cp2k结构优化过程监控shell脚本

参考http://bbs.keinsci.com/thread-28800-1-1.html

主要区别在于将作图改为字符散点图，在远程命令行终端可以直接显示。

#!/bin/bash

# Check if the required file argument is provided
if [ -z "$1" ]; then
    echo -e "\033[31mERROR:\033[0m Missing file operand! Please identify the name of OUTPUT_FILE.out"
    exit 1
fi

output_file="$1"
plot_file="${output_file%.out}__data.csv"

echo "======================================="
echo "In process..."
echo "..."

MAX_SCF=50
OUTER_SCF_CHECK="FALSE"
SCF_OPTIMIZER="DIAGONALIZATION"
GEO_OPTIMIZER="N/A"
TOTAL_TIME=0

# Extract start time
starttime=$(grep "PROGRAM STARTED AT" "$output_file" | awk -F"AT" '{print $2}' | xargs)

# Extract run type and determine line offset
RUN_TYPE=$(grep "Run type" "$output_file" | awk '{print $NF}')
if [ "$RUN_TYPE" == "GEO_OPT" ]; then
    line_added=25
elif [ "$RUN_TYPE" == "CELL_OPT" ]; then
    line_added=32
else
    echo -e "\033[31mERROR:\033[0m This script can only be used for Geometry Optimization results!"
    exit 1
fi

EPS_SCF=$(grep "eps_scf:" "$output_file" | awk -F":" '{print $2}' | xargs)
MAX_SCF=$(grep "max_scf:" "$output_file" | awk -F":" '{print $2}' | xargs)

# Check for Outer SCF
if grep -q "Outer loop SCF in use" "$output_file"; then
    OUTER_SCF_CHECK="TRUE"
fi

# Extract geometry optimizer
GEO_OPTIMIZER=$(grep -A1 "STARTING GEOMETRY OPTIMIZATION" "$output_file" | tail -n 1 | awk -F"***" '{print $2}' | xargs)

# Create or clear the plot file
> "$plot_file"

# Parse the output file
while read -r line; do
    if [[ "$line" == *"*** SCF run converged"* ]]; then
        SCF_NUMBER=$(echo "$line" | awk '{print $(NF-2)}')
    elif [[ "$line" == *"SCF run NOT converged ***"* ]]; then
        SCF_NUMBER="!$MAX_SCF"
    elif [[ "$line" == *"outer SCF loop converged in"* ]]; then
        SCF_NUMBER=$(echo "$line" | awk '{print $(NF-1)}')
    elif [[ "$line" == *"Informations at step"* ]]; then
        CYCLE_NUMBER=$(echo "$line" | awk -F"=" '{print $2}' | awk -F" " '{print $1}' | xargs)
        top_line_number=$(grep -n " $line" "$output_file" | awk -F":" '{print $1}')
        bottom_line_number=$((top_line_number + line_added))

        segment=$(sed -n "${top_line_number},${bottom_line_number}p" "$output_file")
        ENERGY_CHANGE=$(echo "$segment" | grep "Decrease in energy " | awk -F"=" '{print $2}' | xargs)
        TOTAL_ENERGY=$(echo "$segment" | grep "Total Energy" | awk -F"=" '{print $2}' | xargs)
        MAX_D=$(echo "$segment" | grep "Conv. limit for step size" | awk -F"=" '{print $2}' | xargs)
        RMS_D=$(echo "$segment" | grep "Conv. limit for RMS step" | awk -F"=" '{print $2}' | xargs)
        MAX_F=$(echo "$segment" | grep "Conv. limit for gradients" | awk -F"=" '{print $2}' | xargs)
        RMS_F=$(echo "$segment" | grep "Conv. limit for RMS grad" | awk -F"=" '{print $2}' | xargs)
        MAX_D_VALUE=$(echo "$segment" | grep "Max. step size " | awk -F"=" '{print $2}' | xargs)
        RMS_D_VALUE=$(echo "$segment" | grep "RMS step size " | awk -F"=" '{print $2}' | xargs)
        MAX_F_VALUE=$(echo "$segment" | grep "Max. gradient " | awk -F"=" '{print $2}' | xargs)
        RMS_F_VALUE=$(echo "$segment" | grep "RMS gradient " | awk -F"=" '{print $2}' | xargs)
        USEDTIME=$(echo "$segment" | grep "Used time" | awk -F"=" '{print $2}' | xargs)

