3*i+2]=coordinates[3*kk+2];
+ }
+ }
+ }
- if(debug_dd){
- p.cmd("setForces",&dd_forces[0]);
- p.cmd("setPositions",&dd_coordinates[0]);
- p.cmd("setMasses",&dd_masses[0]);
- p.cmd("setCharges",&dd_charges[0]);
- } else {
- p.cmd("setForces",&forces[3*pd_start]);
- p.cmd("setPositions",&coordinates[3*pd_start]);
- p.cmd("setMasses",&masses[pd_start]);
- p.cmd("setCharges",&charges[pd_start]);
+ if(debug_dd){
+ p.cmd("setForces",&dd_forces[0]);
+ p.cmd("setPositions",&dd_coordinates[0]);
+ p.cmd("setMasses",&dd_masses[0]);
+ p.cmd("setCharges",&dd_charges[0]);
+ } else {
+ p.cmd("setForces",&forces[3*pd_start]);
+ p.cmd("setPositions",&coordinates[3*pd_start]);
+ p.cmd("setMasses",&masses[pd_start]);
+ p.cmd("setCharges",&charges[pd_start]);
+ }
+ p.cmd("setBox",&cell[0]);
+ p.cmd("setVirial",&virial[0]);
}
- p.cmd("setBox",&cell[0]);
- p.cmd("setVirial",&virial[0]);
p.cmd("setStep",&step);
p.cmd("calc");
diff --git a/src/tools/PlumedFile.cpp b/src/tools/PlumedFile.cpp
index 18db9242066db9e2104a743d47e73cea4a3ed729..36459164436a194087a04259b969ab4cca3fd2b0 100644
--- a/src/tools/PlumedFile.cpp
+++ b/src/tools/PlumedFile.cpp
@@ -492,15 +492,18 @@ PlumedIFile& PlumedIFile::scanField(Value* val){
}
PlumedIFile& PlumedIFile::scanField(){
- for(unsigned i=0;i<fields.size();i++){
- plumed_assert(fields[i].read);
+ if(!ignoreFields){
+ for(unsigned i=0;i<fields.size();i++){
+ plumed_assert(fields[i].read);
+ }
}
inMiddleOfField=false;
return *this;
}
PlumedIFile::PlumedIFile():
- inMiddleOfField(false)
+ inMiddleOfField(false),
+ ignoreFields(false)
{
}
@@ -537,3 +540,7 @@ void PlumedIFile::reset(bool reset){
if(!reset) clearerr(fp);
return;
}
+
+void PlumedIFile::allowIgnoredFields(){
+ ignoreFields=true;
+}
diff --git a/src/tools/PlumedFile.h b/src/tools/PlumedFile.h
index a402c4427db57ef6b7fbb5cc7ba17668a736316d..430553be851de6587c06fdc0cb9bcfc0ef47051c 100644
--- a/src/tools/PlumedFile.h
+++ b/src/tools/PlumedFile.h
@@ -278,6 +278,8 @@ public virtual PlumedFileBase{
std::vector<Field> fields;
/// Flag set in the middle of a field reading
bool inMiddleOfField;
+/// Set to true if you want to allow fields to be ignored in the read in file
+ bool ignoreFields;
/// Advance to next field (= read one line)
PlumedIFile& advanceField();
/// Find field index by name
@@ -314,6 +316,8 @@ Typically used as
bool FieldExist(const std::string& s);
/// Read in a value
PlumedIFile& scanField(Value* val);
+/// Allow some of the fields in the input to be ignored
+ void allowIgnoredFields();
};
/// Write using << syntax