        # Accumulate total time
        TOTAL_TIME=$(echo "$TOTAL_TIME + $USEDTIME" | bc)

        # Write data to CSV file
        if [[ "$ENERGY_CHANGE" == "NO" ]]; then
            printf "%7s %19s x%6s" "$CYCLE_NUMBER" "$TOTAL_ENERGY" "$SCF_NUMBER" >> "$plot_file"
        else
            printf "%7s %19s %7s" "$CYCLE_NUMBER" "$TOTAL_ENERGY" "$SCF_NUMBER" >> "$plot_file"
        fi

        printf "%12.6f" "$MAX_D_VALUE" >> "$plot_file"
        if (( $(echo "$MAX_D_VALUE > $MAX_D" | bc -l) )); then
            MAX_D_CONVERGENCE="NO"
        else
            MAX_D_CONVERGENCE="YES"
        fi
        printf "%4s" "$MAX_D_CONVERGENCE" >> "$plot_file"

        printf "%12.6f" "$RMS_D_VALUE" >> "$plot_file"
        if (( $(echo "$RMS_D_VALUE > $RMS_D" | bc -l) )); then
            RMS_D_CONVERGENCE="NO"
        else
            RMS_D_CONVERGENCE="YES"
        fi
        printf "%4s" "$RMS_D_CONVERGENCE" >> "$plot_file"

        printf "%14.6f" "$MAX_F_VALUE" >> "$plot_file"
        if (( $(echo "$MAX_F_VALUE > $MAX_F" | bc -l) )); then
            MAX_F_CONVERGENCE="NO"
        else
            MAX_F_CONVERGENCE="YES"
        fi
        printf "%4s" "$MAX_F_CONVERGENCE" >> "$plot_file"

        printf "%13.6f" "$RMS_F_VALUE" >> "$plot_file"
        if (( $(echo "$RMS_F_VALUE > $RMS_F" | bc -l) )); then
            RMS_F_CONVERGENCE="NO"
        else
            RMS_F_CONVERGENCE="YES"
        fi
        printf "%4s" "$RMS_F_CONVERGENCE" >> "$plot_file"

        printf "%13s\n" "$USEDTIME" >> "$plot_file"
    elif [[ "$line" == *"OPTIMIZATION COMPLETED"* ]]; then
        CYCLE_NUMBER=$(echo "$line" | awk -F'=' '{print $2}' | awk -F'-' '{print $1}' | xargs)
        TOTAL_ENERGY=$(grep -A 100 "OPTIMIZATION COMPLETED" "$output_file" | grep "ENERGY" | awk -F':' '{print $2}' | xargs | head -1)
        printf "Final %17.10f %7s\n" "$TOTAL_ENERGY" "$SCF_NUMBER" >> "$plot_file"
        printf "%11s %15s %16s %17s\n" "N/A" "N/A" "N/A" "N/A" >> "$plot_file"
        printf "%17s\n" "N/A" >> "$plot_file"
    fi
done < "$output_file"

# Format total time
TOTAL_TIME=$(printf "%.0f\n" "$TOTAL_TIME")
TOTAL_TIME=$(date -d@$TOTAL_TIME -u +%H:%M:%S)

# Write the header information to the plot file
{
    echo "# Job Starting Date: $starttime"
    echo "# Total used time: $TOTAL_TIME"
    echo "# Directory: $(pwd)"
    echo "# RUN_TYPE: $RUN_TYPE"
    echo "# EPS_SCF: $EPS_SCF"
    echo "# MAX_SCF: $MAX_SCF"
    echo "# SCF_OPTIMIZER: $SCF_OPTIMIZER"
    echo "# OUTER_SCF: $OUTER_SCF_CHECK"
    echo "# GEO_OPTIMIZER: $GEO_OPTIMIZER"
    echo "# CYCLE | TOTAL_ENERGY [a.u.] | SCF | MAX_D.($MAX_D) | RMS_D.($RMS_D) | MAX_F.($MAX_F) | RMS_F.($RMS_F) | USEDTIME [s]"
} | cat - "$plot_file" > temp && mv temp "$plot_file"

echo "======================================="

# plot generation
gnuplot -persist <<-EOFMarker
    set terminal dumb
    set xlabel "Cycle Number"
    set ylabel "Energy (a.u.)"
    set format y "%.4f"
    plot "$plot_file" using 1:2 w l
EOFMarker

temp_data="temp_data.dat"
> $temp_data

# 从文件中提取最后十步的能量数据作图
tail -n 10 "$plot_file"  > "$temp_data"

gnuplot -persist <<-EOFMarker
    set terminal dumb
    set title "Energy vs Step"
    set xlabel "Step"
    set ylabel "Energy"
    set format y "%.4f"
    set key off
    plot "$temp_data" using 1:2 w l
EOFMarker

echo "Done!"
echo "======================================="

用法：保存以上代码为out.sh，命令行输入

./out.sh cp2k.out 

#cp2k.out为结构优化输出文件。

输出：

=======================================
In process...
...
=======================================

    -38280.0000 +----------------------------------------------------------+
                |         +         +         +        +         +         |
    -38300.0000 |-+                     "cp2k__data.csv" using 1:2 *******-|
                |                                                          |
    -38320.0000 |*+                                                      +-|
                |*                                                         |
    -38340.0000 |*+                                                      +-|
                |*                                                         |
    -38360.0000 |-*                                                      +-|
                | *                                                        |
                | *                                                        |
    -38380.0000 |-+*                                                     +-|
                |  *                                                       |
    -38400.0000 |-+ *                                                    +-|
                |   *                                                      |
    -38420.0000 |-+ *                                                    +-|
                |    *                                                     |
    -38440.0000 |-+  *                                                   +-|
                |     *****************************************************|
    -38460.0000 +----------------------------------------------------------+
                0         20        40        60       80       100       120
                                       Cycle Number

                                      Energy vs Step

    -38453.7100 +----------------------------------------------------------+
                |***** +     +      +     +      +     +      +     +      |
    -38453.7120 |-+   *                                                  +-|
    -38453.7140 |-+    ***                                               +-|
                |         *                                                |
    -38453.7160 |-+        **                                            +-|
                |                                                          |
    -38453.7180 |-+          ****                                        +-|
    -38453.7200 |-+              **                                      +-|
                |                  *                                       |
    -38453.7220 |-+                 ***                                  +-|
                |                      **                                  |
    -38453.7240 |-+                      *                               +-|
                |                         *******                          |
    -38453.7260 |-+                              *************           +-|
    -38453.7280 |-+                                           *************|
                |      +     +      +     +      +     +      +     +      |
    -38453.7300 +----------------------------------------------------------+
               109    110   111    112   113    114   115    116   117    118
                                           Step

Done!
=======================================

csv文件结果：

# Job Starting Date: 2024-06-03 15:45:20.173
# Total used time: 23:47:24
# Directory: /home/lily/LLF/cp2k/phenol/cp2k
# RUN_TYPE: GEO_OPT
# EPS_SCF: 1.00E-06
# MAX_SCF: 128
# SCF_OPTIMIZER: DIAGONALIZATION
# OUTER_SCF: FALSE
# GEO_OPTIMIZER: L-BFGS
# CYCLE | TOTAL_ENERGY [a.u.] | SCF | MAX_D.(0.0030000000) | RMS_D.(0.0015000000) | MAX_F.(0.0004500000) | RMS_F.(0.0003000000) | USEDTIME [s]
      1   -38293.9009093772    !128    0.566918  NO    0.517696  NO     13.537421  NO     5.393604  NO     2339.735
      2   -38345.0711337413    !128    0.049864  NO    0.020402  NO     11.347661  NO     2.420294  NO     3615.186
      3   -38347.6119252461    !128    0.009948  NO    0.005308  NO     11.597702  NO     2.215591  NO     2430.807
      4   -38358.7593935025    !128    0.083949  NO    0.018435  NO     13.370634  NO     2.819675  NO     1237.605
      5   -38373.4747662735    !128    0.048048  NO    0.008313  NO     13.689350  NO     2.753831  NO     1235.306
      6   -38385.4430239490    !128    0.098385  NO    0.017551  NO     13.795138  NO     3.163100  NO     2475.502
      7   -38398.3275671691    !128    0.039247  NO    0.010051  NO     14.278510  NO     3.007065  NO     1223.777
      8   -38407.6707794731    !128    0.110714  NO    0.017888  NO     13.767358  NO     3.513500  NO     1222.547
      9   -38424.0415851509    !128    0.037548  NO    0.008126  NO     13.802667  NO     2.680716  NO     1219.407
     10   -38437.3715964221    !128    0.063622  NO    0.011894  NO     13.616962  NO     2.170538  NO     2463.265
     11   -38442.0157973437    !128    0.058363  NO    0.010835  NO     12.542194  NO     2.319541  NO     1238.417
     12   -38448.1099966033    !128    0.029864  NO    0.004923  NO      9.425311  NO     1.216871  NO     1239.613
     13   -38449.5536058381    !128    0.051664  NO    0.006625  NO     11.502005  NO     1.078886  NO     1226.044
     14   -38450.7744174706    !128    0.026048  NO    0.003157  NO      8.941722  NO     0.612406  NO     1227.373
     15   -38451.4243230985    !128    0.032923  NO    0.002444  NO     14.058508  NO     0.614670  NO     1224.183
     16   -38451.8572894509    !128    0.082810  NO    0.003724  NO     11.394319  NO     0.675941  NO     1226.924
     17   -38452.3401525953    !128    0.027161  NO    0.001689  NO      4.987087  NO     0.331008  NO     1225.656
     18   -38452.5155352595    !128    0.018287  NO    0.001354 YES      1.741073  NO     0.154253  NO     1225.290
     19   -38452.5677832827    !128    0.009514  NO    0.000759 YES      1.554650  NO     0.151277  NO     1223.176
     20   -38452.6502578204    !128    0.022160  NO    0.001564  NO      3.221266  NO     0.183821  NO     1225.604
     21   -38452.7107625667    !128    0.045410  NO    0.003302  NO      2.406537  NO     0.227219  NO     1226.349
     22   -38452.7790396656    !128    0.008623  NO    0.001049 YES      1.110677  NO     0.114943  NO     1227.193
     23   -38452.8060171333    !128    0.007565  NO    0.000542 YES      0.874225  NO     0.092893  NO     1223.016
     24   -38452.8513238147     120    0.010166  NO    0.001001 YES      1.165554  NO     0.106416  NO     1154.807
     25   -38452.9763659228    !128    0.033919  NO    0.004598  NO      3.134758  NO     0.195972  NO     1222.316
     26   -38453.0368771456    !128    0.045391  NO    0.005965  NO      4.510042  NO     0.262002  NO     1225.082
     27   -38453.1106225547    !128    0.010515  NO    0.001237 YES      0.814755  NO     0.102952  NO     1224.452
     28   -38453.1317484527    !128    0.008002  NO    0.000596 YES      0.510067  NO     0.057107  NO     1224.220
     29   -38453.1416951662     106    0.005294  NO    0.000579 YES      0.636377  NO     0.062950  NO     1027.885
     30   -38453.1658257423     127    0.015610  NO    0.001577  NO      1.066407  NO     0.089825  NO      997.352
     31   -38453.2014799830    !128    0.025234  NO    0.002532  NO      0.996985  NO     0.118614  NO      547.957
     32   -38453.2360840145     124    0.035358  NO    0.003468  NO      1.179458  NO     0.135713  NO      530.993
     33   -38453.2788908814    !128    0.011234  NO    0.001359 YES      1.147295  NO     0.081889  NO      547.602
     34   -38453.3253798973     115    0.016066  NO    0.002041  NO      1.052968  NO     0.094644  NO      493.633
     35   -38453.3587110808    !128    0.021265  NO    0.001925  NO      1.067494  NO     0.106279  NO      548.158
     36   -38453.3814815270    !128    0.024454  NO    0.001905  NO      0.838873  NO     0.106136  NO     1094.919
     37   -38453.4007859257    !128    0.014422  NO    0.001030 YES      0.484989  NO     0.047869  NO      548.036
     38   -38453.4073257428    !128    0.005331  NO    0.000398 YES      0.456717  NO     0.039658  NO      547.544
     39   -38453.4143332759    !128    0.006557  NO    0.000477 YES      0.480681  NO     0.053184  NO      548.051
     40   -38453.4307623710    !128    0.021882  NO    0.001295 YES      0.696394  NO     0.077216  NO      546.807
     41   -38453.4423080051    !128    0.042476  NO    0.002413  NO      1.648272  NO     0.124604  NO      546.647
     42   -38453.4592114834    !128    0.009067  NO    0.000610 YES      0.363971  NO     0.049756  NO      545.691
     43   -38453.4646087917    !128    0.005141  NO    0.000472 YES      0.309877  NO     0.022359  NO      546.501
     44   -38453.4662032009     119    0.003859  NO    0.000316 YES      0.149075  NO     0.019768  NO      511.400
     45   -38453.4676728431     101    0.003978  NO    0.000327 YES      0.228340  NO     0.021864  NO      437.721
     46   -38453.4700696358      98    0.006811  NO    0.000608 YES      0.241899  NO     0.024803  NO      425.070
     47   -38453.4725093286    !128    0.006641  NO    0.000591 YES      0.277829  NO     0.027853  NO      547.172
     48   -38453.4753551295     108    0.004979  NO    0.000533 YES      0.222803  NO     0.026360  NO      466.572
     49   -38453.4797543371    !128    0.008871  NO    0.000964 YES      0.322469  NO     0.032315  NO      546.653
     50   -38453.4836622007    !128    0.014376  NO    0.001417 YES      0.540455  NO     0.048698  NO      548.108
     51   -38453.4881990688    !128    0.008473  NO    0.000865 YES      0.319379  NO     0.028678  NO      546.961
     52   -38453.4923642961     119    0.008142  NO    0.001003 YES      0.274817  NO     0.025880  NO      510.928
     53   -38453.4954670575    !128    0.006620  NO    0.000905 YES      0.315574  NO     0.028694  NO      547.386
     54   -38453.4987172498    !128    0.012209  NO    0.001638  NO      0.529461  NO     0.042139  NO      548.032
     55   -38453.5023511995     127    0.007364  NO    0.000971 YES      0.364782  NO     0.026311  NO      542.951
     56   -38453.5057121455    !128    0.005645  NO    0.000716 YES      0.352429  NO     0.030186  NO      546.726
     57   -38453.5111359223    !128    0.010985  NO    0.001375 YES      0.565123  NO     0.045769  NO      546.763
     58   -38453.5213540246     101    0.024813  NO    0.003038  NO      0.700710  NO     0.063421  NO      437.382
     59   -38453.5326039384     108    0.059473  NO    0.007248  NO      1.181988  NO     0.095351  NO      466.312
     60   -38453.5466723135     109    0.026251  NO    0.003189  NO      0.451825  NO     0.046147  NO      470.034
     61   -38453.5526489089     103    0.008430  NO    0.001013 YES      0.403029  NO     0.026745  NO      447.132
     62   -38453.5546060930     116    0.006375  NO    0.000736 YES      0.243423  NO     0.024858  NO      498.222
     63   -38453.5556651238     103    0.003236  NO    0.000348 YES      0.155239  NO     0.018363  NO      446.758
     64   -38453.5569261986      88    0.005108  NO    0.000525 YES      0.127348  NO     0.015579  NO      385.401
     65   -38453.5581529340      95    0.006239  NO    0.000593 YES      0.136582  NO     0.016449  NO      414.122
     66   -38453.5596833129      96    0.008871  NO    0.000769 YES      0.192127  NO     0.021433  NO      418.552
     67   -38453.5619982265      90    0.012981  NO    0.001066 YES      0.270557  NO     0.025687  NO      392.991
     68   -38453.5659991143      95    0.018620  NO    0.001476 YES      0.240005  NO     0.029187  NO      413.354
     69   -38453.5754187684     111    0.050312  NO    0.003935  NO      0.365837  NO     0.051956  NO      477.983
     70   -38453.5876075052    !128    0.080000  NO    0.006228  NO      0.460397  NO     0.068926  NO      546.990
     71   -38453.6018972062     117    0.062223  NO    0.004838  NO      0.437872  NO     0.054928  NO      505.473
     72   -38453.6162898744    !128    0.098172  NO    0.007609  NO      0.354021  NO     0.050229  NO      550.201
     73   -38453.6204939352    !128    0.012543  NO    0.001065 YES      0.361459  NO     0.051380  NO      550.131
     74   -38453.6238650643     121    0.013853  NO    0.001119 YES      0.155597  NO     0.024984  NO      522.362
     75   -38453.6267982518     108    0.007894  NO    0.000669 YES      0.147059  NO     0.021417  NO      466.426
     76   -38453.6306628970     102    0.017326  NO    0.001326 YES      0.184631  NO     0.030542  NO      441.362
     77   -38453.6360444614     102    0.028129  NO    0.002155  NO      0.395133  NO     0.040345  NO      442.570
     78   -38453.6384552231     103    0.054547  NO    0.004145  NO      0.481192  NO     0.055446  NO      446.492
     79   -38453.6435224723     117    0.015246  NO    0.001255 YES      0.206357  NO     0.023973  NO      503.186
     80   -38453.6455828065      98    0.004054  NO    0.000401 YES      0.145329  NO     0.019764  NO      426.872
     81   -38453.6472944409     128    0.004866  NO    0.000439 YES      0.149949  NO     0.021695  NO      552.618
     82   -38453.6493814395      87    0.013964  NO    0.001111 YES      0.203396  NO     0.025311  NO      385.179
     83   -38453.6510177956     100    0.009415  NO    0.000736 YES      0.306191  NO     0.025235  NO      436.152
     84   -38453.6523212899      97    0.004500  NO    0.000338 YES      0.152837  NO     0.017139  NO      423.328
     85   -38453.6538856585     101    0.006279  NO    0.000473 YES      0.102953  NO     0.018195  NO      440.124
     86   -38453.6556041322      89    0.007680  NO    0.000569 YES      0.164060  NO     0.022570  NO      393.277
     87   -38453.6585302827      74    0.021391  NO    0.001508  NO      0.273899  NO     0.033458  NO      330.402
     88   -38453.6613369889      78    0.017440  NO    0.001200 YES      0.329912  NO     0.029732  NO      346.576
     89   -38453.6636764580      96    0.008453  NO    0.000557 YES      0.188873  NO     0.022445  NO      420.143
     90   -38453.6672098766      81    0.020111  NO    0.001319 YES      0.222533  NO     0.027323  NO      359.962
     91   -38453.6705914517      95    0.022776  NO    0.001465 YES      0.272270  NO     0.035188  NO      417.479
     92   -38453.6764592106      81    0.043111  NO    0.002722  NO      0.336035  NO     0.037181  NO      359.595
     93   -38453.6861843247     104    0.127895  NO    0.008011  NO      0.754398  NO     0.062662  NO      452.478
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